2021-03-19T17:11:57,596 DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality. 2021-03-19T17:11:58,280 Created temporary directory: /tmp/pip-ephem-wheel-cache-ny6zxp9c 2021-03-19T17:11:58,284 Created temporary directory: /tmp/pip-req-tracker-bezuzveo 2021-03-19T17:11:58,285 Initialized build tracking at /tmp/pip-req-tracker-bezuzveo 2021-03-19T17:11:58,286 Created build tracker: /tmp/pip-req-tracker-bezuzveo 2021-03-19T17:11:58,286 Entered build tracker: /tmp/pip-req-tracker-bezuzveo 2021-03-19T17:11:58,288 Created temporary directory: /tmp/pip-wheel-clob8tvk 2021-03-19T17:11:58,351 1 location(s) to search for versions of pele-platform: 2021-03-19T17:11:58,351 * https://pypi.org/simple/pele-platform/ 2021-03-19T17:11:58,352 Fetching project page and analyzing links: https://pypi.org/simple/pele-platform/ 2021-03-19T17:11:58,354 Getting page https://pypi.org/simple/pele-platform/ 2021-03-19T17:11:58,358 Found index url https://pypi.org/simple 2021-03-19T17:11:58,695 Found link https://files.pythonhosted.org/packages/f0/ac/9497572d7da4e501c8dddc3be3fa338744dbc27b67eb09275b8375fae2fd/pele_platform-1.0.0.1.tar.gz#sha256=e3c8bde654fe3d249714c4ddb1d3471944752f6840a6bcf4b399a3466931b838 (from https://pypi.org/simple/pele-platform/), version: 1.0.0.1 2021-03-19T17:11:58,697 Found link https://files.pythonhosted.org/packages/79/a0/d1b4b9269c3fe9dd2edc878a2dec9d3f4e7701cc932272169f44a025c2a9/pele_platform-1.0.0.2.tar.gz#sha256=919f487c943e6e71a8d82e56dac3051605ffdc6a680d168b5233cea95c9e4701 (from https://pypi.org/simple/pele-platform/), version: 1.0.0.2 2021-03-19T17:11:58,698 Found link https://files.pythonhosted.org/packages/a3/56/3cc9eb3b0ecf0943c4f4eb5b0729cd54906290f84dc4cfb230ad69ce99c6/pele_platform-1.0.0.3.tar.gz#sha256=ea4f3df0aeb65812e72eb9b24605146a7afeeb7f89ce7f769058c2e894654239 (from https://pypi.org/simple/pele-platform/), version: 1.0.0.3 2021-03-19T17:11:58,699 Found link https://files.pythonhosted.org/packages/d0/6d/1ac79163749b10c7f694dde1db24063d4e2f57bcf365db1b8cfa1b9f7f57/pele_platform-1.1.0.tar.gz#sha256=25a644fc27c0c364bfece9addd278a74a5a7ea5f4ab40b31fa8cd961e7485a65 (from https://pypi.org/simple/pele-platform/), version: 1.1.0 2021-03-19T17:11:58,700 Found link https://files.pythonhosted.org/packages/fd/15/306ea35b1d4be507caf1613d05fc16c076f070c2a16e6283a331695fcb5e/pele_platform-1.2.0.tar.gz#sha256=2967a976bafc47884ca49864ca87d40d87aa50c2fc57900c1f0517e84e789153 (from https://pypi.org/simple/pele-platform/), version: 1.2.0 2021-03-19T17:11:58,700 Found link https://files.pythonhosted.org/packages/74/98/cf2442f668f8ad6be1838c3ce7b87a409eee7448a1d7d033862ad0bda36c/pele_platform-1.2.1.tar.gz#sha256=5d30d563960934362ac79eb7a24b8f4b831076dba29bbb498901a0b0a1dca367 (from https://pypi.org/simple/pele-platform/), version: 1.2.1 2021-03-19T17:11:58,701 Found link https://files.pythonhosted.org/packages/1a/78/29b2eb73308b595668a9c22abd93ac88f82c49ebc6b004f332a774166391/pele_platform-1.2.2.tar.gz#sha256=00f579740db5455cea04c82e86b87c8f53045496ba61d9f4e96436f1d0cdfb08 (from https://pypi.org/simple/pele-platform/), version: 1.2.2 2021-03-19T17:11:58,702 Found link https://files.pythonhosted.org/packages/fb/6b/85f262d33a080377ea5202d5779c9402c23aaefc4e1b04bb94d9432aad42/pele_platform-1.2.3.tar.gz#sha256=18713b6811d7689accb54dde5429aa5225dcb8e520164fd7b4037453c63f74d9 (from https://pypi.org/simple/pele-platform/), version: 1.2.3 2021-03-19T17:11:58,703 Found link https://files.pythonhosted.org/packages/d5/15/707e6b89f0ee479d173ef2fe6a41af1ff9d91dd86e45067da5cee56761d9/pele_platform-1.3.0.tar.gz#sha256=fb7fb5dd59f9e3a76d371be6aa0b013209752c464862bf944de6b2a2903424a9 (from https://pypi.org/simple/pele-platform/), version: 1.3.0 2021-03-19T17:11:58,704 Found link https://files.pythonhosted.org/packages/7c/b0/4fda3001d5f13010bc2005e335f799f24d2204fc700a847e28091b57fabb/pele_platform-1.3.1.tar.gz#sha256=c6c0ac764ae30ce8a0650cdf0fc686fd733cb6b11fc15e6cccd5659166be3b33 (from https://pypi.org/simple/pele-platform/), version: 1.3.1 2021-03-19T17:11:58,705 Found link https://files.pythonhosted.org/packages/34/21/2f68d91d200432e0feb4662f6ba5538817335d86df60688e3a6f050dd21b/pele_platform-1.3.2.tar.gz#sha256=14c6e236347a1101f5de04bc25a32f302904bdb46326fb151c14e930a28d7a48 (from https://pypi.org/simple/pele-platform/), version: 1.3.2 2021-03-19T17:11:58,706 Found link https://files.pythonhosted.org/packages/63/a6/ad0bc781b4089093fd8aca4d75d237e0c0ae9d1f6b7e4b86a733f5a91b10/pele_platform-1.3.3.tar.gz#sha256=9e9e49d359bde42485b1c2d23b8a80c3de43064a672c260d18b9f10b55ee666e (from https://pypi.org/simple/pele-platform/), version: 1.3.3 2021-03-19T17:11:58,707 Found link https://files.pythonhosted.org/packages/e7/6a/4d8e75e0dbff74b22c76f4640a72798acfe6f55e35dcf0e9080dc8f36857/pele_platform-1.3.4.tar.gz#sha256=b8f7a2caac267df0381e8a3d73ddfeaec60cccc22336aa76178dbf3d2b2e880b (from https://pypi.org/simple/pele-platform/), version: 1.3.4 2021-03-19T17:11:58,708 Found link https://files.pythonhosted.org/packages/d2/7d/8f6c7c977288ed554723c003a885c118889c3bf76ac343961a84d330f85e/pele_platform-1.4.0.tar.gz#sha256=0190af77e0e24482742b634d120ac9b52135716bbbc93929bf688313f63e4a59 (from https://pypi.org/simple/pele-platform/), version: 1.4.0 2021-03-19T17:11:58,709 Found link https://files.pythonhosted.org/packages/ed/11/ff7cdcb7a17869082a94fc4c066a8bc6407a07f7c542c1dbc4919b1e091a/pele_platform-1.4.1.tar.gz#sha256=2f5327616aeff5be40d54b2771fd43b8cdb75086944c11800339bd44e0866c01 (from https://pypi.org/simple/pele-platform/), version: 1.4.1 2021-03-19T17:11:58,710 Found link https://files.pythonhosted.org/packages/4b/4f/fec23d74e8b1474fe25234fd34972a427234307dc9f7908f916e50036d81/pele_platform-1.4.2.tar.gz#sha256=c1092fb5c5cdb38736f621c434ff3112ea1cd1abc94d0bfe03ea7044b6e06612 (from https://pypi.org/simple/pele-platform/), version: 1.4.2 2021-03-19T17:11:58,711 Found link https://files.pythonhosted.org/packages/7a/b3/8eeb8c773a4fbf6561a929b8bab563f31384a0512a4708b4d0249ebc8c24/pele_platform-1.4.3.tar.gz#sha256=e491ac06c05301a846084e07ab709abf4b0507768710256443b6523b25339c40 (from https://pypi.org/simple/pele-platform/), version: 1.4.3 2021-03-19T17:11:58,712 Found link https://files.pythonhosted.org/packages/92/57/ff446766add00995f3fa0446f9c32ad52b759bab05d3f41e5ee51a8e76a8/pele_platform-1.4.4.tar.gz#sha256=eca94d45d76664106cff9915781740932635878b203b430d62f7aeb252ce59c7 (from https://pypi.org/simple/pele-platform/), version: 1.4.4 2021-03-19T17:11:58,712 Found link https://files.pythonhosted.org/packages/6d/f3/5ad1c5dab958edc8ecfb75883f8ac760308e570f3a0929104ba01a223f02/pele_platform-1.5.0.tar.gz#sha256=0b7eed2abd70f20caadcf9e9c8642cfc51d55d66ab114e42f0d425bfb6603323 (from https://pypi.org/simple/pele-platform/), version: 1.5.0 2021-03-19T17:11:58,713 Found link https://files.pythonhosted.org/packages/1c/b0/44dcc5184b218a7481babe8cd5738129741e29422e226308a583a3dd5629/pele_platform-1.5.1.tar.gz#sha256=9e138403c8fb65450d9841db279140f046a8325791af9983e202c9002bf44b93 (from https://pypi.org/simple/pele-platform/), version: 1.5.1 2021-03-19T17:11:58,714 Found link https://files.pythonhosted.org/packages/05/85/4cfdad270ebf569727204cbc9de66f22ef802d5079846f2631e1e6a11059/pele_platform-1.6.0b1.tar.gz#sha256=a7b5e566ec00598a1991d44c8748267104e5a123f462365a584632c94b36a7bf (from https://pypi.org/simple/pele-platform/), version: 1.6.0b1 2021-03-19T17:11:58,753 Given no hashes to check 1 links for project 'pele-platform': discarding no candidates 2021-03-19T17:11:58,787 Collecting pele-platform==1.6.0b1 2021-03-19T17:11:58,791 Created temporary directory: /tmp/pip-unpack-2o6qboef 2021-03-19T17:11:59,968 Downloading pele_platform-1.6.0b1.tar.gz (10.1 MB) 2021-03-19T17:12:11,912 Added pele-platform==1.6.0b1 from https://files.pythonhosted.org/packages/05/85/4cfdad270ebf569727204cbc9de66f22ef802d5079846f2631e1e6a11059/pele_platform-1.6.0b1.tar.gz#sha256=a7b5e566ec00598a1991d44c8748267104e5a123f462365a584632c94b36a7bf to build tracker '/tmp/pip-req-tracker-bezuzveo' 2021-03-19T17:12:11,915 Running setup.py (path:/tmp/pip-wheel-clob8tvk/pele-platform_54f2dfd5c51943d3ad6cd57c8372550b/setup.py) egg_info for package pele-platform 2021-03-19T17:12:11,916 Created temporary directory: /tmp/pip-pip-egg-info-ufdgj0vx 2021-03-19T17:12:11,917 Running command python setup.py egg_info 2021-03-19T17:12:14,702 running egg_info 2021-03-19T17:12:14,710 creating /tmp/pip-pip-egg-info-ufdgj0vx/pele_platform.egg-info 2021-03-19T17:12:14,713 writing top-level names to /tmp/pip-pip-egg-info-ufdgj0vx/pele_platform.egg-info/top_level.txt 2021-03-19T17:12:14,716 writing /tmp/pip-pip-egg-info-ufdgj0vx/pele_platform.egg-info/PKG-INFO 2021-03-19T17:12:14,722 writing dependency_links to /tmp/pip-pip-egg-info-ufdgj0vx/pele_platform.egg-info/dependency_links.txt 2021-03-19T17:12:14,726 writing requirements to /tmp/pip-pip-egg-info-ufdgj0vx/pele_platform.egg-info/requires.txt 2021-03-19T17:12:14,730 writing manifest file '/tmp/pip-pip-egg-info-ufdgj0vx/pele_platform.egg-info/SOURCES.txt' 2021-03-19T17:12:14,780 reading manifest file '/tmp/pip-pip-egg-info-ufdgj0vx/pele_platform.egg-info/SOURCES.txt' 2021-03-19T17:12:14,783 reading manifest template 'MANIFEST.in' 2021-03-19T17:12:14,788 warning: no files found matching 'pele_platform/Utilities/PlopRotTemp/param/*' 2021-03-19T17:12:14,789 warning: no files found matching 'pele_platform/AdaptivePELE/atomset/*' 2021-03-19T17:12:14,790 warning: no files found matching 'pele_platform/AdaptivePELE/freeEnergies/*' 2021-03-19T17:12:14,791 warning: no files found matching '*' under directory 'pele_platform/Utilities/PPP/Data/' 2021-03-19T17:12:15,325 warning: no files found matching '*' under directory 'tests/data' 2021-03-19T17:12:15,368 writing manifest file '/tmp/pip-pip-egg-info-ufdgj0vx/pele_platform.egg-info/SOURCES.txt' 2021-03-19T17:12:15,521 Source in /tmp/pip-wheel-clob8tvk/pele-platform_54f2dfd5c51943d3ad6cd57c8372550b has version 1.6.0b1, which satisfies requirement pele-platform==1.6.0b1 from https://files.pythonhosted.org/packages/05/85/4cfdad270ebf569727204cbc9de66f22ef802d5079846f2631e1e6a11059/pele_platform-1.6.0b1.tar.gz#sha256=a7b5e566ec00598a1991d44c8748267104e5a123f462365a584632c94b36a7bf 2021-03-19T17:12:15,523 Removed pele-platform==1.6.0b1 from https://files.pythonhosted.org/packages/05/85/4cfdad270ebf569727204cbc9de66f22ef802d5079846f2631e1e6a11059/pele_platform-1.6.0b1.tar.gz#sha256=a7b5e566ec00598a1991d44c8748267104e5a123f462365a584632c94b36a7bf from build tracker '/tmp/pip-req-tracker-bezuzveo' 2021-03-19T17:12:15,533 Created temporary directory: /tmp/pip-unpack-9k6cry4f 2021-03-19T17:12:15,535 Building wheels for collected packages: pele-platform 2021-03-19T17:12:15,545 Created temporary directory: /tmp/pip-wheel-g_xolvmx 2021-03-19T17:12:15,546 Building wheel for pele-platform (setup.py): started 2021-03-19T17:12:15,547 Destination directory: /tmp/pip-wheel-g_xolvmx 2021-03-19T17:12:15,548 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-clob8tvk/pele-platform_54f2dfd5c51943d3ad6cd57c8372550b/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-clob8tvk/pele-platform_54f2dfd5c51943d3ad6cd57c8372550b/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-g_xolvmx 2021-03-19T17:12:18,263 running bdist_wheel 2021-03-19T17:12:18,274 running build 2021-03-19T17:12:18,275 running build_py 2021-03-19T17:12:18,286 creating build 2021-03-19T17:12:18,287 creating build/lib 2021-03-19T17:12:18,289 creating build/lib/pele_platform 2021-03-19T17:12:18,292 copying pele_platform/main.py -> build/lib/pele_platform 2021-03-19T17:12:18,297 copying pele_platform/_version.py -> build/lib/pele_platform 2021-03-19T17:12:18,300 copying pele_platform/__init__.py -> build/lib/pele_platform 2021-03-19T17:12:18,307 creating build/lib/pele_platform/PPI 2021-03-19T17:12:18,310 copying pele_platform/PPI/main.py -> build/lib/pele_platform/PPI 2021-03-19T17:12:18,317 copying pele_platform/PPI/simulation_launcher.py -> build/lib/pele_platform/PPI 2021-03-19T17:12:18,323 copying pele_platform/PPI/preparation.py -> build/lib/pele_platform/PPI 2021-03-19T17:12:18,327 copying pele_platform/PPI/__init__.py -> build/lib/pele_platform/PPI 2021-03-19T17:12:18,332 creating build/lib/pele_platform/Errors 2021-03-19T17:12:18,333 copying pele_platform/Errors/custom_errors.py -> build/lib/pele_platform/Errors 2021-03-19T17:12:18,338 copying pele_platform/Errors/__init__.py -> build/lib/pele_platform/Errors 2021-03-19T17:12:18,342 creating build/lib/pele_platform/Utilities 2021-03-19T17:12:18,344 copying pele_platform/Utilities/__init__.py -> build/lib/pele_platform/Utilities 2021-03-19T17:12:18,351 creating build/lib/pele_platform/out_in 2021-03-19T17:12:18,354 copying pele_platform/out_in/main.py -> build/lib/pele_platform/out_in 2021-03-19T17:12:18,360 copying pele_platform/out_in/__init__.py -> build/lib/pele_platform/out_in 2021-03-19T17:12:18,367 creating build/lib/pele_platform/analysis 2021-03-19T17:12:18,369 copying pele_platform/analysis/clustering.py -> build/lib/pele_platform/analysis 2021-03-19T17:12:18,375 copying pele_platform/analysis/interactive_plot.py -> build/lib/pele_platform/analysis 2021-03-19T17:12:18,382 copying pele_platform/analysis/plot.py -> build/lib/pele_platform/analysis 2021-03-19T17:12:18,389 copying pele_platform/analysis/pdf_report.py -> build/lib/pele_platform/analysis 2021-03-19T17:12:18,395 copying pele_platform/analysis/analysis.py -> build/lib/pele_platform/analysis 2021-03-19T17:12:18,405 copying pele_platform/analysis/to_mae.py -> build/lib/pele_platform/analysis 2021-03-19T17:12:18,411 copying pele_platform/analysis/__init__.py -> build/lib/pele_platform/analysis 2021-03-19T17:12:18,417 copying pele_platform/analysis/data.py -> build/lib/pele_platform/analysis 2021-03-19T17:12:18,428 creating build/lib/pele_platform/constants 2021-03-19T17:12:18,431 copying pele_platform/constants/constants.py -> build/lib/pele_platform/constants 2021-03-19T17:12:18,438 copying pele_platform/constants/pele_params.py -> build/lib/pele_platform/constants 2021-03-19T17:12:18,445 copying pele_platform/constants/__init__.py -> build/lib/pele_platform/constants 2021-03-19T17:12:18,452 creating build/lib/pele_platform/Adaptive 2021-03-19T17:12:18,455 copying pele_platform/Adaptive/pca.py -> build/lib/pele_platform/Adaptive 2021-03-19T17:12:18,461 copying pele_platform/Adaptive/ligand_parametrization.py -> build/lib/pele_platform/Adaptive 2021-03-19T17:12:18,466 copying pele_platform/Adaptive/metrics.py -> build/lib/pele_platform/Adaptive 2021-03-19T17:12:18,470 copying pele_platform/Adaptive/box.py -> build/lib/pele_platform/Adaptive 2021-03-19T17:12:18,474 copying pele_platform/Adaptive/solvent.py -> build/lib/pele_platform/Adaptive 2021-03-19T17:12:18,478 copying pele_platform/Adaptive/interaction_restrictions.py -> build/lib/pele_platform/Adaptive 2021-03-19T17:12:18,483 copying pele_platform/Adaptive/__init__.py -> build/lib/pele_platform/Adaptive 2021-03-19T17:12:18,486 copying pele_platform/Adaptive/simulation.py -> build/lib/pele_platform/Adaptive 2021-03-19T17:12:18,496 creating build/lib/pele_platform/Checker 2021-03-19T17:12:18,499 copying pele_platform/Checker/python_version.py -> build/lib/pele_platform/Checker 2021-03-19T17:12:18,505 copying pele_platform/Checker/main.py -> build/lib/pele_platform/Checker 2021-03-19T17:12:18,510 copying pele_platform/Checker/executable.py -> build/lib/pele_platform/Checker 2021-03-19T17:12:18,514 copying pele_platform/Checker/environment_variables.py -> build/lib/pele_platform/Checker 2021-03-19T17:12:18,518 copying pele_platform/Checker/valid_flags.py -> build/lib/pele_platform/Checker 2021-03-19T17:12:18,523 copying pele_platform/Checker/__init__.py -> build/lib/pele_platform/Checker 2021-03-19T17:12:18,528 creating build/lib/pele_platform/RNA 2021-03-19T17:12:18,530 copying pele_platform/RNA/prep.py -> build/lib/pele_platform/RNA 2021-03-19T17:12:18,537 copying pele_platform/RNA/__init__.py -> build/lib/pele_platform/RNA 2021-03-19T17:12:18,544 creating build/lib/pele_platform/Frag 2021-03-19T17:12:18,547 copying pele_platform/Frag/libraries.py -> build/lib/pele_platform/Frag 2021-03-19T17:12:18,553 copying pele_platform/Frag/generative_model.py -> build/lib/pele_platform/Frag 2021-03-19T17:12:18,558 copying pele_platform/Frag/analysis.py -> build/lib/pele_platform/Frag 2021-03-19T17:12:18,563 copying pele_platform/Frag/checker.py -> build/lib/pele_platform/Frag 2021-03-19T17:12:18,568 copying pele_platform/Frag/fragments.py -> build/lib/pele_platform/Frag 2021-03-19T17:12:18,573 copying pele_platform/Frag/atoms.py -> build/lib/pele_platform/Frag 2021-03-19T17:12:18,579 copying pele_platform/Frag/helpers.py -> build/lib/pele_platform/Frag 2021-03-19T17:12:18,586 copying pele_platform/Frag/__init__.py -> build/lib/pele_platform/Frag 2021-03-19T17:12:18,591 copying pele_platform/Frag/simulation.py -> build/lib/pele_platform/Frag 2021-03-19T17:12:18,599 creating build/lib/pele_platform/site_finder 2021-03-19T17:12:18,602 copying pele_platform/site_finder/cluster.py -> build/lib/pele_platform/site_finder 2021-03-19T17:12:18,608 copying pele_platform/site_finder/main.py -> build/lib/pele_platform/site_finder 2021-03-19T17:12:18,613 copying pele_platform/site_finder/__init__.py -> build/lib/pele_platform/site_finder 2021-03-19T17:12:18,617 creating build/lib/pele_platform/enzyme_engineering 2021-03-19T17:12:18,619 copying pele_platform/enzyme_engineering/saturated_mutagenesis.py -> build/lib/pele_platform/enzyme_engineering 2021-03-19T17:12:18,625 copying pele_platform/enzyme_engineering/__init__.py -> build/lib/pele_platform/enzyme_engineering 2021-03-19T17:12:18,631 creating build/lib/pele_platform/features 2021-03-19T17:12:18,633 copying pele_platform/features/adaptive.py -> build/lib/pele_platform/features 2021-03-19T17:12:18,641 copying pele_platform/features/frag.py -> build/lib/pele_platform/features 2021-03-19T17:12:18,646 copying pele_platform/features/__init__.py -> build/lib/pele_platform/features 2021-03-19T17:12:18,651 creating build/lib/pele_platform/gpcr 2021-03-19T17:12:18,653 copying pele_platform/gpcr/main.py -> build/lib/pele_platform/gpcr 2021-03-19T17:12:18,657 copying pele_platform/gpcr/__init__.py -> build/lib/pele_platform/gpcr 2021-03-19T17:12:18,663 creating build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,665 copying pele_platform/Utilities/Helpers/map_atoms.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,673 copying pele_platform/Utilities/Helpers/plop_launcher.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,679 copying pele_platform/Utilities/Helpers/bestStructs.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,686 copying pele_platform/Utilities/Helpers/interaction_constraints.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,691 copying pele_platform/Utilities/Helpers/yaml_parser.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,699 copying pele_platform/Utilities/Helpers/center_of_mass.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,706 copying pele_platform/Utilities/Helpers/randomize.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,713 copying pele_platform/Utilities/Helpers/missing_residues.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,719 copying pele_platform/Utilities/Helpers/water.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,726 copying pele_platform/Utilities/Helpers/template_builder.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,732 copying pele_platform/Utilities/Helpers/launcher.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,738 copying pele_platform/Utilities/Helpers/solventOBCParamsGenerator.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,745 copying pele_platform/Utilities/Helpers/system_prep.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,752 copying pele_platform/Utilities/Helpers/calculatePCA4PELE.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,760 copying pele_platform/Utilities/Helpers/conda_deployment.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,766 copying pele_platform/Utilities/Helpers/protein_wizard.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,773 copying pele_platform/Utilities/Helpers/helpers.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,779 copying pele_platform/Utilities/Helpers/__init__.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,785 copying pele_platform/Utilities/Helpers/simulation.py -> build/lib/pele_platform/Utilities/Helpers 2021-03-19T17:12:18,793 creating build/lib/pele_platform/Utilities/Parameters 2021-03-19T17:12:18,796 copying pele_platform/Utilities/Parameters/parameters.py -> build/lib/pele_platform/Utilities/Parameters 2021-03-19T17:12:18,807 copying pele_platform/Utilities/Parameters/__init__.py -> build/lib/pele_platform/Utilities/Parameters 2021-03-19T17:12:18,815 creating build/lib/pele_platform/Utilities/Helpers/constraints 2021-03-19T17:12:18,818 copying pele_platform/Utilities/Helpers/constraints/smiles_constraints.py -> build/lib/pele_platform/Utilities/Helpers/constraints 2021-03-19T17:12:18,826 copying pele_platform/Utilities/Helpers/constraints/alpha_constraints.py -> build/lib/pele_platform/Utilities/Helpers/constraints 2021-03-19T17:12:18,832 copying pele_platform/Utilities/Helpers/constraints/__init__.py -> build/lib/pele_platform/Utilities/Helpers/constraints 2021-03-19T17:12:18,836 creating build/lib/pele_platform/Utilities/Helpers/Metals 2021-03-19T17:12:18,839 copying pele_platform/Utilities/Helpers/Metals/metal_polarisation.py -> build/lib/pele_platform/Utilities/Helpers/Metals 2021-03-19T17:12:18,843 copying pele_platform/Utilities/Helpers/Metals/metal_constraints.py -> build/lib/pele_platform/Utilities/Helpers/Metals 2021-03-19T17:12:18,849 copying pele_platform/Utilities/Helpers/Metals/__init__.py -> build/lib/pele_platform/Utilities/Helpers/Metals 2021-03-19T17:12:18,855 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams 2021-03-19T17:12:18,858 copying pele_platform/Utilities/Parameters/SimulationParams/simulation_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams 2021-03-19T17:12:18,867 copying pele_platform/Utilities/Parameters/SimulationParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams 2021-03-19T17:12:18,872 creating build/lib/pele_platform/Utilities/Parameters/SimulationFolders 2021-03-19T17:12:18,875 copying pele_platform/Utilities/Parameters/SimulationFolders/simulation_folders.py -> build/lib/pele_platform/Utilities/Parameters/SimulationFolders 2021-03-19T17:12:18,879 copying pele_platform/Utilities/Parameters/SimulationFolders/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationFolders 2021-03-19T17:12:18,884 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-03-19T17:12:18,886 copying pele_platform/Utilities/Parameters/SimulationParams/PPI/ppi.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-03-19T17:12:18,891 copying pele_platform/Utilities/Parameters/SimulationParams/PPI/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-03-19T17:12:18,898 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-03-19T17:12:18,901 copying pele_platform/Utilities/Parameters/SimulationParams/InOutParams/inout_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-03-19T17:12:18,907 copying pele_platform/Utilities/Parameters/SimulationParams/InOutParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-03-19T17:12:18,913 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-03-19T17:12:18,917 copying pele_platform/Utilities/Parameters/SimulationParams/GlideParams/glide_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-03-19T17:12:18,923 copying pele_platform/Utilities/Parameters/SimulationParams/GlideParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-03-19T17:12:18,929 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-03-19T17:12:18,932 copying pele_platform/Utilities/Parameters/SimulationParams/MSMParams/msm_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-03-19T17:12:18,937 copying pele_platform/Utilities/Parameters/SimulationParams/MSMParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-03-19T17:12:18,941 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-03-19T17:12:18,943 copying pele_platform/Utilities/Parameters/SimulationParams/PCA/pca.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-03-19T17:12:18,948 copying pele_platform/Utilities/Parameters/SimulationParams/PCA/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-03-19T17:12:18,954 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-03-19T17:12:18,957 copying pele_platform/Utilities/Parameters/SimulationParams/BiasParams/bias_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-03-19T17:12:18,963 copying pele_platform/Utilities/Parameters/SimulationParams/BiasParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-03-19T17:12:18,970 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2021-03-19T17:12:18,972 copying pele_platform/Utilities/Parameters/SimulationParams/site_finder/site_finder.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2021-03-19T17:12:18,977 copying pele_platform/Utilities/Parameters/SimulationParams/site_finder/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2021-03-19T17:12:18,982 creating build/lib/pele_platform/Frag/parameters 2021-03-19T17:12:18,984 copying pele_platform/Frag/parameters/optional.py -> build/lib/pele_platform/Frag/parameters 2021-03-19T17:12:18,989 copying pele_platform/Frag/parameters/files.py -> build/lib/pele_platform/Frag/parameters 2021-03-19T17:12:18,995 copying pele_platform/Frag/parameters/main.py -> build/lib/pele_platform/Frag/parameters 2021-03-19T17:12:19,001 copying pele_platform/Frag/parameters/metrics.py -> build/lib/pele_platform/Frag/parameters 2021-03-19T17:12:19,007 copying pele_platform/Frag/parameters/water.py -> build/lib/pele_platform/Frag/parameters 2021-03-19T17:12:19,013 copying pele_platform/Frag/parameters/__init__.py -> build/lib/pele_platform/Frag/parameters 2021-03-19T17:12:19,017 copying pele_platform/Frag/parameters/simulation.py -> build/lib/pele_platform/Frag/parameters 2021-03-19T17:12:19,021 running egg_info 2021-03-19T17:12:19,042 writing requirements to pele_platform.egg-info/requires.txt 2021-03-19T17:12:19,044 writing dependency_links to pele_platform.egg-info/dependency_links.txt 2021-03-19T17:12:19,049 writing top-level names to pele_platform.egg-info/top_level.txt 2021-03-19T17:12:19,051 writing pele_platform.egg-info/PKG-INFO 2021-03-19T17:12:19,105 reading manifest file 'pele_platform.egg-info/SOURCES.txt' 2021-03-19T17:12:19,129 reading manifest template 'MANIFEST.in' 2021-03-19T17:12:19,132 warning: no files found matching 'pele_platform/Utilities/PlopRotTemp/param/*' 2021-03-19T17:12:19,133 warning: no files found matching 'pele_platform/AdaptivePELE/atomset/*' 2021-03-19T17:12:19,133 warning: no files found matching 'pele_platform/AdaptivePELE/freeEnergies/*' 2021-03-19T17:12:19,134 warning: no files found matching '*' under directory 'pele_platform/Utilities/PPP/Data/' 2021-03-19T17:12:19,602 warning: no files found matching '*' under directory 'tests/data' 2021-03-19T17:12:19,665 writing manifest file 'pele_platform.egg-info/SOURCES.txt' 2021-03-19T17:12:19,760 creating build/lib/pele_platform/Examples 2021-03-19T17:12:19,762 copying pele_platform/Examples/test.sl -> build/lib/pele_platform/Examples 2021-03-19T17:12:19,768 creating build/lib/pele_platform/Examples/Adaptive 2021-03-19T17:12:19,770 copying pele_platform/Examples/Adaptive/STR.rot.assign -> build/lib/pele_platform/Examples/Adaptive 2021-03-19T17:12:19,775 copying pele_platform/Examples/Adaptive/adaptive.conf -> build/lib/pele_platform/Examples/Adaptive 2021-03-19T17:12:19,780 copying pele_platform/Examples/Adaptive/pele_file_4Adaptive.conf -> build/lib/pele_platform/Examples/Adaptive 2021-03-19T17:12:19,786 copying pele_platform/Examples/Adaptive/strz -> build/lib/pele_platform/Examples/Adaptive 2021-03-19T17:12:19,796 copying pele_platform/Examples/Adaptive/test.sl -> build/lib/pele_platform/Examples/Adaptive 2021-03-19T17:12:19,803 creating build/lib/pele_platform/Examples/Msm 2021-03-19T17:12:19,805 copying pele_platform/Examples/Msm/AS4_INIT.mae -> build/lib/pele_platform/Examples/Msm 2021-03-19T17:12:19,815 copying pele_platform/Examples/Msm/PR_1A28_protein.pdb -> build/lib/pele_platform/Examples/Msm 2021-03-19T17:12:19,853 copying pele_platform/Examples/Msm/PR_1A28_xray_-_minimized.pdb -> build/lib/pele_platform/Examples/Msm 2021-03-19T17:12:19,889 copying pele_platform/Examples/Msm/PR_1A28_xray_-_minimized_processed.pdb -> build/lib/pele_platform/Examples/Msm 2021-03-19T17:12:20,290 copying pele_platform/Examples/Msm/PR_AS4.pdb -> build/lib/pele_platform/Examples/Msm 2021-03-19T17:12:20,329 copying pele_platform/Examples/Msm/input.yaml -> build/lib/pele_platform/Examples/Msm 2021-03-19T17:12:20,335 creating build/lib/pele_platform/Examples/PPI 2021-03-19T17:12:20,338 copying pele_platform/Examples/PPI/1f47_ligand.pdb -> build/lib/pele_platform/Examples/PPI 2021-03-19T17:12:20,346 copying pele_platform/Examples/PPI/1f47_prep.pdb -> build/lib/pele_platform/Examples/PPI 2021-03-19T17:12:20,370 copying pele_platform/Examples/PPI/1tnf_ligand.pdb -> build/lib/pele_platform/Examples/PPI 2021-03-19T17:12:20,379 copying pele_platform/Examples/PPI/1tnf_prep.pdb -> build/lib/pele_platform/Examples/PPI 2021-03-19T17:12:20,442 copying pele_platform/Examples/PPI/input.yaml -> build/lib/pele_platform/Examples/PPI 2021-03-19T17:12:20,448 copying pele_platform/Examples/PPI/input_folder.yaml -> build/lib/pele_platform/Examples/PPI 2021-03-19T17:12:20,455 copying pele_platform/Examples/PPI/input_skipref.yaml -> build/lib/pele_platform/Examples/PPI 2021-03-19T17:12:20,462 creating build/lib/pele_platform/Examples/RNA 2021-03-19T17:12:20,465 copying pele_platform/Examples/RNA/2l94.yaml -> build/lib/pele_platform/Examples/RNA 2021-03-19T17:12:20,473 copying pele_platform/Examples/RNA/5C45_prep.pdb -> build/lib/pele_platform/Examples/RNA 2021-03-19T17:12:20,517 copying pele_platform/Examples/RNA/5C45_prep_proc.pdb -> build/lib/pele_platform/Examples/RNA 2021-03-19T17:12:20,561 copying pele_platform/Examples/RNA/input.yaml -> build/lib/pele_platform/Examples/RNA 2021-03-19T17:12:20,568 copying pele_platform/Examples/RNA/input_induced.yaml -> build/lib/pele_platform/Examples/RNA 2021-03-19T17:12:20,574 creating build/lib/pele_platform/Examples/analysis 2021-03-19T17:12:20,577 copying pele_platform/Examples/analysis/input.yaml -> build/lib/pele_platform/Examples/analysis 2021-03-19T17:12:20,584 copying pele_platform/Examples/analysis/input_flags.yaml -> build/lib/pele_platform/Examples/analysis 2021-03-19T17:12:20,591 copying pele_platform/Examples/analysis/input_flags0.yaml -> build/lib/pele_platform/Examples/analysis 2021-03-19T17:12:20,598 copying pele_platform/Examples/analysis/input_xtc.yaml -> build/lib/pele_platform/Examples/analysis 2021-03-19T17:12:20,605 creating build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,607 copying pele_platform/Examples/analysis/data/MG.rot.assign -> build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,614 copying pele_platform/Examples/analysis/data/STR.rot.assign -> build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,619 copying pele_platform/Examples/analysis/data/adaptive.conf -> build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,624 copying pele_platform/Examples/analysis/data/input.yaml -> build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,629 copying pele_platform/Examples/analysis/data/input_flags.yaml -> build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,634 copying pele_platform/Examples/analysis/data/input_flags0.yaml -> build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,640 copying pele_platform/Examples/analysis/data/input_mae.yaml -> build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,647 copying pele_platform/Examples/analysis/data/mgz -> build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,653 copying pele_platform/Examples/analysis/data/pele.conf -> build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,660 copying pele_platform/Examples/analysis/data/strz -> build/lib/pele_platform/Examples/analysis/data 2021-03-19T17:12:20,665 creating build/lib/pele_platform/Examples/analysis/data/inputs 2021-03-19T17:12:20,668 copying pele_platform/Examples/analysis/data/inputs/input1.pdb -> build/lib/pele_platform/Examples/analysis/data/inputs 2021-03-19T17:12:20,709 copying pele_platform/Examples/analysis/data/inputs/input2.pdb -> build/lib/pele_platform/Examples/analysis/data/inputs 2021-03-19T17:12:20,751 copying pele_platform/Examples/analysis/data/inputs/input3.pdb -> build/lib/pele_platform/Examples/analysis/data/inputs 2021-03-19T17:12:20,790 creating build/lib/pele_platform/Examples/analysis/data/output 2021-03-19T17:12:20,792 copying pele_platform/Examples/analysis/data/output/originalControlFile.conf -> build/lib/pele_platform/Examples/analysis/data/output 2021-03-19T17:12:20,797 creating build/lib/pele_platform/Examples/analysis/data/output/0 2021-03-19T17:12:20,800 copying pele_platform/Examples/analysis/data/output/0/report_1 -> build/lib/pele_platform/Examples/analysis/data/output/0 2021-03-19T17:12:20,807 copying pele_platform/Examples/analysis/data/output/0/topologyMapping.txt -> build/lib/pele_platform/Examples/analysis/data/output/0 2021-03-19T17:12:20,814 copying pele_platform/Examples/analysis/data/output/0/trajectory_1.pdb -> build/lib/pele_platform/Examples/analysis/data/output/0 2021-03-19T17:12:20,854 creating build/lib/pele_platform/Examples/analysis/data/output/0/clustering 2021-03-19T17:12:20,857 copying pele_platform/Examples/analysis/data/output/0/clustering/object.pkl -> build/lib/pele_platform/Examples/analysis/data/output/0/clustering 2021-03-19T17:12:20,896 copying pele_platform/Examples/analysis/data/output/0/clustering/summary.txt -> build/lib/pele_platform/Examples/analysis/data/output/0/clustering 2021-03-19T17:12:20,901 creating build/lib/pele_platform/Examples/analysis/data/output/synchronization 2021-03-19T17:12:20,903 copying pele_platform/Examples/analysis/data/output/synchronization/syncFile.lock -> build/lib/pele_platform/Examples/analysis/data/output/synchronization 2021-03-19T17:12:20,910 creating build/lib/pele_platform/Examples/analysis/data/output/topologies 2021-03-19T17:12:20,913 copying pele_platform/Examples/analysis/data/output/topologies/topologies.pkl -> build/lib/pele_platform/Examples/analysis/data/output/topologies 2021-03-19T17:12:20,950 copying pele_platform/Examples/analysis/data/output/topologies/topology_0.pdb -> build/lib/pele_platform/Examples/analysis/data/output/topologies 2021-03-19T17:12:20,990 creating build/lib/pele_platform/Examples/analysis/data/results 2021-03-19T17:12:20,992 creating build/lib/pele_platform/Examples/analysis/data/results/BestStructs 2021-03-19T17:12:20,995 copying pele_platform/Examples/analysis/data/results/BestStructs/epoch0_trajectory_1.0_BindingEnergy1.26468.pdb -> build/lib/pele_platform/Examples/analysis/data/results/BestStructs 2021-03-19T17:12:21,011 copying pele_platform/Examples/analysis/data/results/BestStructs/epoch0_trajectory_2.0_BindingEnergy0.644256.pdb -> build/lib/pele_platform/Examples/analysis/data/results/BestStructs 2021-03-19T17:12:21,141 copying pele_platform/Examples/analysis/data/results/BestStructs/epoch0_trajectory_2.1_BindingEnergy1.84474.pdb -> build/lib/pele_platform/Examples/analysis/data/results/BestStructs 2021-03-19T17:12:21,158 creating build/lib/pele_platform/Examples/analysis/data/results/Plots 2021-03-19T17:12:21,161 copying pele_platform/Examples/analysis/data/results/Plots/Binding_Energy.1_Binding_Energy_plot.png -> build/lib/pele_platform/Examples/analysis/data/results/Plots 2021-03-19T17:12:21,170 copying pele_platform/Examples/analysis/data/results/Plots/currentEnergy_Binding_Energy_Binding_Energy.1_plot.png -> build/lib/pele_platform/Examples/analysis/data/results/Plots 2021-03-19T17:12:21,180 copying pele_platform/Examples/analysis/data/results/Plots/currentEnergy_Binding_Energy_sasaLig_plot.png -> build/lib/pele_platform/Examples/analysis/data/results/Plots 2021-03-19T17:12:21,189 copying pele_platform/Examples/analysis/data/results/Plots/sasaLig_Binding_Energy_plot.png -> build/lib/pele_platform/Examples/analysis/data/results/Plots 2021-03-19T17:12:21,198 creating build/lib/pele_platform/Examples/analysis/data/results/clusters 2021-03-19T17:12:21,200 copying pele_platform/Examples/analysis/data/results/clusters/clusters_Binding Energy_boxplot.png -> build/lib/pele_platform/Examples/analysis/data/results/clusters 2021-03-19T17:12:21,209 creating build/lib/pele_platform/Examples/analysis/data/xtc 2021-03-19T17:12:21,212 copying pele_platform/Examples/analysis/data/xtc/summary.csv -> build/lib/pele_platform/Examples/analysis/data/xtc 2021-03-19T17:12:21,219 creating build/lib/pele_platform/Examples/analysis/data/xtc/0 2021-03-19T17:12:21,222 copying pele_platform/Examples/analysis/data/xtc/0/report_1 -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2021-03-19T17:12:21,229 copying pele_platform/Examples/analysis/data/xtc/0/report_2 -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2021-03-19T17:12:21,237 copying pele_platform/Examples/analysis/data/xtc/0/trajectory_1.xtc -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2021-03-19T17:12:21,245 copying pele_platform/Examples/analysis/data/xtc/0/trajectory_2.xtc -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2021-03-19T17:12:21,253 creating build/lib/pele_platform/Examples/analysis/data/xtc/topologies 2021-03-19T17:12:21,256 copying pele_platform/Examples/analysis/data/xtc/topologies/topology_0.pdb -> build/lib/pele_platform/Examples/analysis/data/xtc/topologies 2021-03-19T17:12:21,273 creating build/lib/pele_platform/Examples/bias 2021-03-19T17:12:21,276 copying pele_platform/Examples/bias/complex.pdb -> build/lib/pele_platform/Examples/bias 2021-03-19T17:12:21,316 copying pele_platform/Examples/bias/input_defaults.yaml -> build/lib/pele_platform/Examples/bias 2021-03-19T17:12:21,323 creating build/lib/pele_platform/Examples/box 2021-03-19T17:12:21,326 copying pele_platform/Examples/box/input.yaml -> build/lib/pele_platform/Examples/box 2021-03-19T17:12:21,332 creating build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,335 copying pele_platform/Examples/checker/complex.pdb -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,382 copying pele_platform/Examples/checker/complex2.pdb -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,408 copying pele_platform/Examples/checker/complex_unk.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,473 copying pele_platform/Examples/checker/input.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,480 copying pele_platform/Examples/checker/input_atom_string.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,487 copying pele_platform/Examples/checker/input_env.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,493 copying pele_platform/Examples/checker/input_map_atom_num.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,500 copying pele_platform/Examples/checker/input_map_atom_str.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,506 copying pele_platform/Examples/checker/input_pele_exec.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,512 copying pele_platform/Examples/checker/input_rotamer.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,519 copying pele_platform/Examples/checker/input_space.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,525 copying pele_platform/Examples/checker/input_tab.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,530 copying pele_platform/Examples/checker/input_template.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,535 copying pele_platform/Examples/checker/input_underscore.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,540 copying pele_platform/Examples/checker/input_unk.yaml -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,545 copying pele_platform/Examples/checker/ligand2.pdb -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,552 copying pele_platform/Examples/checker/mapping_complex.pdb -> build/lib/pele_platform/Examples/checker 2021-03-19T17:12:21,620 creating build/lib/pele_platform/Examples/clustering 2021-03-19T17:12:21,622 copying pele_platform/Examples/clustering/summary.csv -> build/lib/pele_platform/Examples/clustering 2021-03-19T17:12:21,627 creating build/lib/pele_platform/Examples/clustering/0 2021-03-19T17:12:21,630 copying pele_platform/Examples/clustering/0/report_1 -> build/lib/pele_platform/Examples/clustering/0 2021-03-19T17:12:21,637 copying pele_platform/Examples/clustering/0/report_2 -> build/lib/pele_platform/Examples/clustering/0 2021-03-19T17:12:21,644 copying pele_platform/Examples/clustering/0/report_3 -> build/lib/pele_platform/Examples/clustering/0 2021-03-19T17:12:21,650 copying pele_platform/Examples/clustering/0/report_4 -> build/lib/pele_platform/Examples/clustering/0 2021-03-19T17:12:21,657 copying pele_platform/Examples/clustering/0/topologyMapping.txt -> build/lib/pele_platform/Examples/clustering/0 2021-03-19T17:12:21,663 copying pele_platform/Examples/clustering/0/trajectory_1.pdb -> build/lib/pele_platform/Examples/clustering/0 2021-03-19T17:12:21,735 copying pele_platform/Examples/clustering/0/trajectory_2.pdb -> build/lib/pele_platform/Examples/clustering/0 2021-03-19T17:12:21,772 copying pele_platform/Examples/clustering/0/trajectory_3.pdb -> build/lib/pele_platform/Examples/clustering/0 2021-03-19T17:12:21,842 copying pele_platform/Examples/clustering/0/trajectory_4.pdb -> build/lib/pele_platform/Examples/clustering/0 2021-03-19T17:12:21,911 creating build/lib/pele_platform/Examples/clustering/0/clustering 2021-03-19T17:12:21,913 copying pele_platform/Examples/clustering/0/clustering/object.pkl -> build/lib/pele_platform/Examples/clustering/0/clustering 2021-03-19T17:12:22,138 copying pele_platform/Examples/clustering/0/clustering/summary.txt -> build/lib/pele_platform/Examples/clustering/0/clustering 2021-03-19T17:12:22,144 creating build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,147 copying pele_platform/Examples/constraints/1zop.pdb -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,178 copying pele_platform/Examples/constraints/4l3a_prep.pdb -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,233 copying pele_platform/Examples/constraints/4qnr_prep.pdb -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,287 copying pele_platform/Examples/constraints/4w4o_prep.pdb -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,320 copying pele_platform/Examples/constraints/4w5i_prep.pdb -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,353 copying pele_platform/Examples/constraints/4zu9_prep.pdb -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,463 copying pele_platform/Examples/constraints/ca_constraints.pdb -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,533 copying pele_platform/Examples/constraints/complex_smiles_error.pdb -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,578 copying pele_platform/Examples/constraints/fail_input_permissive_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,584 copying pele_platform/Examples/constraints/input_all_metal_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,591 copying pele_platform/Examples/constraints/input_ca_noppp.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,598 copying pele_platform/Examples/constraints/input_ca_ppp.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,605 copying pele_platform/Examples/constraints/input_constrain_smarts.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,612 copying pele_platform/Examples/constraints/input_constrain_smiles.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,619 copying pele_platform/Examples/constraints/input_external_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,626 copying pele_platform/Examples/constraints/input_ignore.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,632 copying pele_platform/Examples/constraints/input_k.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,640 copying pele_platform/Examples/constraints/input_metals.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,647 copying pele_platform/Examples/constraints/input_no_metal_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,654 copying pele_platform/Examples/constraints/input_permissive_exception.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,661 copying pele_platform/Examples/constraints/input_smiles_error.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,667 copying pele_platform/Examples/constraints/input_square_planar.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,675 copying pele_platform/Examples/constraints/input_square_planar_polarisation.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,682 copying pele_platform/Examples/constraints/input_tetrahedral.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,688 copying pele_platform/Examples/constraints/pass_input_permissive_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2021-03-19T17:12:22,695 creating build/lib/pele_platform/Examples/enzyme_engineering 2021-03-19T17:12:22,698 copying pele_platform/Examples/enzyme_engineering/restart_saturated_mutagenesis.yaml -> build/lib/pele_platform/Examples/enzyme_engineering 2021-03-19T17:12:22,705 copying pele_platform/Examples/enzyme_engineering/saturated_mutagenesis.yaml -> build/lib/pele_platform/Examples/enzyme_engineering 2021-03-19T17:12:22,712 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart 2021-03-19T17:12:22,715 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/completed_mutations.log -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart 2021-03-19T17:12:22,722 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2021-03-19T17:12:22,725 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 2021-03-19T17:12:22,732 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 2021-03-19T17:12:22,737 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 2021-03-19T17:12:22,744 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 2021-03-19T17:12:22,750 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal 2021-03-19T17:12:22,752 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs 2021-03-19T17:12:22,755 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 2021-03-19T17:12:22,763 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates 2021-03-19T17:12:22,764 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005 2021-03-19T17:12:22,766 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms 2021-03-19T17:12:22,770 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 2021-03-19T17:12:22,777 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2021-03-19T17:12:22,779 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 2021-03-19T17:12:22,942 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 2021-03-19T17:12:23,006 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 2021-03-19T17:12:23,068 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 2021-03-19T17:12:23,127 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 2021-03-19T17:12:23,132 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 2021-03-19T17:12:23,193 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output 2021-03-19T17:12:23,197 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 2021-03-19T17:12:23,203 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0 2021-03-19T17:12:23,205 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 2021-03-19T17:12:23,211 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering 2021-03-19T17:12:23,213 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 2021-03-19T17:12:23,218 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 2021-03-19T17:12:23,226 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2021-03-19T17:12:23,228 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 2021-03-19T17:12:23,236 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 2021-03-19T17:12:23,243 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 2021-03-19T17:12:23,363 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 2021-03-19T17:12:23,552 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2021-03-19T17:12:23,555 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 2021-03-19T17:12:23,562 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 2021-03-19T17:12:23,568 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 2021-03-19T17:12:23,690 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 2021-03-19T17:12:23,809 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization 2021-03-19T17:12:23,812 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 2021-03-19T17:12:23,820 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2021-03-19T17:12:23,823 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 2021-03-19T17:12:23,933 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 2021-03-19T17:12:23,996 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 2021-03-19T17:12:24,060 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2021-03-19T17:12:24,063 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 2021-03-19T17:12:24,071 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 2021-03-19T17:12:24,132 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 2021-03-19T17:12:24,194 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2021-03-19T17:12:24,196 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 2021-03-19T17:12:24,202 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 2021-03-19T17:12:24,208 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 2021-03-19T17:12:24,215 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 2021-03-19T17:12:24,222 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2021-03-19T17:12:24,225 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 2021-03-19T17:12:24,289 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 2021-03-19T17:12:24,353 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 2021-03-19T17:12:24,359 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 2021-03-19T17:12:24,419 creating build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2021-03-19T17:12:24,422 copying pele_platform/Examples/enzyme_engineering/pdb_files/T454A.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2021-03-19T17:12:24,486 copying pele_platform/Examples/enzyme_engineering/pdb_files/T454D.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2021-03-19T17:12:24,550 copying pele_platform/Examples/enzyme_engineering/pdb_files/T454E.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2021-03-19T17:12:24,613 creating build/lib/pele_platform/Examples/exit 2021-03-19T17:12:24,616 copying pele_platform/Examples/exit/input.yaml -> build/lib/pele_platform/Examples/exit 2021-03-19T17:12:24,623 copying pele_platform/Examples/exit/input_defaults.yaml -> build/lib/pele_platform/Examples/exit 2021-03-19T17:12:24,630 creating build/lib/pele_platform/Examples/exit_soft 2021-03-19T17:12:24,632 copying pele_platform/Examples/exit_soft/input.yaml -> build/lib/pele_platform/Examples/exit_soft 2021-03-19T17:12:24,639 copying pele_platform/Examples/exit_soft/input_defaults.yaml -> build/lib/pele_platform/Examples/exit_soft 2021-03-19T17:12:24,646 creating build/lib/pele_platform/Examples/flags 2021-03-19T17:12:24,649 copying pele_platform/Examples/flags/input.yaml -> build/lib/pele_platform/Examples/flags 2021-03-19T17:12:24,656 creating build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,659 copying pele_platform/Examples/frag/1w7h_preparation_structure_2w.pdb -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,711 copying pele_platform/Examples/frag/1w7h_preparation_structure_2w_processed.pdb -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,762 copying pele_platform/Examples/frag/amino.pdb -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,768 copying pele_platform/Examples/frag/core.pdb -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,775 copying pele_platform/Examples/frag/flags.conf -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,781 copying pele_platform/Examples/frag/input_ai.yaml -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,786 copying pele_platform/Examples/frag/input_core.yaml -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,791 copying pele_platform/Examples/frag/input_core_sdf.yaml -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,795 copying pele_platform/Examples/frag/input_flags.yaml -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,800 copying pele_platform/Examples/frag/input_lib_pdb.yaml -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,806 copying pele_platform/Examples/frag/input_lib_sdf.yaml -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,813 copying pele_platform/Examples/frag/input_point_analysis.yaml -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,819 copying pele_platform/Examples/frag/input_sim.yaml -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,825 copying pele_platform/Examples/frag/input_symmetry.yaml -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,829 copying pele_platform/Examples/frag/ligands.sdf -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,834 copying pele_platform/Examples/frag/sequential.conf -> build/lib/pele_platform/Examples/frag 2021-03-19T17:12:24,839 creating build/lib/pele_platform/Examples/frag/analysis_data 2021-03-19T17:12:24,840 creating build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_mol1C3-H2C1-H1 2021-03-19T17:12:24,841 creating build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_mol1C3-H2C1-H1/top_result 2021-03-19T17:12:24,845 copying pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_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_mol1C3-H2C1-H1/top_result 2021-03-19T17:12:24,897 copying pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_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_mol1C3-H2C1-H1/top_result 2021-03-19T17:12:24,948 creating build/lib/pele_platform/Examples/frag/checker 2021-03-19T17:12:24,950 copying pele_platform/Examples/frag/checker/4RFM_proc.pdb -> build/lib/pele_platform/Examples/frag/checker 2021-03-19T17:12:24,958 copying pele_platform/Examples/frag/checker/4RFM_series.sdf -> build/lib/pele_platform/Examples/frag/checker 2021-03-19T17:12:24,966 copying pele_platform/Examples/frag/checker/receptor.sdf -> build/lib/pele_platform/Examples/frag/checker 2021-03-19T17:12:24,998 creating build/lib/pele_platform/Examples/frag/pdb_test_lib 2021-03-19T17:12:25,001 copying pele_platform/Examples/frag/pdb_test_lib/mol1.pdb -> build/lib/pele_platform/Examples/frag/pdb_test_lib 2021-03-19T17:12:25,009 copying pele_platform/Examples/frag/pdb_test_lib/mol2.pdb -> build/lib/pele_platform/Examples/frag/pdb_test_lib 2021-03-19T17:12:25,016 creating build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,019 copying pele_platform/Examples/frag/sdf_joiner/13_serie.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,033 copying pele_platform/Examples/frag/sdf_joiner/4RFM_core_sc.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,084 copying pele_platform/Examples/frag/sdf_joiner/4RFM_proc.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,135 copying pele_platform/Examples/frag/sdf_joiner/4RFM_series.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,144 copying pele_platform/Examples/frag/sdf_joiner/core2.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,184 copying pele_platform/Examples/frag/sdf_joiner/core3.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,204 copying pele_platform/Examples/frag/sdf_joiner/frag.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,213 copying pele_platform/Examples/frag/sdf_joiner/frag.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,219 copying pele_platform/Examples/frag/sdf_joiner/frag2.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,231 copying pele_platform/Examples/frag/sdf_joiner/frag2.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,238 copying pele_platform/Examples/frag/sdf_joiner/frag3.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,249 copying pele_platform/Examples/frag/sdf_joiner/frag3.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,256 copying pele_platform/Examples/frag/sdf_joiner/frag31.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,268 copying pele_platform/Examples/frag/sdf_joiner/frag4.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,274 copying pele_platform/Examples/frag/sdf_joiner/frag5.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,281 copying pele_platform/Examples/frag/sdf_joiner/glide-dockSARS_core.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:25,362 creating build/lib/pele_platform/Examples/frag/sdf_test_lib 2021-03-19T17:12:25,365 copying pele_platform/Examples/frag/sdf_test_lib/test_library.sdf -> build/lib/pele_platform/Examples/frag/sdf_test_lib 2021-03-19T17:12:25,372 creating build/lib/pele_platform/Examples/global 2021-03-19T17:12:25,375 copying pele_platform/Examples/global/input.yaml -> build/lib/pele_platform/Examples/global 2021-03-19T17:12:25,383 copying pele_platform/Examples/global/input_defaults.yaml -> build/lib/pele_platform/Examples/global 2021-03-19T17:12:25,390 copying pele_platform/Examples/global/input_inputs.yaml -> build/lib/pele_platform/Examples/global 2021-03-19T17:12:25,398 copying pele_platform/Examples/global/input_inputs_asterisc.yaml -> build/lib/pele_platform/Examples/global 2021-03-19T17:12:25,405 creating build/lib/pele_platform/Examples/gpcr 2021-03-19T17:12:25,407 copying pele_platform/Examples/gpcr/complex.pdb -> build/lib/pele_platform/Examples/gpcr 2021-03-19T17:12:25,452 copying pele_platform/Examples/gpcr/complex_processed.pdb -> build/lib/pele_platform/Examples/gpcr 2021-03-19T17:12:25,497 copying pele_platform/Examples/gpcr/input.yaml -> build/lib/pele_platform/Examples/gpcr 2021-03-19T17:12:25,504 copying pele_platform/Examples/gpcr/input_atom_error.yaml -> build/lib/pele_platform/Examples/gpcr 2021-03-19T17:12:25,510 copying pele_platform/Examples/gpcr/input_defaults.yaml -> build/lib/pele_platform/Examples/gpcr 2021-03-19T17:12:25,517 copying pele_platform/Examples/gpcr/input_defaults2.yaml -> build/lib/pele_platform/Examples/gpcr 2021-03-19T17:12:25,524 creating build/lib/pele_platform/Examples/induced_fit 2021-03-19T17:12:25,527 copying pele_platform/Examples/induced_fit/input_exhaustive.yaml -> build/lib/pele_platform/Examples/induced_fit 2021-03-19T17:12:25,535 copying pele_platform/Examples/induced_fit/input_exhaustive_defaults.yaml -> build/lib/pele_platform/Examples/induced_fit 2021-03-19T17:12:25,542 copying pele_platform/Examples/induced_fit/input_fast.yaml -> build/lib/pele_platform/Examples/induced_fit 2021-03-19T17:12:25,549 copying pele_platform/Examples/induced_fit/input_fast_defaults.yaml -> build/lib/pele_platform/Examples/induced_fit 2021-03-19T17:12:25,556 copying pele_platform/Examples/induced_fit/input_mae.yaml -> build/lib/pele_platform/Examples/induced_fit 2021-03-19T17:12:25,562 creating build/lib/pele_platform/Examples/inputs 2021-03-19T17:12:25,565 copying pele_platform/Examples/inputs/input.yaml -> build/lib/pele_platform/Examples/inputs 2021-03-19T17:12:25,573 copying pele_platform/Examples/inputs/mn4.sl -> build/lib/pele_platform/Examples/inputs 2021-03-19T17:12:25,580 copying pele_platform/Examples/inputs/nord3.sge -> build/lib/pele_platform/Examples/inputs 2021-03-19T17:12:25,587 creating build/lib/pele_platform/Examples/interaction_restrictions 2021-03-19T17:12:25,590 copying pele_platform/Examples/interaction_restrictions/complex.pdb -> build/lib/pele_platform/Examples/interaction_restrictions 2021-03-19T17:12:25,659 copying pele_platform/Examples/interaction_restrictions/input.yaml -> build/lib/pele_platform/Examples/interaction_restrictions 2021-03-19T17:12:25,667 copying pele_platform/Examples/interaction_restrictions/input_error.yaml -> build/lib/pele_platform/Examples/interaction_restrictions 2021-03-19T17:12:25,674 copying pele_platform/Examples/interaction_restrictions/input_error_2.yaml -> build/lib/pele_platform/Examples/interaction_restrictions 2021-03-19T17:12:25,680 creating build/lib/pele_platform/Examples/interaction_restrictions/out 2021-03-19T17:12:25,683 copying pele_platform/Examples/interaction_restrictions/out/expected_conditions.txt -> build/lib/pele_platform/Examples/interaction_restrictions/out 2021-03-19T17:12:25,691 copying pele_platform/Examples/interaction_restrictions/out/expected_metrics.txt -> build/lib/pele_platform/Examples/interaction_restrictions/out 2021-03-19T17:12:25,698 creating build/lib/pele_platform/Examples/out_in 2021-03-19T17:12:25,701 copying pele_platform/Examples/out_in/1_3ZON_complex.pdb -> build/lib/pele_platform/Examples/out_in 2021-03-19T17:12:25,743 copying pele_platform/Examples/out_in/input.yaml -> build/lib/pele_platform/Examples/out_in 2021-03-19T17:12:25,750 copying pele_platform/Examples/out_in/input_default.yaml -> build/lib/pele_platform/Examples/out_in 2021-03-19T17:12:25,757 copying pele_platform/Examples/out_in/input_flag_error.yaml -> build/lib/pele_platform/Examples/out_in 2021-03-19T17:12:25,762 creating build/lib/pele_platform/Examples/pca 2021-03-19T17:12:25,765 copying pele_platform/Examples/pca/1.pdb -> build/lib/pele_platform/Examples/pca 2021-03-19T17:12:25,812 copying pele_platform/Examples/pca/2.pdb -> build/lib/pele_platform/Examples/pca 2021-03-19T17:12:25,851 copying pele_platform/Examples/pca/3.pdb -> build/lib/pele_platform/Examples/pca 2021-03-19T17:12:25,896 copying pele_platform/Examples/pca/input.yaml -> build/lib/pele_platform/Examples/pca 2021-03-19T17:12:25,903 copying pele_platform/Examples/pca/input_str.yaml -> build/lib/pele_platform/Examples/pca 2021-03-19T17:12:25,910 creating build/lib/pele_platform/Examples/preparation 2021-03-19T17:12:25,913 copying pele_platform/Examples/preparation/6qmk_correct.pdb -> build/lib/pele_platform/Examples/preparation 2021-03-19T17:12:25,964 copying pele_platform/Examples/preparation/6qmk_repeated.pdb -> build/lib/pele_platform/Examples/preparation 2021-03-19T17:12:26,021 copying pele_platform/Examples/preparation/complex.pdb -> build/lib/pele_platform/Examples/preparation 2021-03-19T17:12:26,059 copying pele_platform/Examples/preparation/complex_2.pdb -> build/lib/pele_platform/Examples/preparation 2021-03-19T17:12:26,119 copying pele_platform/Examples/preparation/input.yaml -> build/lib/pele_platform/Examples/preparation 2021-03-19T17:12:26,127 copying pele_platform/Examples/preparation/input_nonstandard.yaml -> build/lib/pele_platform/Examples/preparation 2021-03-19T17:12:26,134 copying pele_platform/Examples/preparation/input_space.yaml -> build/lib/pele_platform/Examples/preparation 2021-03-19T17:12:26,140 creating build/lib/pele_platform/Examples/production 2021-03-19T17:12:26,143 copying pele_platform/Examples/production/input.sl -> build/lib/pele_platform/Examples/production 2021-03-19T17:12:26,151 copying pele_platform/Examples/production/input_mae.yaml -> build/lib/pele_platform/Examples/production 2021-03-19T17:12:26,157 creating build/lib/pele_platform/Examples/rescoring 2021-03-19T17:12:26,160 copying pele_platform/Examples/rescoring/input.yaml -> build/lib/pele_platform/Examples/rescoring 2021-03-19T17:12:26,168 copying pele_platform/Examples/rescoring/input_defaults.yaml -> build/lib/pele_platform/Examples/rescoring 2021-03-19T17:12:26,175 creating build/lib/pele_platform/Examples/restart 2021-03-19T17:12:26,178 copying pele_platform/Examples/restart/input.yaml -> build/lib/pele_platform/Examples/restart 2021-03-19T17:12:26,185 creating build/lib/pele_platform/Examples/site_finder 2021-03-19T17:12:26,188 copying pele_platform/Examples/site_finder/complex.pdb -> build/lib/pele_platform/Examples/site_finder 2021-03-19T17:12:26,236 copying pele_platform/Examples/site_finder/input_folder.yaml -> build/lib/pele_platform/Examples/site_finder 2021-03-19T17:12:26,241 copying pele_platform/Examples/site_finder/input_global.yaml -> build/lib/pele_platform/Examples/site_finder 2021-03-19T17:12:26,246 copying pele_platform/Examples/site_finder/input_global_xtc.yaml -> build/lib/pele_platform/Examples/site_finder 2021-03-19T17:12:26,253 copying pele_platform/Examples/site_finder/input_restart.yaml -> build/lib/pele_platform/Examples/site_finder 2021-03-19T17:12:26,260 copying pele_platform/Examples/site_finder/input_skipref.yaml -> build/lib/pele_platform/Examples/site_finder 2021-03-19T17:12:26,267 creating build/lib/pele_platform/Examples/tutorials 2021-03-19T17:12:26,268 creating build/lib/pele_platform/Examples/tutorials/gpcr 2021-03-19T17:12:26,272 copying pele_platform/Examples/tutorials/gpcr/complex.pdb -> build/lib/pele_platform/Examples/tutorials/gpcr 2021-03-19T17:12:26,317 copying pele_platform/Examples/tutorials/gpcr/input.yaml -> build/lib/pele_platform/Examples/tutorials/gpcr 2021-03-19T17:12:26,324 creating build/lib/pele_platform/Examples/tutorials/induced_fit 2021-03-19T17:12:26,328 copying pele_platform/Examples/tutorials/induced_fit/docking.pdb -> build/lib/pele_platform/Examples/tutorials/induced_fit 2021-03-19T17:12:26,397 copying pele_platform/Examples/tutorials/induced_fit/input.yaml -> build/lib/pele_platform/Examples/tutorials/induced_fit 2021-03-19T17:12:26,404 creating build/lib/pele_platform/Examples/tutorials/ppi 2021-03-19T17:12:26,407 copying pele_platform/Examples/tutorials/ppi/4yy6_ligand.pdb -> build/lib/pele_platform/Examples/tutorials/ppi 2021-03-19T17:12:26,416 copying pele_platform/Examples/tutorials/ppi/4yy6_prep.pdb -> build/lib/pele_platform/Examples/tutorials/ppi 2021-03-19T17:12:26,442 copying pele_platform/Examples/tutorials/ppi/input.yaml -> build/lib/pele_platform/Examples/tutorials/ppi 2021-03-19T17:12:26,447 creating build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,450 copying pele_platform/Examples/water/complex_induced.pdb -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,471 copying pele_platform/Examples/water/complex_ref_LESSH2O.pdb -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,518 copying pele_platform/Examples/water/input_all.yaml -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,526 copying pele_platform/Examples/water/input_bs.yaml -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,533 copying pele_platform/Examples/water/input_bs_defaults.yaml -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,538 copying pele_platform/Examples/water/input_induced.yaml -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,544 copying pele_platform/Examples/water/input_lig.yaml -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,549 copying pele_platform/Examples/water/input_lig_defaults.yaml -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,556 copying pele_platform/Examples/water/input_nwaters.yaml -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,564 copying pele_platform/Examples/water/input_previous_water.yaml -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,571 copying pele_platform/Examples/water/water_processed.pdb -> build/lib/pele_platform/Examples/water 2021-03-19T17:12:26,620 creating build/lib/pele_platform/Templates 2021-03-19T17:12:26,623 copying pele_platform/Templates/pele_template.conf -> build/lib/pele_platform/Templates 2021-03-19T17:12:26,632 copying pele_platform/Templates/solventParamsHCTOBC.txt -> build/lib/pele_platform/Templates 2021-03-19T17:12:26,646 copying pele_platform/Templates/template_adaptive.conf -> build/lib/pele_platform/Templates 2021-03-19T17:12:26,700 UPDATING build/lib/pele_platform/_version.py 2021-03-19T17:12:26,702 set build/lib/pele_platform/_version.py to '1.6.0b1' 2021-03-19T17:12:26,709 installing to build/bdist.linux-armv7l/wheel 2021-03-19T17:12:26,710 running install 2021-03-19T17:12:26,712 running install_lib 2021-03-19T17:12:26,720 creating build/bdist.linux-armv7l 2021-03-19T17:12:26,721 creating build/bdist.linux-armv7l/wheel 2021-03-19T17:12:26,725 creating build/bdist.linux-armv7l/wheel/pele_platform 2021-03-19T17:12:26,728 creating build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-03-19T17:12:26,731 copying build/lib/pele_platform/PPI/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-03-19T17:12:26,736 copying build/lib/pele_platform/PPI/simulation_launcher.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-03-19T17:12:26,741 copying build/lib/pele_platform/PPI/preparation.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-03-19T17:12:26,747 copying build/lib/pele_platform/PPI/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-03-19T17:12:26,753 creating build/bdist.linux-armv7l/wheel/pele_platform/Templates 2021-03-19T17:12:26,756 copying build/lib/pele_platform/Templates/pele_template.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Templates 2021-03-19T17:12:26,761 copying build/lib/pele_platform/Templates/solventParamsHCTOBC.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Templates 2021-03-19T17:12:26,772 copying build/lib/pele_platform/Templates/template_adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Templates 2021-03-19T17:12:26,776 copying build/lib/pele_platform/main.py -> build/bdist.linux-armv7l/wheel/pele_platform 2021-03-19T17:12:26,783 creating build/bdist.linux-armv7l/wheel/pele_platform/Errors 2021-03-19T17:12:26,786 copying build/lib/pele_platform/Errors/custom_errors.py -> build/bdist.linux-armv7l/wheel/pele_platform/Errors 2021-03-19T17:12:26,792 copying build/lib/pele_platform/Errors/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Errors 2021-03-19T17:12:26,798 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities 2021-03-19T17:12:26,803 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:26,806 copying build/lib/pele_platform/Utilities/Helpers/map_atoms.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:26,813 copying build/lib/pele_platform/Utilities/Helpers/plop_launcher.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:26,820 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2021-03-19T17:12:26,822 copying build/lib/pele_platform/Utilities/Helpers/constraints/smiles_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2021-03-19T17:12:26,827 copying build/lib/pele_platform/Utilities/Helpers/constraints/alpha_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2021-03-19T17:12:26,833 copying build/lib/pele_platform/Utilities/Helpers/constraints/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2021-03-19T17:12:26,836 copying build/lib/pele_platform/Utilities/Helpers/bestStructs.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:26,843 copying build/lib/pele_platform/Utilities/Helpers/interaction_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:26,849 copying build/lib/pele_platform/Utilities/Helpers/yaml_parser.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:26,856 copying build/lib/pele_platform/Utilities/Helpers/center_of_mass.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:26,862 copying build/lib/pele_platform/Utilities/Helpers/randomize.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:26,870 copying build/lib/pele_platform/Utilities/Helpers/missing_residues.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:26,876 copying build/lib/pele_platform/Utilities/Helpers/water.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,011 copying build/lib/pele_platform/Utilities/Helpers/template_builder.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,017 copying build/lib/pele_platform/Utilities/Helpers/launcher.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,024 copying build/lib/pele_platform/Utilities/Helpers/solventOBCParamsGenerator.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,030 copying build/lib/pele_platform/Utilities/Helpers/system_prep.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,035 copying build/lib/pele_platform/Utilities/Helpers/calculatePCA4PELE.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,042 copying build/lib/pele_platform/Utilities/Helpers/conda_deployment.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,049 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2021-03-19T17:12:27,051 copying build/lib/pele_platform/Utilities/Helpers/Metals/metal_polarisation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2021-03-19T17:12:27,059 copying build/lib/pele_platform/Utilities/Helpers/Metals/metal_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2021-03-19T17:12:27,066 copying build/lib/pele_platform/Utilities/Helpers/Metals/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2021-03-19T17:12:27,071 copying build/lib/pele_platform/Utilities/Helpers/protein_wizard.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,077 copying build/lib/pele_platform/Utilities/Helpers/helpers.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,084 copying build/lib/pele_platform/Utilities/Helpers/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,090 copying build/lib/pele_platform/Utilities/Helpers/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-03-19T17:12:27,098 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters 2021-03-19T17:12:27,103 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams 2021-03-19T17:12:27,108 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-03-19T17:12:27,110 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI/ppi.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-03-19T17:12:27,115 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-03-19T17:12:27,120 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-03-19T17:12:27,122 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams/inout_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-03-19T17:12:27,127 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-03-19T17:12:27,133 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-03-19T17:12:27,136 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams/glide_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-03-19T17:12:27,142 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-03-19T17:12:27,149 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-03-19T17:12:27,151 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams/msm_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-03-19T17:12:27,156 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-03-19T17:12:27,159 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/simulation_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams 2021-03-19T17:12:27,167 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-03-19T17:12:27,170 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA/pca.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-03-19T17:12:27,176 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-03-19T17:12:27,183 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-03-19T17:12:27,186 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams/bias_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-03-19T17:12:27,192 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-03-19T17:12:27,199 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2021-03-19T17:12:27,202 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 2021-03-19T17:12:27,209 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2021-03-19T17:12:27,213 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams 2021-03-19T17:12:27,218 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationFolders 2021-03-19T17:12:27,220 copying build/lib/pele_platform/Utilities/Parameters/SimulationFolders/simulation_folders.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationFolders 2021-03-19T17:12:27,225 copying build/lib/pele_platform/Utilities/Parameters/SimulationFolders/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationFolders 2021-03-19T17:12:27,228 copying build/lib/pele_platform/Utilities/Parameters/parameters.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters 2021-03-19T17:12:27,236 copying build/lib/pele_platform/Utilities/Parameters/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters 2021-03-19T17:12:27,241 copying build/lib/pele_platform/Utilities/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities 2021-03-19T17:12:27,248 creating build/bdist.linux-armv7l/wheel/pele_platform/out_in 2021-03-19T17:12:27,251 copying build/lib/pele_platform/out_in/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/out_in 2021-03-19T17:12:27,257 copying build/lib/pele_platform/out_in/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/out_in 2021-03-19T17:12:27,263 creating build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-03-19T17:12:27,266 copying build/lib/pele_platform/analysis/clustering.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-03-19T17:12:27,274 copying build/lib/pele_platform/analysis/interactive_plot.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-03-19T17:12:27,283 copying build/lib/pele_platform/analysis/plot.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-03-19T17:12:27,290 copying build/lib/pele_platform/analysis/pdf_report.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-03-19T17:12:27,296 copying build/lib/pele_platform/analysis/analysis.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-03-19T17:12:27,305 copying build/lib/pele_platform/analysis/to_mae.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-03-19T17:12:27,311 copying build/lib/pele_platform/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-03-19T17:12:27,317 copying build/lib/pele_platform/analysis/data.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-03-19T17:12:27,328 creating build/bdist.linux-armv7l/wheel/pele_platform/constants 2021-03-19T17:12:27,330 copying build/lib/pele_platform/constants/constants.py -> build/bdist.linux-armv7l/wheel/pele_platform/constants 2021-03-19T17:12:27,337 copying build/lib/pele_platform/constants/pele_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/constants 2021-03-19T17:12:27,345 copying build/lib/pele_platform/constants/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/constants 2021-03-19T17:12:27,351 creating build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-03-19T17:12:27,354 copying build/lib/pele_platform/Adaptive/pca.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-03-19T17:12:27,360 copying build/lib/pele_platform/Adaptive/ligand_parametrization.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-03-19T17:12:27,366 copying build/lib/pele_platform/Adaptive/metrics.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-03-19T17:12:27,372 copying build/lib/pele_platform/Adaptive/box.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-03-19T17:12:27,378 copying build/lib/pele_platform/Adaptive/solvent.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-03-19T17:12:27,383 copying build/lib/pele_platform/Adaptive/interaction_restrictions.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-03-19T17:12:27,389 copying build/lib/pele_platform/Adaptive/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-03-19T17:12:27,394 copying build/lib/pele_platform/Adaptive/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-03-19T17:12:27,405 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples 2021-03-19T17:12:27,409 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-03-19T17:12:27,412 copying build/lib/pele_platform/Examples/PPI/1f47_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-03-19T17:12:27,436 copying build/lib/pele_platform/Examples/PPI/input_folder.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-03-19T17:12:27,440 copying build/lib/pele_platform/Examples/PPI/1tnf_ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-03-19T17:12:27,446 copying build/lib/pele_platform/Examples/PPI/1f47_ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-03-19T17:12:27,451 copying build/lib/pele_platform/Examples/PPI/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-03-19T17:12:27,456 copying build/lib/pele_platform/Examples/PPI/input_skipref.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-03-19T17:12:27,462 copying build/lib/pele_platform/Examples/PPI/1tnf_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-03-19T17:12:27,525 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/rescoring 2021-03-19T17:12:27,528 copying build/lib/pele_platform/Examples/rescoring/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/rescoring 2021-03-19T17:12:27,535 copying build/lib/pele_platform/Examples/rescoring/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/rescoring 2021-03-19T17:12:27,542 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/box 2021-03-19T17:12:27,544 copying build/lib/pele_platform/Examples/box/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/box 2021-03-19T17:12:27,552 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2021-03-19T17:12:27,555 copying build/lib/pele_platform/Examples/interaction_restrictions/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2021-03-19T17:12:27,620 copying build/lib/pele_platform/Examples/interaction_restrictions/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2021-03-19T17:12:27,626 copying build/lib/pele_platform/Examples/interaction_restrictions/input_error_2.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2021-03-19T17:12:27,633 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions/out 2021-03-19T17:12:27,636 copying build/lib/pele_platform/Examples/interaction_restrictions/out/expected_metrics.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions/out 2021-03-19T17:12:27,642 copying build/lib/pele_platform/Examples/interaction_restrictions/out/expected_conditions.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions/out 2021-03-19T17:12:27,648 copying build/lib/pele_platform/Examples/interaction_restrictions/input_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2021-03-19T17:12:27,657 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,660 copying build/lib/pele_platform/Examples/constraints/input_square_planar_polarisation.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,666 copying build/lib/pele_platform/Examples/constraints/input_constrain_smarts.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,672 copying build/lib/pele_platform/Examples/constraints/input_k.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,678 copying build/lib/pele_platform/Examples/constraints/input_all_metal_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,683 copying build/lib/pele_platform/Examples/constraints/4zu9_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,790 copying build/lib/pele_platform/Examples/constraints/input_ignore.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,795 copying build/lib/pele_platform/Examples/constraints/input_ca_noppp.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,799 copying build/lib/pele_platform/Examples/constraints/input_ca_ppp.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,805 copying build/lib/pele_platform/Examples/constraints/input_smiles_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,810 copying build/lib/pele_platform/Examples/constraints/pass_input_permissive_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,816 copying build/lib/pele_platform/Examples/constraints/input_square_planar.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,822 copying build/lib/pele_platform/Examples/constraints/4l3a_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,877 copying build/lib/pele_platform/Examples/constraints/input_external_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,883 copying build/lib/pele_platform/Examples/constraints/input_no_metal_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,888 copying build/lib/pele_platform/Examples/constraints/input_constrain_smiles.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,894 copying build/lib/pele_platform/Examples/constraints/input_tetrahedral.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,900 copying build/lib/pele_platform/Examples/constraints/input_permissive_exception.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,904 copying build/lib/pele_platform/Examples/constraints/fail_input_permissive_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,909 copying build/lib/pele_platform/Examples/constraints/4qnr_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,959 copying build/lib/pele_platform/Examples/constraints/4w4o_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,992 copying build/lib/pele_platform/Examples/constraints/input_metals.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:27,996 copying build/lib/pele_platform/Examples/constraints/complex_smiles_error.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:28,036 copying build/lib/pele_platform/Examples/constraints/1zop.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:28,066 copying build/lib/pele_platform/Examples/constraints/4w5i_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:28,099 copying build/lib/pele_platform/Examples/constraints/ca_constraints.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-03-19T17:12:28,165 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-03-19T17:12:28,167 copying build/lib/pele_platform/Examples/Msm/AS4_INIT.mae -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-03-19T17:12:28,176 copying build/lib/pele_platform/Examples/Msm/PR_1A28_xray_-_minimized.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-03-19T17:12:28,215 copying build/lib/pele_platform/Examples/Msm/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-03-19T17:12:28,221 copying build/lib/pele_platform/Examples/Msm/PR_AS4.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-03-19T17:12:28,261 copying build/lib/pele_platform/Examples/Msm/PR_1A28_xray_-_minimized_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-03-19T17:12:28,299 copying build/lib/pele_platform/Examples/Msm/PR_1A28_protein.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-03-19T17:12:28,338 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit_soft 2021-03-19T17:12:28,340 copying build/lib/pele_platform/Examples/exit_soft/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit_soft 2021-03-19T17:12:28,347 copying build/lib/pele_platform/Examples/exit_soft/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit_soft 2021-03-19T17:12:28,354 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,357 copying build/lib/pele_platform/Examples/water/input_previous_water.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,363 copying build/lib/pele_platform/Examples/water/input_lig_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,369 copying build/lib/pele_platform/Examples/water/input_induced.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,375 copying build/lib/pele_platform/Examples/water/complex_induced.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,393 copying build/lib/pele_platform/Examples/water/input_lig.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,397 copying build/lib/pele_platform/Examples/water/input_bs.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,402 copying build/lib/pele_platform/Examples/water/input_nwaters.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,406 copying build/lib/pele_platform/Examples/water/water_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,454 copying build/lib/pele_platform/Examples/water/complex_ref_LESSH2O.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,500 copying build/lib/pele_platform/Examples/water/input_bs_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,505 copying build/lib/pele_platform/Examples/water/input_all.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-03-19T17:12:28,510 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/bias 2021-03-19T17:12:28,513 copying build/lib/pele_platform/Examples/bias/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/bias 2021-03-19T17:12:28,519 copying build/lib/pele_platform/Examples/bias/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/bias 2021-03-19T17:12:28,559 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2021-03-19T17:12:28,562 copying build/lib/pele_platform/Examples/global/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2021-03-19T17:12:28,568 copying build/lib/pele_platform/Examples/global/input_inputs.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2021-03-19T17:12:28,574 copying build/lib/pele_platform/Examples/global/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2021-03-19T17:12:28,580 copying build/lib/pele_platform/Examples/global/input_inputs_asterisc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2021-03-19T17:12:28,587 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2021-03-19T17:12:28,589 copying build/lib/pele_platform/Examples/inputs/mn4.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2021-03-19T17:12:28,596 copying build/lib/pele_platform/Examples/inputs/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2021-03-19T17:12:28,601 copying build/lib/pele_platform/Examples/inputs/nord3.sge -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2021-03-19T17:12:28,609 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit 2021-03-19T17:12:28,611 copying build/lib/pele_platform/Examples/exit/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit 2021-03-19T17:12:28,617 copying build/lib/pele_platform/Examples/exit/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit 2021-03-19T17:12:28,624 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-03-19T17:12:28,627 copying build/lib/pele_platform/Examples/induced_fit/input_fast.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-03-19T17:12:28,633 copying build/lib/pele_platform/Examples/induced_fit/input_mae.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-03-19T17:12:28,638 copying build/lib/pele_platform/Examples/induced_fit/input_exhaustive.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-03-19T17:12:28,644 copying build/lib/pele_platform/Examples/induced_fit/input_fast_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-03-19T17:12:28,649 copying build/lib/pele_platform/Examples/induced_fit/input_exhaustive_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-03-19T17:12:28,656 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-03-19T17:12:28,659 copying build/lib/pele_platform/Examples/out_in/1_3ZON_complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-03-19T17:12:28,699 copying build/lib/pele_platform/Examples/out_in/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-03-19T17:12:28,705 copying build/lib/pele_platform/Examples/out_in/input_flag_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-03-19T17:12:28,711 copying build/lib/pele_platform/Examples/out_in/input_default.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-03-19T17:12:28,718 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2021-03-19T17:12:28,720 copying build/lib/pele_platform/Examples/analysis/input_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2021-03-19T17:12:28,726 copying build/lib/pele_platform/Examples/analysis/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2021-03-19T17:12:28,732 copying build/lib/pele_platform/Examples/analysis/input_flags0.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2021-03-19T17:12:28,737 copying build/lib/pele_platform/Examples/analysis/input_xtc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2021-03-19T17:12:28,745 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:28,749 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc 2021-03-19T17:12:28,754 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2021-03-19T17:12:28,756 copying build/lib/pele_platform/Examples/analysis/data/xtc/0/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2021-03-19T17:12:28,761 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 2021-03-19T17:12:28,775 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 2021-03-19T17:12:28,781 copying build/lib/pele_platform/Examples/analysis/data/xtc/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2021-03-19T17:12:28,788 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/topologies 2021-03-19T17:12:28,791 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 2021-03-19T17:12:28,807 copying build/lib/pele_platform/Examples/analysis/data/xtc/summary.csv -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc 2021-03-19T17:12:28,813 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output 2021-03-19T17:12:28,817 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/synchronization 2021-03-19T17:12:28,820 copying build/lib/pele_platform/Examples/analysis/data/output/synchronization/syncFile.lock -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/synchronization 2021-03-19T17:12:28,828 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0 2021-03-19T17:12:28,830 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 2021-03-19T17:12:28,870 copying build/lib/pele_platform/Examples/analysis/data/output/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0 2021-03-19T17:12:28,878 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0/clustering 2021-03-19T17:12:28,880 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 2021-03-19T17:12:28,921 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 2021-03-19T17:12:28,927 copying build/lib/pele_platform/Examples/analysis/data/output/0/topologyMapping.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0 2021-03-19T17:12:28,933 copying build/lib/pele_platform/Examples/analysis/data/output/originalControlFile.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output 2021-03-19T17:12:28,941 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/topologies 2021-03-19T17:12:28,944 copying build/lib/pele_platform/Examples/analysis/data/output/topologies/topologies.pkl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/topologies 2021-03-19T17:12:28,980 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 2021-03-19T17:12:29,021 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2021-03-19T17:12:29,024 copying build/lib/pele_platform/Examples/analysis/data/inputs/input1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2021-03-19T17:12:29,063 copying build/lib/pele_platform/Examples/analysis/data/inputs/input3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2021-03-19T17:12:29,101 copying build/lib/pele_platform/Examples/analysis/data/inputs/input2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2021-03-19T17:12:29,141 copying build/lib/pele_platform/Examples/analysis/data/adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:29,147 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results 2021-03-19T17:12:29,150 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/clusters 2021-03-19T17:12:29,152 copying build/lib/pele_platform/Examples/analysis/data/results/clusters/clusters_Binding Energy_boxplot.png -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/clusters 2021-03-19T17:12:29,161 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/BestStructs 2021-03-19T17:12:29,163 copying build/lib/pele_platform/Examples/analysis/data/results/BestStructs/epoch0_trajectory_2.1_BindingEnergy1.84474.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/BestStructs 2021-03-19T17:12:29,181 copying build/lib/pele_platform/Examples/analysis/data/results/BestStructs/epoch0_trajectory_1.0_BindingEnergy1.26468.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/BestStructs 2021-03-19T17:12:29,197 copying build/lib/pele_platform/Examples/analysis/data/results/BestStructs/epoch0_trajectory_2.0_BindingEnergy0.644256.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/BestStructs 2021-03-19T17:12:29,215 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/Plots 2021-03-19T17:12:29,218 copying build/lib/pele_platform/Examples/analysis/data/results/Plots/currentEnergy_Binding_Energy_sasaLig_plot.png -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/Plots 2021-03-19T17:12:29,227 copying build/lib/pele_platform/Examples/analysis/data/results/Plots/Binding_Energy.1_Binding_Energy_plot.png -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/Plots 2021-03-19T17:12:29,235 copying build/lib/pele_platform/Examples/analysis/data/results/Plots/currentEnergy_Binding_Energy_Binding_Energy.1_plot.png -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/Plots 2021-03-19T17:12:29,243 copying build/lib/pele_platform/Examples/analysis/data/results/Plots/sasaLig_Binding_Energy_plot.png -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/results/Plots 2021-03-19T17:12:29,250 copying build/lib/pele_platform/Examples/analysis/data/input_mae.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:29,254 copying build/lib/pele_platform/Examples/analysis/data/input_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:29,258 copying build/lib/pele_platform/Examples/analysis/data/strz -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:29,262 copying build/lib/pele_platform/Examples/analysis/data/pele.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:29,268 copying build/lib/pele_platform/Examples/analysis/data/STR.rot.assign -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:29,273 copying build/lib/pele_platform/Examples/analysis/data/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:29,279 copying build/lib/pele_platform/Examples/analysis/data/input_flags0.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:29,284 copying build/lib/pele_platform/Examples/analysis/data/MG.rot.assign -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:29,289 copying build/lib/pele_platform/Examples/analysis/data/mgz -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-03-19T17:12:29,296 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-03-19T17:12:29,298 copying build/lib/pele_platform/Examples/pca/3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-03-19T17:12:29,342 copying build/lib/pele_platform/Examples/pca/2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-03-19T17:12:29,383 copying build/lib/pele_platform/Examples/pca/input_str.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-03-19T17:12:29,388 copying build/lib/pele_platform/Examples/pca/1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-03-19T17:12:29,429 copying build/lib/pele_platform/Examples/pca/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-03-19T17:12:29,436 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/restart 2021-03-19T17:12:29,439 copying build/lib/pele_platform/Examples/restart/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/restart 2021-03-19T17:12:29,447 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials 2021-03-19T17:12:29,452 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/induced_fit 2021-03-19T17:12:29,455 copying build/lib/pele_platform/Examples/tutorials/induced_fit/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/induced_fit 2021-03-19T17:12:29,461 copying build/lib/pele_platform/Examples/tutorials/induced_fit/docking.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/induced_fit 2021-03-19T17:12:29,528 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2021-03-19T17:12:29,530 copying build/lib/pele_platform/Examples/tutorials/ppi/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2021-03-19T17:12:29,537 copying build/lib/pele_platform/Examples/tutorials/ppi/4yy6_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2021-03-19T17:12:29,561 copying build/lib/pele_platform/Examples/tutorials/ppi/4yy6_ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2021-03-19T17:12:29,568 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/gpcr 2021-03-19T17:12:29,570 copying build/lib/pele_platform/Examples/tutorials/gpcr/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/gpcr 2021-03-19T17:12:29,617 copying build/lib/pele_platform/Examples/tutorials/gpcr/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/gpcr 2021-03-19T17:12:29,624 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-03-19T17:12:29,627 copying build/lib/pele_platform/Examples/Adaptive/pele_file_4Adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-03-19T17:12:29,635 copying build/lib/pele_platform/Examples/Adaptive/adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-03-19T17:12:29,641 copying build/lib/pele_platform/Examples/Adaptive/strz -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-03-19T17:12:29,651 copying build/lib/pele_platform/Examples/Adaptive/STR.rot.assign -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-03-19T17:12:29,656 copying build/lib/pele_platform/Examples/Adaptive/test.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-03-19T17:12:29,661 copying build/lib/pele_platform/Examples/test.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples 2021-03-19T17:12:29,667 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/flags 2021-03-19T17:12:29,669 copying build/lib/pele_platform/Examples/flags/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/flags 2021-03-19T17:12:29,676 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,681 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_test_lib 2021-03-19T17:12:29,683 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 2021-03-19T17:12:29,690 copying build/lib/pele_platform/Examples/frag/input_ai.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,696 copying build/lib/pele_platform/Examples/frag/sequential.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,703 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data 2021-03-19T17:12:29,708 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_mol1C3-H2C1-H1 2021-03-19T17:12:29,713 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_mol1C3-H2C1-H1/top_result 2021-03-19T17:12:29,716 copying build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_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_mol1C3-H2C1-H1/top_result 2021-03-19T17:12:29,763 copying build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_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_mol1C3-H2C1-H1/top_result 2021-03-19T17:12:29,810 copying build/lib/pele_platform/Examples/frag/input_lib_sdf.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,814 copying build/lib/pele_platform/Examples/frag/input_core_sdf.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,820 copying build/lib/pele_platform/Examples/frag/flags.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,826 copying build/lib/pele_platform/Examples/frag/core.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,831 copying build/lib/pele_platform/Examples/frag/input_sim.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,837 copying build/lib/pele_platform/Examples/frag/input_core.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,842 copying build/lib/pele_platform/Examples/frag/input_symmetry.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,846 copying build/lib/pele_platform/Examples/frag/input_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,850 copying build/lib/pele_platform/Examples/frag/amino.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,855 copying build/lib/pele_platform/Examples/frag/1w7h_preparation_structure_2w_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,903 copying build/lib/pele_platform/Examples/frag/ligands.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,910 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2021-03-19T17:12:29,913 copying build/lib/pele_platform/Examples/frag/checker/4RFM_proc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2021-03-19T17:12:29,920 copying build/lib/pele_platform/Examples/frag/checker/receptor.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2021-03-19T17:12:29,950 copying build/lib/pele_platform/Examples/frag/checker/4RFM_series.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2021-03-19T17:12:29,955 copying build/lib/pele_platform/Examples/frag/input_point_analysis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:29,961 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/pdb_test_lib 2021-03-19T17:12:29,964 copying build/lib/pele_platform/Examples/frag/pdb_test_lib/mol2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/pdb_test_lib 2021-03-19T17:12:29,971 copying build/lib/pele_platform/Examples/frag/pdb_test_lib/mol1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/pdb_test_lib 2021-03-19T17:12:29,978 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:29,981 copying build/lib/pele_platform/Examples/frag/sdf_joiner/4RFM_proc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,033 copying build/lib/pele_platform/Examples/frag/sdf_joiner/core2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,074 copying build/lib/pele_platform/Examples/frag/sdf_joiner/13_serie.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,086 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag3.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,092 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,101 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,106 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag2.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,112 copying build/lib/pele_platform/Examples/frag/sdf_joiner/glide-dockSARS_core.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,190 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag2.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,200 copying build/lib/pele_platform/Examples/frag/sdf_joiner/4RFM_core_sc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,248 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag4.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,254 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag5.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,260 copying build/lib/pele_platform/Examples/frag/sdf_joiner/core3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,277 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag3.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,287 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag31.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,298 copying build/lib/pele_platform/Examples/frag/sdf_joiner/4RFM_series.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-03-19T17:12:30,306 copying build/lib/pele_platform/Examples/frag/1w7h_preparation_structure_2w.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:30,359 copying build/lib/pele_platform/Examples/frag/input_lib_pdb.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-03-19T17:12:30,367 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,369 copying build/lib/pele_platform/Examples/checker/input_rotamer.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,376 copying build/lib/pele_platform/Examples/checker/mapping_complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,442 copying build/lib/pele_platform/Examples/checker/input_atom_string.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,447 copying build/lib/pele_platform/Examples/checker/input_map_atom_str.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,452 copying build/lib/pele_platform/Examples/checker/complex_unk.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,518 copying build/lib/pele_platform/Examples/checker/ligand2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,524 copying build/lib/pele_platform/Examples/checker/input_map_atom_num.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,530 copying build/lib/pele_platform/Examples/checker/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,578 copying build/lib/pele_platform/Examples/checker/input_tab.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,583 copying build/lib/pele_platform/Examples/checker/input_template.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,589 copying build/lib/pele_platform/Examples/checker/input_underscore.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,595 copying build/lib/pele_platform/Examples/checker/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,601 copying build/lib/pele_platform/Examples/checker/input_space.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,606 copying build/lib/pele_platform/Examples/checker/input_env.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,611 copying build/lib/pele_platform/Examples/checker/input_pele_exec.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,614 copying build/lib/pele_platform/Examples/checker/complex2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,640 copying build/lib/pele_platform/Examples/checker/input_unk.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-03-19T17:12:30,647 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-03-19T17:12:30,649 copying build/lib/pele_platform/Examples/RNA/5C45_prep_proc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-03-19T17:12:30,693 copying build/lib/pele_platform/Examples/RNA/input_induced.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-03-19T17:12:30,699 copying build/lib/pele_platform/Examples/RNA/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-03-19T17:12:30,705 copying build/lib/pele_platform/Examples/RNA/2l94.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-03-19T17:12:30,712 copying build/lib/pele_platform/Examples/RNA/5C45_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-03-19T17:12:30,758 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-03-19T17:12:30,762 copying build/lib/pele_platform/Examples/preparation/complex_2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-03-19T17:12:30,826 copying build/lib/pele_platform/Examples/preparation/6qmk_correct.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-03-19T17:12:30,875 copying build/lib/pele_platform/Examples/preparation/6qmk_repeated.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-03-19T17:12:30,931 copying build/lib/pele_platform/Examples/preparation/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-03-19T17:12:30,968 copying build/lib/pele_platform/Examples/preparation/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-03-19T17:12:30,972 copying build/lib/pele_platform/Examples/preparation/input_space.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-03-19T17:12:30,978 copying build/lib/pele_platform/Examples/preparation/input_nonstandard.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-03-19T17:12:30,986 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering 2021-03-19T17:12:30,991 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-03-19T17:12:30,994 copying build/lib/pele_platform/Examples/clustering/0/report_3 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-03-19T17:12:31,001 copying build/lib/pele_platform/Examples/clustering/0/trajectory_4.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-03-19T17:12:31,072 copying build/lib/pele_platform/Examples/clustering/0/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-03-19T17:12:31,078 copying build/lib/pele_platform/Examples/clustering/0/report_4 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-03-19T17:12:31,084 copying build/lib/pele_platform/Examples/clustering/0/trajectory_2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-03-19T17:12:31,122 copying build/lib/pele_platform/Examples/clustering/0/trajectory_1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-03-19T17:12:31,190 copying build/lib/pele_platform/Examples/clustering/0/trajectory_3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-03-19T17:12:31,261 copying build/lib/pele_platform/Examples/clustering/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-03-19T17:12:31,268 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0/clustering 2021-03-19T17:12:31,271 copying build/lib/pele_platform/Examples/clustering/0/clustering/object.pkl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0/clustering 2021-03-19T17:12:31,500 copying build/lib/pele_platform/Examples/clustering/0/clustering/summary.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0/clustering 2021-03-19T17:12:31,507 copying build/lib/pele_platform/Examples/clustering/0/topologyMapping.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-03-19T17:12:31,511 copying build/lib/pele_platform/Examples/clustering/summary.csv -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering 2021-03-19T17:12:31,517 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-03-19T17:12:31,518 copying build/lib/pele_platform/Examples/site_finder/input_folder.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-03-19T17:12:31,523 copying build/lib/pele_platform/Examples/site_finder/input_restart.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-03-19T17:12:31,528 copying build/lib/pele_platform/Examples/site_finder/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-03-19T17:12:31,574 copying build/lib/pele_platform/Examples/site_finder/input_global_xtc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-03-19T17:12:31,579 copying build/lib/pele_platform/Examples/site_finder/input_skipref.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-03-19T17:12:31,585 copying build/lib/pele_platform/Examples/site_finder/input_global.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-03-19T17:12:31,591 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2021-03-19T17:12:31,600 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2021-03-19T17:12:31,603 copying build/lib/pele_platform/Examples/enzyme_engineering/pdb_files/T454E.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2021-03-19T17:12:31,665 copying build/lib/pele_platform/Examples/enzyme_engineering/pdb_files/T454D.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2021-03-19T17:12:31,728 copying build/lib/pele_platform/Examples/enzyme_engineering/pdb_files/T454A.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2021-03-19T17:12:31,790 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart 2021-03-19T17:12:31,796 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2021-03-19T17:12:31,801 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal 2021-03-19T17:12:31,805 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates 2021-03-19T17:12:31,809 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005 2021-03-19T17:12:31,814 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms 2021-03-19T17:12:31,818 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 2021-03-19T17:12:31,826 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs 2021-03-19T17:12:31,829 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 2021-03-19T17:12:31,836 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output 2021-03-19T17:12:31,841 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2021-03-19T17:12:31,844 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 2021-03-19T17:12:31,850 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 2021-03-19T17:12:31,965 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 2021-03-19T17:12:32,085 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 2021-03-19T17:12:32,095 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization 2021-03-19T17:12:32,099 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 2021-03-19T17:12:32,108 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2021-03-19T17:12:32,111 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 2021-03-19T17:12:32,226 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 2021-03-19T17:12:32,234 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 2021-03-19T17:12:32,242 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 2021-03-19T17:12:32,357 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0 2021-03-19T17:12:32,361 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering 2021-03-19T17:12:32,364 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 2021-03-19T17:12:32,372 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 2021-03-19T17:12:32,379 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 2021-03-19T17:12:32,387 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 2021-03-19T17:12:32,394 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2021-03-19T17:12:32,397 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 2021-03-19T17:12:32,458 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 2021-03-19T17:12:32,568 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 2021-03-19T17:12:32,631 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 2021-03-19T17:12:32,637 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 2021-03-19T17:12:32,644 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 2021-03-19T17:12:32,655 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2021-03-19T17:12:32,659 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 2021-03-19T17:12:32,719 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 2021-03-19T17:12:32,726 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 2021-03-19T17:12:32,789 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2021-03-19T17:12:32,793 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 2021-03-19T17:12:32,855 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 2021-03-19T17:12:32,919 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 2021-03-19T17:12:32,983 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 2021-03-19T17:12:33,049 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 2021-03-19T17:12:33,055 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 2021-03-19T17:12:33,119 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 2021-03-19T17:12:33,127 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2021-03-19T17:12:33,130 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 2021-03-19T17:12:33,138 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 2021-03-19T17:12:33,144 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 2021-03-19T17:12:33,153 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2021-03-19T17:12:33,156 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 2021-03-19T17:12:33,330 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 2021-03-19T17:12:33,393 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 2021-03-19T17:12:33,455 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 2021-03-19T17:12:33,461 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 2021-03-19T17:12:33,467 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 2021-03-19T17:12:33,473 copying build/lib/pele_platform/Examples/enzyme_engineering/restart_saturated_mutagenesis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2021-03-19T17:12:33,478 copying build/lib/pele_platform/Examples/enzyme_engineering/saturated_mutagenesis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2021-03-19T17:12:33,486 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/production 2021-03-19T17:12:33,488 copying build/lib/pele_platform/Examples/production/input_mae.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/production 2021-03-19T17:12:33,493 copying build/lib/pele_platform/Examples/production/input.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/production 2021-03-19T17:12:33,499 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-03-19T17:12:33,501 copying build/lib/pele_platform/Examples/gpcr/input_defaults2.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-03-19T17:12:33,505 copying build/lib/pele_platform/Examples/gpcr/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-03-19T17:12:33,510 copying build/lib/pele_platform/Examples/gpcr/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-03-19T17:12:33,554 copying build/lib/pele_platform/Examples/gpcr/complex_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-03-19T17:12:33,597 copying build/lib/pele_platform/Examples/gpcr/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-03-19T17:12:33,602 copying build/lib/pele_platform/Examples/gpcr/input_atom_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-03-19T17:12:33,617 creating build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-03-19T17:12:33,620 copying build/lib/pele_platform/Checker/python_version.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-03-19T17:12:33,626 copying build/lib/pele_platform/Checker/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-03-19T17:12:33,632 copying build/lib/pele_platform/Checker/executable.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-03-19T17:12:33,637 copying build/lib/pele_platform/Checker/environment_variables.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-03-19T17:12:33,643 copying build/lib/pele_platform/Checker/valid_flags.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-03-19T17:12:33,650 copying build/lib/pele_platform/Checker/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-03-19T17:12:33,656 creating build/bdist.linux-armv7l/wheel/pele_platform/RNA 2021-03-19T17:12:33,659 copying build/lib/pele_platform/RNA/prep.py -> build/bdist.linux-armv7l/wheel/pele_platform/RNA 2021-03-19T17:12:33,665 copying build/lib/pele_platform/RNA/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/RNA 2021-03-19T17:12:33,671 creating build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-03-19T17:12:33,674 copying build/lib/pele_platform/Frag/libraries.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-03-19T17:12:33,681 copying build/lib/pele_platform/Frag/generative_model.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-03-19T17:12:33,687 copying build/lib/pele_platform/Frag/analysis.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-03-19T17:12:33,693 copying build/lib/pele_platform/Frag/checker.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-03-19T17:12:33,699 copying build/lib/pele_platform/Frag/fragments.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-03-19T17:12:33,705 copying build/lib/pele_platform/Frag/atoms.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-03-19T17:12:33,712 creating build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-03-19T17:12:33,715 copying build/lib/pele_platform/Frag/parameters/optional.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-03-19T17:12:33,720 copying build/lib/pele_platform/Frag/parameters/files.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-03-19T17:12:33,725 copying build/lib/pele_platform/Frag/parameters/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-03-19T17:12:33,729 copying build/lib/pele_platform/Frag/parameters/metrics.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-03-19T17:12:33,734 copying build/lib/pele_platform/Frag/parameters/water.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-03-19T17:12:33,738 copying build/lib/pele_platform/Frag/parameters/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-03-19T17:12:33,744 copying build/lib/pele_platform/Frag/parameters/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-03-19T17:12:33,750 copying build/lib/pele_platform/Frag/helpers.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-03-19T17:12:33,756 copying build/lib/pele_platform/Frag/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-03-19T17:12:33,761 copying build/lib/pele_platform/Frag/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-03-19T17:12:33,770 creating build/bdist.linux-armv7l/wheel/pele_platform/site_finder 2021-03-19T17:12:33,773 copying build/lib/pele_platform/site_finder/cluster.py -> build/bdist.linux-armv7l/wheel/pele_platform/site_finder 2021-03-19T17:12:33,780 copying build/lib/pele_platform/site_finder/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/site_finder 2021-03-19T17:12:33,786 copying build/lib/pele_platform/site_finder/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/site_finder 2021-03-19T17:12:33,793 creating build/bdist.linux-armv7l/wheel/pele_platform/enzyme_engineering 2021-03-19T17:12:33,795 copying build/lib/pele_platform/enzyme_engineering/saturated_mutagenesis.py -> build/bdist.linux-armv7l/wheel/pele_platform/enzyme_engineering 2021-03-19T17:12:33,802 copying build/lib/pele_platform/enzyme_engineering/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/enzyme_engineering 2021-03-19T17:12:33,807 copying build/lib/pele_platform/_version.py -> build/bdist.linux-armv7l/wheel/pele_platform 2021-03-19T17:12:33,813 creating build/bdist.linux-armv7l/wheel/pele_platform/features 2021-03-19T17:12:33,815 copying build/lib/pele_platform/features/adaptive.py -> build/bdist.linux-armv7l/wheel/pele_platform/features 2021-03-19T17:12:33,821 copying build/lib/pele_platform/features/frag.py -> build/bdist.linux-armv7l/wheel/pele_platform/features 2021-03-19T17:12:33,827 copying build/lib/pele_platform/features/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/features 2021-03-19T17:12:33,834 creating build/bdist.linux-armv7l/wheel/pele_platform/gpcr 2021-03-19T17:12:33,836 copying build/lib/pele_platform/gpcr/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/gpcr 2021-03-19T17:12:33,843 copying build/lib/pele_platform/gpcr/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/gpcr 2021-03-19T17:12:33,848 copying build/lib/pele_platform/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform 2021-03-19T17:12:33,853 running install_egg_info 2021-03-19T17:12:33,873 Copying pele_platform.egg-info to build/bdist.linux-armv7l/wheel/pele_platform-1.6.0b1-py3.5.egg-info 2021-03-19T17:12:33,903 running install_scripts 2021-03-19T17:12:34,152 creating build/bdist.linux-armv7l/wheel/pele_platform-1.6.0b1.dist-info/WHEEL 2021-03-19T17:12:49,407 Building wheel for pele-platform (setup.py): finished with status 'done' 2021-03-19T17:12:49,588 Created wheel for pele-platform: filename=pele_platform-1.6.0b1-py3-none-any.whl size=10369832 sha256=d11c7ac7f6e793af3a339a75fe273ad0a8257511394b6e6949f7f8ac3638c822 2021-03-19T17:12:49,589 Stored in directory: /tmp/pip-ephem-wheel-cache-ny6zxp9c/wheels/e3/ea/b0/2d8fafa1c0b67f2726e7d234545ab188af49b0af84a96b875f 2021-03-19T17:12:49,651 Successfully built pele-platform 2021-03-19T17:12:51,446 Removed build tracker: '/tmp/pip-req-tracker-bezuzveo'