2022-08-01T11:16:13,834 Created temporary directory: /tmp/pip-ephem-wheel-cache-j4547t5q 2022-08-01T11:16:13,839 Created temporary directory: /tmp/pip-build-tracker-38w_f5aw 2022-08-01T11:16:13,840 Initialized build tracking at /tmp/pip-build-tracker-38w_f5aw 2022-08-01T11:16:13,840 Created build tracker: /tmp/pip-build-tracker-38w_f5aw 2022-08-01T11:16:13,841 Entered build tracker: /tmp/pip-build-tracker-38w_f5aw 2022-08-01T11:16:13,842 Created temporary directory: /tmp/pip-wheel-oriy7x17 2022-08-01T11:16:13,911 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-08-01T11:16:13,920 2 location(s) to search for versions of pele-platform: 2022-08-01T11:16:13,920 * https://pypi.org/simple/pele-platform/ 2022-08-01T11:16:13,920 * https://www.piwheels.org/simple/pele-platform/ 2022-08-01T11:16:13,921 Fetching project page and analyzing links: https://pypi.org/simple/pele-platform/ 2022-08-01T11:16:13,922 Getting page https://pypi.org/simple/pele-platform/ 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https://www.piwheels.org/simple/pele-platform/pele_platform-1.5.1-py3-none-any.whl#sha256=1e2441185afe5cc09f11dd375ad35a722a8557cfa6d58dafa105b6cc82f8dace (from https://www.piwheels.org/simple/pele-platform/) 2022-08-01T11:16:14,422 Skipping link: No binaries permitted for pele-platform: https://www.piwheels.org/simple/pele-platform/pele_platform-1.5.0-py3-none-any.whl#sha256=6e46958311c83d72e2c0f5f9b84d2453ab73469c2b58f0e559093aaf935dfde3 (from https://www.piwheels.org/simple/pele-platform/) 2022-08-01T11:16:14,423 Skipping link: No binaries permitted for pele-platform: https://www.piwheels.org/simple/pele-platform/pele_platform-1.4.4-py3-none-any.whl#sha256=c335d006901d5acc5b99a37758afcf124c3dbc76cf935ebcbecf2031883da70f (from https://www.piwheels.org/simple/pele-platform/) 2022-08-01T11:16:14,423 Skipping link: No binaries permitted for pele-platform: 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https://pypi.org/simple/pele-platform/ 2022-08-01T11:16:14,489 Given no hashes to check 1 links for project 'pele-platform': discarding no candidates 2022-08-01T11:16:14,524 Collecting pele-platform==1.6.4 2022-08-01T11:16:14,528 Created temporary directory: /tmp/pip-unpack-cinyr8op 2022-08-01T11:16:15,727 Downloading pele_platform-1.6.4.tar.gz (12.3 MB) 2022-08-01T11:16:26,028 Added pele-platform==1.6.4 from https://files.pythonhosted.org/packages/ed/c6/d0bed283cb52725f3de771dca5a44915ca192e19f4b13384957b0b99e6ee/pele_platform-1.6.4.tar.gz#sha256=8fc7df3aeacf738df7be54f45ff1371ead1799e4f5ffad614dbce6135c3aba21 to build tracker '/tmp/pip-build-tracker-38w_f5aw' 2022-08-01T11:16:26,031 Running setup.py (path:/tmp/pip-wheel-oriy7x17/pele-platform_4d1d3be08eae4d3eb1012048ed9b6310/setup.py) egg_info for package pele-platform 2022-08-01T11:16:26,033 Created temporary directory: /tmp/pip-pip-egg-info-nhfe24_r 2022-08-01T11:16:26,033 Preparing metadata (setup.py): started 2022-08-01T11:16:26,035 Running command python setup.py egg_info 2022-08-01T11:16:33,201 running egg_info 2022-08-01T11:16:33,206 creating /tmp/pip-pip-egg-info-nhfe24_r/pele_platform.egg-info 2022-08-01T11:16:33,871 writing /tmp/pip-pip-egg-info-nhfe24_r/pele_platform.egg-info/PKG-INFO 2022-08-01T11:16:34,461 writing dependency_links to /tmp/pip-pip-egg-info-nhfe24_r/pele_platform.egg-info/dependency_links.txt 2022-08-01T11:16:37,407 writing requirements to /tmp/pip-pip-egg-info-nhfe24_r/pele_platform.egg-info/requires.txt 2022-08-01T11:16:37,999 writing top-level names to /tmp/pip-pip-egg-info-nhfe24_r/pele_platform.egg-info/top_level.txt 2022-08-01T11:16:38,002 writing manifest file '/tmp/pip-pip-egg-info-nhfe24_r/pele_platform.egg-info/SOURCES.txt' 2022-08-01T11:16:38,239 reading manifest file '/tmp/pip-pip-egg-info-nhfe24_r/pele_platform.egg-info/SOURCES.txt' 2022-08-01T11:16:38,242 reading manifest template 'MANIFEST.in' 2022-08-01T11:16:38,245 warning: no files found matching 'pele_platform/Utilities/PlopRotTemp/param/*' 2022-08-01T11:16:38,246 warning: no files found matching 'pele_platform/AdaptivePELE/atomset/*' 2022-08-01T11:16:38,246 warning: no files found matching 'pele_platform/AdaptivePELE/freeEnergies/*' 2022-08-01T11:16:38,247 warning: no files found matching '*' under directory 'pele_platform/Utilities/PPP/Data/' 2022-08-01T11:16:38,637 warning: no files found matching '*' under directory 'tests/data' 2022-08-01T11:16:38,638 adding license file 'LICENSE' 2022-08-01T11:16:38,683 writing manifest file '/tmp/pip-pip-egg-info-nhfe24_r/pele_platform.egg-info/SOURCES.txt' 2022-08-01T11:16:38,901 Preparing metadata (setup.py): finished with status 'done' 2022-08-01T11:16:38,912 Source in /tmp/pip-wheel-oriy7x17/pele-platform_4d1d3be08eae4d3eb1012048ed9b6310 has version 1.6.4, which satisfies requirement pele-platform==1.6.4 from https://files.pythonhosted.org/packages/ed/c6/d0bed283cb52725f3de771dca5a44915ca192e19f4b13384957b0b99e6ee/pele_platform-1.6.4.tar.gz#sha256=8fc7df3aeacf738df7be54f45ff1371ead1799e4f5ffad614dbce6135c3aba21 2022-08-01T11:16:38,914 Removed pele-platform==1.6.4 from https://files.pythonhosted.org/packages/ed/c6/d0bed283cb52725f3de771dca5a44915ca192e19f4b13384957b0b99e6ee/pele_platform-1.6.4.tar.gz#sha256=8fc7df3aeacf738df7be54f45ff1371ead1799e4f5ffad614dbce6135c3aba21 from build tracker '/tmp/pip-build-tracker-38w_f5aw' 2022-08-01T11:16:38,922 Created temporary directory: /tmp/pip-unpack-00y4tc4w 2022-08-01T11:16:38,924 Building wheels for collected packages: pele-platform 2022-08-01T11:16:38,933 Created temporary directory: /tmp/pip-wheel-0ji81ool 2022-08-01T11:16:38,934 Building wheel for pele-platform (setup.py): started 2022-08-01T11:16:38,936 Destination directory: /tmp/pip-wheel-0ji81ool 2022-08-01T11:16:38,937 Running command python setup.py bdist_wheel 2022-08-01T11:16:45,461 running bdist_wheel 2022-08-01T11:16:45,693 running build 2022-08-01T11:16:45,693 running build_py 2022-08-01T11:16:45,705 creating build 2022-08-01T11:16:45,706 creating build/lib 2022-08-01T11:16:45,707 creating build/lib/pele_platform 2022-08-01T11:16:45,709 copying pele_platform/__init__.py -> build/lib/pele_platform 2022-08-01T11:16:45,713 copying pele_platform/pathway_extractor.py -> build/lib/pele_platform 2022-08-01T11:16:45,717 copying pele_platform/plotter.py -> build/lib/pele_platform 2022-08-01T11:16:45,726 copying pele_platform/converter.py -> build/lib/pele_platform 2022-08-01T11:16:45,730 copying pele_platform/main.py -> build/lib/pele_platform 2022-08-01T11:16:45,734 copying pele_platform/_version.py -> build/lib/pele_platform 2022-08-01T11:16:45,738 creating build/lib/pele_platform/constants 2022-08-01T11:16:45,739 copying pele_platform/constants/pele_params.py -> build/lib/pele_platform/constants 2022-08-01T11:16:45,743 copying pele_platform/constants/__init__.py -> build/lib/pele_platform/constants 2022-08-01T11:16:45,746 copying pele_platform/constants/constants.py -> build/lib/pele_platform/constants 2022-08-01T11:16:45,751 creating build/lib/pele_platform/out_in 2022-08-01T11:16:45,753 copying pele_platform/out_in/__init__.py -> build/lib/pele_platform/out_in 2022-08-01T11:16:45,756 copying pele_platform/out_in/main.py -> build/lib/pele_platform/out_in 2022-08-01T11:16:45,760 creating build/lib/pele_platform/covalent_docking 2022-08-01T11:16:45,762 copying pele_platform/covalent_docking/__init__.py -> build/lib/pele_platform/covalent_docking 2022-08-01T11:16:45,765 copying pele_platform/covalent_docking/main.py -> build/lib/pele_platform/covalent_docking 2022-08-01T11:16:45,770 creating build/lib/pele_platform/Utilities 2022-08-01T11:16:45,771 copying pele_platform/Utilities/__init__.py -> build/lib/pele_platform/Utilities 2022-08-01T11:16:45,776 creating build/lib/pele_platform/Frag 2022-08-01T11:16:45,778 copying pele_platform/Frag/simulation.py -> build/lib/pele_platform/Frag 2022-08-01T11:16:45,782 copying pele_platform/Frag/fragments.py -> build/lib/pele_platform/Frag 2022-08-01T11:16:45,785 copying pele_platform/Frag/__init__.py -> build/lib/pele_platform/Frag 2022-08-01T11:16:45,788 copying pele_platform/Frag/libraries.py -> build/lib/pele_platform/Frag 2022-08-01T11:16:45,791 copying pele_platform/Frag/checker.py -> build/lib/pele_platform/Frag 2022-08-01T11:16:45,795 copying pele_platform/Frag/generative_model.py -> build/lib/pele_platform/Frag 2022-08-01T11:16:45,798 copying pele_platform/Frag/atoms.py -> build/lib/pele_platform/Frag 2022-08-01T11:16:45,801 copying pele_platform/Frag/analysis.py -> build/lib/pele_platform/Frag 2022-08-01T11:16:45,805 copying pele_platform/Frag/helpers.py -> build/lib/pele_platform/Frag 2022-08-01T11:16:45,811 creating build/lib/pele_platform/analysis 2022-08-01T11:16:45,813 copying pele_platform/analysis/clustering.py -> build/lib/pele_platform/analysis 2022-08-01T11:16:45,818 copying pele_platform/analysis/__init__.py -> build/lib/pele_platform/analysis 2022-08-01T11:16:45,822 copying pele_platform/analysis/pdf_report.py -> build/lib/pele_platform/analysis 2022-08-01T11:16:45,826 copying pele_platform/analysis/data.py -> build/lib/pele_platform/analysis 2022-08-01T11:16:45,832 copying pele_platform/analysis/plot.py -> build/lib/pele_platform/analysis 2022-08-01T11:16:45,838 copying pele_platform/analysis/analysis.py -> build/lib/pele_platform/analysis 2022-08-01T11:16:45,846 copying pele_platform/analysis/interactive_plot.py -> build/lib/pele_platform/analysis 2022-08-01T11:16:45,853 creating build/lib/pele_platform/RNA 2022-08-01T11:16:45,855 copying pele_platform/RNA/__init__.py -> build/lib/pele_platform/RNA 2022-08-01T11:16:45,859 copying pele_platform/RNA/prep.py -> build/lib/pele_platform/RNA 2022-08-01T11:16:45,865 creating build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,867 copying pele_platform/Adaptive/plop_solvent.py -> build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,871 copying pele_platform/Adaptive/interaction_restrictions.py -> build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,875 copying pele_platform/Adaptive/simulation.py -> build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,881 copying pele_platform/Adaptive/__init__.py -> build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,885 copying pele_platform/Adaptive/box.py -> build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,889 copying pele_platform/Adaptive/plop_ligand_parametrization.py -> build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,894 copying pele_platform/Adaptive/pca.py -> build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,897 copying pele_platform/Adaptive/parametrizer.py -> build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,904 copying pele_platform/Adaptive/metrics.py -> build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,907 copying pele_platform/Adaptive/preequilibrator.py -> build/lib/pele_platform/Adaptive 2022-08-01T11:16:45,913 creating build/lib/pele_platform/gpcr 2022-08-01T11:16:45,915 copying pele_platform/gpcr/__init__.py -> build/lib/pele_platform/gpcr 2022-08-01T11:16:45,918 copying pele_platform/gpcr/main.py -> build/lib/pele_platform/gpcr 2022-08-01T11:16:45,923 creating build/lib/pele_platform/features 2022-08-01T11:16:45,924 copying pele_platform/features/__init__.py -> build/lib/pele_platform/features 2022-08-01T11:16:45,927 copying pele_platform/features/adaptive.py -> build/lib/pele_platform/features 2022-08-01T11:16:45,932 copying pele_platform/features/frag.py -> build/lib/pele_platform/features 2022-08-01T11:16:45,936 creating build/lib/pele_platform/Checker 2022-08-01T11:16:45,937 copying pele_platform/Checker/executable.py -> build/lib/pele_platform/Checker 2022-08-01T11:16:45,941 copying pele_platform/Checker/environment_variables.py -> build/lib/pele_platform/Checker 2022-08-01T11:16:45,944 copying pele_platform/Checker/__init__.py -> build/lib/pele_platform/Checker 2022-08-01T11:16:45,947 copying pele_platform/Checker/python_version.py -> build/lib/pele_platform/Checker 2022-08-01T11:16:45,950 copying pele_platform/Checker/valid_flags.py -> build/lib/pele_platform/Checker 2022-08-01T11:16:45,954 copying pele_platform/Checker/pdb_checker.py -> build/lib/pele_platform/Checker 2022-08-01T11:16:45,958 copying pele_platform/Checker/main.py -> build/lib/pele_platform/Checker 2022-08-01T11:16:45,962 creating build/lib/pele_platform/Errors 2022-08-01T11:16:45,964 copying pele_platform/Errors/__init__.py -> build/lib/pele_platform/Errors 2022-08-01T11:16:45,967 copying pele_platform/Errors/custom_errors.py -> build/lib/pele_platform/Errors 2022-08-01T11:16:45,972 creating build/lib/pele_platform/PPI 2022-08-01T11:16:45,973 copying pele_platform/PPI/__init__.py -> build/lib/pele_platform/PPI 2022-08-01T11:16:45,976 copying pele_platform/PPI/simulation_launcher.py -> build/lib/pele_platform/PPI 2022-08-01T11:16:45,980 copying pele_platform/PPI/cluster.py -> build/lib/pele_platform/PPI 2022-08-01T11:16:45,983 copying pele_platform/PPI/preparation.py -> build/lib/pele_platform/PPI 2022-08-01T11:16:45,987 copying pele_platform/PPI/main.py -> build/lib/pele_platform/PPI 2022-08-01T11:16:45,992 creating build/lib/pele_platform/enzyme_engineering 2022-08-01T11:16:45,994 copying pele_platform/enzyme_engineering/saturated_mutagenesis.py -> build/lib/pele_platform/enzyme_engineering 2022-08-01T11:16:45,998 copying pele_platform/enzyme_engineering/__init__.py -> build/lib/pele_platform/enzyme_engineering 2022-08-01T11:16:46,003 creating build/lib/pele_platform/site_finder 2022-08-01T11:16:46,005 copying pele_platform/site_finder/__init__.py -> build/lib/pele_platform/site_finder 2022-08-01T11:16:46,009 copying pele_platform/site_finder/main.py -> build/lib/pele_platform/site_finder 2022-08-01T11:16:46,017 creating build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,019 copying pele_platform/Utilities/Helpers/interaction_constraints.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,024 copying pele_platform/Utilities/Helpers/plop_launcher.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,028 copying pele_platform/Utilities/Helpers/system_prep.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,034 copying pele_platform/Utilities/Helpers/simulation.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,038 copying pele_platform/Utilities/Helpers/randomize.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,042 copying pele_platform/Utilities/Helpers/__init__.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,046 copying pele_platform/Utilities/Helpers/conda_deployment.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,049 copying pele_platform/Utilities/Helpers/launcher.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,052 copying pele_platform/Utilities/Helpers/center_of_mass.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,056 copying pele_platform/Utilities/Helpers/yaml_parser.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,061 copying pele_platform/Utilities/Helpers/ligand_conformations.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,065 copying pele_platform/Utilities/Helpers/calculatePCA4PELE.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,071 copying pele_platform/Utilities/Helpers/water.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,075 copying pele_platform/Utilities/Helpers/bestStructs.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,080 copying pele_platform/Utilities/Helpers/template_builder.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,083 copying pele_platform/Utilities/Helpers/solventOBCParamsGenerator.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,088 copying pele_platform/Utilities/Helpers/helpers.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,093 copying pele_platform/Utilities/Helpers/map_atoms.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,097 copying pele_platform/Utilities/Helpers/protein_wizard.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,101 copying pele_platform/Utilities/Helpers/missing_residues.py -> build/lib/pele_platform/Utilities/Helpers 2022-08-01T11:16:46,105 creating build/lib/pele_platform/Utilities/Parameters 2022-08-01T11:16:46,107 copying pele_platform/Utilities/Parameters/__init__.py -> build/lib/pele_platform/Utilities/Parameters 2022-08-01T11:16:46,111 copying pele_platform/Utilities/Parameters/parameters.py -> build/lib/pele_platform/Utilities/Parameters 2022-08-01T11:16:46,116 creating build/lib/pele_platform/Utilities/Helpers/Metals 2022-08-01T11:16:46,118 copying pele_platform/Utilities/Helpers/Metals/__init__.py -> build/lib/pele_platform/Utilities/Helpers/Metals 2022-08-01T11:16:46,121 copying pele_platform/Utilities/Helpers/Metals/metal_polarisation.py -> build/lib/pele_platform/Utilities/Helpers/Metals 2022-08-01T11:16:46,124 copying pele_platform/Utilities/Helpers/Metals/metal_constraints.py -> build/lib/pele_platform/Utilities/Helpers/Metals 2022-08-01T11:16:46,129 creating build/lib/pele_platform/Utilities/Helpers/constraints 2022-08-01T11:16:46,131 copying pele_platform/Utilities/Helpers/constraints/alpha_constraints.py -> build/lib/pele_platform/Utilities/Helpers/constraints 2022-08-01T11:16:46,135 copying pele_platform/Utilities/Helpers/constraints/__init__.py -> build/lib/pele_platform/Utilities/Helpers/constraints 2022-08-01T11:16:46,138 copying pele_platform/Utilities/Helpers/constraints/smiles_constraints.py -> build/lib/pele_platform/Utilities/Helpers/constraints 2022-08-01T11:16:46,143 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams 2022-08-01T11:16:46,145 copying pele_platform/Utilities/Parameters/SimulationParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams 2022-08-01T11:16:46,148 copying pele_platform/Utilities/Parameters/SimulationParams/simulation_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams 2022-08-01T11:16:46,154 creating build/lib/pele_platform/Utilities/Parameters/SimulationFolders 2022-08-01T11:16:46,156 copying pele_platform/Utilities/Parameters/SimulationFolders/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationFolders 2022-08-01T11:16:46,158 copying pele_platform/Utilities/Parameters/SimulationFolders/simulation_folders.py -> build/lib/pele_platform/Utilities/Parameters/SimulationFolders 2022-08-01T11:16:46,163 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2022-08-01T11:16:46,165 copying pele_platform/Utilities/Parameters/SimulationParams/InOutParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2022-08-01T11:16:46,168 copying pele_platform/Utilities/Parameters/SimulationParams/InOutParams/inout_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2022-08-01T11:16:46,172 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2022-08-01T11:16:46,173 copying pele_platform/Utilities/Parameters/SimulationParams/GlideParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2022-08-01T11:16:46,176 copying pele_platform/Utilities/Parameters/SimulationParams/GlideParams/glide_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2022-08-01T11:16:46,181 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2022-08-01T11:16:46,182 copying pele_platform/Utilities/Parameters/SimulationParams/BiasParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2022-08-01T11:16:46,185 copying pele_platform/Utilities/Parameters/SimulationParams/BiasParams/bias_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2022-08-01T11:16:46,190 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2022-08-01T11:16:46,191 copying pele_platform/Utilities/Parameters/SimulationParams/MSMParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2022-08-01T11:16:46,194 copying pele_platform/Utilities/Parameters/SimulationParams/MSMParams/msm_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2022-08-01T11:16:46,198 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA 2022-08-01T11:16:46,200 copying pele_platform/Utilities/Parameters/SimulationParams/PCA/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA 2022-08-01T11:16:46,203 copying pele_platform/Utilities/Parameters/SimulationParams/PCA/pca.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA 2022-08-01T11:16:46,208 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI 2022-08-01T11:16:46,209 copying pele_platform/Utilities/Parameters/SimulationParams/PPI/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI 2022-08-01T11:16:46,212 copying pele_platform/Utilities/Parameters/SimulationParams/PPI/ppi.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI 2022-08-01T11:16:46,216 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2022-08-01T11:16:46,218 copying pele_platform/Utilities/Parameters/SimulationParams/site_finder/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2022-08-01T11:16:46,221 copying pele_platform/Utilities/Parameters/SimulationParams/site_finder/site_finder.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2022-08-01T11:16:46,226 creating build/lib/pele_platform/Frag/parameters 2022-08-01T11:16:46,227 copying pele_platform/Frag/parameters/simulation.py -> build/lib/pele_platform/Frag/parameters 2022-08-01T11:16:46,230 copying pele_platform/Frag/parameters/__init__.py -> build/lib/pele_platform/Frag/parameters 2022-08-01T11:16:46,234 copying pele_platform/Frag/parameters/files.py -> build/lib/pele_platform/Frag/parameters 2022-08-01T11:16:46,237 copying pele_platform/Frag/parameters/metrics.py -> build/lib/pele_platform/Frag/parameters 2022-08-01T11:16:46,240 copying pele_platform/Frag/parameters/optional.py -> build/lib/pele_platform/Frag/parameters 2022-08-01T11:16:46,243 copying pele_platform/Frag/parameters/water.py -> build/lib/pele_platform/Frag/parameters 2022-08-01T11:16:46,247 running egg_info 2022-08-01T11:16:47,599 writing pele_platform.egg-info/PKG-INFO 2022-08-01T11:16:48,199 writing dependency_links to pele_platform.egg-info/dependency_links.txt 2022-08-01T11:16:51,168 writing requirements to pele_platform.egg-info/requires.txt 2022-08-01T11:16:51,764 writing top-level names to pele_platform.egg-info/top_level.txt 2022-08-01T11:16:51,885 reading manifest file 'pele_platform.egg-info/SOURCES.txt' 2022-08-01T11:16:51,999 reading manifest template 'MANIFEST.in' 2022-08-01T11:16:52,001 warning: no files found matching 'pele_platform/Utilities/PlopRotTemp/param/*' 2022-08-01T11:16:52,002 warning: no files found matching 'pele_platform/AdaptivePELE/atomset/*' 2022-08-01T11:16:52,002 warning: no files found matching 'pele_platform/AdaptivePELE/freeEnergies/*' 2022-08-01T11:16:52,003 warning: no files found matching '*' under directory 'pele_platform/Utilities/PPP/Data/' 2022-08-01T11:16:52,339 warning: no files found matching '*' under directory 'tests/data' 2022-08-01T11:16:52,340 adding license file 'LICENSE' 2022-08-01T11:16:52,404 writing manifest file 'pele_platform.egg-info/SOURCES.txt' 2022-08-01T11:16:52,410 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,412 ############################ 2022-08-01T11:16:52,412 # Package would be ignored # 2022-08-01T11:16:52,412 ############################ 2022-08-01T11:16:52,412 Python recognizes 'pele_platform.Examples' as an importable package, however it is 2022-08-01T11:16:52,413 included in the distribution as "data". 2022-08-01T11:16:52,413 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,413 therefore is considered deprecated). 2022-08-01T11:16:52,414 Please make sure that 'pele_platform.Examples' is included as a package by using 2022-08-01T11:16:52,414 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,415 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,415 documentation page. 2022-08-01T11:16:52,416 !! 2022-08-01T11:16:52,417 check.warn(importable) 2022-08-01T11:16:52,417 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,418 ############################ 2022-08-01T11:16:52,418 # Package would be ignored # 2022-08-01T11:16:52,419 ############################ 2022-08-01T11:16:52,419 Python recognizes 'pele_platform.Examples.Adaptive' as an importable package, however it is 2022-08-01T11:16:52,419 included in the distribution as "data". 2022-08-01T11:16:52,420 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,420 therefore is considered deprecated). 2022-08-01T11:16:52,421 Please make sure that 'pele_platform.Examples.Adaptive' is included as a package by using 2022-08-01T11:16:52,421 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,421 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,422 documentation page. 2022-08-01T11:16:52,423 !! 2022-08-01T11:16:52,423 check.warn(importable) 2022-08-01T11:16:52,424 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,424 ############################ 2022-08-01T11:16:52,425 # Package would be ignored # 2022-08-01T11:16:52,425 ############################ 2022-08-01T11:16:52,425 Python recognizes 'pele_platform.Examples.Msm' as an importable package, however it is 2022-08-01T11:16:52,426 included in the distribution as "data". 2022-08-01T11:16:52,426 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,426 therefore is considered deprecated). 2022-08-01T11:16:52,427 Please make sure that 'pele_platform.Examples.Msm' is included as a package by using 2022-08-01T11:16:52,427 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,428 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,428 documentation page. 2022-08-01T11:16:52,429 !! 2022-08-01T11:16:52,429 check.warn(importable) 2022-08-01T11:16:52,430 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,430 ############################ 2022-08-01T11:16:52,431 # Package would be ignored # 2022-08-01T11:16:52,431 ############################ 2022-08-01T11:16:52,431 Python recognizes 'pele_platform.Examples.PPI' as an importable package, however it is 2022-08-01T11:16:52,432 included in the distribution as "data". 2022-08-01T11:16:52,432 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,432 therefore is considered deprecated). 2022-08-01T11:16:52,433 Please make sure that 'pele_platform.Examples.PPI' is included as a package by using 2022-08-01T11:16:52,433 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,434 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,434 documentation page. 2022-08-01T11:16:52,435 !! 2022-08-01T11:16:52,436 check.warn(importable) 2022-08-01T11:16:52,436 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,437 ############################ 2022-08-01T11:16:52,437 # Package would be ignored # 2022-08-01T11:16:52,437 ############################ 2022-08-01T11:16:52,438 Python recognizes 'pele_platform.Examples.RNA' as an importable package, however it is 2022-08-01T11:16:52,438 included in the distribution as "data". 2022-08-01T11:16:52,438 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,438 therefore is considered deprecated). 2022-08-01T11:16:52,439 Please make sure that 'pele_platform.Examples.RNA' is included as a package by using 2022-08-01T11:16:52,439 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,440 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,440 documentation page. 2022-08-01T11:16:52,441 !! 2022-08-01T11:16:52,442 check.warn(importable) 2022-08-01T11:16:52,442 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,443 ############################ 2022-08-01T11:16:52,443 # Package would be ignored # 2022-08-01T11:16:52,443 ############################ 2022-08-01T11:16:52,444 Python recognizes 'pele_platform.Examples.analysis' as an importable package, however it is 2022-08-01T11:16:52,444 included in the distribution as "data". 2022-08-01T11:16:52,444 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,444 therefore is considered deprecated). 2022-08-01T11:16:52,445 Please make sure that 'pele_platform.Examples.analysis' is included as a package by using 2022-08-01T11:16:52,445 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,446 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,446 documentation page. 2022-08-01T11:16:52,447 !! 2022-08-01T11:16:52,448 check.warn(importable) 2022-08-01T11:16:52,448 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,449 ############################ 2022-08-01T11:16:52,449 # Package would be ignored # 2022-08-01T11:16:52,450 ############################ 2022-08-01T11:16:52,450 Python recognizes 'pele_platform.Examples.analysis.data' as an importable package, however it is 2022-08-01T11:16:52,450 included in the distribution as "data". 2022-08-01T11:16:52,450 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,451 therefore is considered deprecated). 2022-08-01T11:16:52,451 Please make sure that 'pele_platform.Examples.analysis.data' is included as a package by using 2022-08-01T11:16:52,452 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,452 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,452 documentation page. 2022-08-01T11:16:52,453 !! 2022-08-01T11:16:52,454 check.warn(importable) 2022-08-01T11:16:52,454 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,455 ############################ 2022-08-01T11:16:52,456 # Package would be ignored # 2022-08-01T11:16:52,456 ############################ 2022-08-01T11:16:52,456 Python recognizes 'pele_platform.Examples.analysis.data.empty_reports_output' as an importable package, however it is 2022-08-01T11:16:52,456 included in the distribution as "data". 2022-08-01T11:16:52,457 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,457 therefore is considered deprecated). 2022-08-01T11:16:52,458 Please make sure that 'pele_platform.Examples.analysis.data.empty_reports_output' is included as a package by using 2022-08-01T11:16:52,458 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,458 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,459 documentation page. 2022-08-01T11:16:52,460 !! 2022-08-01T11:16:52,460 check.warn(importable) 2022-08-01T11:16:52,460 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,461 ############################ 2022-08-01T11:16:52,462 # Package would be ignored # 2022-08-01T11:16:52,462 ############################ 2022-08-01T11:16:52,462 Python recognizes 'pele_platform.Examples.analysis.data.inputs' as an importable package, however it is 2022-08-01T11:16:52,462 included in the distribution as "data". 2022-08-01T11:16:52,463 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,463 therefore is considered deprecated). 2022-08-01T11:16:52,464 Please make sure that 'pele_platform.Examples.analysis.data.inputs' is included as a package by using 2022-08-01T11:16:52,464 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,465 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,465 documentation page. 2022-08-01T11:16:52,466 !! 2022-08-01T11:16:52,466 check.warn(importable) 2022-08-01T11:16:52,467 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,467 ############################ 2022-08-01T11:16:52,468 # Package would be ignored # 2022-08-01T11:16:52,468 ############################ 2022-08-01T11:16:52,468 Python recognizes 'pele_platform.Examples.analysis.data.output' as an importable package, however it is 2022-08-01T11:16:52,469 included in the distribution as "data". 2022-08-01T11:16:52,469 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,469 therefore is considered deprecated). 2022-08-01T11:16:52,470 Please make sure that 'pele_platform.Examples.analysis.data.output' is included as a package by using 2022-08-01T11:16:52,470 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,471 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,471 documentation page. 2022-08-01T11:16:52,472 !! 2022-08-01T11:16:52,472 check.warn(importable) 2022-08-01T11:16:52,473 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,474 ############################ 2022-08-01T11:16:52,474 # Package would be ignored # 2022-08-01T11:16:52,474 ############################ 2022-08-01T11:16:52,474 Python recognizes 'pele_platform.Examples.analysis.data.output.synchronization' as an importable package, however it is 2022-08-01T11:16:52,475 included in the distribution as "data". 2022-08-01T11:16:52,475 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,475 therefore is considered deprecated). 2022-08-01T11:16:52,476 Please make sure that 'pele_platform.Examples.analysis.data.output.synchronization' is included as a package by using 2022-08-01T11:16:52,476 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,477 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,477 documentation page. 2022-08-01T11:16:52,478 !! 2022-08-01T11:16:52,479 check.warn(importable) 2022-08-01T11:16:52,479 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,480 ############################ 2022-08-01T11:16:52,480 # Package would be ignored # 2022-08-01T11:16:52,480 ############################ 2022-08-01T11:16:52,481 Python recognizes 'pele_platform.Examples.analysis.data.output.topologies' as an importable package, however it is 2022-08-01T11:16:52,481 included in the distribution as "data". 2022-08-01T11:16:52,481 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,481 therefore is considered deprecated). 2022-08-01T11:16:52,482 Please make sure that 'pele_platform.Examples.analysis.data.output.topologies' is included as a package by using 2022-08-01T11:16:52,482 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,483 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,483 documentation page. 2022-08-01T11:16:52,484 !! 2022-08-01T11:16:52,485 check.warn(importable) 2022-08-01T11:16:52,485 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,486 ############################ 2022-08-01T11:16:52,486 # Package would be ignored # 2022-08-01T11:16:52,486 ############################ 2022-08-01T11:16:52,487 Python recognizes 'pele_platform.Examples.analysis.data.xtc' as an importable package, however it is 2022-08-01T11:16:52,487 included in the distribution as "data". 2022-08-01T11:16:52,487 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,487 therefore is considered deprecated). 2022-08-01T11:16:52,488 Please make sure that 'pele_platform.Examples.analysis.data.xtc' is included as a package by using 2022-08-01T11:16:52,488 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,489 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,489 documentation page. 2022-08-01T11:16:52,490 !! 2022-08-01T11:16:52,491 check.warn(importable) 2022-08-01T11:16:52,491 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,492 ############################ 2022-08-01T11:16:52,492 # Package would be ignored # 2022-08-01T11:16:52,492 ############################ 2022-08-01T11:16:52,493 Python recognizes 'pele_platform.Examples.analysis.data.xtc.topologies' as an importable package, however it is 2022-08-01T11:16:52,493 included in the distribution as "data". 2022-08-01T11:16:52,493 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,493 therefore is considered deprecated). 2022-08-01T11:16:52,494 Please make sure that 'pele_platform.Examples.analysis.data.xtc.topologies' is included as a package by using 2022-08-01T11:16:52,494 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,495 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,495 documentation page. 2022-08-01T11:16:52,496 !! 2022-08-01T11:16:52,497 check.warn(importable) 2022-08-01T11:16:52,497 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,498 ############################ 2022-08-01T11:16:52,498 # Package would be ignored # 2022-08-01T11:16:52,498 ############################ 2022-08-01T11:16:52,499 Python recognizes 'pele_platform.Examples.bias' as an importable package, however it is 2022-08-01T11:16:52,499 included in the distribution as "data". 2022-08-01T11:16:52,499 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,500 therefore is considered deprecated). 2022-08-01T11:16:52,500 Please make sure that 'pele_platform.Examples.bias' is included as a package by using 2022-08-01T11:16:52,500 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,501 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,501 documentation page. 2022-08-01T11:16:52,502 !! 2022-08-01T11:16:52,503 check.warn(importable) 2022-08-01T11:16:52,503 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,504 ############################ 2022-08-01T11:16:52,504 # Package would be ignored # 2022-08-01T11:16:52,504 ############################ 2022-08-01T11:16:52,505 Python recognizes 'pele_platform.Examples.box' as an importable package, however it is 2022-08-01T11:16:52,505 included in the distribution as "data". 2022-08-01T11:16:52,505 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,506 therefore is considered deprecated). 2022-08-01T11:16:52,506 Please make sure that 'pele_platform.Examples.box' is included as a package by using 2022-08-01T11:16:52,506 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,507 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,507 documentation page. 2022-08-01T11:16:52,508 !! 2022-08-01T11:16:52,509 check.warn(importable) 2022-08-01T11:16:52,509 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,510 ############################ 2022-08-01T11:16:52,510 # Package would be ignored # 2022-08-01T11:16:52,511 ############################ 2022-08-01T11:16:52,511 Python recognizes 'pele_platform.Examples.checker' as an importable package, however it is 2022-08-01T11:16:52,511 included in the distribution as "data". 2022-08-01T11:16:52,511 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,512 therefore is considered deprecated). 2022-08-01T11:16:52,512 Please make sure that 'pele_platform.Examples.checker' is included as a package by using 2022-08-01T11:16:52,513 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,513 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,514 documentation page. 2022-08-01T11:16:52,514 !! 2022-08-01T11:16:52,515 check.warn(importable) 2022-08-01T11:16:52,515 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,516 ############################ 2022-08-01T11:16:52,516 # Package would be ignored # 2022-08-01T11:16:52,517 ############################ 2022-08-01T11:16:52,517 Python recognizes 'pele_platform.Examples.clustering' as an importable package, however it is 2022-08-01T11:16:52,517 included in the distribution as "data". 2022-08-01T11:16:52,518 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,518 therefore is considered deprecated). 2022-08-01T11:16:52,518 Please make sure that 'pele_platform.Examples.clustering' is included as a package by using 2022-08-01T11:16:52,519 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,519 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,520 documentation page. 2022-08-01T11:16:52,520 !! 2022-08-01T11:16:52,521 check.warn(importable) 2022-08-01T11:16:52,521 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,522 ############################ 2022-08-01T11:16:52,522 # Package would be ignored # 2022-08-01T11:16:52,523 ############################ 2022-08-01T11:16:52,523 Python recognizes 'pele_platform.Examples.clustering_xtc' as an importable package, however it is 2022-08-01T11:16:52,523 included in the distribution as "data". 2022-08-01T11:16:52,524 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,524 therefore is considered deprecated). 2022-08-01T11:16:52,524 Please make sure that 'pele_platform.Examples.clustering_xtc' is included as a package by using 2022-08-01T11:16:52,525 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,525 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,526 documentation page. 2022-08-01T11:16:52,526 !! 2022-08-01T11:16:52,527 check.warn(importable) 2022-08-01T11:16:52,527 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,528 ############################ 2022-08-01T11:16:52,528 # Package would be ignored # 2022-08-01T11:16:52,529 ############################ 2022-08-01T11:16:52,529 Python recognizes 'pele_platform.Examples.constraints' as an importable package, however it is 2022-08-01T11:16:52,529 included in the distribution as "data". 2022-08-01T11:16:52,530 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,530 therefore is considered deprecated). 2022-08-01T11:16:52,531 Please make sure that 'pele_platform.Examples.constraints' is included as a package by using 2022-08-01T11:16:52,531 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,531 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,532 documentation page. 2022-08-01T11:16:52,533 !! 2022-08-01T11:16:52,533 check.warn(importable) 2022-08-01T11:16:52,533 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,534 ############################ 2022-08-01T11:16:52,535 # Package would be ignored # 2022-08-01T11:16:52,535 ############################ 2022-08-01T11:16:52,535 Python recognizes 'pele_platform.Examples.covalent_docking' as an importable package, however it is 2022-08-01T11:16:52,535 included in the distribution as "data". 2022-08-01T11:16:52,536 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,536 therefore is considered deprecated). 2022-08-01T11:16:52,537 Please make sure that 'pele_platform.Examples.covalent_docking' is included as a package by using 2022-08-01T11:16:52,537 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,537 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,538 documentation page. 2022-08-01T11:16:52,539 !! 2022-08-01T11:16:52,539 check.warn(importable) 2022-08-01T11:16:52,539 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,540 ############################ 2022-08-01T11:16:52,541 # Package would be ignored # 2022-08-01T11:16:52,541 ############################ 2022-08-01T11:16:52,541 Python recognizes 'pele_platform.Examples.enzyme_engineering' as an importable package, however it is 2022-08-01T11:16:52,541 included in the distribution as "data". 2022-08-01T11:16:52,542 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,542 therefore is considered deprecated). 2022-08-01T11:16:52,543 Please make sure that 'pele_platform.Examples.enzyme_engineering' is included as a package by using 2022-08-01T11:16:52,543 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,543 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,544 documentation page. 2022-08-01T11:16:52,545 !! 2022-08-01T11:16:52,545 check.warn(importable) 2022-08-01T11:16:52,545 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,546 ############################ 2022-08-01T11:16:52,547 # Package would be ignored # 2022-08-01T11:16:52,547 ############################ 2022-08-01T11:16:52,547 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart' as an importable package, however it is 2022-08-01T11:16:52,547 included in the distribution as "data". 2022-08-01T11:16:52,548 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,548 therefore is considered deprecated). 2022-08-01T11:16:52,549 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart' is included as a package by using 2022-08-01T11:16:52,549 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,549 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,550 documentation page. 2022-08-01T11:16:52,550 !! 2022-08-01T11:16:52,551 check.warn(importable) 2022-08-01T11:16:52,551 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,552 ############################ 2022-08-01T11:16:52,552 # Package would be ignored # 2022-08-01T11:16:52,553 ############################ 2022-08-01T11:16:52,553 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1' as an importable package, however it is 2022-08-01T11:16:52,553 included in the distribution as "data". 2022-08-01T11:16:52,554 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,554 therefore is considered deprecated). 2022-08-01T11:16:52,554 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1' is included as a package by using 2022-08-01T11:16:52,555 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,555 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,556 documentation page. 2022-08-01T11:16:52,557 !! 2022-08-01T11:16:52,557 check.warn(importable) 2022-08-01T11:16:52,557 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,558 ############################ 2022-08-01T11:16:52,558 # Package would be ignored # 2022-08-01T11:16:52,559 ############################ 2022-08-01T11:16:52,559 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.DataLocal.LigandRotamerLibs' as an importable package, however it is 2022-08-01T11:16:52,559 included in the distribution as "data". 2022-08-01T11:16:52,560 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,560 therefore is considered deprecated). 2022-08-01T11:16:52,560 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.DataLocal.LigandRotamerLibs' is included as a package by using 2022-08-01T11:16:52,561 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,561 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,562 documentation page. 2022-08-01T11:16:52,562 !! 2022-08-01T11:16:52,563 check.warn(importable) 2022-08-01T11:16:52,563 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,564 ############################ 2022-08-01T11:16:52,565 # Package would be ignored # 2022-08-01T11:16:52,565 ############################ 2022-08-01T11:16:52,565 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.DataLocal.Templates.OPLS2005.HeteroAtoms' as an importable package, however it is 2022-08-01T11:16:52,565 included in the distribution as "data". 2022-08-01T11:16:52,566 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,566 therefore is considered deprecated). 2022-08-01T11:16:52,567 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.DataLocal.Templates.OPLS2005.HeteroAtoms' is included as a package by using 2022-08-01T11:16:52,567 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,567 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,568 documentation page. 2022-08-01T11:16:52,569 !! 2022-08-01T11:16:52,569 check.warn(importable) 2022-08-01T11:16:52,570 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,570 ############################ 2022-08-01T11:16:52,571 # Package would be ignored # 2022-08-01T11:16:52,571 ############################ 2022-08-01T11:16:52,571 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.input' as an importable package, however it is 2022-08-01T11:16:52,572 included in the distribution as "data". 2022-08-01T11:16:52,572 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,572 therefore is considered deprecated). 2022-08-01T11:16:52,573 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.input' is included as a package by using 2022-08-01T11:16:52,573 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,574 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,574 documentation page. 2022-08-01T11:16:52,575 !! 2022-08-01T11:16:52,576 check.warn(importable) 2022-08-01T11:16:52,576 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,577 ############################ 2022-08-01T11:16:52,577 # Package would be ignored # 2022-08-01T11:16:52,578 ############################ 2022-08-01T11:16:52,578 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.output' as an importable package, however it is 2022-08-01T11:16:52,578 included in the distribution as "data". 2022-08-01T11:16:52,579 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,579 therefore is considered deprecated). 2022-08-01T11:16:52,580 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.output' is included as a package by using 2022-08-01T11:16:52,580 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,580 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,581 documentation page. 2022-08-01T11:16:52,582 !! 2022-08-01T11:16:52,582 check.warn(importable) 2022-08-01T11:16:52,583 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,584 ############################ 2022-08-01T11:16:52,584 # Package would be ignored # 2022-08-01T11:16:52,584 ############################ 2022-08-01T11:16:52,585 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.output.T454A' as an importable package, however it is 2022-08-01T11:16:52,585 included in the distribution as "data". 2022-08-01T11:16:52,585 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,586 therefore is considered deprecated). 2022-08-01T11:16:52,586 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.output.T454A' is included as a package by using 2022-08-01T11:16:52,587 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,587 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,588 documentation page. 2022-08-01T11:16:52,589 !! 2022-08-01T11:16:52,589 check.warn(importable) 2022-08-01T11:16:52,590 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,591 ############################ 2022-08-01T11:16:52,591 # Package would be ignored # 2022-08-01T11:16:52,591 ############################ 2022-08-01T11:16:52,591 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.output.T454D' as an importable package, however it is 2022-08-01T11:16:52,592 included in the distribution as "data". 2022-08-01T11:16:52,592 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,592 therefore is considered deprecated). 2022-08-01T11:16:52,593 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.output.T454D' is included as a package by using 2022-08-01T11:16:52,593 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,594 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,595 documentation page. 2022-08-01T11:16:52,596 !! 2022-08-01T11:16:52,596 check.warn(importable) 2022-08-01T11:16:52,597 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,598 ############################ 2022-08-01T11:16:52,598 # Package would be ignored # 2022-08-01T11:16:52,598 ############################ 2022-08-01T11:16:52,599 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.output.synchronization' as an importable package, however it is 2022-08-01T11:16:52,599 included in the distribution as "data". 2022-08-01T11:16:52,600 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,601 therefore is considered deprecated). 2022-08-01T11:16:52,602 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.output.synchronization' is included as a package by using 2022-08-01T11:16:52,603 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,603 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,604 documentation page. 2022-08-01T11:16:52,605 !! 2022-08-01T11:16:52,605 check.warn(importable) 2022-08-01T11:16:52,606 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,607 ############################ 2022-08-01T11:16:52,607 # Package would be ignored # 2022-08-01T11:16:52,608 ############################ 2022-08-01T11:16:52,608 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.output.topologies' as an importable package, however it is 2022-08-01T11:16:52,608 included in the distribution as "data". 2022-08-01T11:16:52,609 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,609 therefore is considered deprecated). 2022-08-01T11:16:52,610 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.output.topologies' is included as a package by using 2022-08-01T11:16:52,610 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,611 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,611 documentation page. 2022-08-01T11:16:52,612 !! 2022-08-01T11:16:52,613 check.warn(importable) 2022-08-01T11:16:52,614 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,615 ############################ 2022-08-01T11:16:52,615 # Package would be ignored # 2022-08-01T11:16:52,616 ############################ 2022-08-01T11:16:52,616 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.tmp_output' as an importable package, however it is 2022-08-01T11:16:52,616 included in the distribution as "data". 2022-08-01T11:16:52,617 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,617 therefore is considered deprecated). 2022-08-01T11:16:52,618 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_1.tmp_output' is included as a package by using 2022-08-01T11:16:52,618 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,619 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,619 documentation page. 2022-08-01T11:16:52,620 !! 2022-08-01T11:16:52,620 check.warn(importable) 2022-08-01T11:16:52,621 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,622 ############################ 2022-08-01T11:16:52,622 # Package would be ignored # 2022-08-01T11:16:52,624 ############################ 2022-08-01T11:16:52,625 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_2' as an importable package, however it is 2022-08-01T11:16:52,626 included in the distribution as "data". 2022-08-01T11:16:52,626 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,627 therefore is considered deprecated). 2022-08-01T11:16:52,628 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_2' is included as a package by using 2022-08-01T11:16:52,629 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,629 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,630 documentation page. 2022-08-01T11:16:52,631 !! 2022-08-01T11:16:52,631 check.warn(importable) 2022-08-01T11:16:52,632 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,632 ############################ 2022-08-01T11:16:52,633 # Package would be ignored # 2022-08-01T11:16:52,633 ############################ 2022-08-01T11:16:52,634 Python recognizes 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_2.input' as an importable package, however it is 2022-08-01T11:16:52,634 included in the distribution as "data". 2022-08-01T11:16:52,634 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,634 therefore is considered deprecated). 2022-08-01T11:16:52,635 Please make sure that 'pele_platform.Examples.enzyme_engineering.directory_to_restart.Subset_2.input' is included as a package by using 2022-08-01T11:16:52,635 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,636 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,636 documentation page. 2022-08-01T11:16:52,637 !! 2022-08-01T11:16:52,638 check.warn(importable) 2022-08-01T11:16:52,638 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,639 ############################ 2022-08-01T11:16:52,639 # Package would be ignored # 2022-08-01T11:16:52,640 ############################ 2022-08-01T11:16:52,640 Python recognizes 'pele_platform.Examples.enzyme_engineering.pdb_files' as an importable package, however it is 2022-08-01T11:16:52,641 included in the distribution as "data". 2022-08-01T11:16:52,641 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,641 therefore is considered deprecated). 2022-08-01T11:16:52,642 Please make sure that 'pele_platform.Examples.enzyme_engineering.pdb_files' is included as a package by using 2022-08-01T11:16:52,642 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,643 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,643 documentation page. 2022-08-01T11:16:52,644 !! 2022-08-01T11:16:52,645 check.warn(importable) 2022-08-01T11:16:52,645 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,646 ############################ 2022-08-01T11:16:52,646 # Package would be ignored # 2022-08-01T11:16:52,647 ############################ 2022-08-01T11:16:52,647 Python recognizes 'pele_platform.Examples.exit' as an importable package, however it is 2022-08-01T11:16:52,647 included in the distribution as "data". 2022-08-01T11:16:52,648 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,648 therefore is considered deprecated). 2022-08-01T11:16:52,649 Please make sure that 'pele_platform.Examples.exit' is included as a package by using 2022-08-01T11:16:52,649 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,650 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,650 documentation page. 2022-08-01T11:16:52,651 !! 2022-08-01T11:16:52,652 check.warn(importable) 2022-08-01T11:16:52,652 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,653 ############################ 2022-08-01T11:16:52,654 # Package would be ignored # 2022-08-01T11:16:52,654 ############################ 2022-08-01T11:16:52,654 Python recognizes 'pele_platform.Examples.exit_soft' as an importable package, however it is 2022-08-01T11:16:52,655 included in the distribution as "data". 2022-08-01T11:16:52,655 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,655 therefore is considered deprecated). 2022-08-01T11:16:52,656 Please make sure that 'pele_platform.Examples.exit_soft' is included as a package by using 2022-08-01T11:16:52,656 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,657 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,657 documentation page. 2022-08-01T11:16:52,658 !! 2022-08-01T11:16:52,658 check.warn(importable) 2022-08-01T11:16:52,659 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,660 ############################ 2022-08-01T11:16:52,660 # Package would be ignored # 2022-08-01T11:16:52,660 ############################ 2022-08-01T11:16:52,661 Python recognizes 'pele_platform.Examples.flags' as an importable package, however it is 2022-08-01T11:16:52,661 included in the distribution as "data". 2022-08-01T11:16:52,661 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,662 therefore is considered deprecated). 2022-08-01T11:16:52,662 Please make sure that 'pele_platform.Examples.flags' is included as a package by using 2022-08-01T11:16:52,663 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,663 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,664 documentation page. 2022-08-01T11:16:52,664 !! 2022-08-01T11:16:52,665 check.warn(importable) 2022-08-01T11:16:52,665 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,666 ############################ 2022-08-01T11:16:52,666 # Package would be ignored # 2022-08-01T11:16:52,667 ############################ 2022-08-01T11:16:52,667 Python recognizes 'pele_platform.Examples.frag' as an importable package, however it is 2022-08-01T11:16:52,667 included in the distribution as "data". 2022-08-01T11:16:52,668 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,668 therefore is considered deprecated). 2022-08-01T11:16:52,669 Please make sure that 'pele_platform.Examples.frag' is included as a package by using 2022-08-01T11:16:52,669 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,670 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,670 documentation page. 2022-08-01T11:16:52,671 !! 2022-08-01T11:16:52,672 check.warn(importable) 2022-08-01T11:16:52,672 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,673 ############################ 2022-08-01T11:16:52,674 # Package would be ignored # 2022-08-01T11:16:52,674 ############################ 2022-08-01T11:16:52,674 Python recognizes 'pele_platform.Examples.frag.analysis_data' as an importable package, however it is 2022-08-01T11:16:52,675 included in the distribution as "data". 2022-08-01T11:16:52,675 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,675 therefore is considered deprecated). 2022-08-01T11:16:52,676 Please make sure that 'pele_platform.Examples.frag.analysis_data' is included as a package by using 2022-08-01T11:16:52,676 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,677 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,677 documentation page. 2022-08-01T11:16:52,678 !! 2022-08-01T11:16:52,679 check.warn(importable) 2022-08-01T11:16:52,679 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,680 ############################ 2022-08-01T11:16:52,681 # Package would be ignored # 2022-08-01T11:16:52,681 ############################ 2022-08-01T11:16:52,681 Python recognizes 'pele_platform.Examples.frag.checker' as an importable package, however it is 2022-08-01T11:16:52,682 included in the distribution as "data". 2022-08-01T11:16:52,682 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,682 therefore is considered deprecated). 2022-08-01T11:16:52,683 Please make sure that 'pele_platform.Examples.frag.checker' is included as a package by using 2022-08-01T11:16:52,683 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,684 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,684 documentation page. 2022-08-01T11:16:52,685 !! 2022-08-01T11:16:52,686 check.warn(importable) 2022-08-01T11:16:52,686 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,687 ############################ 2022-08-01T11:16:52,688 # Package would be ignored # 2022-08-01T11:16:52,688 ############################ 2022-08-01T11:16:52,688 Python recognizes 'pele_platform.Examples.frag.pdb_test_lib' as an importable package, however it is 2022-08-01T11:16:52,688 included in the distribution as "data". 2022-08-01T11:16:52,689 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,689 therefore is considered deprecated). 2022-08-01T11:16:52,690 Please make sure that 'pele_platform.Examples.frag.pdb_test_lib' is included as a package by using 2022-08-01T11:16:52,690 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,691 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,691 documentation page. 2022-08-01T11:16:52,692 !! 2022-08-01T11:16:52,692 check.warn(importable) 2022-08-01T11:16:52,693 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,694 ############################ 2022-08-01T11:16:52,694 # Package would be ignored # 2022-08-01T11:16:52,694 ############################ 2022-08-01T11:16:52,695 Python recognizes 'pele_platform.Examples.frag.sdf_joiner' as an importable package, however it is 2022-08-01T11:16:52,695 included in the distribution as "data". 2022-08-01T11:16:52,695 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,695 therefore is considered deprecated). 2022-08-01T11:16:52,696 Please make sure that 'pele_platform.Examples.frag.sdf_joiner' is included as a package by using 2022-08-01T11:16:52,696 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,697 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,697 documentation page. 2022-08-01T11:16:52,698 !! 2022-08-01T11:16:52,699 check.warn(importable) 2022-08-01T11:16:52,699 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,700 ############################ 2022-08-01T11:16:52,701 # Package would be ignored # 2022-08-01T11:16:52,701 ############################ 2022-08-01T11:16:52,701 Python recognizes 'pele_platform.Examples.frag.sdf_test_lib' as an importable package, however it is 2022-08-01T11:16:52,701 included in the distribution as "data". 2022-08-01T11:16:52,702 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,702 therefore is considered deprecated). 2022-08-01T11:16:52,703 Please make sure that 'pele_platform.Examples.frag.sdf_test_lib' is included as a package by using 2022-08-01T11:16:52,703 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,704 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,704 documentation page. 2022-08-01T11:16:52,707 !! 2022-08-01T11:16:52,708 check.warn(importable) 2022-08-01T11:16:52,708 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,709 ############################ 2022-08-01T11:16:52,709 # Package would be ignored # 2022-08-01T11:16:52,710 ############################ 2022-08-01T11:16:52,710 Python recognizes 'pele_platform.Examples.global' as an importable package, however it is 2022-08-01T11:16:52,711 included in the distribution as "data". 2022-08-01T11:16:52,711 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,711 therefore is considered deprecated). 2022-08-01T11:16:52,712 Please make sure that 'pele_platform.Examples.global' is included as a package by using 2022-08-01T11:16:52,712 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,713 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,713 documentation page. 2022-08-01T11:16:52,714 !! 2022-08-01T11:16:52,715 check.warn(importable) 2022-08-01T11:16:52,715 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,716 ############################ 2022-08-01T11:16:52,716 # Package would be ignored # 2022-08-01T11:16:52,717 ############################ 2022-08-01T11:16:52,717 Python recognizes 'pele_platform.Examples.gpcr' as an importable package, however it is 2022-08-01T11:16:52,717 included in the distribution as "data". 2022-08-01T11:16:52,718 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,718 therefore is considered deprecated). 2022-08-01T11:16:52,719 Please make sure that 'pele_platform.Examples.gpcr' is included as a package by using 2022-08-01T11:16:52,719 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,720 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,720 documentation page. 2022-08-01T11:16:52,721 !! 2022-08-01T11:16:52,722 check.warn(importable) 2022-08-01T11:16:52,722 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,723 ############################ 2022-08-01T11:16:52,723 # Package would be ignored # 2022-08-01T11:16:52,724 ############################ 2022-08-01T11:16:52,724 Python recognizes 'pele_platform.Examples.induced_fit' as an importable package, however it is 2022-08-01T11:16:52,724 included in the distribution as "data". 2022-08-01T11:16:52,725 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,725 therefore is considered deprecated). 2022-08-01T11:16:52,726 Please make sure that 'pele_platform.Examples.induced_fit' is included as a package by using 2022-08-01T11:16:52,726 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,727 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,727 documentation page. 2022-08-01T11:16:52,728 !! 2022-08-01T11:16:52,729 check.warn(importable) 2022-08-01T11:16:52,729 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,730 ############################ 2022-08-01T11:16:52,730 # Package would be ignored # 2022-08-01T11:16:52,731 ############################ 2022-08-01T11:16:52,731 Python recognizes 'pele_platform.Examples.inputs' as an importable package, however it is 2022-08-01T11:16:52,732 included in the distribution as "data". 2022-08-01T11:16:52,733 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,734 therefore is considered deprecated). 2022-08-01T11:16:52,735 Please make sure that 'pele_platform.Examples.inputs' is included as a package by using 2022-08-01T11:16:52,735 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,736 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,736 documentation page. 2022-08-01T11:16:52,737 !! 2022-08-01T11:16:52,738 check.warn(importable) 2022-08-01T11:16:52,738 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,739 ############################ 2022-08-01T11:16:52,740 # Package would be ignored # 2022-08-01T11:16:52,740 ############################ 2022-08-01T11:16:52,740 Python recognizes 'pele_platform.Examples.interaction_restrictions' as an importable package, however it is 2022-08-01T11:16:52,741 included in the distribution as "data". 2022-08-01T11:16:52,741 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,741 therefore is considered deprecated). 2022-08-01T11:16:52,742 Please make sure that 'pele_platform.Examples.interaction_restrictions' is included as a package by using 2022-08-01T11:16:52,742 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,743 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,743 documentation page. 2022-08-01T11:16:52,744 !! 2022-08-01T11:16:52,745 check.warn(importable) 2022-08-01T11:16:52,745 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,746 ############################ 2022-08-01T11:16:52,746 # Package would be ignored # 2022-08-01T11:16:52,746 ############################ 2022-08-01T11:16:52,747 Python recognizes 'pele_platform.Examples.interaction_restrictions.out' as an importable package, however it is 2022-08-01T11:16:52,747 included in the distribution as "data". 2022-08-01T11:16:52,747 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,748 therefore is considered deprecated). 2022-08-01T11:16:52,748 Please make sure that 'pele_platform.Examples.interaction_restrictions.out' is included as a package by using 2022-08-01T11:16:52,749 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,749 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,749 documentation page. 2022-08-01T11:16:52,750 !! 2022-08-01T11:16:52,751 check.warn(importable) 2022-08-01T11:16:52,751 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,752 ############################ 2022-08-01T11:16:52,753 # Package would be ignored # 2022-08-01T11:16:52,753 ############################ 2022-08-01T11:16:52,754 Python recognizes 'pele_platform.Examples.ligand_conformations' as an importable package, however it is 2022-08-01T11:16:52,754 included in the distribution as "data". 2022-08-01T11:16:52,754 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,755 therefore is considered deprecated). 2022-08-01T11:16:52,755 Please make sure that 'pele_platform.Examples.ligand_conformations' is included as a package by using 2022-08-01T11:16:52,756 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,756 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,757 documentation page. 2022-08-01T11:16:52,758 !! 2022-08-01T11:16:52,758 check.warn(importable) 2022-08-01T11:16:52,759 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,760 ############################ 2022-08-01T11:16:52,760 # Package would be ignored # 2022-08-01T11:16:52,760 ############################ 2022-08-01T11:16:52,761 Python recognizes 'pele_platform.Examples.minimum_steps' as an importable package, however it is 2022-08-01T11:16:52,761 included in the distribution as "data". 2022-08-01T11:16:52,761 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,762 therefore is considered deprecated). 2022-08-01T11:16:52,762 Please make sure that 'pele_platform.Examples.minimum_steps' is included as a package by using 2022-08-01T11:16:52,762 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,763 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,763 documentation page. 2022-08-01T11:16:52,764 !! 2022-08-01T11:16:52,765 check.warn(importable) 2022-08-01T11:16:52,765 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,766 ############################ 2022-08-01T11:16:52,767 # Package would be ignored # 2022-08-01T11:16:52,767 ############################ 2022-08-01T11:16:52,768 Python recognizes 'pele_platform.Examples.out_in' as an importable package, however it is 2022-08-01T11:16:52,768 included in the distribution as "data". 2022-08-01T11:16:52,769 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,769 therefore is considered deprecated). 2022-08-01T11:16:52,770 Please make sure that 'pele_platform.Examples.out_in' is included as a package by using 2022-08-01T11:16:52,770 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,771 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,771 documentation page. 2022-08-01T11:16:52,772 !! 2022-08-01T11:16:52,772 check.warn(importable) 2022-08-01T11:16:52,773 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,774 ############################ 2022-08-01T11:16:52,774 # Package would be ignored # 2022-08-01T11:16:52,774 ############################ 2022-08-01T11:16:52,774 Python recognizes 'pele_platform.Examples.pca' as an importable package, however it is 2022-08-01T11:16:52,775 included in the distribution as "data". 2022-08-01T11:16:52,775 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,775 therefore is considered deprecated). 2022-08-01T11:16:52,776 Please make sure that 'pele_platform.Examples.pca' is included as a package by using 2022-08-01T11:16:52,776 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,777 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,777 documentation page. 2022-08-01T11:16:52,778 !! 2022-08-01T11:16:52,779 check.warn(importable) 2022-08-01T11:16:52,779 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,780 ############################ 2022-08-01T11:16:52,780 # Package would be ignored # 2022-08-01T11:16:52,780 ############################ 2022-08-01T11:16:52,781 Python recognizes 'pele_platform.Examples.preparation' as an importable package, however it is 2022-08-01T11:16:52,781 included in the distribution as "data". 2022-08-01T11:16:52,781 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,782 therefore is considered deprecated). 2022-08-01T11:16:52,782 Please make sure that 'pele_platform.Examples.preparation' is included as a package by using 2022-08-01T11:16:52,782 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,783 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,783 documentation page. 2022-08-01T11:16:52,784 !! 2022-08-01T11:16:52,785 check.warn(importable) 2022-08-01T11:16:52,785 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,786 ############################ 2022-08-01T11:16:52,787 # Package would be ignored # 2022-08-01T11:16:52,787 ############################ 2022-08-01T11:16:52,787 Python recognizes 'pele_platform.Examples.production' as an importable package, however it is 2022-08-01T11:16:52,788 included in the distribution as "data". 2022-08-01T11:16:52,788 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,788 therefore is considered deprecated). 2022-08-01T11:16:52,789 Please make sure that 'pele_platform.Examples.production' is included as a package by using 2022-08-01T11:16:52,789 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,790 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,790 documentation page. 2022-08-01T11:16:52,791 !! 2022-08-01T11:16:52,792 check.warn(importable) 2022-08-01T11:16:52,792 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,793 ############################ 2022-08-01T11:16:52,793 # Package would be ignored # 2022-08-01T11:16:52,794 ############################ 2022-08-01T11:16:52,794 Python recognizes 'pele_platform.Examples.randomize' as an importable package, however it is 2022-08-01T11:16:52,794 included in the distribution as "data". 2022-08-01T11:16:52,795 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,795 therefore is considered deprecated). 2022-08-01T11:16:52,796 Please make sure that 'pele_platform.Examples.randomize' is included as a package by using 2022-08-01T11:16:52,796 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,797 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,797 documentation page. 2022-08-01T11:16:52,798 !! 2022-08-01T11:16:52,798 check.warn(importable) 2022-08-01T11:16:52,799 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,800 ############################ 2022-08-01T11:16:52,800 # Package would be ignored # 2022-08-01T11:16:52,800 ############################ 2022-08-01T11:16:52,801 Python recognizes 'pele_platform.Examples.rescoring' as an importable package, however it is 2022-08-01T11:16:52,801 included in the distribution as "data". 2022-08-01T11:16:52,801 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,802 therefore is considered deprecated). 2022-08-01T11:16:52,803 Please make sure that 'pele_platform.Examples.rescoring' is included as a package by using 2022-08-01T11:16:52,803 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,804 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,804 documentation page. 2022-08-01T11:16:52,805 !! 2022-08-01T11:16:52,806 check.warn(importable) 2022-08-01T11:16:52,806 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,807 ############################ 2022-08-01T11:16:52,808 # Package would be ignored # 2022-08-01T11:16:52,808 ############################ 2022-08-01T11:16:52,808 Python recognizes 'pele_platform.Examples.restart' as an importable package, however it is 2022-08-01T11:16:52,808 included in the distribution as "data". 2022-08-01T11:16:52,809 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,809 therefore is considered deprecated). 2022-08-01T11:16:52,810 Please make sure that 'pele_platform.Examples.restart' is included as a package by using 2022-08-01T11:16:52,810 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,811 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,811 documentation page. 2022-08-01T11:16:52,812 !! 2022-08-01T11:16:52,813 check.warn(importable) 2022-08-01T11:16:52,813 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,814 ############################ 2022-08-01T11:16:52,815 # Package would be ignored # 2022-08-01T11:16:52,815 ############################ 2022-08-01T11:16:52,815 Python recognizes 'pele_platform.Examples.singularity' as an importable package, however it is 2022-08-01T11:16:52,816 included in the distribution as "data". 2022-08-01T11:16:52,816 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,816 therefore is considered deprecated). 2022-08-01T11:16:52,817 Please make sure that 'pele_platform.Examples.singularity' is included as a package by using 2022-08-01T11:16:52,817 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,818 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,818 documentation page. 2022-08-01T11:16:52,819 !! 2022-08-01T11:16:52,820 check.warn(importable) 2022-08-01T11:16:52,820 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,821 ############################ 2022-08-01T11:16:52,821 # Package would be ignored # 2022-08-01T11:16:52,822 ############################ 2022-08-01T11:16:52,822 Python recognizes 'pele_platform.Examples.site_finder' as an importable package, however it is 2022-08-01T11:16:52,822 included in the distribution as "data". 2022-08-01T11:16:52,822 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,823 therefore is considered deprecated). 2022-08-01T11:16:52,823 Please make sure that 'pele_platform.Examples.site_finder' is included as a package by using 2022-08-01T11:16:52,824 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,824 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,825 documentation page. 2022-08-01T11:16:52,826 !! 2022-08-01T11:16:52,826 check.warn(importable) 2022-08-01T11:16:52,827 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,827 ############################ 2022-08-01T11:16:52,828 # Package would be ignored # 2022-08-01T11:16:52,828 ############################ 2022-08-01T11:16:52,828 Python recognizes 'pele_platform.Examples.tutorials.gpcr' as an importable package, however it is 2022-08-01T11:16:52,829 included in the distribution as "data". 2022-08-01T11:16:52,829 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,829 therefore is considered deprecated). 2022-08-01T11:16:52,830 Please make sure that 'pele_platform.Examples.tutorials.gpcr' is included as a package by using 2022-08-01T11:16:52,830 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,831 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,831 documentation page. 2022-08-01T11:16:52,832 !! 2022-08-01T11:16:52,833 check.warn(importable) 2022-08-01T11:16:52,833 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,834 ############################ 2022-08-01T11:16:52,834 # Package would be ignored # 2022-08-01T11:16:52,835 ############################ 2022-08-01T11:16:52,835 Python recognizes 'pele_platform.Examples.tutorials.induced_fit' as an importable package, however it is 2022-08-01T11:16:52,835 included in the distribution as "data". 2022-08-01T11:16:52,836 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,836 therefore is considered deprecated). 2022-08-01T11:16:52,836 Please make sure that 'pele_platform.Examples.tutorials.induced_fit' is included as a package by using 2022-08-01T11:16:52,837 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,837 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,838 documentation page. 2022-08-01T11:16:52,839 !! 2022-08-01T11:16:52,839 check.warn(importable) 2022-08-01T11:16:52,840 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,841 ############################ 2022-08-01T11:16:52,841 # Package would be ignored # 2022-08-01T11:16:52,841 ############################ 2022-08-01T11:16:52,842 Python recognizes 'pele_platform.Examples.tutorials.ppi' as an importable package, however it is 2022-08-01T11:16:52,842 included in the distribution as "data". 2022-08-01T11:16:52,842 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,843 therefore is considered deprecated). 2022-08-01T11:16:52,843 Please make sure that 'pele_platform.Examples.tutorials.ppi' is included as a package by using 2022-08-01T11:16:52,844 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,844 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,845 documentation page. 2022-08-01T11:16:52,845 !! 2022-08-01T11:16:52,846 check.warn(importable) 2022-08-01T11:16:52,846 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,847 ############################ 2022-08-01T11:16:52,848 # Package would be ignored # 2022-08-01T11:16:52,848 ############################ 2022-08-01T11:16:52,848 Python recognizes 'pele_platform.Examples.water' as an importable package, however it is 2022-08-01T11:16:52,848 included in the distribution as "data". 2022-08-01T11:16:52,849 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,849 therefore is considered deprecated). 2022-08-01T11:16:52,850 Please make sure that 'pele_platform.Examples.water' is included as a package by using 2022-08-01T11:16:52,850 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,851 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,851 documentation page. 2022-08-01T11:16:52,852 !! 2022-08-01T11:16:52,852 check.warn(importable) 2022-08-01T11:16:52,853 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-08-01T11:16:52,854 ############################ 2022-08-01T11:16:52,854 # Package would be ignored # 2022-08-01T11:16:52,854 ############################ 2022-08-01T11:16:52,855 Python recognizes 'pele_platform.Templates' as an importable package, however it is 2022-08-01T11:16:52,855 included in the distribution as "data". 2022-08-01T11:16:52,855 This behavior is likely to change in future versions of setuptools (and 2022-08-01T11:16:52,856 therefore is considered deprecated). 2022-08-01T11:16:52,856 Please make sure that 'pele_platform.Templates' is included as a package by using 2022-08-01T11:16:52,857 setuptools' `packages` configuration field or the proper discovery methods. 2022-08-01T11:16:52,857 You can read more about "package discovery" and "data files" on setuptools 2022-08-01T11:16:52,858 documentation page. 2022-08-01T11:16:52,859 !! 2022-08-01T11:16:52,859 check.warn(importable) 2022-08-01T11:16:52,859 creating build/lib/pele_platform/Examples 2022-08-01T11:16:52,860 copying pele_platform/Examples/test.sl -> build/lib/pele_platform/Examples 2022-08-01T11:16:52,860 creating build/lib/pele_platform/Examples/Adaptive 2022-08-01T11:16:52,860 copying pele_platform/Examples/Adaptive/STR.rot.assign -> build/lib/pele_platform/Examples/Adaptive 2022-08-01T11:16:52,861 copying pele_platform/Examples/Adaptive/adaptive.conf -> build/lib/pele_platform/Examples/Adaptive 2022-08-01T11:16:52,861 copying pele_platform/Examples/Adaptive/pele_file_4Adaptive.conf -> build/lib/pele_platform/Examples/Adaptive 2022-08-01T11:16:52,861 copying pele_platform/Examples/Adaptive/strz -> build/lib/pele_platform/Examples/Adaptive 2022-08-01T11:16:52,862 copying pele_platform/Examples/Adaptive/test.sl -> build/lib/pele_platform/Examples/Adaptive 2022-08-01T11:16:52,862 creating build/lib/pele_platform/Examples/Msm 2022-08-01T11:16:52,862 copying pele_platform/Examples/Msm/AS4_INIT.mae -> build/lib/pele_platform/Examples/Msm 2022-08-01T11:16:52,863 copying pele_platform/Examples/Msm/PR_1A28_protein.pdb -> build/lib/pele_platform/Examples/Msm 2022-08-01T11:16:52,863 copying pele_platform/Examples/Msm/PR_1A28_xray_-_minimized.pdb -> build/lib/pele_platform/Examples/Msm 2022-08-01T11:16:52,863 copying pele_platform/Examples/Msm/PR_1A28_xray_-_minimized_processed.pdb -> build/lib/pele_platform/Examples/Msm 2022-08-01T11:16:52,864 copying pele_platform/Examples/Msm/PR_AS4.pdb -> build/lib/pele_platform/Examples/Msm 2022-08-01T11:16:52,864 copying pele_platform/Examples/Msm/input.yaml -> build/lib/pele_platform/Examples/Msm 2022-08-01T11:16:52,864 creating build/lib/pele_platform/Examples/PPI 2022-08-01T11:16:52,865 copying pele_platform/Examples/PPI/1f47_ligand.pdb -> build/lib/pele_platform/Examples/PPI 2022-08-01T11:16:52,865 copying pele_platform/Examples/PPI/1f47_prep.pdb -> build/lib/pele_platform/Examples/PPI 2022-08-01T11:16:52,865 copying pele_platform/Examples/PPI/1tnf_ligand.pdb -> build/lib/pele_platform/Examples/PPI 2022-08-01T11:16:52,865 copying pele_platform/Examples/PPI/1tnf_prep.pdb -> build/lib/pele_platform/Examples/PPI 2022-08-01T11:16:52,866 copying pele_platform/Examples/PPI/input.yaml -> build/lib/pele_platform/Examples/PPI 2022-08-01T11:16:52,866 copying pele_platform/Examples/PPI/input_folder.yaml -> build/lib/pele_platform/Examples/PPI 2022-08-01T11:16:52,867 copying pele_platform/Examples/PPI/input_skipref.yaml -> build/lib/pele_platform/Examples/PPI 2022-08-01T11:16:52,867 creating build/lib/pele_platform/Examples/RNA 2022-08-01T11:16:52,867 copying pele_platform/Examples/RNA/2l94.yaml -> build/lib/pele_platform/Examples/RNA 2022-08-01T11:16:52,868 copying pele_platform/Examples/RNA/5C45_prep.pdb -> build/lib/pele_platform/Examples/RNA 2022-08-01T11:16:52,868 copying pele_platform/Examples/RNA/5C45_prep_proc.pdb -> build/lib/pele_platform/Examples/RNA 2022-08-01T11:16:52,868 copying pele_platform/Examples/RNA/input.yaml -> build/lib/pele_platform/Examples/RNA 2022-08-01T11:16:52,869 copying pele_platform/Examples/RNA/input_induced.yaml -> build/lib/pele_platform/Examples/RNA 2022-08-01T11:16:52,869 creating build/lib/pele_platform/Examples/analysis 2022-08-01T11:16:52,869 copying pele_platform/Examples/analysis/input.yaml -> build/lib/pele_platform/Examples/analysis 2022-08-01T11:16:52,870 copying pele_platform/Examples/analysis/input_flags.yaml -> build/lib/pele_platform/Examples/analysis 2022-08-01T11:16:52,871 copying pele_platform/Examples/analysis/input_flags0.yaml -> build/lib/pele_platform/Examples/analysis 2022-08-01T11:16:52,875 copying pele_platform/Examples/analysis/input_xtc.yaml -> build/lib/pele_platform/Examples/analysis 2022-08-01T11:16:52,879 creating build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,880 copying pele_platform/Examples/analysis/data/MG.rot.assign -> build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,884 copying pele_platform/Examples/analysis/data/STR.rot.assign -> build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,887 copying pele_platform/Examples/analysis/data/adaptive.conf -> build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,891 copying pele_platform/Examples/analysis/data/input.yaml -> build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,895 copying pele_platform/Examples/analysis/data/input_flags.yaml -> build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,898 copying pele_platform/Examples/analysis/data/input_flags0.yaml -> build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,902 copying pele_platform/Examples/analysis/data/input_mae.yaml -> build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,906 copying pele_platform/Examples/analysis/data/mgz -> build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,909 copying pele_platform/Examples/analysis/data/pele.conf -> build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,913 copying pele_platform/Examples/analysis/data/strz -> build/lib/pele_platform/Examples/analysis/data 2022-08-01T11:16:52,916 creating build/lib/pele_platform/Examples/analysis/data/empty_reports_output 2022-08-01T11:16:52,917 creating build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:16:52,919 copying pele_platform/Examples/analysis/data/empty_reports_output/0/report_1 -> build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:16:52,923 copying pele_platform/Examples/analysis/data/empty_reports_output/0/report_2 -> build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:16:52,927 copying pele_platform/Examples/analysis/data/empty_reports_output/0/topologyMapping.txt -> build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:16:52,931 copying pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_1.pdb -> build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:16:52,953 copying pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_2.pdb -> build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:16:53,013 creating build/lib/pele_platform/Examples/analysis/data/inputs 2022-08-01T11:16:53,014 copying pele_platform/Examples/analysis/data/inputs/input1.pdb -> build/lib/pele_platform/Examples/analysis/data/inputs 2022-08-01T11:16:53,037 copying pele_platform/Examples/analysis/data/inputs/input2.pdb -> build/lib/pele_platform/Examples/analysis/data/inputs 2022-08-01T11:16:53,059 copying pele_platform/Examples/analysis/data/inputs/input3.pdb -> build/lib/pele_platform/Examples/analysis/data/inputs 2022-08-01T11:16:53,086 creating build/lib/pele_platform/Examples/analysis/data/output 2022-08-01T11:16:53,087 copying pele_platform/Examples/analysis/data/output/originalControlFile.conf -> build/lib/pele_platform/Examples/analysis/data/output 2022-08-01T11:16:53,091 creating build/lib/pele_platform/Examples/analysis/data/output/0 2022-08-01T11:16:53,092 copying pele_platform/Examples/analysis/data/output/0/report_1 -> build/lib/pele_platform/Examples/analysis/data/output/0 2022-08-01T11:16:53,097 copying pele_platform/Examples/analysis/data/output/0/topologyMapping.txt -> build/lib/pele_platform/Examples/analysis/data/output/0 2022-08-01T11:16:53,100 copying pele_platform/Examples/analysis/data/output/0/trajectory_1.pdb -> build/lib/pele_platform/Examples/analysis/data/output/0 2022-08-01T11:16:53,122 creating build/lib/pele_platform/Examples/analysis/data/output/0/clustering 2022-08-01T11:16:53,123 copying pele_platform/Examples/analysis/data/output/0/clustering/object.pkl -> build/lib/pele_platform/Examples/analysis/data/output/0/clustering 2022-08-01T11:16:53,145 copying pele_platform/Examples/analysis/data/output/0/clustering/summary.txt -> build/lib/pele_platform/Examples/analysis/data/output/0/clustering 2022-08-01T11:16:53,149 creating build/lib/pele_platform/Examples/analysis/data/output/synchronization 2022-08-01T11:16:53,151 copying pele_platform/Examples/analysis/data/output/synchronization/syncFile.lock -> build/lib/pele_platform/Examples/analysis/data/output/synchronization 2022-08-01T11:16:53,155 creating build/lib/pele_platform/Examples/analysis/data/output/topologies 2022-08-01T11:16:53,156 copying pele_platform/Examples/analysis/data/output/topologies/topologies.pkl -> build/lib/pele_platform/Examples/analysis/data/output/topologies 2022-08-01T11:16:53,177 copying pele_platform/Examples/analysis/data/output/topologies/topology_0.pdb -> build/lib/pele_platform/Examples/analysis/data/output/topologies 2022-08-01T11:16:53,202 creating build/lib/pele_platform/Examples/analysis/data/xtc 2022-08-01T11:16:53,204 copying pele_platform/Examples/analysis/data/xtc/summary.csv -> build/lib/pele_platform/Examples/analysis/data/xtc 2022-08-01T11:16:53,208 creating build/lib/pele_platform/Examples/analysis/data/xtc/0 2022-08-01T11:16:53,209 copying pele_platform/Examples/analysis/data/xtc/0/report_1 -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2022-08-01T11:16:53,213 copying pele_platform/Examples/analysis/data/xtc/0/report_2 -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2022-08-01T11:16:53,217 copying pele_platform/Examples/analysis/data/xtc/0/trajectory_1.xtc -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2022-08-01T11:16:53,222 copying pele_platform/Examples/analysis/data/xtc/0/trajectory_2.xtc -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2022-08-01T11:16:53,226 creating build/lib/pele_platform/Examples/analysis/data/xtc/topologies 2022-08-01T11:16:53,228 copying pele_platform/Examples/analysis/data/xtc/topologies/topology_0.pdb -> build/lib/pele_platform/Examples/analysis/data/xtc/topologies 2022-08-01T11:16:53,237 creating build/lib/pele_platform/Examples/bias 2022-08-01T11:16:53,239 copying pele_platform/Examples/bias/complex.pdb -> build/lib/pele_platform/Examples/bias 2022-08-01T11:16:53,261 copying pele_platform/Examples/bias/input_defaults.yaml -> build/lib/pele_platform/Examples/bias 2022-08-01T11:16:53,265 creating build/lib/pele_platform/Examples/box 2022-08-01T11:16:53,266 copying pele_platform/Examples/box/input.yaml -> build/lib/pele_platform/Examples/box 2022-08-01T11:16:53,270 creating build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,272 copying pele_platform/Examples/checker/capped.pdb -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,346 copying pele_platform/Examples/checker/capped_no_connects.pdb -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,425 copying pele_platform/Examples/checker/complex.pdb -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,454 copying pele_platform/Examples/checker/complex2.pdb -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,470 copying pele_platform/Examples/checker/complex_unk.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,502 copying pele_platform/Examples/checker/incompatible_flags.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,506 copying pele_platform/Examples/checker/input.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,509 copying pele_platform/Examples/checker/input_atom_string.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,513 copying pele_platform/Examples/checker/input_env.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,517 copying pele_platform/Examples/checker/input_map_atom_num.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,521 copying pele_platform/Examples/checker/input_map_atom_str.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,525 copying pele_platform/Examples/checker/input_pele_exec.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,528 copying pele_platform/Examples/checker/input_rotamer.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,531 copying pele_platform/Examples/checker/input_space.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,535 copying pele_platform/Examples/checker/input_tab.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,539 copying pele_platform/Examples/checker/input_template.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,542 copying pele_platform/Examples/checker/input_underscore.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,546 copying pele_platform/Examples/checker/input_unk.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,550 copying pele_platform/Examples/checker/ligand2.pdb -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,554 copying pele_platform/Examples/checker/mapping_complex.pdb -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,590 copying pele_platform/Examples/checker/multiple_simulations.yaml -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,594 copying pele_platform/Examples/checker/negative_residues.pdb -> build/lib/pele_platform/Examples/checker 2022-08-01T11:16:53,599 creating build/lib/pele_platform/Examples/clustering 2022-08-01T11:16:53,601 copying pele_platform/Examples/clustering/summary.csv -> build/lib/pele_platform/Examples/clustering 2022-08-01T11:16:53,605 creating build/lib/pele_platform/Examples/clustering/0 2022-08-01T11:16:53,607 copying pele_platform/Examples/clustering/0/report_1 -> build/lib/pele_platform/Examples/clustering/0 2022-08-01T11:16:53,612 copying pele_platform/Examples/clustering/0/report_2 -> build/lib/pele_platform/Examples/clustering/0 2022-08-01T11:16:53,616 copying pele_platform/Examples/clustering/0/report_3 -> build/lib/pele_platform/Examples/clustering/0 2022-08-01T11:16:53,620 copying pele_platform/Examples/clustering/0/report_4 -> build/lib/pele_platform/Examples/clustering/0 2022-08-01T11:16:53,625 copying pele_platform/Examples/clustering/0/topologyMapping.txt -> build/lib/pele_platform/Examples/clustering/0 2022-08-01T11:16:53,629 copying pele_platform/Examples/clustering/0/trajectory_1.pdb -> build/lib/pele_platform/Examples/clustering/0 2022-08-01T11:16:53,665 copying pele_platform/Examples/clustering/0/trajectory_2.pdb -> build/lib/pele_platform/Examples/clustering/0 2022-08-01T11:16:53,692 copying pele_platform/Examples/clustering/0/trajectory_3.pdb -> build/lib/pele_platform/Examples/clustering/0 2022-08-01T11:16:53,728 copying pele_platform/Examples/clustering/0/trajectory_4.pdb -> build/lib/pele_platform/Examples/clustering/0 2022-08-01T11:16:53,771 creating build/lib/pele_platform/Examples/clustering/0/clustering 2022-08-01T11:16:53,772 copying pele_platform/Examples/clustering/0/clustering/object.pkl -> build/lib/pele_platform/Examples/clustering/0/clustering 2022-08-01T11:16:53,907 copying pele_platform/Examples/clustering/0/clustering/summary.txt -> build/lib/pele_platform/Examples/clustering/0/clustering 2022-08-01T11:16:53,911 creating build/lib/pele_platform/Examples/clustering_xtc 2022-08-01T11:16:53,912 copying pele_platform/Examples/clustering_xtc/water_clustering.yaml -> build/lib/pele_platform/Examples/clustering_xtc 2022-08-01T11:16:53,917 creating build/lib/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:16:53,918 copying pele_platform/Examples/clustering_xtc/0/report_1 -> build/lib/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:16:53,922 copying pele_platform/Examples/clustering_xtc/0/report_2 -> build/lib/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:16:53,926 copying pele_platform/Examples/clustering_xtc/0/report_3 -> build/lib/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:16:53,930 copying pele_platform/Examples/clustering_xtc/0/report_4 -> build/lib/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:16:53,934 copying pele_platform/Examples/clustering_xtc/0/topology.pdb -> build/lib/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:16:53,955 copying pele_platform/Examples/clustering_xtc/0/trajectory_1.xtc -> build/lib/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:16:53,962 copying pele_platform/Examples/clustering_xtc/0/trajectory_2.xtc -> build/lib/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:16:53,967 copying pele_platform/Examples/clustering_xtc/0/trajectory_3.xtc -> build/lib/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:16:53,974 copying pele_platform/Examples/clustering_xtc/0/trajectory_4.xtc -> build/lib/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:16:53,980 creating build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:53,982 copying pele_platform/Examples/constraints/1zop.pdb -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:53,999 copying pele_platform/Examples/constraints/4l3a_prep.pdb -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,027 copying pele_platform/Examples/constraints/4qnr_prep.pdb -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,056 copying pele_platform/Examples/constraints/4w4o_prep.pdb -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,076 copying pele_platform/Examples/constraints/4w5i_prep.pdb -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,096 copying pele_platform/Examples/constraints/4zu9_prep.pdb -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,161 copying pele_platform/Examples/constraints/ca_constraints.pdb -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,201 copying pele_platform/Examples/constraints/complex_smiles_error.pdb -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,234 copying pele_platform/Examples/constraints/fail_input_permissive_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,238 copying pele_platform/Examples/constraints/input_all_metal_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,242 copying pele_platform/Examples/constraints/input_ca_noppp.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,247 copying pele_platform/Examples/constraints/input_ca_ppp.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,251 copying pele_platform/Examples/constraints/input_constrain_smarts.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,256 copying pele_platform/Examples/constraints/input_constrain_smiles.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,260 copying pele_platform/Examples/constraints/input_external_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,265 copying pele_platform/Examples/constraints/input_ignore.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,269 copying pele_platform/Examples/constraints/input_k.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,274 copying pele_platform/Examples/constraints/input_metals.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,278 copying pele_platform/Examples/constraints/input_no_metal_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,282 copying pele_platform/Examples/constraints/input_permissive_exception.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,287 copying pele_platform/Examples/constraints/input_smiles_error.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,291 copying pele_platform/Examples/constraints/input_square_planar.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,296 copying pele_platform/Examples/constraints/input_square_planar_polarisation.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,300 copying pele_platform/Examples/constraints/input_tetrahedral.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,305 copying pele_platform/Examples/constraints/no_connects.pdb -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,309 copying pele_platform/Examples/constraints/pass_input_permissive_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2022-08-01T11:16:54,313 creating build/lib/pele_platform/Examples/covalent_docking 2022-08-01T11:16:54,315 copying pele_platform/Examples/covalent_docking/5XXD_prepared.pdb -> build/lib/pele_platform/Examples/covalent_docking 2022-08-01T11:16:54,345 copying pele_platform/Examples/covalent_docking/6M06_prepared.pdb -> build/lib/pele_platform/Examples/covalent_docking 2022-08-01T11:16:54,373 copying pele_platform/Examples/covalent_docking/6P0M_prepared.pdb -> build/lib/pele_platform/Examples/covalent_docking 2022-08-01T11:16:54,393 copying pele_platform/Examples/covalent_docking/input1.yaml -> build/lib/pele_platform/Examples/covalent_docking 2022-08-01T11:16:54,397 copying pele_platform/Examples/covalent_docking/input2.yaml -> build/lib/pele_platform/Examples/covalent_docking 2022-08-01T11:16:54,401 copying pele_platform/Examples/covalent_docking/input3.yaml -> build/lib/pele_platform/Examples/covalent_docking 2022-08-01T11:16:54,405 copying pele_platform/Examples/covalent_docking/input_defaults.yaml -> build/lib/pele_platform/Examples/covalent_docking 2022-08-01T11:16:54,408 copying pele_platform/Examples/covalent_docking/input_defaults_refinement.yaml -> build/lib/pele_platform/Examples/covalent_docking 2022-08-01T11:16:54,412 creating build/lib/pele_platform/Examples/enzyme_engineering 2022-08-01T11:16:54,413 copying pele_platform/Examples/enzyme_engineering/restart_saturated_mutagenesis.yaml -> build/lib/pele_platform/Examples/enzyme_engineering 2022-08-01T11:16:54,417 copying pele_platform/Examples/enzyme_engineering/saturated_mutagenesis.yaml -> build/lib/pele_platform/Examples/enzyme_engineering 2022-08-01T11:16:54,421 copying pele_platform/Examples/enzyme_engineering/wrong_cpus.yaml -> build/lib/pele_platform/Examples/enzyme_engineering 2022-08-01T11:16:54,425 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart 2022-08-01T11:16:54,426 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/completed_mutations.log -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart 2022-08-01T11:16:54,430 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2022-08-01T11:16:54,431 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/ANL.mae -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2022-08-01T11:16:54,435 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/adaptive.conf -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2022-08-01T11:16:54,439 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/pele.conf -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2022-08-01T11:16:54,444 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/restart_saturated_mutagenesis.yaml -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2022-08-01T11:16:54,448 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal 2022-08-01T11:16:54,448 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs 2022-08-01T11:16:54,450 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs/ANL.rot.assign -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs 2022-08-01T11:16:54,454 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates 2022-08-01T11:16:54,455 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005 2022-08-01T11:16:54,456 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms 2022-08-01T11:16:54,458 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms/anlz -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms 2022-08-01T11:16:54,463 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:16:54,464 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454A.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:16:54,498 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454A_processed.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:16:54,531 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454D.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:16:54,569 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454D_processed.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:16:54,606 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/ligand.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:16:54,610 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/receptor.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:16:54,643 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output 2022-08-01T11:16:54,645 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/originalControlFile.conf -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output 2022-08-01T11:16:54,649 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0 2022-08-01T11:16:54,651 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/topologyMapping.txt -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0 2022-08-01T11:16:54,655 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering 2022-08-01T11:16:54,656 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering/object.pkl -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering 2022-08-01T11:16:54,661 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering/summary.txt -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering 2022-08-01T11:16:54,665 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2022-08-01T11:16:54,666 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/report_1 -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2022-08-01T11:16:54,670 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/report_3 -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2022-08-01T11:16:54,674 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/trajectory_1.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2022-08-01T11:16:54,738 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/trajectory_3.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2022-08-01T11:16:54,800 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2022-08-01T11:16:54,802 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/report_2 -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2022-08-01T11:16:54,806 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/report_4 -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2022-08-01T11:16:54,810 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/trajectory_2.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2022-08-01T11:16:54,876 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/trajectory_4.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2022-08-01T11:16:54,937 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization 2022-08-01T11:16:54,939 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization/syncFile.lock -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization 2022-08-01T11:16:54,944 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2022-08-01T11:16:54,946 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topologies.pkl -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2022-08-01T11:16:55,002 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topology_0.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2022-08-01T11:16:55,039 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topology_1.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2022-08-01T11:16:55,072 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2022-08-01T11:16:55,074 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/controlFile0.conf -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2022-08-01T11:16:55,080 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/initial_0_0.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2022-08-01T11:16:55,116 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/initial_0_1.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2022-08-01T11:16:55,149 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2022-08-01T11:16:55,150 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/ANL.mae -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2022-08-01T11:16:55,155 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/adaptive.conf -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2022-08-01T11:16:55,159 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/pele.conf -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2022-08-01T11:16:55,163 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/restart_saturated_mutagenesis.yaml -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2022-08-01T11:16:55,167 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2022-08-01T11:16:55,168 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/T454E.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2022-08-01T11:16:55,204 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/T454E_processed.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2022-08-01T11:16:55,237 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/ligand.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2022-08-01T11:16:55,241 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/receptor.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2022-08-01T11:16:55,282 creating build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2022-08-01T11:16:55,283 copying pele_platform/Examples/enzyme_engineering/pdb_files/T454A.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2022-08-01T11:16:55,318 copying pele_platform/Examples/enzyme_engineering/pdb_files/T454D.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2022-08-01T11:16:55,351 copying pele_platform/Examples/enzyme_engineering/pdb_files/T454E.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2022-08-01T11:16:55,385 creating build/lib/pele_platform/Examples/exit 2022-08-01T11:16:55,387 copying pele_platform/Examples/exit/input.yaml -> build/lib/pele_platform/Examples/exit 2022-08-01T11:16:55,391 copying pele_platform/Examples/exit/input_defaults.yaml -> build/lib/pele_platform/Examples/exit 2022-08-01T11:16:55,394 creating build/lib/pele_platform/Examples/exit_soft 2022-08-01T11:16:55,396 copying pele_platform/Examples/exit_soft/input.yaml -> build/lib/pele_platform/Examples/exit_soft 2022-08-01T11:16:55,400 copying pele_platform/Examples/exit_soft/input_defaults.yaml -> build/lib/pele_platform/Examples/exit_soft 2022-08-01T11:16:55,404 creating build/lib/pele_platform/Examples/flags 2022-08-01T11:16:55,405 copying pele_platform/Examples/flags/input.yaml -> build/lib/pele_platform/Examples/flags 2022-08-01T11:16:55,409 creating build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,411 copying pele_platform/Examples/frag/1dyi_no_waters.pdb -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,426 copying pele_platform/Examples/frag/1dyi_waters.pdb -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,442 copying pele_platform/Examples/frag/1w7h_preparation_structure_2w.pdb -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,471 copying pele_platform/Examples/frag/1w7h_preparation_structure_2w_processed.pdb -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,499 copying pele_platform/Examples/frag/amino.pdb -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,503 copying pele_platform/Examples/frag/analysis.conf -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,507 copying pele_platform/Examples/frag/core.pdb -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,510 copying pele_platform/Examples/frag/flags.conf -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,514 copying pele_platform/Examples/frag/input_ai.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,518 copying pele_platform/Examples/frag/input_core.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,521 copying pele_platform/Examples/frag/input_core_bond.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,525 copying pele_platform/Examples/frag/input_core_sdf.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,529 copying pele_platform/Examples/frag/input_flags.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,533 copying pele_platform/Examples/frag/input_frag_waters.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,536 copying pele_platform/Examples/frag/input_fragment_atom.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,540 copying pele_platform/Examples/frag/input_lib_pdb.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,544 copying pele_platform/Examples/frag/input_lib_sdf.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,547 copying pele_platform/Examples/frag/input_point_analysis.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,551 copying pele_platform/Examples/frag/input_sim.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,555 copying pele_platform/Examples/frag/input_sim_xtc.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,559 copying pele_platform/Examples/frag/input_symmetry.yaml -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,562 copying pele_platform/Examples/frag/ligands.sdf -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,566 copying pele_platform/Examples/frag/ligands_water.sdf -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,571 copying pele_platform/Examples/frag/sequential.conf -> build/lib/pele_platform/Examples/frag 2022-08-01T11:16:55,575 creating build/lib/pele_platform/Examples/frag/analysis_data 2022-08-01T11:16:55,575 creating build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1 2022-08-01T11:16:55,576 creating build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result 2022-08-01T11:16:55,578 copying pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/report_1 -> build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result 2022-08-01T11:16:55,583 copying pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/report_2 -> build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result 2022-08-01T11:16:55,587 copying pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/trajectory_1.pdb -> build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result 2022-08-01T11:16:55,638 copying pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/trajectory_2.pdb -> build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result 2022-08-01T11:16:55,687 creating build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result 2022-08-01T11:16:55,689 copying pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result/epochsampling_result_trajectory_1.1_BindingEnergy-23.4636.pdb -> build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result 2022-08-01T11:16:55,710 copying pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result/epochsampling_result_trajectory_2.1_BindingEnergy-25.1634.pdb -> build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result 2022-08-01T11:16:55,744 creating build/lib/pele_platform/Examples/frag/checker 2022-08-01T11:16:55,745 copying pele_platform/Examples/frag/checker/4RFM_proc.pdb -> build/lib/pele_platform/Examples/frag/checker 2022-08-01T11:16:55,749 copying pele_platform/Examples/frag/checker/4RFM_series.sdf -> build/lib/pele_platform/Examples/frag/checker 2022-08-01T11:16:55,753 copying pele_platform/Examples/frag/checker/receptor.sdf -> build/lib/pele_platform/Examples/frag/checker 2022-08-01T11:16:55,775 creating build/lib/pele_platform/Examples/frag/pdb_test_lib 2022-08-01T11:16:55,776 copying pele_platform/Examples/frag/pdb_test_lib/mol1.pdb -> build/lib/pele_platform/Examples/frag/pdb_test_lib 2022-08-01T11:16:55,780 copying pele_platform/Examples/frag/pdb_test_lib/mol2.pdb -> build/lib/pele_platform/Examples/frag/pdb_test_lib 2022-08-01T11:16:55,784 creating build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,785 copying pele_platform/Examples/frag/sdf_joiner/13_serie.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,793 copying pele_platform/Examples/frag/sdf_joiner/4RFM_core_sc.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,823 copying pele_platform/Examples/frag/sdf_joiner/4RFM_proc.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,853 copying pele_platform/Examples/frag/sdf_joiner/4RFM_series.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,858 copying pele_platform/Examples/frag/sdf_joiner/core2.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,881 copying pele_platform/Examples/frag/sdf_joiner/core3.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,894 copying pele_platform/Examples/frag/sdf_joiner/frag.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,899 copying pele_platform/Examples/frag/sdf_joiner/frag.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,903 copying pele_platform/Examples/frag/sdf_joiner/frag2.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,912 copying pele_platform/Examples/frag/sdf_joiner/frag2.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,916 copying pele_platform/Examples/frag/sdf_joiner/frag3.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,924 copying pele_platform/Examples/frag/sdf_joiner/frag3.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,928 copying pele_platform/Examples/frag/sdf_joiner/frag31.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,936 copying pele_platform/Examples/frag/sdf_joiner/frag4.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,940 copying pele_platform/Examples/frag/sdf_joiner/frag5.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,945 copying pele_platform/Examples/frag/sdf_joiner/glide-dockSARS_core.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:16:55,987 creating build/lib/pele_platform/Examples/frag/sdf_test_lib 2022-08-01T11:16:55,988 copying pele_platform/Examples/frag/sdf_test_lib/test_library.sdf -> build/lib/pele_platform/Examples/frag/sdf_test_lib 2022-08-01T11:16:55,992 creating build/lib/pele_platform/Examples/global 2022-08-01T11:16:55,993 copying pele_platform/Examples/global/input.yaml -> build/lib/pele_platform/Examples/global 2022-08-01T11:16:55,997 copying pele_platform/Examples/global/input_defaults.yaml -> build/lib/pele_platform/Examples/global 2022-08-01T11:16:56,001 copying pele_platform/Examples/global/input_inputs.yaml -> build/lib/pele_platform/Examples/global 2022-08-01T11:16:56,005 copying pele_platform/Examples/global/input_inputs_asterisc.yaml -> build/lib/pele_platform/Examples/global 2022-08-01T11:16:56,009 creating build/lib/pele_platform/Examples/gpcr 2022-08-01T11:16:56,010 copying pele_platform/Examples/gpcr/complex.pdb -> build/lib/pele_platform/Examples/gpcr 2022-08-01T11:16:56,041 copying pele_platform/Examples/gpcr/complex_processed.pdb -> build/lib/pele_platform/Examples/gpcr 2022-08-01T11:16:56,078 copying pele_platform/Examples/gpcr/input.yaml -> build/lib/pele_platform/Examples/gpcr 2022-08-01T11:16:56,082 copying pele_platform/Examples/gpcr/input_atom_error.yaml -> build/lib/pele_platform/Examples/gpcr 2022-08-01T11:16:56,085 copying pele_platform/Examples/gpcr/input_defaults.yaml -> build/lib/pele_platform/Examples/gpcr 2022-08-01T11:16:56,089 copying pele_platform/Examples/gpcr/input_defaults2.yaml -> build/lib/pele_platform/Examples/gpcr 2022-08-01T11:16:56,093 creating build/lib/pele_platform/Examples/induced_fit 2022-08-01T11:16:56,094 copying pele_platform/Examples/induced_fit/input_auto_clustering.yaml -> build/lib/pele_platform/Examples/induced_fit 2022-08-01T11:16:56,098 copying pele_platform/Examples/induced_fit/input_exhaustive.yaml -> build/lib/pele_platform/Examples/induced_fit 2022-08-01T11:16:56,102 copying pele_platform/Examples/induced_fit/input_exhaustive_defaults.yaml -> build/lib/pele_platform/Examples/induced_fit 2022-08-01T11:16:56,106 copying pele_platform/Examples/induced_fit/input_fast.yaml -> build/lib/pele_platform/Examples/induced_fit 2022-08-01T11:16:56,109 copying pele_platform/Examples/induced_fit/input_fast_defaults.yaml -> build/lib/pele_platform/Examples/induced_fit 2022-08-01T11:16:56,113 copying pele_platform/Examples/induced_fit/input_mae.yaml -> build/lib/pele_platform/Examples/induced_fit 2022-08-01T11:16:56,117 creating build/lib/pele_platform/Examples/inputs 2022-08-01T11:16:56,118 copying pele_platform/Examples/inputs/input.yaml -> build/lib/pele_platform/Examples/inputs 2022-08-01T11:16:56,122 copying pele_platform/Examples/inputs/mn4.sl -> build/lib/pele_platform/Examples/inputs 2022-08-01T11:16:56,126 copying pele_platform/Examples/inputs/nord3.sge -> build/lib/pele_platform/Examples/inputs 2022-08-01T11:16:56,130 creating build/lib/pele_platform/Examples/interaction_restrictions 2022-08-01T11:16:56,131 copying pele_platform/Examples/interaction_restrictions/complex.pdb -> build/lib/pele_platform/Examples/interaction_restrictions 2022-08-01T11:16:56,174 copying pele_platform/Examples/interaction_restrictions/input.yaml -> build/lib/pele_platform/Examples/interaction_restrictions 2022-08-01T11:16:56,178 copying pele_platform/Examples/interaction_restrictions/input_error.yaml -> build/lib/pele_platform/Examples/interaction_restrictions 2022-08-01T11:16:56,182 copying pele_platform/Examples/interaction_restrictions/input_error_2.yaml -> build/lib/pele_platform/Examples/interaction_restrictions 2022-08-01T11:16:56,186 creating build/lib/pele_platform/Examples/interaction_restrictions/out 2022-08-01T11:16:56,187 copying pele_platform/Examples/interaction_restrictions/out/expected_conditions.txt -> build/lib/pele_platform/Examples/interaction_restrictions/out 2022-08-01T11:16:56,191 copying pele_platform/Examples/interaction_restrictions/out/expected_metrics.txt -> build/lib/pele_platform/Examples/interaction_restrictions/out 2022-08-01T11:16:56,196 creating build/lib/pele_platform/Examples/ligand_conformations 2022-08-01T11:16:56,198 copying pele_platform/Examples/ligand_conformations/1.pdb -> build/lib/pele_platform/Examples/ligand_conformations 2022-08-01T11:16:56,204 copying pele_platform/Examples/ligand_conformations/2.pdb -> build/lib/pele_platform/Examples/ligand_conformations 2022-08-01T11:16:56,208 copying pele_platform/Examples/ligand_conformations/3.pdb -> build/lib/pele_platform/Examples/ligand_conformations 2022-08-01T11:16:56,212 copying pele_platform/Examples/ligand_conformations/input.yaml -> build/lib/pele_platform/Examples/ligand_conformations 2022-08-01T11:16:56,216 creating build/lib/pele_platform/Examples/minimum_steps 2022-08-01T11:16:56,217 copying pele_platform/Examples/minimum_steps/complex.pdb -> build/lib/pele_platform/Examples/minimum_steps 2022-08-01T11:16:56,256 copying pele_platform/Examples/minimum_steps/input.yaml -> build/lib/pele_platform/Examples/minimum_steps 2022-08-01T11:16:56,260 creating build/lib/pele_platform/Examples/out_in 2022-08-01T11:16:56,261 copying pele_platform/Examples/out_in/1_3ZON_complex.pdb -> build/lib/pele_platform/Examples/out_in 2022-08-01T11:16:56,284 copying pele_platform/Examples/out_in/input.yaml -> build/lib/pele_platform/Examples/out_in 2022-08-01T11:16:56,289 copying pele_platform/Examples/out_in/input_auto_clustering.yaml -> build/lib/pele_platform/Examples/out_in 2022-08-01T11:16:56,294 copying pele_platform/Examples/out_in/input_box_center.yaml -> build/lib/pele_platform/Examples/out_in 2022-08-01T11:16:56,299 copying pele_platform/Examples/out_in/input_default.yaml -> build/lib/pele_platform/Examples/out_in 2022-08-01T11:16:56,303 copying pele_platform/Examples/out_in/input_flag_error.yaml -> build/lib/pele_platform/Examples/out_in 2022-08-01T11:16:56,307 copying pele_platform/Examples/out_in/input_metrics.yaml -> build/lib/pele_platform/Examples/out_in 2022-08-01T11:16:56,311 creating build/lib/pele_platform/Examples/pca 2022-08-01T11:16:56,312 copying pele_platform/Examples/pca/1.pdb -> build/lib/pele_platform/Examples/pca 2022-08-01T11:16:56,336 copying pele_platform/Examples/pca/2.pdb -> build/lib/pele_platform/Examples/pca 2022-08-01T11:16:56,360 copying pele_platform/Examples/pca/3.pdb -> build/lib/pele_platform/Examples/pca 2022-08-01T11:16:56,385 copying pele_platform/Examples/pca/input.yaml -> build/lib/pele_platform/Examples/pca 2022-08-01T11:16:56,389 copying pele_platform/Examples/pca/input_str.yaml -> build/lib/pele_platform/Examples/pca 2022-08-01T11:16:56,392 creating build/lib/pele_platform/Examples/preparation 2022-08-01T11:16:56,394 copying pele_platform/Examples/preparation/6qmk_correct.pdb -> build/lib/pele_platform/Examples/preparation 2022-08-01T11:16:56,422 copying pele_platform/Examples/preparation/6qmk_repeated.pdb -> build/lib/pele_platform/Examples/preparation 2022-08-01T11:16:56,453 copying pele_platform/Examples/preparation/complex.pdb -> build/lib/pele_platform/Examples/preparation 2022-08-01T11:16:56,476 copying pele_platform/Examples/preparation/complex_2.pdb -> build/lib/pele_platform/Examples/preparation 2022-08-01T11:16:56,508 copying pele_platform/Examples/preparation/input.yaml -> build/lib/pele_platform/Examples/preparation 2022-08-01T11:16:56,512 copying pele_platform/Examples/preparation/input_nonstandard.yaml -> build/lib/pele_platform/Examples/preparation 2022-08-01T11:16:56,516 copying pele_platform/Examples/preparation/input_space.yaml -> build/lib/pele_platform/Examples/preparation 2022-08-01T11:16:56,519 copying pele_platform/Examples/preparation/parametrization_flags.yaml -> build/lib/pele_platform/Examples/preparation 2022-08-01T11:16:56,523 creating build/lib/pele_platform/Examples/production 2022-08-01T11:16:56,525 copying pele_platform/Examples/production/input.sl -> build/lib/pele_platform/Examples/production 2022-08-01T11:16:56,529 copying pele_platform/Examples/production/input_mae.yaml -> build/lib/pele_platform/Examples/production 2022-08-01T11:16:56,533 creating build/lib/pele_platform/Examples/randomize 2022-08-01T11:16:56,534 copying pele_platform/Examples/randomize/ligand1.pdb -> build/lib/pele_platform/Examples/randomize 2022-08-01T11:16:56,538 copying pele_platform/Examples/randomize/ligand2.pdb -> build/lib/pele_platform/Examples/randomize 2022-08-01T11:16:56,542 copying pele_platform/Examples/randomize/ligand3.pdb -> build/lib/pele_platform/Examples/randomize 2022-08-01T11:16:56,547 copying pele_platform/Examples/randomize/receptor.pdb -> build/lib/pele_platform/Examples/randomize 2022-08-01T11:16:56,577 copying pele_platform/Examples/randomize/ref_ligand.pdb -> build/lib/pele_platform/Examples/randomize 2022-08-01T11:16:56,581 creating build/lib/pele_platform/Examples/rescoring 2022-08-01T11:16:56,582 copying pele_platform/Examples/rescoring/input.yaml -> build/lib/pele_platform/Examples/rescoring 2022-08-01T11:16:56,586 copying pele_platform/Examples/rescoring/input_defaults.yaml -> build/lib/pele_platform/Examples/rescoring 2022-08-01T11:16:56,590 creating build/lib/pele_platform/Examples/restart 2022-08-01T11:16:56,591 copying pele_platform/Examples/restart/restart.yaml -> build/lib/pele_platform/Examples/restart 2022-08-01T11:16:56,596 creating build/lib/pele_platform/Examples/singularity 2022-08-01T11:16:56,597 copying pele_platform/Examples/singularity/input_adaptive.yaml -> build/lib/pele_platform/Examples/singularity 2022-08-01T11:16:56,601 copying pele_platform/Examples/singularity/input_adaptive_mpi_params.yaml -> build/lib/pele_platform/Examples/singularity 2022-08-01T11:16:56,605 copying pele_platform/Examples/singularity/input_frag.yaml -> build/lib/pele_platform/Examples/singularity 2022-08-01T11:16:56,609 creating build/lib/pele_platform/Examples/site_finder 2022-08-01T11:16:56,610 copying pele_platform/Examples/site_finder/complex.pdb -> build/lib/pele_platform/Examples/site_finder 2022-08-01T11:16:56,643 copying pele_platform/Examples/site_finder/global.yaml -> build/lib/pele_platform/Examples/site_finder 2022-08-01T11:16:56,646 copying pele_platform/Examples/site_finder/input_custom_box.yaml -> build/lib/pele_platform/Examples/site_finder 2022-08-01T11:16:56,650 copying pele_platform/Examples/site_finder/input_folder.yaml -> build/lib/pele_platform/Examples/site_finder 2022-08-01T11:16:56,654 copying pele_platform/Examples/site_finder/input_global.yaml -> build/lib/pele_platform/Examples/site_finder 2022-08-01T11:16:56,658 copying pele_platform/Examples/site_finder/input_global_xtc.yaml -> build/lib/pele_platform/Examples/site_finder 2022-08-01T11:16:56,662 copying pele_platform/Examples/site_finder/input_restart.yaml -> build/lib/pele_platform/Examples/site_finder 2022-08-01T11:16:56,665 copying pele_platform/Examples/site_finder/input_skipref.yaml -> build/lib/pele_platform/Examples/site_finder 2022-08-01T11:16:56,669 copying pele_platform/Examples/site_finder/local.yaml -> build/lib/pele_platform/Examples/site_finder 2022-08-01T11:16:56,673 creating build/lib/pele_platform/Examples/tutorials 2022-08-01T11:16:56,674 creating build/lib/pele_platform/Examples/tutorials/gpcr 2022-08-01T11:16:56,676 copying pele_platform/Examples/tutorials/gpcr/complex.pdb -> build/lib/pele_platform/Examples/tutorials/gpcr 2022-08-01T11:16:56,701 copying pele_platform/Examples/tutorials/gpcr/input.yaml -> build/lib/pele_platform/Examples/tutorials/gpcr 2022-08-01T11:16:56,705 creating build/lib/pele_platform/Examples/tutorials/induced_fit 2022-08-01T11:16:56,707 copying pele_platform/Examples/tutorials/induced_fit/docking.pdb -> build/lib/pele_platform/Examples/tutorials/induced_fit 2022-08-01T11:16:56,744 copying pele_platform/Examples/tutorials/induced_fit/input.yaml -> build/lib/pele_platform/Examples/tutorials/induced_fit 2022-08-01T11:16:56,748 creating build/lib/pele_platform/Examples/tutorials/ppi 2022-08-01T11:16:56,750 copying pele_platform/Examples/tutorials/ppi/4yy6_ligand.pdb -> build/lib/pele_platform/Examples/tutorials/ppi 2022-08-01T11:16:56,755 copying pele_platform/Examples/tutorials/ppi/4yy6_prep.pdb -> build/lib/pele_platform/Examples/tutorials/ppi 2022-08-01T11:16:56,769 copying pele_platform/Examples/tutorials/ppi/input.yaml -> build/lib/pele_platform/Examples/tutorials/ppi 2022-08-01T11:16:56,774 creating build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,776 copying pele_platform/Examples/water/complex_induced.pdb -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,787 copying pele_platform/Examples/water/complex_ref_LESSH2O.pdb -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,812 copying pele_platform/Examples/water/input_all.yaml -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,816 copying pele_platform/Examples/water/input_bs.yaml -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,820 copying pele_platform/Examples/water/input_bs_defaults.yaml -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,825 copying pele_platform/Examples/water/input_induced.yaml -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,829 copying pele_platform/Examples/water/input_lig.yaml -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,834 copying pele_platform/Examples/water/input_lig_defaults.yaml -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,838 copying pele_platform/Examples/water/input_nwaters.yaml -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,842 copying pele_platform/Examples/water/input_previous_water.yaml -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,847 copying pele_platform/Examples/water/water2_pele.conf -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,851 copying pele_platform/Examples/water/water_pele.conf -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,856 copying pele_platform/Examples/water/water_processed.pdb -> build/lib/pele_platform/Examples/water 2022-08-01T11:16:56,891 creating build/lib/pele_platform/Templates 2022-08-01T11:16:56,894 copying pele_platform/Templates/pele_template.conf -> build/lib/pele_platform/Templates 2022-08-01T11:16:56,898 copying pele_platform/Templates/solventParamsHCTOBC.txt -> build/lib/pele_platform/Templates 2022-08-01T11:16:56,908 copying pele_platform/Templates/template_adaptive.conf -> build/lib/pele_platform/Templates 2022-08-01T11:16:56,953 UPDATING build/lib/pele_platform/_version.py 2022-08-01T11:16:56,956 set build/lib/pele_platform/_version.py to '1.6.4' 2022-08-01T11:16:57,639 /usr/local/lib/python3.7/dist-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. 2022-08-01T11:16:57,639 setuptools.SetuptoolsDeprecationWarning, 2022-08-01T11:16:58,322 installing to build/bdist.linux-armv7l/wheel 2022-08-01T11:16:58,323 running install 2022-08-01T11:16:58,385 running install_lib 2022-08-01T11:16:59,067 creating build/bdist.linux-armv7l 2022-08-01T11:16:59,068 creating build/bdist.linux-armv7l/wheel 2022-08-01T11:16:59,073 creating build/bdist.linux-armv7l/wheel/pele_platform 2022-08-01T11:16:59,076 creating build/bdist.linux-armv7l/wheel/pele_platform/constants 2022-08-01T11:16:59,079 copying build/lib/pele_platform/constants/pele_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/constants 2022-08-01T11:16:59,084 copying build/lib/pele_platform/constants/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/constants 2022-08-01T11:16:59,088 copying build/lib/pele_platform/constants/constants.py -> build/bdist.linux-armv7l/wheel/pele_platform/constants 2022-08-01T11:16:59,094 creating build/bdist.linux-armv7l/wheel/pele_platform/out_in 2022-08-01T11:16:59,097 copying build/lib/pele_platform/out_in/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/out_in 2022-08-01T11:16:59,101 copying build/lib/pele_platform/out_in/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/out_in 2022-08-01T11:16:59,106 creating build/bdist.linux-armv7l/wheel/pele_platform/covalent_docking 2022-08-01T11:16:59,108 copying build/lib/pele_platform/covalent_docking/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/covalent_docking 2022-08-01T11:16:59,112 copying build/lib/pele_platform/covalent_docking/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/covalent_docking 2022-08-01T11:16:59,118 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities 2022-08-01T11:16:59,120 copying build/lib/pele_platform/Utilities/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities 2022-08-01T11:16:59,125 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,128 copying build/lib/pele_platform/Utilities/Helpers/interaction_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,132 copying build/lib/pele_platform/Utilities/Helpers/plop_launcher.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,136 copying build/lib/pele_platform/Utilities/Helpers/system_prep.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,140 copying build/lib/pele_platform/Utilities/Helpers/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,146 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2022-08-01T11:16:59,148 copying build/lib/pele_platform/Utilities/Helpers/Metals/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2022-08-01T11:16:59,152 copying build/lib/pele_platform/Utilities/Helpers/Metals/metal_polarisation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2022-08-01T11:16:59,156 copying build/lib/pele_platform/Utilities/Helpers/Metals/metal_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2022-08-01T11:16:59,161 copying build/lib/pele_platform/Utilities/Helpers/randomize.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,166 copying build/lib/pele_platform/Utilities/Helpers/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,169 copying build/lib/pele_platform/Utilities/Helpers/conda_deployment.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,173 copying build/lib/pele_platform/Utilities/Helpers/launcher.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,176 copying build/lib/pele_platform/Utilities/Helpers/center_of_mass.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,179 copying build/lib/pele_platform/Utilities/Helpers/yaml_parser.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,184 copying build/lib/pele_platform/Utilities/Helpers/ligand_conformations.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,187 copying build/lib/pele_platform/Utilities/Helpers/calculatePCA4PELE.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,193 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2022-08-01T11:16:59,195 copying build/lib/pele_platform/Utilities/Helpers/constraints/alpha_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2022-08-01T11:16:59,199 copying build/lib/pele_platform/Utilities/Helpers/constraints/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2022-08-01T11:16:59,202 copying build/lib/pele_platform/Utilities/Helpers/constraints/smiles_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2022-08-01T11:16:59,206 copying build/lib/pele_platform/Utilities/Helpers/water.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,211 copying build/lib/pele_platform/Utilities/Helpers/bestStructs.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,215 copying build/lib/pele_platform/Utilities/Helpers/template_builder.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,218 copying build/lib/pele_platform/Utilities/Helpers/solventOBCParamsGenerator.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,222 copying build/lib/pele_platform/Utilities/Helpers/helpers.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,227 copying build/lib/pele_platform/Utilities/Helpers/map_atoms.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,231 copying build/lib/pele_platform/Utilities/Helpers/protein_wizard.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,235 copying build/lib/pele_platform/Utilities/Helpers/missing_residues.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2022-08-01T11:16:59,239 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters 2022-08-01T11:16:59,242 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams 2022-08-01T11:16:59,244 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams 2022-08-01T11:16:59,248 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2022-08-01T11:16:59,249 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2022-08-01T11:16:59,252 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams/inout_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2022-08-01T11:16:59,257 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2022-08-01T11:16:59,258 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2022-08-01T11:16:59,261 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams/glide_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2022-08-01T11:16:59,266 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2022-08-01T11:16:59,267 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2022-08-01T11:16:59,270 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams/bias_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2022-08-01T11:16:59,274 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2022-08-01T11:16:59,276 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2022-08-01T11:16:59,279 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams/msm_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2022-08-01T11:16:59,283 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PCA 2022-08-01T11:16:59,285 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PCA 2022-08-01T11:16:59,288 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA/pca.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PCA 2022-08-01T11:16:59,291 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/simulation_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams 2022-08-01T11:16:59,297 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PPI 2022-08-01T11:16:59,299 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PPI 2022-08-01T11:16:59,302 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI/ppi.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PPI 2022-08-01T11:16:59,306 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2022-08-01T11:16:59,308 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2022-08-01T11:16:59,311 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder/site_finder.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2022-08-01T11:16:59,314 copying build/lib/pele_platform/Utilities/Parameters/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters 2022-08-01T11:16:59,317 copying build/lib/pele_platform/Utilities/Parameters/parameters.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters 2022-08-01T11:16:59,322 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationFolders 2022-08-01T11:16:59,324 copying build/lib/pele_platform/Utilities/Parameters/SimulationFolders/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationFolders 2022-08-01T11:16:59,327 copying build/lib/pele_platform/Utilities/Parameters/SimulationFolders/simulation_folders.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationFolders 2022-08-01T11:16:59,330 copying build/lib/pele_platform/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform 2022-08-01T11:16:59,335 creating build/bdist.linux-armv7l/wheel/pele_platform/Frag 2022-08-01T11:16:59,336 copying build/lib/pele_platform/Frag/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2022-08-01T11:16:59,341 copying build/lib/pele_platform/Frag/fragments.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2022-08-01T11:16:59,344 copying build/lib/pele_platform/Frag/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2022-08-01T11:16:59,348 creating build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2022-08-01T11:16:59,349 copying build/lib/pele_platform/Frag/parameters/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2022-08-01T11:16:59,352 copying build/lib/pele_platform/Frag/parameters/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2022-08-01T11:16:59,356 copying build/lib/pele_platform/Frag/parameters/files.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2022-08-01T11:16:59,359 copying build/lib/pele_platform/Frag/parameters/metrics.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2022-08-01T11:16:59,362 copying build/lib/pele_platform/Frag/parameters/optional.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2022-08-01T11:16:59,366 copying build/lib/pele_platform/Frag/parameters/water.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2022-08-01T11:16:59,369 copying build/lib/pele_platform/Frag/libraries.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2022-08-01T11:16:59,373 copying build/lib/pele_platform/Frag/checker.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2022-08-01T11:16:59,376 copying build/lib/pele_platform/Frag/generative_model.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2022-08-01T11:16:59,379 copying build/lib/pele_platform/Frag/atoms.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2022-08-01T11:16:59,382 copying build/lib/pele_platform/Frag/analysis.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2022-08-01T11:16:59,386 copying build/lib/pele_platform/Frag/helpers.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2022-08-01T11:16:59,392 creating build/bdist.linux-armv7l/wheel/pele_platform/analysis 2022-08-01T11:16:59,393 copying build/lib/pele_platform/analysis/clustering.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2022-08-01T11:16:59,398 copying build/lib/pele_platform/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2022-08-01T11:16:59,401 copying build/lib/pele_platform/analysis/pdf_report.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2022-08-01T11:16:59,404 copying build/lib/pele_platform/analysis/data.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2022-08-01T11:16:59,409 copying build/lib/pele_platform/analysis/plot.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2022-08-01T11:16:59,414 copying build/lib/pele_platform/analysis/analysis.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2022-08-01T11:16:59,422 copying build/lib/pele_platform/analysis/interactive_plot.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2022-08-01T11:16:59,428 copying build/lib/pele_platform/pathway_extractor.py -> build/bdist.linux-armv7l/wheel/pele_platform 2022-08-01T11:16:59,432 creating build/bdist.linux-armv7l/wheel/pele_platform/RNA 2022-08-01T11:16:59,434 copying build/lib/pele_platform/RNA/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/RNA 2022-08-01T11:16:59,437 copying build/lib/pele_platform/RNA/prep.py -> build/bdist.linux-armv7l/wheel/pele_platform/RNA 2022-08-01T11:16:59,440 copying build/lib/pele_platform/plotter.py -> build/bdist.linux-armv7l/wheel/pele_platform 2022-08-01T11:16:59,452 creating build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,454 copying build/lib/pele_platform/Adaptive/plop_solvent.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,457 copying build/lib/pele_platform/Adaptive/interaction_restrictions.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,461 copying build/lib/pele_platform/Adaptive/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,465 copying build/lib/pele_platform/Adaptive/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,469 copying build/lib/pele_platform/Adaptive/box.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,472 copying build/lib/pele_platform/Adaptive/plop_ligand_parametrization.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,475 copying build/lib/pele_platform/Adaptive/pca.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,478 copying build/lib/pele_platform/Adaptive/parametrizer.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,485 copying build/lib/pele_platform/Adaptive/metrics.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,488 copying build/lib/pele_platform/Adaptive/preequilibrator.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2022-08-01T11:16:59,492 creating build/bdist.linux-armv7l/wheel/pele_platform/gpcr 2022-08-01T11:16:59,494 copying build/lib/pele_platform/gpcr/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/gpcr 2022-08-01T11:16:59,497 copying build/lib/pele_platform/gpcr/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/gpcr 2022-08-01T11:16:59,501 creating build/bdist.linux-armv7l/wheel/pele_platform/features 2022-08-01T11:16:59,503 copying build/lib/pele_platform/features/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/features 2022-08-01T11:16:59,506 copying build/lib/pele_platform/features/adaptive.py -> build/bdist.linux-armv7l/wheel/pele_platform/features 2022-08-01T11:16:59,510 copying build/lib/pele_platform/features/frag.py -> build/bdist.linux-armv7l/wheel/pele_platform/features 2022-08-01T11:16:59,514 creating build/bdist.linux-armv7l/wheel/pele_platform/Checker 2022-08-01T11:16:59,515 copying build/lib/pele_platform/Checker/executable.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2022-08-01T11:16:59,519 copying build/lib/pele_platform/Checker/environment_variables.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2022-08-01T11:16:59,522 copying build/lib/pele_platform/Checker/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2022-08-01T11:16:59,525 copying build/lib/pele_platform/Checker/python_version.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2022-08-01T11:16:59,528 copying build/lib/pele_platform/Checker/valid_flags.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2022-08-01T11:16:59,532 copying build/lib/pele_platform/Checker/pdb_checker.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2022-08-01T11:16:59,535 copying build/lib/pele_platform/Checker/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2022-08-01T11:16:59,540 creating build/bdist.linux-armv7l/wheel/pele_platform/Errors 2022-08-01T11:16:59,542 copying build/lib/pele_platform/Errors/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Errors 2022-08-01T11:16:59,545 copying build/lib/pele_platform/Errors/custom_errors.py -> build/bdist.linux-armv7l/wheel/pele_platform/Errors 2022-08-01T11:16:59,549 creating build/bdist.linux-armv7l/wheel/pele_platform/Templates 2022-08-01T11:16:59,550 copying build/lib/pele_platform/Templates/template_adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Templates 2022-08-01T11:16:59,554 copying build/lib/pele_platform/Templates/solventParamsHCTOBC.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Templates 2022-08-01T11:16:59,562 copying build/lib/pele_platform/Templates/pele_template.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Templates 2022-08-01T11:16:59,567 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples 2022-08-01T11:16:59,570 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/minimum_steps 2022-08-01T11:16:59,571 copying build/lib/pele_platform/Examples/minimum_steps/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/minimum_steps 2022-08-01T11:16:59,608 copying build/lib/pele_platform/Examples/minimum_steps/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/minimum_steps 2022-08-01T11:16:59,612 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/restart 2022-08-01T11:16:59,613 copying build/lib/pele_platform/Examples/restart/restart.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/restart 2022-08-01T11:16:59,618 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials 2022-08-01T11:16:59,620 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/induced_fit 2022-08-01T11:16:59,622 copying build/lib/pele_platform/Examples/tutorials/induced_fit/docking.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/induced_fit 2022-08-01T11:16:59,652 copying build/lib/pele_platform/Examples/tutorials/induced_fit/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/induced_fit 2022-08-01T11:16:59,657 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/gpcr 2022-08-01T11:16:59,659 copying build/lib/pele_platform/Examples/tutorials/gpcr/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/gpcr 2022-08-01T11:16:59,683 copying build/lib/pele_platform/Examples/tutorials/gpcr/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/gpcr 2022-08-01T11:16:59,688 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2022-08-01T11:16:59,689 copying build/lib/pele_platform/Examples/tutorials/ppi/4yy6_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2022-08-01T11:16:59,703 copying build/lib/pele_platform/Examples/tutorials/ppi/4yy6_ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2022-08-01T11:16:59,708 copying build/lib/pele_platform/Examples/tutorials/ppi/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2022-08-01T11:16:59,712 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2022-08-01T11:16:59,714 copying build/lib/pele_platform/Examples/out_in/input_default.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2022-08-01T11:16:59,717 copying build/lib/pele_platform/Examples/out_in/input_flag_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2022-08-01T11:16:59,720 copying build/lib/pele_platform/Examples/out_in/input_auto_clustering.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2022-08-01T11:16:59,724 copying build/lib/pele_platform/Examples/out_in/input_box_center.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2022-08-01T11:16:59,727 copying build/lib/pele_platform/Examples/out_in/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2022-08-01T11:16:59,730 copying build/lib/pele_platform/Examples/out_in/1_3ZON_complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2022-08-01T11:16:59,752 copying build/lib/pele_platform/Examples/out_in/input_metrics.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2022-08-01T11:16:59,756 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2022-08-01T11:16:59,758 copying build/lib/pele_platform/Examples/covalent_docking/5XXD_prepared.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2022-08-01T11:16:59,791 copying build/lib/pele_platform/Examples/covalent_docking/input3.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2022-08-01T11:16:59,794 copying build/lib/pele_platform/Examples/covalent_docking/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2022-08-01T11:16:59,797 copying build/lib/pele_platform/Examples/covalent_docking/6P0M_prepared.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2022-08-01T11:16:59,818 copying build/lib/pele_platform/Examples/covalent_docking/input2.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2022-08-01T11:16:59,822 copying build/lib/pele_platform/Examples/covalent_docking/6M06_prepared.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2022-08-01T11:16:59,847 copying build/lib/pele_platform/Examples/covalent_docking/input_defaults_refinement.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2022-08-01T11:16:59,850 copying build/lib/pele_platform/Examples/covalent_docking/input1.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2022-08-01T11:16:59,855 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/bias 2022-08-01T11:16:59,856 copying build/lib/pele_platform/Examples/bias/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/bias 2022-08-01T11:16:59,877 copying build/lib/pele_platform/Examples/bias/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/bias 2022-08-01T11:16:59,882 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/production 2022-08-01T11:16:59,883 copying build/lib/pele_platform/Examples/production/input_mae.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/production 2022-08-01T11:16:59,887 copying build/lib/pele_platform/Examples/production/input.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/production 2022-08-01T11:16:59,891 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering 2022-08-01T11:16:59,894 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2022-08-01T11:16:59,896 copying build/lib/pele_platform/Examples/clustering/0/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2022-08-01T11:16:59,900 copying build/lib/pele_platform/Examples/clustering/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2022-08-01T11:16:59,904 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0/clustering 2022-08-01T11:16:59,905 copying build/lib/pele_platform/Examples/clustering/0/clustering/object.pkl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0/clustering 2022-08-01T11:17:00,023 copying build/lib/pele_platform/Examples/clustering/0/clustering/summary.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0/clustering 2022-08-01T11:17:00,026 copying build/lib/pele_platform/Examples/clustering/0/trajectory_3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2022-08-01T11:17:00,064 copying build/lib/pele_platform/Examples/clustering/0/trajectory_1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2022-08-01T11:17:00,099 copying build/lib/pele_platform/Examples/clustering/0/report_4 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2022-08-01T11:17:00,102 copying build/lib/pele_platform/Examples/clustering/0/trajectory_2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2022-08-01T11:17:00,132 copying build/lib/pele_platform/Examples/clustering/0/trajectory_4.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2022-08-01T11:17:00,173 copying build/lib/pele_platform/Examples/clustering/0/report_3 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2022-08-01T11:17:00,177 copying build/lib/pele_platform/Examples/clustering/0/topologyMapping.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2022-08-01T11:17:00,180 copying build/lib/pele_platform/Examples/clustering/summary.csv -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering 2022-08-01T11:17:00,184 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit 2022-08-01T11:17:00,186 copying build/lib/pele_platform/Examples/exit/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit 2022-08-01T11:17:00,189 copying build/lib/pele_platform/Examples/exit/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit 2022-08-01T11:17:00,193 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2022-08-01T11:17:00,195 copying build/lib/pele_platform/Examples/inputs/nord3.sge -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2022-08-01T11:17:00,198 copying build/lib/pele_platform/Examples/inputs/mn4.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2022-08-01T11:17:00,201 copying build/lib/pele_platform/Examples/inputs/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2022-08-01T11:17:00,206 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2022-08-01T11:17:00,208 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,210 copying build/lib/pele_platform/Examples/analysis/data/strz -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,213 copying build/lib/pele_platform/Examples/analysis/data/input_mae.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,218 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2022-08-01T11:17:00,219 copying build/lib/pele_platform/Examples/analysis/data/inputs/input1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2022-08-01T11:17:00,241 copying build/lib/pele_platform/Examples/analysis/data/inputs/input3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2022-08-01T11:17:00,261 copying build/lib/pele_platform/Examples/analysis/data/inputs/input2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2022-08-01T11:17:00,292 copying build/lib/pele_platform/Examples/analysis/data/STR.rot.assign -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,295 copying build/lib/pele_platform/Examples/analysis/data/input_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,299 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc 2022-08-01T11:17:00,302 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2022-08-01T11:17:00,303 copying build/lib/pele_platform/Examples/analysis/data/xtc/0/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2022-08-01T11:17:00,307 copying build/lib/pele_platform/Examples/analysis/data/xtc/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2022-08-01T11:17:00,310 copying build/lib/pele_platform/Examples/analysis/data/xtc/0/trajectory_2.xtc -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2022-08-01T11:17:00,314 copying build/lib/pele_platform/Examples/analysis/data/xtc/0/trajectory_1.xtc -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2022-08-01T11:17:00,319 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/topologies 2022-08-01T11:17:00,320 copying build/lib/pele_platform/Examples/analysis/data/xtc/topologies/topology_0.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/topologies 2022-08-01T11:17:00,330 copying build/lib/pele_platform/Examples/analysis/data/xtc/summary.csv -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc 2022-08-01T11:17:00,334 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output 2022-08-01T11:17:00,336 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0 2022-08-01T11:17:00,338 copying build/lib/pele_platform/Examples/analysis/data/output/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0 2022-08-01T11:17:00,342 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0/clustering 2022-08-01T11:17:00,344 copying build/lib/pele_platform/Examples/analysis/data/output/0/clustering/object.pkl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0/clustering 2022-08-01T11:17:00,367 copying build/lib/pele_platform/Examples/analysis/data/output/0/clustering/summary.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0/clustering 2022-08-01T11:17:00,370 copying build/lib/pele_platform/Examples/analysis/data/output/0/trajectory_1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0 2022-08-01T11:17:00,392 copying build/lib/pele_platform/Examples/analysis/data/output/0/topologyMapping.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0 2022-08-01T11:17:00,395 copying build/lib/pele_platform/Examples/analysis/data/output/originalControlFile.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output 2022-08-01T11:17:00,400 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/synchronization 2022-08-01T11:17:00,401 copying build/lib/pele_platform/Examples/analysis/data/output/synchronization/syncFile.lock -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/synchronization 2022-08-01T11:17:00,405 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/topologies 2022-08-01T11:17:00,407 copying build/lib/pele_platform/Examples/analysis/data/output/topologies/topology_0.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/topologies 2022-08-01T11:17:00,431 copying build/lib/pele_platform/Examples/analysis/data/output/topologies/topologies.pkl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/topologies 2022-08-01T11:17:00,453 copying build/lib/pele_platform/Examples/analysis/data/adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,458 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output 2022-08-01T11:17:00,460 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:17:00,462 copying build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:17:00,465 copying build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:17:00,468 copying build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:17:00,498 copying build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:17:00,559 copying build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0/topologyMapping.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2022-08-01T11:17:00,563 copying build/lib/pele_platform/Examples/analysis/data/pele.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,566 copying build/lib/pele_platform/Examples/analysis/data/mgz -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,568 copying build/lib/pele_platform/Examples/analysis/data/MG.rot.assign -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,571 copying build/lib/pele_platform/Examples/analysis/data/input_flags0.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,574 copying build/lib/pele_platform/Examples/analysis/data/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2022-08-01T11:17:00,577 copying build/lib/pele_platform/Examples/analysis/input_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2022-08-01T11:17:00,580 copying build/lib/pele_platform/Examples/analysis/input_xtc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2022-08-01T11:17:00,583 copying build/lib/pele_platform/Examples/analysis/input_flags0.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2022-08-01T11:17:00,586 copying build/lib/pele_platform/Examples/analysis/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2022-08-01T11:17:00,591 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2022-08-01T11:17:00,592 copying build/lib/pele_platform/Examples/Msm/PR_AS4.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2022-08-01T11:17:00,613 copying build/lib/pele_platform/Examples/Msm/AS4_INIT.mae -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2022-08-01T11:17:00,617 copying build/lib/pele_platform/Examples/Msm/PR_1A28_xray_-_minimized.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2022-08-01T11:17:00,639 copying build/lib/pele_platform/Examples/Msm/PR_1A28_protein.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2022-08-01T11:17:00,660 copying build/lib/pele_platform/Examples/Msm/PR_1A28_xray_-_minimized_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2022-08-01T11:17:00,681 copying build/lib/pele_platform/Examples/Msm/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2022-08-01T11:17:00,684 copying build/lib/pele_platform/Examples/test.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples 2022-08-01T11:17:00,689 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,690 copying build/lib/pele_platform/Examples/water/input_induced.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,693 copying build/lib/pele_platform/Examples/water/water_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,720 copying build/lib/pele_platform/Examples/water/complex_induced.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,734 copying build/lib/pele_platform/Examples/water/input_lig.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,737 copying build/lib/pele_platform/Examples/water/water2_pele.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,740 copying build/lib/pele_platform/Examples/water/input_nwaters.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,743 copying build/lib/pele_platform/Examples/water/input_all.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,747 copying build/lib/pele_platform/Examples/water/input_bs.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,750 copying build/lib/pele_platform/Examples/water/water_pele.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,753 copying build/lib/pele_platform/Examples/water/complex_ref_LESSH2O.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,785 copying build/lib/pele_platform/Examples/water/input_bs_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,788 copying build/lib/pele_platform/Examples/water/input_lig_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,791 copying build/lib/pele_platform/Examples/water/input_previous_water.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2022-08-01T11:17:00,796 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/randomize 2022-08-01T11:17:00,797 copying build/lib/pele_platform/Examples/randomize/ligand2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/randomize 2022-08-01T11:17:00,801 copying build/lib/pele_platform/Examples/randomize/ref_ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/randomize 2022-08-01T11:17:00,804 copying build/lib/pele_platform/Examples/randomize/ligand3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/randomize 2022-08-01T11:17:00,807 copying build/lib/pele_platform/Examples/randomize/receptor.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/randomize 2022-08-01T11:17:00,833 copying build/lib/pele_platform/Examples/randomize/ligand1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/randomize 2022-08-01T11:17:00,838 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2022-08-01T11:17:00,839 copying build/lib/pele_platform/Examples/RNA/input_induced.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2022-08-01T11:17:00,842 copying build/lib/pele_platform/Examples/RNA/2l94.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2022-08-01T11:17:00,846 copying build/lib/pele_platform/Examples/RNA/5C45_prep_proc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2022-08-01T11:17:00,869 copying build/lib/pele_platform/Examples/RNA/5C45_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2022-08-01T11:17:00,891 copying build/lib/pele_platform/Examples/RNA/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2022-08-01T11:17:00,896 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2022-08-01T11:17:00,897 copying build/lib/pele_platform/Examples/induced_fit/input_fast.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2022-08-01T11:17:00,901 copying build/lib/pele_platform/Examples/induced_fit/input_mae.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2022-08-01T11:17:00,904 copying build/lib/pele_platform/Examples/induced_fit/input_fast_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2022-08-01T11:17:00,907 copying build/lib/pele_platform/Examples/induced_fit/input_exhaustive_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2022-08-01T11:17:00,910 copying build/lib/pele_platform/Examples/induced_fit/input_auto_clustering.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2022-08-01T11:17:00,914 copying build/lib/pele_platform/Examples/induced_fit/input_exhaustive.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2022-08-01T11:17:00,918 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:00,919 copying build/lib/pele_platform/Examples/checker/input_unk.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:00,923 copying build/lib/pele_platform/Examples/checker/input_space.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:00,926 copying build/lib/pele_platform/Examples/checker/input_rotamer.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:00,929 copying build/lib/pele_platform/Examples/checker/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:00,956 copying build/lib/pele_platform/Examples/checker/complex_unk.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:00,997 copying build/lib/pele_platform/Examples/checker/input_template.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,001 copying build/lib/pele_platform/Examples/checker/mapping_complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,038 copying build/lib/pele_platform/Examples/checker/input_tab.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,041 copying build/lib/pele_platform/Examples/checker/ligand2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,046 copying build/lib/pele_platform/Examples/checker/incompatible_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,049 copying build/lib/pele_platform/Examples/checker/input_env.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,052 copying build/lib/pele_platform/Examples/checker/negative_residues.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,055 copying build/lib/pele_platform/Examples/checker/input_map_atom_str.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,058 copying build/lib/pele_platform/Examples/checker/input_underscore.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,061 copying build/lib/pele_platform/Examples/checker/complex2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,074 copying build/lib/pele_platform/Examples/checker/capped_no_connects.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,154 copying build/lib/pele_platform/Examples/checker/capped.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,266 copying build/lib/pele_platform/Examples/checker/input_atom_string.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,269 copying build/lib/pele_platform/Examples/checker/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,273 copying build/lib/pele_platform/Examples/checker/input_map_atom_num.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,276 copying build/lib/pele_platform/Examples/checker/input_pele_exec.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,279 copying build/lib/pele_platform/Examples/checker/multiple_simulations.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2022-08-01T11:17:01,284 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2022-08-01T11:17:01,286 copying build/lib/pele_platform/Examples/Adaptive/strz -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2022-08-01T11:17:01,293 copying build/lib/pele_platform/Examples/Adaptive/STR.rot.assign -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2022-08-01T11:17:01,297 copying build/lib/pele_platform/Examples/Adaptive/test.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2022-08-01T11:17:01,300 copying build/lib/pele_platform/Examples/Adaptive/adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2022-08-01T11:17:01,303 copying build/lib/pele_platform/Examples/Adaptive/pele_file_4Adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2022-08-01T11:17:01,308 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/rescoring 2022-08-01T11:17:01,309 copying build/lib/pele_platform/Examples/rescoring/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/rescoring 2022-08-01T11:17:01,312 copying build/lib/pele_platform/Examples/rescoring/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/rescoring 2022-08-01T11:17:01,317 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2022-08-01T11:17:01,318 copying build/lib/pele_platform/Examples/pca/3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2022-08-01T11:17:01,341 copying build/lib/pele_platform/Examples/pca/2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2022-08-01T11:17:01,362 copying build/lib/pele_platform/Examples/pca/input_str.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2022-08-01T11:17:01,366 copying build/lib/pele_platform/Examples/pca/1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2022-08-01T11:17:01,389 copying build/lib/pele_platform/Examples/pca/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2022-08-01T11:17:01,394 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2022-08-01T11:17:01,395 copying build/lib/pele_platform/Examples/gpcr/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2022-08-01T11:17:01,420 copying build/lib/pele_platform/Examples/gpcr/input_atom_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2022-08-01T11:17:01,423 copying build/lib/pele_platform/Examples/gpcr/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2022-08-01T11:17:01,426 copying build/lib/pele_platform/Examples/gpcr/complex_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2022-08-01T11:17:01,460 copying build/lib/pele_platform/Examples/gpcr/input_defaults2.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2022-08-01T11:17:01,464 copying build/lib/pele_platform/Examples/gpcr/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2022-08-01T11:17:01,469 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,471 copying build/lib/pele_platform/Examples/constraints/input_permissive_exception.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,475 copying build/lib/pele_platform/Examples/constraints/1zop.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,492 copying build/lib/pele_platform/Examples/constraints/input_ca_ppp.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,495 copying build/lib/pele_platform/Examples/constraints/input_ignore.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,498 copying build/lib/pele_platform/Examples/constraints/4w4o_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,523 copying build/lib/pele_platform/Examples/constraints/4qnr_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,553 copying build/lib/pele_platform/Examples/constraints/no_connects.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,557 copying build/lib/pele_platform/Examples/constraints/ca_constraints.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,600 copying build/lib/pele_platform/Examples/constraints/input_all_metal_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,605 copying build/lib/pele_platform/Examples/constraints/input_tetrahedral.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,609 copying build/lib/pele_platform/Examples/constraints/fail_input_permissive_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,613 copying build/lib/pele_platform/Examples/constraints/input_k.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,621 copying build/lib/pele_platform/Examples/constraints/4w5i_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,639 copying build/lib/pele_platform/Examples/constraints/pass_input_permissive_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,642 copying build/lib/pele_platform/Examples/constraints/input_external_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,646 copying build/lib/pele_platform/Examples/constraints/input_constrain_smarts.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,649 copying build/lib/pele_platform/Examples/constraints/input_metals.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,655 copying build/lib/pele_platform/Examples/constraints/input_smiles_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,659 copying build/lib/pele_platform/Examples/constraints/complex_smiles_error.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,682 copying build/lib/pele_platform/Examples/constraints/4zu9_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,743 copying build/lib/pele_platform/Examples/constraints/4l3a_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,771 copying build/lib/pele_platform/Examples/constraints/input_constrain_smiles.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,774 copying build/lib/pele_platform/Examples/constraints/input_no_metal_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,777 copying build/lib/pele_platform/Examples/constraints/input_ca_noppp.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,780 copying build/lib/pele_platform/Examples/constraints/input_square_planar.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,783 copying build/lib/pele_platform/Examples/constraints/input_square_planar_polarisation.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2022-08-01T11:17:01,787 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit_soft 2022-08-01T11:17:01,788 copying build/lib/pele_platform/Examples/exit_soft/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit_soft 2022-08-01T11:17:01,792 copying build/lib/pele_platform/Examples/exit_soft/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit_soft 2022-08-01T11:17:01,796 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc 2022-08-01T11:17:01,797 copying build/lib/pele_platform/Examples/clustering_xtc/water_clustering.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc 2022-08-01T11:17:01,801 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:17:01,803 copying build/lib/pele_platform/Examples/clustering_xtc/0/trajectory_3.xtc -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:17:01,808 copying build/lib/pele_platform/Examples/clustering_xtc/0/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:17:01,811 copying build/lib/pele_platform/Examples/clustering_xtc/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:17:01,815 copying build/lib/pele_platform/Examples/clustering_xtc/0/trajectory_2.xtc -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:17:01,819 copying build/lib/pele_platform/Examples/clustering_xtc/0/trajectory_4.xtc -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:17:01,824 copying build/lib/pele_platform/Examples/clustering_xtc/0/topology.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:17:01,845 copying build/lib/pele_platform/Examples/clustering_xtc/0/report_4 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:17:01,848 copying build/lib/pele_platform/Examples/clustering_xtc/0/report_3 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:17:01,851 copying build/lib/pele_platform/Examples/clustering_xtc/0/trajectory_1.xtc -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2022-08-01T11:17:01,858 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,860 copying build/lib/pele_platform/Examples/frag/input_core_bond.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,863 copying build/lib/pele_platform/Examples/frag/flags.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,867 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/pdb_test_lib 2022-08-01T11:17:01,868 copying build/lib/pele_platform/Examples/frag/pdb_test_lib/mol2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/pdb_test_lib 2022-08-01T11:17:01,872 copying build/lib/pele_platform/Examples/frag/pdb_test_lib/mol1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/pdb_test_lib 2022-08-01T11:17:01,875 copying build/lib/pele_platform/Examples/frag/input_symmetry.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,878 copying build/lib/pele_platform/Examples/frag/1dyi_no_waters.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,892 copying build/lib/pele_platform/Examples/frag/input_core.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,895 copying build/lib/pele_platform/Examples/frag/input_fragment_atom.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,898 copying build/lib/pele_platform/Examples/frag/ligands_water.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,902 copying build/lib/pele_platform/Examples/frag/input_frag_waters.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,905 copying build/lib/pele_platform/Examples/frag/input_ai.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,908 copying build/lib/pele_platform/Examples/frag/sequential.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,912 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2022-08-01T11:17:01,914 copying build/lib/pele_platform/Examples/frag/checker/4RFM_proc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2022-08-01T11:17:01,917 copying build/lib/pele_platform/Examples/frag/checker/receptor.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2022-08-01T11:17:01,933 copying build/lib/pele_platform/Examples/frag/checker/4RFM_series.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2022-08-01T11:17:01,937 copying build/lib/pele_platform/Examples/frag/input_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,940 copying build/lib/pele_platform/Examples/frag/1w7h_preparation_structure_2w_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,969 copying build/lib/pele_platform/Examples/frag/input_sim.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,972 copying build/lib/pele_platform/Examples/frag/input_sim_xtc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,976 copying build/lib/pele_platform/Examples/frag/input_core_sdf.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,979 copying build/lib/pele_platform/Examples/frag/input_lib_pdb.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,982 copying build/lib/pele_platform/Examples/frag/ligands.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,985 copying build/lib/pele_platform/Examples/frag/core.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,989 copying build/lib/pele_platform/Examples/frag/input_lib_sdf.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:01,993 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:01,995 copying build/lib/pele_platform/Examples/frag/sdf_joiner/core2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,021 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag2.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,025 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,029 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag2.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,035 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,038 copying build/lib/pele_platform/Examples/frag/sdf_joiner/4RFM_proc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,070 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag3.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,077 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag3.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,080 copying build/lib/pele_platform/Examples/frag/sdf_joiner/core3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,096 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag4.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,099 copying build/lib/pele_platform/Examples/frag/sdf_joiner/13_serie.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,106 copying build/lib/pele_platform/Examples/frag/sdf_joiner/4RFM_series.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,111 copying build/lib/pele_platform/Examples/frag/sdf_joiner/glide-dockSARS_core.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,154 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag31.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,161 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag5.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,165 copying build/lib/pele_platform/Examples/frag/sdf_joiner/4RFM_core_sc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2022-08-01T11:17:02,192 copying build/lib/pele_platform/Examples/frag/amino.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:02,197 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_test_lib 2022-08-01T11:17:02,198 copying build/lib/pele_platform/Examples/frag/sdf_test_lib/test_library.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_test_lib 2022-08-01T11:17:02,202 copying build/lib/pele_platform/Examples/frag/input_point_analysis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:02,206 copying build/lib/pele_platform/Examples/frag/analysis.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:02,209 copying build/lib/pele_platform/Examples/frag/1w7h_preparation_structure_2w.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:02,242 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data 2022-08-01T11:17:02,245 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1 2022-08-01T11:17:02,248 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result 2022-08-01T11:17:02,249 copying build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result/epochsampling_result_trajectory_1.1_BindingEnergy-23.4636.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result 2022-08-01T11:17:02,277 copying build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result/epochsampling_result_trajectory_2.1_BindingEnergy-25.1634.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result 2022-08-01T11:17:02,307 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result 2022-08-01T11:17:02,309 copying build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result 2022-08-01T11:17:02,313 copying build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result 2022-08-01T11:17:02,317 copying build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/trajectory_1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result 2022-08-01T11:17:02,368 copying build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/trajectory_2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result 2022-08-01T11:17:02,418 copying build/lib/pele_platform/Examples/frag/1dyi_waters.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2022-08-01T11:17:02,433 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2022-08-01T11:17:02,435 copying build/lib/pele_platform/Examples/global/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2022-08-01T11:17:02,438 copying build/lib/pele_platform/Examples/global/input_inputs.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2022-08-01T11:17:02,441 copying build/lib/pele_platform/Examples/global/input_inputs_asterisc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2022-08-01T11:17:02,444 copying build/lib/pele_platform/Examples/global/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2022-08-01T11:17:02,448 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/ligand_conformations 2022-08-01T11:17:02,449 copying build/lib/pele_platform/Examples/ligand_conformations/3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/ligand_conformations 2022-08-01T11:17:02,453 copying build/lib/pele_platform/Examples/ligand_conformations/2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/ligand_conformations 2022-08-01T11:17:02,456 copying build/lib/pele_platform/Examples/ligand_conformations/1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/ligand_conformations 2022-08-01T11:17:02,459 copying build/lib/pele_platform/Examples/ligand_conformations/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/ligand_conformations 2022-08-01T11:17:02,464 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2022-08-01T11:17:02,465 copying build/lib/pele_platform/Examples/PPI/1f47_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2022-08-01T11:17:02,477 copying build/lib/pele_platform/Examples/PPI/1tnf_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2022-08-01T11:17:02,510 copying build/lib/pele_platform/Examples/PPI/input_folder.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2022-08-01T11:17:02,514 copying build/lib/pele_platform/Examples/PPI/input_skipref.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2022-08-01T11:17:02,517 copying build/lib/pele_platform/Examples/PPI/1f47_ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2022-08-01T11:17:02,521 copying build/lib/pele_platform/Examples/PPI/1tnf_ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2022-08-01T11:17:02,525 copying build/lib/pele_platform/Examples/PPI/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2022-08-01T11:17:02,529 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2022-08-01T11:17:02,530 copying build/lib/pele_platform/Examples/enzyme_engineering/saturated_mutagenesis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2022-08-01T11:17:02,534 copying build/lib/pele_platform/Examples/enzyme_engineering/restart_saturated_mutagenesis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2022-08-01T11:17:02,537 copying build/lib/pele_platform/Examples/enzyme_engineering/wrong_cpus.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2022-08-01T11:17:02,541 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart 2022-08-01T11:17:02,542 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/completed_mutations.log -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart 2022-08-01T11:17:02,547 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2022-08-01T11:17:02,549 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal 2022-08-01T11:17:02,552 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs 2022-08-01T11:17:02,554 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs/ANL.rot.assign -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs 2022-08-01T11:17:02,558 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates 2022-08-01T11:17:02,560 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005 2022-08-01T11:17:02,563 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms 2022-08-01T11:17:02,565 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms/anlz -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms 2022-08-01T11:17:02,570 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/ANL.mae -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2022-08-01T11:17:02,573 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/restart_saturated_mutagenesis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2022-08-01T11:17:02,577 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2022-08-01T11:17:02,579 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/initial_0_1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2022-08-01T11:17:02,616 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/initial_0_0.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2022-08-01T11:17:02,650 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/controlFile0.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2022-08-01T11:17:02,656 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output 2022-08-01T11:17:02,658 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0 2022-08-01T11:17:02,661 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering 2022-08-01T11:17:02,663 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering/object.pkl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering 2022-08-01T11:17:02,666 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering/summary.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering 2022-08-01T11:17:02,669 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/topologyMapping.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0 2022-08-01T11:17:02,672 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/originalControlFile.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output 2022-08-01T11:17:02,677 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2022-08-01T11:17:02,678 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2022-08-01T11:17:02,681 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/report_4 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2022-08-01T11:17:02,685 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/trajectory_2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2022-08-01T11:17:02,748 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/trajectory_4.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2022-08-01T11:17:02,816 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2022-08-01T11:17:02,817 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2022-08-01T11:17:02,821 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/trajectory_3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2022-08-01T11:17:02,885 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/trajectory_1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2022-08-01T11:17:02,959 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/report_3 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2022-08-01T11:17:02,964 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization 2022-08-01T11:17:02,966 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization/syncFile.lock -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization 2022-08-01T11:17:02,971 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2022-08-01T11:17:02,973 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topology_1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2022-08-01T11:17:03,008 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topology_0.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2022-08-01T11:17:03,045 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topologies.pkl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2022-08-01T11:17:03,128 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2022-08-01T11:17:03,132 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:17:03,133 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454D_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:17:03,166 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454A.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:17:03,200 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454D.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:17:03,237 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/receptor.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:17:03,273 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454A_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:17:03,308 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2022-08-01T11:17:03,312 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/pele.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2022-08-01T11:17:03,317 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2022-08-01T11:17:03,318 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/ANL.mae -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2022-08-01T11:17:03,322 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/restart_saturated_mutagenesis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2022-08-01T11:17:03,325 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2022-08-01T11:17:03,329 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2022-08-01T11:17:03,330 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/T454E_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2022-08-01T11:17:03,365 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/T454E.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2022-08-01T11:17:03,398 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/receptor.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2022-08-01T11:17:03,431 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2022-08-01T11:17:03,434 copying build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/pele.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2022-08-01T11:17:03,438 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2022-08-01T11:17:03,440 copying build/lib/pele_platform/Examples/enzyme_engineering/pdb_files/T454A.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2022-08-01T11:17:03,475 copying build/lib/pele_platform/Examples/enzyme_engineering/pdb_files/T454D.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2022-08-01T11:17:03,505 copying build/lib/pele_platform/Examples/enzyme_engineering/pdb_files/T454E.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2022-08-01T11:17:03,542 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/flags 2022-08-01T11:17:03,543 copying build/lib/pele_platform/Examples/flags/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/flags 2022-08-01T11:17:03,548 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2022-08-01T11:17:03,549 copying build/lib/pele_platform/Examples/preparation/input_space.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2022-08-01T11:17:03,553 copying build/lib/pele_platform/Examples/preparation/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2022-08-01T11:17:03,574 copying build/lib/pele_platform/Examples/preparation/input_nonstandard.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2022-08-01T11:17:03,577 copying build/lib/pele_platform/Examples/preparation/complex_2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2022-08-01T11:17:03,613 copying build/lib/pele_platform/Examples/preparation/parametrization_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2022-08-01T11:17:03,617 copying build/lib/pele_platform/Examples/preparation/6qmk_correct.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2022-08-01T11:17:03,642 copying build/lib/pele_platform/Examples/preparation/6qmk_repeated.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2022-08-01T11:17:03,673 copying build/lib/pele_platform/Examples/preparation/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2022-08-01T11:17:03,677 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2022-08-01T11:17:03,678 copying build/lib/pele_platform/Examples/interaction_restrictions/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2022-08-01T11:17:03,714 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions/out 2022-08-01T11:17:03,716 copying build/lib/pele_platform/Examples/interaction_restrictions/out/expected_conditions.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions/out 2022-08-01T11:17:03,719 copying build/lib/pele_platform/Examples/interaction_restrictions/out/expected_metrics.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions/out 2022-08-01T11:17:03,722 copying build/lib/pele_platform/Examples/interaction_restrictions/input_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2022-08-01T11:17:03,725 copying build/lib/pele_platform/Examples/interaction_restrictions/input_error_2.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2022-08-01T11:17:03,728 copying build/lib/pele_platform/Examples/interaction_restrictions/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2022-08-01T11:17:03,733 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2022-08-01T11:17:03,734 copying build/lib/pele_platform/Examples/site_finder/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2022-08-01T11:17:03,761 copying build/lib/pele_platform/Examples/site_finder/input_global.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2022-08-01T11:17:03,765 copying build/lib/pele_platform/Examples/site_finder/input_global_xtc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2022-08-01T11:17:03,768 copying build/lib/pele_platform/Examples/site_finder/input_folder.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2022-08-01T11:17:03,771 copying build/lib/pele_platform/Examples/site_finder/input_restart.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2022-08-01T11:17:03,774 copying build/lib/pele_platform/Examples/site_finder/input_skipref.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2022-08-01T11:17:03,777 copying build/lib/pele_platform/Examples/site_finder/input_custom_box.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2022-08-01T11:17:03,780 copying build/lib/pele_platform/Examples/site_finder/global.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2022-08-01T11:17:03,784 copying build/lib/pele_platform/Examples/site_finder/local.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2022-08-01T11:17:03,788 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/singularity 2022-08-01T11:17:03,789 copying build/lib/pele_platform/Examples/singularity/input_adaptive_mpi_params.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/singularity 2022-08-01T11:17:03,793 copying build/lib/pele_platform/Examples/singularity/input_adaptive.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/singularity 2022-08-01T11:17:03,796 copying build/lib/pele_platform/Examples/singularity/input_frag.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/singularity 2022-08-01T11:17:03,800 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/box 2022-08-01T11:17:03,801 copying build/lib/pele_platform/Examples/box/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/box 2022-08-01T11:17:03,806 creating build/bdist.linux-armv7l/wheel/pele_platform/PPI 2022-08-01T11:17:03,807 copying build/lib/pele_platform/PPI/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2022-08-01T11:17:03,810 copying build/lib/pele_platform/PPI/simulation_launcher.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2022-08-01T11:17:03,813 copying build/lib/pele_platform/PPI/cluster.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2022-08-01T11:17:03,817 copying build/lib/pele_platform/PPI/preparation.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2022-08-01T11:17:03,820 copying build/lib/pele_platform/PPI/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2022-08-01T11:17:03,823 copying build/lib/pele_platform/converter.py -> build/bdist.linux-armv7l/wheel/pele_platform 2022-08-01T11:17:03,829 creating build/bdist.linux-armv7l/wheel/pele_platform/enzyme_engineering 2022-08-01T11:17:03,831 copying build/lib/pele_platform/enzyme_engineering/saturated_mutagenesis.py -> build/bdist.linux-armv7l/wheel/pele_platform/enzyme_engineering 2022-08-01T11:17:03,835 copying build/lib/pele_platform/enzyme_engineering/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/enzyme_engineering 2022-08-01T11:17:03,838 copying build/lib/pele_platform/main.py -> build/bdist.linux-armv7l/wheel/pele_platform 2022-08-01T11:17:03,841 copying build/lib/pele_platform/_version.py -> build/bdist.linux-armv7l/wheel/pele_platform 2022-08-01T11:17:03,845 creating build/bdist.linux-armv7l/wheel/pele_platform/site_finder 2022-08-01T11:17:03,847 copying build/lib/pele_platform/site_finder/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/site_finder 2022-08-01T11:17:03,849 copying build/lib/pele_platform/site_finder/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/site_finder 2022-08-01T11:17:03,853 running install_egg_info 2022-08-01T11:17:04,534 Copying pele_platform.egg-info to build/bdist.linux-armv7l/wheel/pele_platform-1.6.4-py3.7.egg-info 2022-08-01T11:17:04,556 running install_scripts 2022-08-01T11:17:04,806 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-08-01T11:17:04,815 creating build/bdist.linux-armv7l/wheel/pele_platform-1.6.4.dist-info/WHEEL 2022-08-01T11:17:04,820 creating '/tmp/pip-wheel-0ji81ool/pele_platform-1.6.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-08-01T11:17:04,824 adding 'pele_platform/__init__.py' 2022-08-01T11:17:04,827 adding 'pele_platform/_version.py' 2022-08-01T11:17:04,832 adding 'pele_platform/converter.py' 2022-08-01T11:17:04,836 adding 'pele_platform/main.py' 2022-08-01T11:17:04,838 adding 'pele_platform/pathway_extractor.py' 2022-08-01T11:17:04,854 adding 'pele_platform/plotter.py' 2022-08-01T11:17:04,858 adding 'pele_platform/Adaptive/__init__.py' 2022-08-01T11:17:04,861 adding 'pele_platform/Adaptive/box.py' 2022-08-01T11:17:04,864 adding 'pele_platform/Adaptive/interaction_restrictions.py' 2022-08-01T11:17:04,866 adding 'pele_platform/Adaptive/metrics.py' 2022-08-01T11:17:04,877 adding 'pele_platform/Adaptive/parametrizer.py' 2022-08-01T11:17:04,880 adding 'pele_platform/Adaptive/pca.py' 2022-08-01T11:17:04,882 adding 'pele_platform/Adaptive/plop_ligand_parametrization.py' 2022-08-01T11:17:04,885 adding 'pele_platform/Adaptive/plop_solvent.py' 2022-08-01T11:17:04,888 adding 'pele_platform/Adaptive/preequilibrator.py' 2022-08-01T11:17:04,893 adding 'pele_platform/Adaptive/simulation.py' 2022-08-01T11:17:04,896 adding 'pele_platform/Checker/__init__.py' 2022-08-01T11:17:04,899 adding 'pele_platform/Checker/environment_variables.py' 2022-08-01T11:17:04,901 adding 'pele_platform/Checker/executable.py' 2022-08-01T11:17:04,904 adding 'pele_platform/Checker/main.py' 2022-08-01T11:17:04,907 adding 'pele_platform/Checker/pdb_checker.py' 2022-08-01T11:17:04,909 adding 'pele_platform/Checker/python_version.py' 2022-08-01T11:17:04,913 adding 'pele_platform/Checker/valid_flags.py' 2022-08-01T11:17:04,916 adding 'pele_platform/Errors/__init__.py' 2022-08-01T11:17:04,918 adding 'pele_platform/Errors/custom_errors.py' 2022-08-01T11:17:04,923 adding 'pele_platform/Examples/test.sl' 2022-08-01T11:17:04,926 adding 'pele_platform/Examples/Adaptive/STR.rot.assign' 2022-08-01T11:17:04,928 adding 'pele_platform/Examples/Adaptive/adaptive.conf' 2022-08-01T11:17:04,931 adding 'pele_platform/Examples/Adaptive/pele_file_4Adaptive.conf' 2022-08-01T11:17:04,942 adding 'pele_platform/Examples/Adaptive/strz' 2022-08-01T11:17:04,945 adding 'pele_platform/Examples/Adaptive/test.sl' 2022-08-01T11:17:04,952 adding 'pele_platform/Examples/Msm/AS4_INIT.mae' 2022-08-01T11:17:05,089 adding 'pele_platform/Examples/Msm/PR_1A28_protein.pdb' 2022-08-01T11:17:05,235 adding 'pele_platform/Examples/Msm/PR_1A28_xray_-_minimized.pdb' 2022-08-01T11:17:05,381 adding 'pele_platform/Examples/Msm/PR_1A28_xray_-_minimized_processed.pdb' 2022-08-01T11:17:05,526 adding 'pele_platform/Examples/Msm/PR_AS4.pdb' 2022-08-01T11:17:05,535 adding 'pele_platform/Examples/Msm/input.yaml' 2022-08-01T11:17:05,539 adding 'pele_platform/Examples/PPI/1f47_ligand.pdb' 2022-08-01T11:17:05,615 adding 'pele_platform/Examples/PPI/1f47_prep.pdb' 2022-08-01T11:17:05,623 adding 'pele_platform/Examples/PPI/1tnf_ligand.pdb' 2022-08-01T11:17:05,862 adding 'pele_platform/Examples/PPI/1tnf_prep.pdb' 2022-08-01T11:17:05,876 adding 'pele_platform/Examples/PPI/input.yaml' 2022-08-01T11:17:05,878 adding 'pele_platform/Examples/PPI/input_folder.yaml' 2022-08-01T11:17:05,880 adding 'pele_platform/Examples/PPI/input_skipref.yaml' 2022-08-01T11:17:05,884 adding 'pele_platform/Examples/RNA/2l94.yaml' 2022-08-01T11:17:06,066 adding 'pele_platform/Examples/RNA/5C45_prep.pdb' 2022-08-01T11:17:06,255 adding 'pele_platform/Examples/RNA/5C45_prep_proc.pdb' 2022-08-01T11:17:06,265 adding 'pele_platform/Examples/RNA/input.yaml' 2022-08-01T11:17:06,267 adding 'pele_platform/Examples/RNA/input_induced.yaml' 2022-08-01T11:17:06,270 adding 'pele_platform/Examples/analysis/input.yaml' 2022-08-01T11:17:06,272 adding 'pele_platform/Examples/analysis/input_flags.yaml' 2022-08-01T11:17:06,274 adding 'pele_platform/Examples/analysis/input_flags0.yaml' 2022-08-01T11:17:06,277 adding 'pele_platform/Examples/analysis/input_xtc.yaml' 2022-08-01T11:17:06,280 adding 'pele_platform/Examples/analysis/data/MG.rot.assign' 2022-08-01T11:17:06,282 adding 'pele_platform/Examples/analysis/data/STR.rot.assign' 2022-08-01T11:17:06,284 adding 'pele_platform/Examples/analysis/data/adaptive.conf' 2022-08-01T11:17:06,286 adding 'pele_platform/Examples/analysis/data/input.yaml' 2022-08-01T11:17:06,289 adding 'pele_platform/Examples/analysis/data/input_flags.yaml' 2022-08-01T11:17:06,291 adding 'pele_platform/Examples/analysis/data/input_flags0.yaml' 2022-08-01T11:17:06,293 adding 'pele_platform/Examples/analysis/data/input_mae.yaml' 2022-08-01T11:17:06,295 adding 'pele_platform/Examples/analysis/data/mgz' 2022-08-01T11:17:06,298 adding 'pele_platform/Examples/analysis/data/pele.conf' 2022-08-01T11:17:06,300 adding 'pele_platform/Examples/analysis/data/strz' 2022-08-01T11:17:06,304 adding 'pele_platform/Examples/analysis/data/empty_reports_output/0/report_1' 2022-08-01T11:17:06,306 adding 'pele_platform/Examples/analysis/data/empty_reports_output/0/report_2' 2022-08-01T11:17:06,308 adding 'pele_platform/Examples/analysis/data/empty_reports_output/0/topologyMapping.txt' 2022-08-01T11:17:06,467 adding 'pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_1.pdb' 2022-08-01T11:17:06,956 adding 'pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_2.pdb' 2022-08-01T11:17:07,125 adding 'pele_platform/Examples/analysis/data/inputs/input1.pdb' 2022-08-01T11:17:07,276 adding 'pele_platform/Examples/analysis/data/inputs/input2.pdb' 2022-08-01T11:17:07,427 adding 'pele_platform/Examples/analysis/data/inputs/input3.pdb' 2022-08-01T11:17:07,438 adding 'pele_platform/Examples/analysis/data/output/originalControlFile.conf' 2022-08-01T11:17:07,441 adding 'pele_platform/Examples/analysis/data/output/0/report_1' 2022-08-01T11:17:07,443 adding 'pele_platform/Examples/analysis/data/output/0/topologyMapping.txt' 2022-08-01T11:17:07,580 adding 'pele_platform/Examples/analysis/data/output/0/trajectory_1.pdb' 2022-08-01T11:17:07,727 adding 'pele_platform/Examples/analysis/data/output/0/clustering/object.pkl' 2022-08-01T11:17:07,736 adding 'pele_platform/Examples/analysis/data/output/0/clustering/summary.txt' 2022-08-01T11:17:07,739 adding 'pele_platform/Examples/analysis/data/output/synchronization/syncFile.lock' 2022-08-01T11:17:07,824 adding 'pele_platform/Examples/analysis/data/output/topologies/topologies.pkl' 2022-08-01T11:17:07,968 adding 'pele_platform/Examples/analysis/data/output/topologies/topology_0.pdb' 2022-08-01T11:17:07,978 adding 'pele_platform/Examples/analysis/data/xtc/summary.csv' 2022-08-01T11:17:07,981 adding 'pele_platform/Examples/analysis/data/xtc/0/report_1' 2022-08-01T11:17:07,984 adding 'pele_platform/Examples/analysis/data/xtc/0/report_2' 2022-08-01T11:17:07,987 adding 'pele_platform/Examples/analysis/data/xtc/0/trajectory_1.xtc' 2022-08-01T11:17:07,991 adding 'pele_platform/Examples/analysis/data/xtc/0/trajectory_2.xtc' 2022-08-01T11:17:08,033 adding 'pele_platform/Examples/analysis/data/xtc/topologies/topology_0.pdb' 2022-08-01T11:17:08,171 adding 'pele_platform/Examples/bias/complex.pdb' 2022-08-01T11:17:08,180 adding 'pele_platform/Examples/bias/input_defaults.yaml' 2022-08-01T11:17:08,183 adding 'pele_platform/Examples/box/input.yaml' 2022-08-01T11:17:08,783 adding 'pele_platform/Examples/checker/capped.pdb' 2022-08-01T11:17:09,402 adding 'pele_platform/Examples/checker/capped_no_connects.pdb' 2022-08-01T11:17:09,600 adding 'pele_platform/Examples/checker/complex.pdb' 2022-08-01T11:17:09,698 adding 'pele_platform/Examples/checker/complex2.pdb' 2022-08-01T11:17:09,964 adding 'pele_platform/Examples/checker/complex_unk.yaml' 2022-08-01T11:17:09,979 adding 'pele_platform/Examples/checker/incompatible_flags.yaml' 2022-08-01T11:17:09,981 adding 'pele_platform/Examples/checker/input.yaml' 2022-08-01T11:17:09,983 adding 'pele_platform/Examples/checker/input_atom_string.yaml' 2022-08-01T11:17:09,985 adding 'pele_platform/Examples/checker/input_env.yaml' 2022-08-01T11:17:09,987 adding 'pele_platform/Examples/checker/input_map_atom_num.yaml' 2022-08-01T11:17:09,990 adding 'pele_platform/Examples/checker/input_map_atom_str.yaml' 2022-08-01T11:17:09,992 adding 'pele_platform/Examples/checker/input_pele_exec.yaml' 2022-08-01T11:17:09,994 adding 'pele_platform/Examples/checker/input_rotamer.yaml' 2022-08-01T11:17:09,996 adding 'pele_platform/Examples/checker/input_space.yaml' 2022-08-01T11:17:09,998 adding 'pele_platform/Examples/checker/input_tab.yaml' 2022-08-01T11:17:10,000 adding 'pele_platform/Examples/checker/input_template.yaml' 2022-08-01T11:17:10,002 adding 'pele_platform/Examples/checker/input_underscore.yaml' 2022-08-01T11:17:10,004 adding 'pele_platform/Examples/checker/input_unk.yaml' 2022-08-01T11:17:10,008 adding 'pele_platform/Examples/checker/ligand2.pdb' 2022-08-01T11:17:10,272 adding 'pele_platform/Examples/checker/mapping_complex.pdb' 2022-08-01T11:17:10,287 adding 'pele_platform/Examples/checker/multiple_simulations.yaml' 2022-08-01T11:17:10,289 adding 'pele_platform/Examples/checker/negative_residues.pdb' 2022-08-01T11:17:10,293 adding 'pele_platform/Examples/clustering/summary.csv' 2022-08-01T11:17:10,298 adding 'pele_platform/Examples/clustering/0/report_1' 2022-08-01T11:17:10,300 adding 'pele_platform/Examples/clustering/0/report_2' 2022-08-01T11:17:10,302 adding 'pele_platform/Examples/clustering/0/report_3' 2022-08-01T11:17:10,305 adding 'pele_platform/Examples/clustering/0/report_4' 2022-08-01T11:17:10,308 adding 'pele_platform/Examples/clustering/0/topologyMapping.txt' 2022-08-01T11:17:10,584 adding 'pele_platform/Examples/clustering/0/trajectory_1.pdb' 2022-08-01T11:17:10,734 adding 'pele_platform/Examples/clustering/0/trajectory_2.pdb' 2022-08-01T11:17:11,016 adding 'pele_platform/Examples/clustering/0/trajectory_3.pdb' 2022-08-01T11:17:11,305 adding 'pele_platform/Examples/clustering/0/trajectory_4.pdb' 2022-08-01T11:17:12,297 adding 'pele_platform/Examples/clustering/0/clustering/object.pkl' 2022-08-01T11:17:12,348 adding 'pele_platform/Examples/clustering/0/clustering/summary.txt' 2022-08-01T11:17:12,352 adding 'pele_platform/Examples/clustering_xtc/water_clustering.yaml' 2022-08-01T11:17:12,356 adding 'pele_platform/Examples/clustering_xtc/0/report_1' 2022-08-01T11:17:12,359 adding 'pele_platform/Examples/clustering_xtc/0/report_2' 2022-08-01T11:17:12,362 adding 'pele_platform/Examples/clustering_xtc/0/report_3' 2022-08-01T11:17:12,364 adding 'pele_platform/Examples/clustering_xtc/0/report_4' 2022-08-01T11:17:12,500 adding 'pele_platform/Examples/clustering_xtc/0/topology.pdb' 2022-08-01T11:17:12,513 adding 'pele_platform/Examples/clustering_xtc/0/trajectory_1.xtc' 2022-08-01T11:17:12,520 adding 'pele_platform/Examples/clustering_xtc/0/trajectory_2.xtc' 2022-08-01T11:17:12,529 adding 'pele_platform/Examples/clustering_xtc/0/trajectory_3.xtc' 2022-08-01T11:17:12,539 adding 'pele_platform/Examples/clustering_xtc/0/trajectory_4.xtc' 2022-08-01T11:17:12,644 adding 'pele_platform/Examples/constraints/1zop.pdb' 2022-08-01T11:17:12,856 adding 'pele_platform/Examples/constraints/4l3a_prep.pdb' 2022-08-01T11:17:13,087 adding 'pele_platform/Examples/constraints/4qnr_prep.pdb' 2022-08-01T11:17:13,216 adding 'pele_platform/Examples/constraints/4w4o_prep.pdb' 2022-08-01T11:17:13,339 adding 'pele_platform/Examples/constraints/4w5i_prep.pdb' 2022-08-01T11:17:13,846 adding 'pele_platform/Examples/constraints/4zu9_prep.pdb' 2022-08-01T11:17:14,130 adding 'pele_platform/Examples/constraints/ca_constraints.pdb' 2022-08-01T11:17:14,297 adding 'pele_platform/Examples/constraints/complex_smiles_error.pdb' 2022-08-01T11:17:14,308 adding 'pele_platform/Examples/constraints/fail_input_permissive_constraints.yaml' 2022-08-01T11:17:14,311 adding 'pele_platform/Examples/constraints/input_all_metal_constraints.yaml' 2022-08-01T11:17:14,313 adding 'pele_platform/Examples/constraints/input_ca_noppp.yaml' 2022-08-01T11:17:14,316 adding 'pele_platform/Examples/constraints/input_ca_ppp.yaml' 2022-08-01T11:17:14,319 adding 'pele_platform/Examples/constraints/input_constrain_smarts.yaml' 2022-08-01T11:17:14,322 adding 'pele_platform/Examples/constraints/input_constrain_smiles.yaml' 2022-08-01T11:17:14,325 adding 'pele_platform/Examples/constraints/input_external_constraints.yaml' 2022-08-01T11:17:14,328 adding 'pele_platform/Examples/constraints/input_ignore.yaml' 2022-08-01T11:17:14,331 adding 'pele_platform/Examples/constraints/input_k.yaml' 2022-08-01T11:17:14,333 adding 'pele_platform/Examples/constraints/input_metals.yaml' 2022-08-01T11:17:14,336 adding 'pele_platform/Examples/constraints/input_no_metal_constraints.yaml' 2022-08-01T11:17:14,339 adding 'pele_platform/Examples/constraints/input_permissive_exception.yaml' 2022-08-01T11:17:14,342 adding 'pele_platform/Examples/constraints/input_smiles_error.yaml' 2022-08-01T11:17:14,345 adding 'pele_platform/Examples/constraints/input_square_planar.yaml' 2022-08-01T11:17:14,347 adding 'pele_platform/Examples/constraints/input_square_planar_polarisation.yaml' 2022-08-01T11:17:14,350 adding 'pele_platform/Examples/constraints/input_tetrahedral.yaml' 2022-08-01T11:17:14,353 adding 'pele_platform/Examples/constraints/no_connects.pdb' 2022-08-01T11:17:14,356 adding 'pele_platform/Examples/constraints/pass_input_permissive_constraints.yaml' 2022-08-01T11:17:14,591 adding 'pele_platform/Examples/covalent_docking/5XXD_prepared.pdb' 2022-08-01T11:17:14,799 adding 'pele_platform/Examples/covalent_docking/6M06_prepared.pdb' 2022-08-01T11:17:14,953 adding 'pele_platform/Examples/covalent_docking/6P0M_prepared.pdb' 2022-08-01T11:17:14,962 adding 'pele_platform/Examples/covalent_docking/input1.yaml' 2022-08-01T11:17:14,965 adding 'pele_platform/Examples/covalent_docking/input2.yaml' 2022-08-01T11:17:14,968 adding 'pele_platform/Examples/covalent_docking/input3.yaml' 2022-08-01T11:17:14,970 adding 'pele_platform/Examples/covalent_docking/input_defaults.yaml' 2022-08-01T11:17:14,973 adding 'pele_platform/Examples/covalent_docking/input_defaults_refinement.yaml' 2022-08-01T11:17:14,977 adding 'pele_platform/Examples/enzyme_engineering/restart_saturated_mutagenesis.yaml' 2022-08-01T11:17:14,980 adding 'pele_platform/Examples/enzyme_engineering/saturated_mutagenesis.yaml' 2022-08-01T11:17:14,982 adding 'pele_platform/Examples/enzyme_engineering/wrong_cpus.yaml' 2022-08-01T11:17:14,986 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/completed_mutations.log' 2022-08-01T11:17:14,990 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/ANL.mae' 2022-08-01T11:17:14,993 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/adaptive.conf' 2022-08-01T11:17:14,998 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/pele.conf' 2022-08-01T11:17:15,001 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/restart_saturated_mutagenesis.yaml' 2022-08-01T11:17:15,005 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs/ANL.rot.assign' 2022-08-01T11:17:15,012 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms/anlz' 2022-08-01T11:17:15,262 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454A.pdb' 2022-08-01T11:17:15,523 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454A_processed.pdb' 2022-08-01T11:17:15,794 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454D.pdb' 2022-08-01T11:17:16,056 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/T454D_processed.pdb' 2022-08-01T11:17:16,070 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/ligand.pdb' 2022-08-01T11:17:16,320 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input/receptor.pdb' 2022-08-01T11:17:16,335 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/originalControlFile.conf' 2022-08-01T11:17:16,339 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/topologyMapping.txt' 2022-08-01T11:17:16,342 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering/object.pkl' 2022-08-01T11:17:16,344 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering/summary.txt' 2022-08-01T11:17:16,347 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/report_1' 2022-08-01T11:17:16,350 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/report_3' 2022-08-01T11:17:16,855 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/trajectory_1.pdb' 2022-08-01T11:17:17,383 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A/trajectory_3.pdb' 2022-08-01T11:17:17,410 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/report_2' 2022-08-01T11:17:17,412 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/report_4' 2022-08-01T11:17:17,917 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/trajectory_2.pdb' 2022-08-01T11:17:18,444 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D/trajectory_4.pdb' 2022-08-01T11:17:18,471 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization/syncFile.lock' 2022-08-01T11:17:18,772 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topologies.pkl' 2022-08-01T11:17:19,044 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topology_0.pdb' 2022-08-01T11:17:19,305 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies/topology_1.pdb' 2022-08-01T11:17:19,322 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/controlFile0.conf' 2022-08-01T11:17:19,572 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/initial_0_0.pdb' 2022-08-01T11:17:19,835 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output/initial_0_1.pdb' 2022-08-01T11:17:19,851 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/ANL.mae' 2022-08-01T11:17:19,853 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/adaptive.conf' 2022-08-01T11:17:19,856 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/pele.conf' 2022-08-01T11:17:19,858 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/restart_saturated_mutagenesis.yaml' 2022-08-01T11:17:20,109 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/T454E.pdb' 2022-08-01T11:17:20,371 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/T454E_processed.pdb' 2022-08-01T11:17:20,386 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/ligand.pdb' 2022-08-01T11:17:20,636 adding 'pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input/receptor.pdb' 2022-08-01T11:17:20,900 adding 'pele_platform/Examples/enzyme_engineering/pdb_files/T454A.pdb' 2022-08-01T11:17:21,161 adding 'pele_platform/Examples/enzyme_engineering/pdb_files/T454D.pdb' 2022-08-01T11:17:21,423 adding 'pele_platform/Examples/enzyme_engineering/pdb_files/T454E.pdb' 2022-08-01T11:17:21,439 adding 'pele_platform/Examples/exit/input.yaml' 2022-08-01T11:17:21,441 adding 'pele_platform/Examples/exit/input_defaults.yaml' 2022-08-01T11:17:21,444 adding 'pele_platform/Examples/exit_soft/input.yaml' 2022-08-01T11:17:21,447 adding 'pele_platform/Examples/exit_soft/input_defaults.yaml' 2022-08-01T11:17:21,451 adding 'pele_platform/Examples/flags/input.yaml' 2022-08-01T11:17:21,537 adding 'pele_platform/Examples/frag/1dyi_no_waters.pdb' 2022-08-01T11:17:21,626 adding 'pele_platform/Examples/frag/1dyi_waters.pdb' 2022-08-01T11:17:21,822 adding 'pele_platform/Examples/frag/1w7h_preparation_structure_2w.pdb' 2022-08-01T11:17:22,023 adding 'pele_platform/Examples/frag/1w7h_preparation_structure_2w_processed.pdb' 2022-08-01T11:17:22,035 adding 'pele_platform/Examples/frag/amino.pdb' 2022-08-01T11:17:22,037 adding 'pele_platform/Examples/frag/analysis.conf' 2022-08-01T11:17:22,040 adding 'pele_platform/Examples/frag/core.pdb' 2022-08-01T11:17:22,042 adding 'pele_platform/Examples/frag/flags.conf' 2022-08-01T11:17:22,044 adding 'pele_platform/Examples/frag/input_ai.yaml' 2022-08-01T11:17:22,046 adding 'pele_platform/Examples/frag/input_core.yaml' 2022-08-01T11:17:22,048 adding 'pele_platform/Examples/frag/input_core_bond.yaml' 2022-08-01T11:17:22,050 adding 'pele_platform/Examples/frag/input_core_sdf.yaml' 2022-08-01T11:17:22,053 adding 'pele_platform/Examples/frag/input_flags.yaml' 2022-08-01T11:17:22,055 adding 'pele_platform/Examples/frag/input_frag_waters.yaml' 2022-08-01T11:17:22,057 adding 'pele_platform/Examples/frag/input_fragment_atom.yaml' 2022-08-01T11:17:22,059 adding 'pele_platform/Examples/frag/input_lib_pdb.yaml' 2022-08-01T11:17:22,061 adding 'pele_platform/Examples/frag/input_lib_sdf.yaml' 2022-08-01T11:17:22,063 adding 'pele_platform/Examples/frag/input_point_analysis.yaml' 2022-08-01T11:17:22,066 adding 'pele_platform/Examples/frag/input_sim.yaml' 2022-08-01T11:17:22,068 adding 'pele_platform/Examples/frag/input_sim_xtc.yaml' 2022-08-01T11:17:22,070 adding 'pele_platform/Examples/frag/input_symmetry.yaml' 2022-08-01T11:17:22,072 adding 'pele_platform/Examples/frag/ligands.sdf' 2022-08-01T11:17:22,076 adding 'pele_platform/Examples/frag/ligands_water.sdf' 2022-08-01T11:17:22,078 adding 'pele_platform/Examples/frag/sequential.conf' 2022-08-01T11:17:22,083 adding 'pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/report_1' 2022-08-01T11:17:22,086 adding 'pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/report_2' 2022-08-01T11:17:22,468 adding 'pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/trajectory_1.pdb' 2022-08-01T11:17:22,870 adding 'pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/sampling_result/trajectory_2.pdb' 2022-08-01T11:17:23,080 adding 'pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result/epochsampling_result_trajectory_1.1_BindingEnergy-23.4636.pdb' 2022-08-01T11:17:23,278 adding 'pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_frag_mol1C3-H2C1-H1/top_result/epochsampling_result_trajectory_2.1_BindingEnergy-25.1634.pdb' 2022-08-01T11:17:23,291 adding 'pele_platform/Examples/frag/checker/4RFM_proc.pdb' 2022-08-01T11:17:23,295 adding 'pele_platform/Examples/frag/checker/4RFM_series.sdf' 2022-08-01T11:17:23,442 adding 'pele_platform/Examples/frag/checker/receptor.sdf' 2022-08-01T11:17:23,451 adding 'pele_platform/Examples/frag/pdb_test_lib/mol1.pdb' 2022-08-01T11:17:23,453 adding 'pele_platform/Examples/frag/pdb_test_lib/mol2.pdb' 2022-08-01T11:17:23,471 adding 'pele_platform/Examples/frag/sdf_joiner/13_serie.sdf' 2022-08-01T11:17:23,676 adding 'pele_platform/Examples/frag/sdf_joiner/4RFM_core_sc.pdb' 2022-08-01T11:17:23,890 adding 'pele_platform/Examples/frag/sdf_joiner/4RFM_proc.pdb' 2022-08-01T11:17:23,904 adding 'pele_platform/Examples/frag/sdf_joiner/4RFM_series.sdf' 2022-08-01T11:17:24,046 adding 'pele_platform/Examples/frag/sdf_joiner/core2.pdb' 2022-08-01T11:17:24,104 adding 'pele_platform/Examples/frag/sdf_joiner/core3.pdb' 2022-08-01T11:17:24,110 adding 'pele_platform/Examples/frag/sdf_joiner/frag.sdf' 2022-08-01T11:17:24,113 adding 'pele_platform/Examples/frag/sdf_joiner/frag.yml' 2022-08-01T11:17:24,119 adding 'pele_platform/Examples/frag/sdf_joiner/frag2.sdf' 2022-08-01T11:17:24,122 adding 'pele_platform/Examples/frag/sdf_joiner/frag2.yml' 2022-08-01T11:17:24,129 adding 'pele_platform/Examples/frag/sdf_joiner/frag3.sdf' 2022-08-01T11:17:24,132 adding 'pele_platform/Examples/frag/sdf_joiner/frag3.yml' 2022-08-01T11:17:24,141 adding 'pele_platform/Examples/frag/sdf_joiner/frag31.sdf' 2022-08-01T11:17:24,144 adding 'pele_platform/Examples/frag/sdf_joiner/frag4.yml' 2022-08-01T11:17:24,146 adding 'pele_platform/Examples/frag/sdf_joiner/frag5.yml' 2022-08-01T11:17:24,493 adding 'pele_platform/Examples/frag/sdf_joiner/glide-dockSARS_core.pdb' 2022-08-01T11:17:24,511 adding 'pele_platform/Examples/frag/sdf_test_lib/test_library.sdf' 2022-08-01T11:17:24,515 adding 'pele_platform/Examples/global/input.yaml' 2022-08-01T11:17:24,517 adding 'pele_platform/Examples/global/input_defaults.yaml' 2022-08-01T11:17:24,519 adding 'pele_platform/Examples/global/input_inputs.yaml' 2022-08-01T11:17:24,521 adding 'pele_platform/Examples/global/input_inputs_asterisc.yaml' 2022-08-01T11:17:24,683 adding 'pele_platform/Examples/gpcr/complex.pdb' 2022-08-01T11:17:24,849 adding 'pele_platform/Examples/gpcr/complex_processed.pdb' 2022-08-01T11:17:24,859 adding 'pele_platform/Examples/gpcr/input.yaml' 2022-08-01T11:17:24,861 adding 'pele_platform/Examples/gpcr/input_atom_error.yaml' 2022-08-01T11:17:24,864 adding 'pele_platform/Examples/gpcr/input_defaults.yaml' 2022-08-01T11:17:24,866 adding 'pele_platform/Examples/gpcr/input_defaults2.yaml' 2022-08-01T11:17:24,869 adding 'pele_platform/Examples/induced_fit/input_auto_clustering.yaml' 2022-08-01T11:17:24,871 adding 'pele_platform/Examples/induced_fit/input_exhaustive.yaml' 2022-08-01T11:17:24,874 adding 'pele_platform/Examples/induced_fit/input_exhaustive_defaults.yaml' 2022-08-01T11:17:24,876 adding 'pele_platform/Examples/induced_fit/input_fast.yaml' 2022-08-01T11:17:24,878 adding 'pele_platform/Examples/induced_fit/input_fast_defaults.yaml' 2022-08-01T11:17:24,880 adding 'pele_platform/Examples/induced_fit/input_mae.yaml' 2022-08-01T11:17:24,883 adding 'pele_platform/Examples/inputs/input.yaml' 2022-08-01T11:17:24,886 adding 'pele_platform/Examples/inputs/mn4.sl' 2022-08-01T11:17:24,888 adding 'pele_platform/Examples/inputs/nord3.sge' 2022-08-01T11:17:25,151 adding 'pele_platform/Examples/interaction_restrictions/complex.pdb' 2022-08-01T11:17:25,166 adding 'pele_platform/Examples/interaction_restrictions/input.yaml' 2022-08-01T11:17:25,169 adding 'pele_platform/Examples/interaction_restrictions/input_error.yaml' 2022-08-01T11:17:25,171 adding 'pele_platform/Examples/interaction_restrictions/input_error_2.yaml' 2022-08-01T11:17:25,174 adding 'pele_platform/Examples/interaction_restrictions/out/expected_conditions.txt' 2022-08-01T11:17:25,176 adding 'pele_platform/Examples/interaction_restrictions/out/expected_metrics.txt' 2022-08-01T11:17:25,180 adding 'pele_platform/Examples/ligand_conformations/1.pdb' 2022-08-01T11:17:25,183 adding 'pele_platform/Examples/ligand_conformations/2.pdb' 2022-08-01T11:17:25,186 adding 'pele_platform/Examples/ligand_conformations/3.pdb' 2022-08-01T11:17:25,188 adding 'pele_platform/Examples/ligand_conformations/input.yaml' 2022-08-01T11:17:25,453 adding 'pele_platform/Examples/minimum_steps/complex.pdb' 2022-08-01T11:17:25,468 adding 'pele_platform/Examples/minimum_steps/input.yaml' 2022-08-01T11:17:25,616 adding 'pele_platform/Examples/out_in/1_3ZON_complex.pdb' 2022-08-01T11:17:25,625 adding 'pele_platform/Examples/out_in/input.yaml' 2022-08-01T11:17:25,627 adding 'pele_platform/Examples/out_in/input_auto_clustering.yaml' 2022-08-01T11:17:25,629 adding 'pele_platform/Examples/out_in/input_box_center.yaml' 2022-08-01T11:17:25,631 adding 'pele_platform/Examples/out_in/input_default.yaml' 2022-08-01T11:17:25,634 adding 'pele_platform/Examples/out_in/input_flag_error.yaml' 2022-08-01T11:17:25,636 adding 'pele_platform/Examples/out_in/input_metrics.yaml' 2022-08-01T11:17:25,794 adding 'pele_platform/Examples/pca/1.pdb' 2022-08-01T11:17:25,959 adding 'pele_platform/Examples/pca/2.pdb' 2022-08-01T11:17:26,123 adding 'pele_platform/Examples/pca/3.pdb' 2022-08-01T11:17:26,133 adding 'pele_platform/Examples/pca/input.yaml' 2022-08-01T11:17:26,136 adding 'pele_platform/Examples/pca/input_str.yaml' 2022-08-01T11:17:26,321 adding 'pele_platform/Examples/preparation/6qmk_correct.pdb' 2022-08-01T11:17:26,572 adding 'pele_platform/Examples/preparation/6qmk_repeated.pdb' 2022-08-01T11:17:26,717 adding 'pele_platform/Examples/preparation/complex.pdb' 2022-08-01T11:17:26,984 adding 'pele_platform/Examples/preparation/complex_2.pdb' 2022-08-01T11:17:26,997 adding 'pele_platform/Examples/preparation/input.yaml' 2022-08-01T11:17:26,999 adding 'pele_platform/Examples/preparation/input_nonstandard.yaml' 2022-08-01T11:17:27,001 adding 'pele_platform/Examples/preparation/input_space.yaml' 2022-08-01T11:17:27,004 adding 'pele_platform/Examples/preparation/parametrization_flags.yaml' 2022-08-01T11:17:27,007 adding 'pele_platform/Examples/production/input.sl' 2022-08-01T11:17:27,009 adding 'pele_platform/Examples/production/input_mae.yaml' 2022-08-01T11:17:27,013 adding 'pele_platform/Examples/randomize/ligand1.pdb' 2022-08-01T11:17:27,015 adding 'pele_platform/Examples/randomize/ligand2.pdb' 2022-08-01T11:17:27,018 adding 'pele_platform/Examples/randomize/ligand3.pdb' 2022-08-01T11:17:27,185 adding 'pele_platform/Examples/randomize/receptor.pdb' 2022-08-01T11:17:27,196 adding 'pele_platform/Examples/randomize/ref_ligand.pdb' 2022-08-01T11:17:27,200 adding 'pele_platform/Examples/rescoring/input.yaml' 2022-08-01T11:17:27,202 adding 'pele_platform/Examples/rescoring/input_defaults.yaml' 2022-08-01T11:17:27,205 adding 'pele_platform/Examples/restart/restart.yaml' 2022-08-01T11:17:27,209 adding 'pele_platform/Examples/singularity/input_adaptive.yaml' 2022-08-01T11:17:27,211 adding 'pele_platform/Examples/singularity/input_adaptive_mpi_params.yaml' 2022-08-01T11:17:27,213 adding 'pele_platform/Examples/singularity/input_frag.yaml' 2022-08-01T11:17:27,385 adding 'pele_platform/Examples/site_finder/complex.pdb' 2022-08-01T11:17:27,396 adding 'pele_platform/Examples/site_finder/global.yaml' 2022-08-01T11:17:27,398 adding 'pele_platform/Examples/site_finder/input_custom_box.yaml' 2022-08-01T11:17:27,400 adding 'pele_platform/Examples/site_finder/input_folder.yaml' 2022-08-01T11:17:27,402 adding 'pele_platform/Examples/site_finder/input_global.yaml' 2022-08-01T11:17:27,405 adding 'pele_platform/Examples/site_finder/input_global_xtc.yaml' 2022-08-01T11:17:27,407 adding 'pele_platform/Examples/site_finder/input_restart.yaml' 2022-08-01T11:17:27,409 adding 'pele_platform/Examples/site_finder/input_skipref.yaml' 2022-08-01T11:17:27,411 adding 'pele_platform/Examples/site_finder/local.yaml' 2022-08-01T11:17:27,571 adding 'pele_platform/Examples/tutorials/gpcr/complex.pdb' 2022-08-01T11:17:27,581 adding 'pele_platform/Examples/tutorials/gpcr/input.yaml' 2022-08-01T11:17:27,846 adding 'pele_platform/Examples/tutorials/induced_fit/docking.pdb' 2022-08-01T11:17:27,861 adding 'pele_platform/Examples/tutorials/induced_fit/input.yaml' 2022-08-01T11:17:27,866 adding 'pele_platform/Examples/tutorials/ppi/4yy6_ligand.pdb' 2022-08-01T11:17:27,953 adding 'pele_platform/Examples/tutorials/ppi/4yy6_prep.pdb' 2022-08-01T11:17:27,960 adding 'pele_platform/Examples/tutorials/ppi/input.yaml' 2022-08-01T11:17:28,018 adding 'pele_platform/Examples/water/complex_induced.pdb' 2022-08-01T11:17:28,200 adding 'pele_platform/Examples/water/complex_ref_LESSH2O.pdb' 2022-08-01T11:17:28,211 adding 'pele_platform/Examples/water/input_all.yaml' 2022-08-01T11:17:28,213 adding 'pele_platform/Examples/water/input_bs.yaml' 2022-08-01T11:17:28,215 adding 'pele_platform/Examples/water/input_bs_defaults.yaml' 2022-08-01T11:17:28,217 adding 'pele_platform/Examples/water/input_induced.yaml' 2022-08-01T11:17:28,219 adding 'pele_platform/Examples/water/input_lig.yaml' 2022-08-01T11:17:28,222 adding 'pele_platform/Examples/water/input_lig_defaults.yaml' 2022-08-01T11:17:28,224 adding 'pele_platform/Examples/water/input_nwaters.yaml' 2022-08-01T11:17:28,226 adding 'pele_platform/Examples/water/input_previous_water.yaml' 2022-08-01T11:17:28,228 adding 'pele_platform/Examples/water/water2_pele.conf' 2022-08-01T11:17:28,232 adding 'pele_platform/Examples/water/water_pele.conf' 2022-08-01T11:17:28,424 adding 'pele_platform/Examples/water/water_processed.pdb' 2022-08-01T11:17:28,436 adding 'pele_platform/Frag/__init__.py' 2022-08-01T11:17:28,439 adding 'pele_platform/Frag/analysis.py' 2022-08-01T11:17:28,442 adding 'pele_platform/Frag/atoms.py' 2022-08-01T11:17:28,444 adding 'pele_platform/Frag/checker.py' 2022-08-01T11:17:28,446 adding 'pele_platform/Frag/fragments.py' 2022-08-01T11:17:28,449 adding 'pele_platform/Frag/generative_model.py' 2022-08-01T11:17:28,453 adding 'pele_platform/Frag/helpers.py' 2022-08-01T11:17:28,457 adding 'pele_platform/Frag/libraries.py' 2022-08-01T11:17:28,461 adding 'pele_platform/Frag/simulation.py' 2022-08-01T11:17:28,465 adding 'pele_platform/Frag/parameters/__init__.py' 2022-08-01T11:17:28,467 adding 'pele_platform/Frag/parameters/files.py' 2022-08-01T11:17:28,470 adding 'pele_platform/Frag/parameters/metrics.py' 2022-08-01T11:17:28,472 adding 'pele_platform/Frag/parameters/optional.py' 2022-08-01T11:17:28,475 adding 'pele_platform/Frag/parameters/simulation.py' 2022-08-01T11:17:28,477 adding 'pele_platform/Frag/parameters/water.py' 2022-08-01T11:17:28,481 adding 'pele_platform/PPI/__init__.py' 2022-08-01T11:17:28,484 adding 'pele_platform/PPI/cluster.py' 2022-08-01T11:17:28,487 adding 'pele_platform/PPI/main.py' 2022-08-01T11:17:28,490 adding 'pele_platform/PPI/preparation.py' 2022-08-01T11:17:28,492 adding 'pele_platform/PPI/simulation_launcher.py' 2022-08-01T11:17:28,495 adding 'pele_platform/RNA/__init__.py' 2022-08-01T11:17:28,498 adding 'pele_platform/RNA/prep.py' 2022-08-01T11:17:28,501 adding 'pele_platform/Templates/pele_template.conf' 2022-08-01T11:17:28,517 adding 'pele_platform/Templates/solventParamsHCTOBC.txt' 2022-08-01T11:17:28,520 adding 'pele_platform/Templates/template_adaptive.conf' 2022-08-01T11:17:28,523 adding 'pele_platform/Utilities/__init__.py' 2022-08-01T11:17:28,527 adding 'pele_platform/Utilities/Helpers/__init__.py' 2022-08-01T11:17:28,531 adding 'pele_platform/Utilities/Helpers/bestStructs.py' 2022-08-01T11:17:28,538 adding 'pele_platform/Utilities/Helpers/calculatePCA4PELE.py' 2022-08-01T11:17:28,541 adding 'pele_platform/Utilities/Helpers/center_of_mass.py' 2022-08-01T11:17:28,543 adding 'pele_platform/Utilities/Helpers/conda_deployment.py' 2022-08-01T11:17:28,549 adding 'pele_platform/Utilities/Helpers/helpers.py' 2022-08-01T11:17:28,552 adding 'pele_platform/Utilities/Helpers/interaction_constraints.py' 2022-08-01T11:17:28,555 adding 'pele_platform/Utilities/Helpers/launcher.py' 2022-08-01T11:17:28,557 adding 'pele_platform/Utilities/Helpers/ligand_conformations.py' 2022-08-01T11:17:28,561 adding 'pele_platform/Utilities/Helpers/map_atoms.py' 2022-08-01T11:17:28,563 adding 'pele_platform/Utilities/Helpers/missing_residues.py' 2022-08-01T11:17:28,566 adding 'pele_platform/Utilities/Helpers/plop_launcher.py' 2022-08-01T11:17:28,568 adding 'pele_platform/Utilities/Helpers/protein_wizard.py' 2022-08-01T11:17:28,573 adding 'pele_platform/Utilities/Helpers/randomize.py' 2022-08-01T11:17:28,576 adding 'pele_platform/Utilities/Helpers/simulation.py' 2022-08-01T11:17:28,580 adding 'pele_platform/Utilities/Helpers/solventOBCParamsGenerator.py' 2022-08-01T11:17:28,583 adding 'pele_platform/Utilities/Helpers/system_prep.py' 2022-08-01T11:17:28,586 adding 'pele_platform/Utilities/Helpers/template_builder.py' 2022-08-01T11:17:28,591 adding 'pele_platform/Utilities/Helpers/water.py' 2022-08-01T11:17:28,597 adding 'pele_platform/Utilities/Helpers/yaml_parser.py' 2022-08-01T11:17:28,600 adding 'pele_platform/Utilities/Helpers/Metals/__init__.py' 2022-08-01T11:17:28,604 adding 'pele_platform/Utilities/Helpers/Metals/metal_constraints.py' 2022-08-01T11:17:28,607 adding 'pele_platform/Utilities/Helpers/Metals/metal_polarisation.py' 2022-08-01T11:17:28,610 adding 'pele_platform/Utilities/Helpers/constraints/__init__.py' 2022-08-01T11:17:28,614 adding 'pele_platform/Utilities/Helpers/constraints/alpha_constraints.py' 2022-08-01T11:17:28,617 adding 'pele_platform/Utilities/Helpers/constraints/smiles_constraints.py' 2022-08-01T11:17:28,620 adding 'pele_platform/Utilities/Parameters/__init__.py' 2022-08-01T11:17:28,625 adding 'pele_platform/Utilities/Parameters/parameters.py' 2022-08-01T11:17:28,628 adding 'pele_platform/Utilities/Parameters/SimulationFolders/__init__.py' 2022-08-01T11:17:28,631 adding 'pele_platform/Utilities/Parameters/SimulationFolders/simulation_folders.py' 2022-08-01T11:17:28,634 adding 'pele_platform/Utilities/Parameters/SimulationParams/__init__.py' 2022-08-01T11:17:28,642 adding 'pele_platform/Utilities/Parameters/SimulationParams/simulation_params.py' 2022-08-01T11:17:28,646 adding 'pele_platform/Utilities/Parameters/SimulationParams/BiasParams/__init__.py' 2022-08-01T11:17:28,648 adding 'pele_platform/Utilities/Parameters/SimulationParams/BiasParams/bias_params.py' 2022-08-01T11:17:28,651 adding 'pele_platform/Utilities/Parameters/SimulationParams/GlideParams/__init__.py' 2022-08-01T11:17:28,654 adding 'pele_platform/Utilities/Parameters/SimulationParams/GlideParams/glide_params.py' 2022-08-01T11:17:28,657 adding 'pele_platform/Utilities/Parameters/SimulationParams/InOutParams/__init__.py' 2022-08-01T11:17:28,659 adding 'pele_platform/Utilities/Parameters/SimulationParams/InOutParams/inout_params.py' 2022-08-01T11:17:28,662 adding 'pele_platform/Utilities/Parameters/SimulationParams/MSMParams/__init__.py' 2022-08-01T11:17:28,665 adding 'pele_platform/Utilities/Parameters/SimulationParams/MSMParams/msm_params.py' 2022-08-01T11:17:28,668 adding 'pele_platform/Utilities/Parameters/SimulationParams/PCA/__init__.py' 2022-08-01T11:17:28,670 adding 'pele_platform/Utilities/Parameters/SimulationParams/PCA/pca.py' 2022-08-01T11:17:28,673 adding 'pele_platform/Utilities/Parameters/SimulationParams/PPI/__init__.py' 2022-08-01T11:17:28,676 adding 'pele_platform/Utilities/Parameters/SimulationParams/PPI/ppi.py' 2022-08-01T11:17:28,679 adding 'pele_platform/Utilities/Parameters/SimulationParams/site_finder/__init__.py' 2022-08-01T11:17:28,681 adding 'pele_platform/Utilities/Parameters/SimulationParams/site_finder/site_finder.py' 2022-08-01T11:17:28,685 adding 'pele_platform/analysis/__init__.py' 2022-08-01T11:17:28,703 adding 'pele_platform/analysis/analysis.py' 2022-08-01T11:17:28,709 adding 'pele_platform/analysis/clustering.py' 2022-08-01T11:17:28,718 adding 'pele_platform/analysis/data.py' 2022-08-01T11:17:28,725 adding 'pele_platform/analysis/interactive_plot.py' 2022-08-01T11:17:28,728 adding 'pele_platform/analysis/pdf_report.py' 2022-08-01T11:17:28,733 adding 'pele_platform/analysis/plot.py' 2022-08-01T11:17:28,736 adding 'pele_platform/constants/__init__.py' 2022-08-01T11:17:28,740 adding 'pele_platform/constants/constants.py' 2022-08-01T11:17:28,744 adding 'pele_platform/constants/pele_params.py' 2022-08-01T11:17:28,747 adding 'pele_platform/covalent_docking/__init__.py' 2022-08-01T11:17:28,751 adding 'pele_platform/covalent_docking/main.py' 2022-08-01T11:17:28,754 adding 'pele_platform/enzyme_engineering/__init__.py' 2022-08-01T11:17:28,758 adding 'pele_platform/enzyme_engineering/saturated_mutagenesis.py' 2022-08-01T11:17:28,762 adding 'pele_platform/features/__init__.py' 2022-08-01T11:17:28,765 adding 'pele_platform/features/adaptive.py' 2022-08-01T11:17:28,767 adding 'pele_platform/features/frag.py' 2022-08-01T11:17:28,771 adding 'pele_platform/gpcr/__init__.py' 2022-08-01T11:17:28,773 adding 'pele_platform/gpcr/main.py' 2022-08-01T11:17:28,776 adding 'pele_platform/out_in/__init__.py' 2022-08-01T11:17:28,779 adding 'pele_platform/out_in/main.py' 2022-08-01T11:17:28,782 adding 'pele_platform/site_finder/__init__.py' 2022-08-01T11:17:28,785 adding 'pele_platform/site_finder/main.py' 2022-08-01T11:17:28,792 adding 'pele_platform-1.6.4.dist-info/LICENSE' 2022-08-01T11:17:28,795 adding 'pele_platform-1.6.4.dist-info/METADATA' 2022-08-01T11:17:28,797 adding 'pele_platform-1.6.4.dist-info/WHEEL' 2022-08-01T11:17:28,798 adding 'pele_platform-1.6.4.dist-info/top_level.txt' 2022-08-01T11:17:28,811 adding 'pele_platform-1.6.4.dist-info/RECORD' 2022-08-01T11:17:29,263 removing build/bdist.linux-armv7l/wheel 2022-08-01T11:17:29,837 Building wheel for pele-platform (setup.py): finished with status 'done' 2022-08-01T11:17:30,216 Created wheel for pele-platform: filename=pele_platform-1.6.4-py3-none-any.whl size=12620214 sha256=d5a23b3065a9f40c6e48426e0103faeb5c52a77f3becca0ef89e39d73a4f77dc 2022-08-01T11:17:30,218 Stored in directory: /tmp/pip-ephem-wheel-cache-j4547t5q/wheels/8b/f1/73/090565d4bb2dc2495e2d2d3bb3a0ae9672f5f71d7622a71d1b 2022-08-01T11:17:30,292 Successfully built pele-platform 2022-08-01T11:17:31,211 Removed build tracker: '/tmp/pip-build-tracker-38w_f5aw'