2021-07-14T15:44:46,024 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 Please upgrade your Python as Python 3.5 is no longer maintained.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. 2021-07-14T15:44:46,625 Created temporary directory: /tmp/pip-ephem-wheel-cache-ai8xuh7r 2021-07-14T15:44:46,629 Created temporary directory: /tmp/pip-req-tracker-g5s86_lb 2021-07-14T15:44:46,629 Initialized build tracking at /tmp/pip-req-tracker-g5s86_lb 2021-07-14T15:44:46,630 Created build tracker: /tmp/pip-req-tracker-g5s86_lb 2021-07-14T15:44:46,630 Entered build tracker: /tmp/pip-req-tracker-g5s86_lb 2021-07-14T15:44:46,631 Created temporary directory: /tmp/pip-wheel-kur70afe 2021-07-14T15:44:46,690 1 location(s) to search for versions of pele-platform: 2021-07-14T15:44:46,690 * https://pypi.org/simple/pele-platform/ 2021-07-14T15:44:46,691 Fetching project page and analyzing links: https://pypi.org/simple/pele-platform/ 2021-07-14T15:44:46,693 Getting page https://pypi.org/simple/pele-platform/ 2021-07-14T15:44:46,697 Found index url https://pypi.org/simple 2021-07-14T15:44:47,023 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 2021-07-14T15:44:47,024 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 2021-07-14T15:44:47,025 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 2021-07-14T15:44:47,025 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 2021-07-14T15:44:47,026 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 2021-07-14T15:44:47,027 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 2021-07-14T15:44:47,028 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 2021-07-14T15:44:47,029 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 2021-07-14T15:44:47,029 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 2021-07-14T15:44:47,030 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 2021-07-14T15:44:47,031 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 2021-07-14T15:44:47,032 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 2021-07-14T15:44:47,032 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 2021-07-14T15:44:47,033 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 2021-07-14T15:44:47,034 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 2021-07-14T15:44:47,035 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 2021-07-14T15:44:47,036 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 2021-07-14T15:44:47,036 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 2021-07-14T15:44:47,037 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 2021-07-14T15:44:47,038 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 2021-07-14T15:44:47,039 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 2021-07-14T15:44:47,040 Found link https://files.pythonhosted.org/packages/c0/d6/f49f102325943cd3a82086e4740dfabd416c278d21ef9f3097fc1bb0ba7a/pele_platform-1.6.0b2.tar.gz#sha256=6bf2be383e50f6654f49f87e44dfc548f2aa1f5f002b25089ae2089ab0a92654 (from https://pypi.org/simple/pele-platform/), version: 1.6.0b2 2021-07-14T15:44:47,040 Found link https://files.pythonhosted.org/packages/f7/16/8db67212a622716e71ea8a9664e4da6207ae136369f2d1b3b802ca39baee/pele_platform-1.6.0b3.tar.gz#sha256=916a0f278c53e5eec786008a498654481c2e76b90b4385e75398872fd28b1f6e (from https://pypi.org/simple/pele-platform/), version: 1.6.0b3 2021-07-14T15:44:47,041 Found link https://files.pythonhosted.org/packages/f3/46/ecebcaed96148f710c2aa716f1a4862033073dfe8c1da1c7283d32b766b4/pele_platform-1.6.0b4.tar.gz#sha256=1e6cdaab94470fa0de99010c2e51ed94e1634b14c9a53206b6f33e838616b361 (from https://pypi.org/simple/pele-platform/), version: 1.6.0b4 2021-07-14T15:44:47,042 Found link https://files.pythonhosted.org/packages/7a/03/3f391e98e553a1cea233c87fe3d33171be5b3851fbf37869ccdfebca58c4/pele_platform-1.6.0b5.tar.gz#sha256=9e98fe723a6e9b2d67e7c95441f23bc98f550d4d824a47614981b39643e4781d (from https://pypi.org/simple/pele-platform/), version: 1.6.0b5 2021-07-14T15:44:47,043 Found link https://files.pythonhosted.org/packages/e1/28/b31c1b1b3daf0bc65f6c3d09cad23ec355868feb94787f0adc4407c60364/pele_platform-1.6.0b6.tar.gz#sha256=63327ad61bcbfa4e69c138e5ec38621194b929c5e271b21d01c359961fd8e805 (from https://pypi.org/simple/pele-platform/), version: 1.6.0b6 2021-07-14T15:44:47,044 Found link https://files.pythonhosted.org/packages/3c/b6/8ebb9f0d293a32db481b1bd6e620d5b04e73b2bf516bcedbd22033f16016/pele_platform-1.6.0b7.tar.gz#sha256=e5e3a57d5eb74bf3f664714017549f773f71f325da381666f8f872c38c12d06e (from https://pypi.org/simple/pele-platform/), version: 1.6.0b7 2021-07-14T15:44:47,044 Found link https://files.pythonhosted.org/packages/bf/83/ff52f07ec4bc23a134b0fcb5ea792d20ee925939a73bc0a2cc867e47378c/pele_platform-1.6.0rc1.tar.gz#sha256=34a396a464e091c199e16e4d7fdce545eb8e1acde49096d61f5c5f04a220b1d7 (from https://pypi.org/simple/pele-platform/), version: 1.6.0rc1 2021-07-14T15:44:47,081 Given no hashes to check 1 links for project 'pele-platform': discarding no candidates 2021-07-14T15:44:47,110 Collecting pele-platform==1.6.0rc1 2021-07-14T15:44:47,113 Created temporary directory: /tmp/pip-unpack-yxiht_zd 2021-07-14T15:44:49,173 Downloading pele_platform-1.6.0rc1.tar.gz (11.1 MB) 2021-07-14T15:44:57,018 Added pele-platform==1.6.0rc1 from https://files.pythonhosted.org/packages/bf/83/ff52f07ec4bc23a134b0fcb5ea792d20ee925939a73bc0a2cc867e47378c/pele_platform-1.6.0rc1.tar.gz#sha256=34a396a464e091c199e16e4d7fdce545eb8e1acde49096d61f5c5f04a220b1d7 to build tracker '/tmp/pip-req-tracker-g5s86_lb' 2021-07-14T15:44:57,020 Running setup.py (path:/tmp/pip-wheel-kur70afe/pele-platform_af77d133fd71479680d58f7c217ebcaa/setup.py) egg_info for package pele-platform 2021-07-14T15:44:57,021 Created temporary directory: /tmp/pip-pip-egg-info-qyma10w9 2021-07-14T15:44:57,022 Running command python setup.py egg_info 2021-07-14T15:44:59,491 running egg_info 2021-07-14T15:44:59,496 creating /tmp/pip-pip-egg-info-qyma10w9/pele_platform.egg-info 2021-07-14T15:44:59,498 writing dependency_links to /tmp/pip-pip-egg-info-qyma10w9/pele_platform.egg-info/dependency_links.txt 2021-07-14T15:44:59,501 writing top-level names to /tmp/pip-pip-egg-info-qyma10w9/pele_platform.egg-info/top_level.txt 2021-07-14T15:44:59,503 writing requirements to /tmp/pip-pip-egg-info-qyma10w9/pele_platform.egg-info/requires.txt 2021-07-14T15:44:59,505 writing /tmp/pip-pip-egg-info-qyma10w9/pele_platform.egg-info/PKG-INFO 2021-07-14T15:44:59,510 writing manifest file '/tmp/pip-pip-egg-info-qyma10w9/pele_platform.egg-info/SOURCES.txt' 2021-07-14T15:44:59,554 reading manifest file '/tmp/pip-pip-egg-info-qyma10w9/pele_platform.egg-info/SOURCES.txt' 2021-07-14T15:44:59,557 reading manifest template 'MANIFEST.in' 2021-07-14T15:44:59,560 warning: no files found matching 'pele_platform/Utilities/PlopRotTemp/param/*' 2021-07-14T15:44:59,561 warning: no files found matching 'pele_platform/AdaptivePELE/atomset/*' 2021-07-14T15:44:59,561 warning: no files found matching 'pele_platform/AdaptivePELE/freeEnergies/*' 2021-07-14T15:44:59,562 warning: no files found matching '*' under directory 'pele_platform/Utilities/PPP/Data/' 2021-07-14T15:44:59,854 warning: no files found matching '*' under directory 'tests/data' 2021-07-14T15:44:59,894 writing manifest file '/tmp/pip-pip-egg-info-qyma10w9/pele_platform.egg-info/SOURCES.txt' 2021-07-14T15:45:00,021 Source in /tmp/pip-wheel-kur70afe/pele-platform_af77d133fd71479680d58f7c217ebcaa has version 1.6.0rc1, which satisfies requirement pele-platform==1.6.0rc1 from https://files.pythonhosted.org/packages/bf/83/ff52f07ec4bc23a134b0fcb5ea792d20ee925939a73bc0a2cc867e47378c/pele_platform-1.6.0rc1.tar.gz#sha256=34a396a464e091c199e16e4d7fdce545eb8e1acde49096d61f5c5f04a220b1d7 2021-07-14T15:45:00,023 Removed pele-platform==1.6.0rc1 from https://files.pythonhosted.org/packages/bf/83/ff52f07ec4bc23a134b0fcb5ea792d20ee925939a73bc0a2cc867e47378c/pele_platform-1.6.0rc1.tar.gz#sha256=34a396a464e091c199e16e4d7fdce545eb8e1acde49096d61f5c5f04a220b1d7 from build tracker '/tmp/pip-req-tracker-g5s86_lb' 2021-07-14T15:45:00,030 Created temporary directory: /tmp/pip-unpack-9okuhqgo 2021-07-14T15:45:00,031 Building wheels for collected packages: pele-platform 2021-07-14T15:45:00,037 Created temporary directory: /tmp/pip-wheel-mlxs7fn5 2021-07-14T15:45:00,038 Building wheel for pele-platform (setup.py): started 2021-07-14T15:45:00,039 Destination directory: /tmp/pip-wheel-mlxs7fn5 2021-07-14T15:45:00,039 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-kur70afe/pele-platform_af77d133fd71479680d58f7c217ebcaa/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-kur70afe/pele-platform_af77d133fd71479680d58f7c217ebcaa/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-mlxs7fn5 2021-07-14T15:45:02,652 running bdist_wheel 2021-07-14T15:45:02,662 running build 2021-07-14T15:45:02,663 running build_py 2021-07-14T15:45:02,678 creating build 2021-07-14T15:45:02,679 creating build/lib 2021-07-14T15:45:02,680 creating build/lib/pele_platform 2021-07-14T15:45:02,682 copying pele_platform/__init__.py -> build/lib/pele_platform 2021-07-14T15:45:02,685 copying pele_platform/main.py -> build/lib/pele_platform 2021-07-14T15:45:02,688 copying pele_platform/_version.py -> build/lib/pele_platform 2021-07-14T15:45:02,691 creating build/lib/pele_platform/out_in 2021-07-14T15:45:02,692 copying pele_platform/out_in/__init__.py -> build/lib/pele_platform/out_in 2021-07-14T15:45:02,695 copying pele_platform/out_in/main.py -> build/lib/pele_platform/out_in 2021-07-14T15:45:02,699 creating build/lib/pele_platform/enzyme_engineering 2021-07-14T15:45:02,704 copying pele_platform/enzyme_engineering/__init__.py -> build/lib/pele_platform/enzyme_engineering 2021-07-14T15:45:02,707 copying pele_platform/enzyme_engineering/saturated_mutagenesis.py -> build/lib/pele_platform/enzyme_engineering 2021-07-14T15:45:02,712 creating build/lib/pele_platform/Frag 2021-07-14T15:45:02,713 copying pele_platform/Frag/__init__.py -> build/lib/pele_platform/Frag 2021-07-14T15:45:02,716 copying pele_platform/Frag/checker.py -> build/lib/pele_platform/Frag 2021-07-14T15:45:02,719 copying pele_platform/Frag/analysis.py -> build/lib/pele_platform/Frag 2021-07-14T15:45:02,723 copying pele_platform/Frag/generative_model.py -> build/lib/pele_platform/Frag 2021-07-14T15:45:02,726 copying pele_platform/Frag/fragments.py -> build/lib/pele_platform/Frag 2021-07-14T15:45:02,729 copying pele_platform/Frag/helpers.py -> build/lib/pele_platform/Frag 2021-07-14T15:45:02,733 copying pele_platform/Frag/simulation.py -> build/lib/pele_platform/Frag 2021-07-14T15:45:02,737 copying pele_platform/Frag/libraries.py -> build/lib/pele_platform/Frag 2021-07-14T15:45:02,741 copying pele_platform/Frag/atoms.py -> build/lib/pele_platform/Frag 2021-07-14T15:45:02,745 creating build/lib/pele_platform/analysis 2021-07-14T15:45:02,746 copying pele_platform/analysis/data.py -> build/lib/pele_platform/analysis 2021-07-14T15:45:02,752 copying pele_platform/analysis/__init__.py -> build/lib/pele_platform/analysis 2021-07-14T15:45:02,755 copying pele_platform/analysis/plot.py -> build/lib/pele_platform/analysis 2021-07-14T15:45:02,760 copying pele_platform/analysis/pdf_report.py -> build/lib/pele_platform/analysis 2021-07-14T15:45:02,766 copying pele_platform/analysis/analysis.py -> build/lib/pele_platform/analysis 2021-07-14T15:45:02,776 copying pele_platform/analysis/interactive_plot.py -> build/lib/pele_platform/analysis 2021-07-14T15:45:02,783 copying pele_platform/analysis/clustering.py -> build/lib/pele_platform/analysis 2021-07-14T15:45:02,788 creating build/lib/pele_platform/Checker 2021-07-14T15:45:02,790 copying pele_platform/Checker/valid_flags.py -> build/lib/pele_platform/Checker 2021-07-14T15:45:02,795 copying pele_platform/Checker/__init__.py -> build/lib/pele_platform/Checker 2021-07-14T15:45:02,801 copying pele_platform/Checker/environment_variables.py -> build/lib/pele_platform/Checker 2021-07-14T15:45:02,805 copying pele_platform/Checker/executable.py -> build/lib/pele_platform/Checker 2021-07-14T15:45:02,808 copying pele_platform/Checker/python_version.py -> build/lib/pele_platform/Checker 2021-07-14T15:45:02,812 copying pele_platform/Checker/pdb_checker.py -> build/lib/pele_platform/Checker 2021-07-14T15:45:02,815 copying pele_platform/Checker/main.py -> build/lib/pele_platform/Checker 2021-07-14T15:45:02,820 creating build/lib/pele_platform/site_finder 2021-07-14T15:45:02,822 copying pele_platform/site_finder/__init__.py -> build/lib/pele_platform/site_finder 2021-07-14T15:45:02,826 copying pele_platform/site_finder/main.py -> build/lib/pele_platform/site_finder 2021-07-14T15:45:02,831 creating build/lib/pele_platform/PPI 2021-07-14T15:45:02,833 copying pele_platform/PPI/preparation.py -> build/lib/pele_platform/PPI 2021-07-14T15:45:02,837 copying pele_platform/PPI/__init__.py -> build/lib/pele_platform/PPI 2021-07-14T15:45:02,841 copying pele_platform/PPI/cluster.py -> build/lib/pele_platform/PPI 2021-07-14T15:45:02,844 copying pele_platform/PPI/main.py -> build/lib/pele_platform/PPI 2021-07-14T15:45:02,849 copying pele_platform/PPI/simulation_launcher.py -> build/lib/pele_platform/PPI 2021-07-14T15:45:02,853 creating build/lib/pele_platform/constants 2021-07-14T15:45:02,855 copying pele_platform/constants/__init__.py -> build/lib/pele_platform/constants 2021-07-14T15:45:02,859 copying pele_platform/constants/pele_params.py -> build/lib/pele_platform/constants 2021-07-14T15:45:02,863 copying pele_platform/constants/constants.py -> build/lib/pele_platform/constants 2021-07-14T15:45:02,869 creating build/lib/pele_platform/covalent_docking 2021-07-14T15:45:02,871 copying pele_platform/covalent_docking/__init__.py -> build/lib/pele_platform/covalent_docking 2021-07-14T15:45:02,874 copying pele_platform/covalent_docking/main.py -> build/lib/pele_platform/covalent_docking 2021-07-14T15:45:02,879 creating build/lib/pele_platform/gpcr 2021-07-14T15:45:02,881 copying pele_platform/gpcr/__init__.py -> build/lib/pele_platform/gpcr 2021-07-14T15:45:02,885 copying pele_platform/gpcr/main.py -> build/lib/pele_platform/gpcr 2021-07-14T15:45:02,890 creating build/lib/pele_platform/Errors 2021-07-14T15:45:02,892 copying pele_platform/Errors/__init__.py -> build/lib/pele_platform/Errors 2021-07-14T15:45:02,895 copying pele_platform/Errors/custom_errors.py -> build/lib/pele_platform/Errors 2021-07-14T15:45:02,900 creating build/lib/pele_platform/Adaptive 2021-07-14T15:45:02,902 copying pele_platform/Adaptive/__init__.py -> build/lib/pele_platform/Adaptive 2021-07-14T15:45:02,906 copying pele_platform/Adaptive/pca.py -> build/lib/pele_platform/Adaptive 2021-07-14T15:45:02,910 copying pele_platform/Adaptive/parametrizer.py -> build/lib/pele_platform/Adaptive 2021-07-14T15:45:02,915 copying pele_platform/Adaptive/plop_solvent.py -> build/lib/pele_platform/Adaptive 2021-07-14T15:45:02,918 copying pele_platform/Adaptive/plop_ligand_parametrization.py -> build/lib/pele_platform/Adaptive 2021-07-14T15:45:02,921 copying pele_platform/Adaptive/interaction_restrictions.py -> build/lib/pele_platform/Adaptive 2021-07-14T15:45:02,926 copying pele_platform/Adaptive/box.py -> build/lib/pele_platform/Adaptive 2021-07-14T15:45:02,931 copying pele_platform/Adaptive/metrics.py -> build/lib/pele_platform/Adaptive 2021-07-14T15:45:02,935 copying pele_platform/Adaptive/simulation.py -> build/lib/pele_platform/Adaptive 2021-07-14T15:45:02,943 creating build/lib/pele_platform/features 2021-07-14T15:45:02,944 copying pele_platform/features/__init__.py -> build/lib/pele_platform/features 2021-07-14T15:45:02,947 copying pele_platform/features/frag.py -> build/lib/pele_platform/features 2021-07-14T15:45:02,950 copying pele_platform/features/adaptive.py -> build/lib/pele_platform/features 2021-07-14T15:45:02,954 creating build/lib/pele_platform/RNA 2021-07-14T15:45:02,955 copying pele_platform/RNA/__init__.py -> build/lib/pele_platform/RNA 2021-07-14T15:45:02,958 copying pele_platform/RNA/prep.py -> build/lib/pele_platform/RNA 2021-07-14T15:45:02,962 creating build/lib/pele_platform/Utilities 2021-07-14T15:45:02,963 copying pele_platform/Utilities/__init__.py -> build/lib/pele_platform/Utilities 2021-07-14T15:45:02,967 creating build/lib/pele_platform/Frag/parameters 2021-07-14T15:45:02,968 copying pele_platform/Frag/parameters/__init__.py -> build/lib/pele_platform/Frag/parameters 2021-07-14T15:45:02,971 copying pele_platform/Frag/parameters/files.py -> build/lib/pele_platform/Frag/parameters 2021-07-14T15:45:02,974 copying pele_platform/Frag/parameters/water.py -> build/lib/pele_platform/Frag/parameters 2021-07-14T15:45:02,977 copying pele_platform/Frag/parameters/optional.py -> build/lib/pele_platform/Frag/parameters 2021-07-14T15:45:02,980 copying pele_platform/Frag/parameters/metrics.py -> build/lib/pele_platform/Frag/parameters 2021-07-14T15:45:02,983 copying pele_platform/Frag/parameters/simulation.py -> build/lib/pele_platform/Frag/parameters 2021-07-14T15:45:02,987 creating build/lib/pele_platform/Utilities/Parameters 2021-07-14T15:45:02,988 copying pele_platform/Utilities/Parameters/__init__.py -> build/lib/pele_platform/Utilities/Parameters 2021-07-14T15:45:02,991 copying pele_platform/Utilities/Parameters/parameters.py -> build/lib/pele_platform/Utilities/Parameters 2021-07-14T15:45:02,997 creating build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:02,999 copying pele_platform/Utilities/Helpers/__init__.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,002 copying pele_platform/Utilities/Helpers/launcher.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,005 copying pele_platform/Utilities/Helpers/system_prep.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,009 copying pele_platform/Utilities/Helpers/map_atoms.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,012 copying pele_platform/Utilities/Helpers/solventOBCParamsGenerator.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,016 copying pele_platform/Utilities/Helpers/conda_deployment.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,019 copying pele_platform/Utilities/Helpers/water.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,023 copying pele_platform/Utilities/Helpers/template_builder.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,026 copying pele_platform/Utilities/Helpers/missing_residues.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,029 copying pele_platform/Utilities/Helpers/ligand_conformations.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,032 copying pele_platform/Utilities/Helpers/helpers.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,036 copying pele_platform/Utilities/Helpers/plop_launcher.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,039 copying pele_platform/Utilities/Helpers/bestStructs.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,043 copying pele_platform/Utilities/Helpers/randomize.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,048 copying pele_platform/Utilities/Helpers/interaction_constraints.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,053 copying pele_platform/Utilities/Helpers/yaml_parser.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,059 copying pele_platform/Utilities/Helpers/calculatePCA4PELE.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,066 copying pele_platform/Utilities/Helpers/simulation.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,070 copying pele_platform/Utilities/Helpers/protein_wizard.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,073 copying pele_platform/Utilities/Helpers/center_of_mass.py -> build/lib/pele_platform/Utilities/Helpers 2021-07-14T15:45:03,077 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams 2021-07-14T15:45:03,078 copying pele_platform/Utilities/Parameters/SimulationParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams 2021-07-14T15:45:03,081 copying pele_platform/Utilities/Parameters/SimulationParams/simulation_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams 2021-07-14T15:45:03,086 creating build/lib/pele_platform/Utilities/Parameters/SimulationFolders 2021-07-14T15:45:03,087 copying pele_platform/Utilities/Parameters/SimulationFolders/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationFolders 2021-07-14T15:45:03,090 copying pele_platform/Utilities/Parameters/SimulationFolders/simulation_folders.py -> build/lib/pele_platform/Utilities/Parameters/SimulationFolders 2021-07-14T15:45:03,093 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-07-14T15:45:03,094 copying pele_platform/Utilities/Parameters/SimulationParams/InOutParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-07-14T15:45:03,097 copying pele_platform/Utilities/Parameters/SimulationParams/InOutParams/inout_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-07-14T15:45:03,101 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-07-14T15:45:03,102 copying pele_platform/Utilities/Parameters/SimulationParams/PCA/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-07-14T15:45:03,105 copying pele_platform/Utilities/Parameters/SimulationParams/PCA/pca.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-07-14T15:45:03,108 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2021-07-14T15:45:03,110 copying pele_platform/Utilities/Parameters/SimulationParams/site_finder/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2021-07-14T15:45:03,112 copying pele_platform/Utilities/Parameters/SimulationParams/site_finder/site_finder.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2021-07-14T15:45:03,116 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-07-14T15:45:03,117 copying pele_platform/Utilities/Parameters/SimulationParams/PPI/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-07-14T15:45:03,120 copying pele_platform/Utilities/Parameters/SimulationParams/PPI/ppi.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-07-14T15:45:03,123 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-07-14T15:45:03,124 copying pele_platform/Utilities/Parameters/SimulationParams/GlideParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-07-14T15:45:03,127 copying pele_platform/Utilities/Parameters/SimulationParams/GlideParams/glide_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-07-14T15:45:03,131 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-07-14T15:45:03,132 copying pele_platform/Utilities/Parameters/SimulationParams/MSMParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-07-14T15:45:03,135 copying pele_platform/Utilities/Parameters/SimulationParams/MSMParams/msm_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-07-14T15:45:03,138 creating build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-07-14T15:45:03,140 copying pele_platform/Utilities/Parameters/SimulationParams/BiasParams/__init__.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-07-14T15:45:03,142 copying pele_platform/Utilities/Parameters/SimulationParams/BiasParams/bias_params.py -> build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-07-14T15:45:03,146 creating build/lib/pele_platform/Utilities/Helpers/constraints 2021-07-14T15:45:03,147 copying pele_platform/Utilities/Helpers/constraints/__init__.py -> build/lib/pele_platform/Utilities/Helpers/constraints 2021-07-14T15:45:03,150 copying pele_platform/Utilities/Helpers/constraints/alpha_constraints.py -> build/lib/pele_platform/Utilities/Helpers/constraints 2021-07-14T15:45:03,154 copying pele_platform/Utilities/Helpers/constraints/smiles_constraints.py -> build/lib/pele_platform/Utilities/Helpers/constraints 2021-07-14T15:45:03,160 creating build/lib/pele_platform/Utilities/Helpers/Metals 2021-07-14T15:45:03,161 copying pele_platform/Utilities/Helpers/Metals/__init__.py -> build/lib/pele_platform/Utilities/Helpers/Metals 2021-07-14T15:45:03,164 copying pele_platform/Utilities/Helpers/Metals/metal_polarisation.py -> build/lib/pele_platform/Utilities/Helpers/Metals 2021-07-14T15:45:03,167 copying pele_platform/Utilities/Helpers/Metals/metal_constraints.py -> build/lib/pele_platform/Utilities/Helpers/Metals 2021-07-14T15:45:03,173 running egg_info 2021-07-14T15:45:03,198 writing dependency_links to pele_platform.egg-info/dependency_links.txt 2021-07-14T15:45:03,201 writing pele_platform.egg-info/PKG-INFO 2021-07-14T15:45:03,205 writing requirements to pele_platform.egg-info/requires.txt 2021-07-14T15:45:03,207 writing top-level names to pele_platform.egg-info/top_level.txt 2021-07-14T15:45:03,244 reading manifest file 'pele_platform.egg-info/SOURCES.txt' 2021-07-14T15:45:03,268 reading manifest template 'MANIFEST.in' 2021-07-14T15:45:03,270 warning: no files found matching 'pele_platform/Utilities/PlopRotTemp/param/*' 2021-07-14T15:45:03,271 warning: no files found matching 'pele_platform/AdaptivePELE/atomset/*' 2021-07-14T15:45:03,271 warning: no files found matching 'pele_platform/AdaptivePELE/freeEnergies/*' 2021-07-14T15:45:03,272 warning: no files found matching '*' under directory 'pele_platform/Utilities/PPP/Data/' 2021-07-14T15:45:03,586 warning: no files found matching '*' under directory 'tests/data' 2021-07-14T15:45:03,646 writing manifest file 'pele_platform.egg-info/SOURCES.txt' 2021-07-14T15:45:03,736 creating build/lib/pele_platform/Examples 2021-07-14T15:45:03,737 copying pele_platform/Examples/test.sl -> build/lib/pele_platform/Examples 2021-07-14T15:45:03,742 creating build/lib/pele_platform/Examples/Adaptive 2021-07-14T15:45:03,743 copying pele_platform/Examples/Adaptive/STR.rot.assign -> build/lib/pele_platform/Examples/Adaptive 2021-07-14T15:45:03,748 copying pele_platform/Examples/Adaptive/adaptive.conf -> build/lib/pele_platform/Examples/Adaptive 2021-07-14T15:45:03,751 copying pele_platform/Examples/Adaptive/pele_file_4Adaptive.conf -> build/lib/pele_platform/Examples/Adaptive 2021-07-14T15:45:03,755 copying pele_platform/Examples/Adaptive/strz -> build/lib/pele_platform/Examples/Adaptive 2021-07-14T15:45:03,761 copying pele_platform/Examples/Adaptive/test.sl -> build/lib/pele_platform/Examples/Adaptive 2021-07-14T15:45:03,765 creating build/lib/pele_platform/Examples/Msm 2021-07-14T15:45:03,767 copying pele_platform/Examples/Msm/AS4_INIT.mae -> build/lib/pele_platform/Examples/Msm 2021-07-14T15:45:03,773 copying pele_platform/Examples/Msm/PR_1A28_protein.pdb -> build/lib/pele_platform/Examples/Msm 2021-07-14T15:45:03,797 copying pele_platform/Examples/Msm/PR_1A28_xray_-_minimized.pdb -> build/lib/pele_platform/Examples/Msm 2021-07-14T15:45:03,817 copying pele_platform/Examples/Msm/PR_1A28_xray_-_minimized_processed.pdb -> build/lib/pele_platform/Examples/Msm 2021-07-14T15:45:03,836 copying pele_platform/Examples/Msm/PR_AS4.pdb -> build/lib/pele_platform/Examples/Msm 2021-07-14T15:45:03,854 copying pele_platform/Examples/Msm/input.yaml -> build/lib/pele_platform/Examples/Msm 2021-07-14T15:45:03,857 creating build/lib/pele_platform/Examples/PPI 2021-07-14T15:45:03,858 copying pele_platform/Examples/PPI/1f47_ligand.pdb -> build/lib/pele_platform/Examples/PPI 2021-07-14T15:45:03,863 copying pele_platform/Examples/PPI/1f47_prep.pdb -> build/lib/pele_platform/Examples/PPI 2021-07-14T15:45:03,874 copying pele_platform/Examples/PPI/1tnf_ligand.pdb -> build/lib/pele_platform/Examples/PPI 2021-07-14T15:45:03,878 copying pele_platform/Examples/PPI/1tnf_prep.pdb -> build/lib/pele_platform/Examples/PPI 2021-07-14T15:45:03,907 copying pele_platform/Examples/PPI/input.yaml -> build/lib/pele_platform/Examples/PPI 2021-07-14T15:45:03,910 copying pele_platform/Examples/PPI/input_folder.yaml -> build/lib/pele_platform/Examples/PPI 2021-07-14T15:45:03,913 copying pele_platform/Examples/PPI/input_skipref.yaml -> build/lib/pele_platform/Examples/PPI 2021-07-14T15:45:03,916 creating build/lib/pele_platform/Examples/RNA 2021-07-14T15:45:03,917 copying pele_platform/Examples/RNA/2l94.yaml -> build/lib/pele_platform/Examples/RNA 2021-07-14T15:45:03,920 copying pele_platform/Examples/RNA/5C45_prep.pdb -> build/lib/pele_platform/Examples/RNA 2021-07-14T15:45:03,941 copying pele_platform/Examples/RNA/5C45_prep_proc.pdb -> build/lib/pele_platform/Examples/RNA 2021-07-14T15:45:03,961 copying pele_platform/Examples/RNA/input.yaml -> build/lib/pele_platform/Examples/RNA 2021-07-14T15:45:03,964 copying pele_platform/Examples/RNA/input_induced.yaml -> build/lib/pele_platform/Examples/RNA 2021-07-14T15:45:03,967 creating build/lib/pele_platform/Examples/analysis 2021-07-14T15:45:03,968 copying pele_platform/Examples/analysis/input.yaml -> build/lib/pele_platform/Examples/analysis 2021-07-14T15:45:03,971 copying pele_platform/Examples/analysis/input_flags.yaml -> build/lib/pele_platform/Examples/analysis 2021-07-14T15:45:03,975 copying pele_platform/Examples/analysis/input_flags0.yaml -> build/lib/pele_platform/Examples/analysis 2021-07-14T15:45:03,978 copying pele_platform/Examples/analysis/input_xtc.yaml -> build/lib/pele_platform/Examples/analysis 2021-07-14T15:45:03,981 creating build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:03,982 copying pele_platform/Examples/analysis/data/MG.rot.assign -> build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:03,985 copying pele_platform/Examples/analysis/data/STR.rot.assign -> build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:03,988 copying pele_platform/Examples/analysis/data/adaptive.conf -> build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:03,991 copying pele_platform/Examples/analysis/data/input.yaml -> build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:03,994 copying pele_platform/Examples/analysis/data/input_flags.yaml -> build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:03,997 copying pele_platform/Examples/analysis/data/input_flags0.yaml -> build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:04,001 copying pele_platform/Examples/analysis/data/input_mae.yaml -> build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:04,004 copying pele_platform/Examples/analysis/data/mgz -> build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:04,006 copying pele_platform/Examples/analysis/data/pele.conf -> build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:04,010 copying pele_platform/Examples/analysis/data/strz -> build/lib/pele_platform/Examples/analysis/data 2021-07-14T15:45:04,013 creating build/lib/pele_platform/Examples/analysis/data/empty_reports_output 2021-07-14T15:45:04,013 creating build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:04,015 copying pele_platform/Examples/analysis/data/empty_reports_output/0/report_1 -> build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:04,018 copying pele_platform/Examples/analysis/data/empty_reports_output/0/report_2 -> build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:04,022 copying pele_platform/Examples/analysis/data/empty_reports_output/0/topologyMapping.txt -> build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:04,025 copying pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_1.pdb -> build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:04,045 copying pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_2.pdb -> build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:04,101 creating build/lib/pele_platform/Examples/analysis/data/inputs 2021-07-14T15:45:04,103 copying pele_platform/Examples/analysis/data/inputs/input1.pdb -> build/lib/pele_platform/Examples/analysis/data/inputs 2021-07-14T15:45:04,125 copying pele_platform/Examples/analysis/data/inputs/input2.pdb -> build/lib/pele_platform/Examples/analysis/data/inputs 2021-07-14T15:45:04,145 copying pele_platform/Examples/analysis/data/inputs/input3.pdb -> build/lib/pele_platform/Examples/analysis/data/inputs 2021-07-14T15:45:04,163 creating build/lib/pele_platform/Examples/analysis/data/output 2021-07-14T15:45:04,165 copying pele_platform/Examples/analysis/data/output/originalControlFile.conf -> build/lib/pele_platform/Examples/analysis/data/output 2021-07-14T15:45:04,168 creating build/lib/pele_platform/Examples/analysis/data/output/0 2021-07-14T15:45:04,170 copying pele_platform/Examples/analysis/data/output/0/report_1 -> build/lib/pele_platform/Examples/analysis/data/output/0 2021-07-14T15:45:04,173 copying pele_platform/Examples/analysis/data/output/0/topologyMapping.txt -> build/lib/pele_platform/Examples/analysis/data/output/0 2021-07-14T15:45:04,176 copying pele_platform/Examples/analysis/data/output/0/trajectory_1.pdb -> build/lib/pele_platform/Examples/analysis/data/output/0 2021-07-14T15:45:04,195 creating build/lib/pele_platform/Examples/analysis/data/output/0/clustering 2021-07-14T15:45:04,196 copying pele_platform/Examples/analysis/data/output/0/clustering/object.pkl -> build/lib/pele_platform/Examples/analysis/data/output/0/clustering 2021-07-14T15:45:04,215 copying pele_platform/Examples/analysis/data/output/0/clustering/summary.txt -> build/lib/pele_platform/Examples/analysis/data/output/0/clustering 2021-07-14T15:45:04,218 creating build/lib/pele_platform/Examples/analysis/data/output/synchronization 2021-07-14T15:45:04,219 copying pele_platform/Examples/analysis/data/output/synchronization/syncFile.lock -> build/lib/pele_platform/Examples/analysis/data/output/synchronization 2021-07-14T15:45:04,222 creating build/lib/pele_platform/Examples/analysis/data/output/topologies 2021-07-14T15:45:04,224 copying pele_platform/Examples/analysis/data/output/topologies/topologies.pkl -> build/lib/pele_platform/Examples/analysis/data/output/topologies 2021-07-14T15:45:04,241 copying pele_platform/Examples/analysis/data/output/topologies/topology_0.pdb -> build/lib/pele_platform/Examples/analysis/data/output/topologies 2021-07-14T15:45:04,259 creating build/lib/pele_platform/Examples/analysis/data/xtc 2021-07-14T15:45:04,261 copying pele_platform/Examples/analysis/data/xtc/summary.csv -> build/lib/pele_platform/Examples/analysis/data/xtc 2021-07-14T15:45:04,264 creating build/lib/pele_platform/Examples/analysis/data/xtc/0 2021-07-14T15:45:04,265 copying pele_platform/Examples/analysis/data/xtc/0/report_1 -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2021-07-14T15:45:04,269 copying pele_platform/Examples/analysis/data/xtc/0/report_2 -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2021-07-14T15:45:04,272 copying pele_platform/Examples/analysis/data/xtc/0/trajectory_1.xtc -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2021-07-14T15:45:04,276 copying pele_platform/Examples/analysis/data/xtc/0/trajectory_2.xtc -> build/lib/pele_platform/Examples/analysis/data/xtc/0 2021-07-14T15:45:04,280 creating build/lib/pele_platform/Examples/analysis/data/xtc/topologies 2021-07-14T15:45:04,281 copying pele_platform/Examples/analysis/data/xtc/topologies/topology_0.pdb -> build/lib/pele_platform/Examples/analysis/data/xtc/topologies 2021-07-14T15:45:04,290 creating build/lib/pele_platform/Examples/bias 2021-07-14T15:45:04,292 copying pele_platform/Examples/bias/complex.pdb -> build/lib/pele_platform/Examples/bias 2021-07-14T15:45:04,310 copying pele_platform/Examples/bias/input_defaults.yaml -> build/lib/pele_platform/Examples/bias 2021-07-14T15:45:04,314 creating build/lib/pele_platform/Examples/box 2021-07-14T15:45:04,316 copying pele_platform/Examples/box/input.yaml -> build/lib/pele_platform/Examples/box 2021-07-14T15:45:04,320 creating build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,322 copying pele_platform/Examples/checker/complex.pdb -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,345 copying pele_platform/Examples/checker/complex2.pdb -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,358 copying pele_platform/Examples/checker/complex_unk.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,390 copying pele_platform/Examples/checker/incompatible_flags.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,394 copying pele_platform/Examples/checker/input.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,399 copying pele_platform/Examples/checker/input_atom_string.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,405 copying pele_platform/Examples/checker/input_env.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,412 copying pele_platform/Examples/checker/input_map_atom_num.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,418 copying pele_platform/Examples/checker/input_map_atom_str.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,422 copying pele_platform/Examples/checker/input_pele_exec.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,425 copying pele_platform/Examples/checker/input_rotamer.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,429 copying pele_platform/Examples/checker/input_space.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,433 copying pele_platform/Examples/checker/input_tab.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,437 copying pele_platform/Examples/checker/input_template.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,441 copying pele_platform/Examples/checker/input_underscore.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,444 copying pele_platform/Examples/checker/input_unk.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,448 copying pele_platform/Examples/checker/ligand2.pdb -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,453 copying pele_platform/Examples/checker/mapping_complex.pdb -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,487 copying pele_platform/Examples/checker/multiple_simulations.yaml -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,492 copying pele_platform/Examples/checker/negative_residues.pdb -> build/lib/pele_platform/Examples/checker 2021-07-14T15:45:04,498 creating build/lib/pele_platform/Examples/clustering 2021-07-14T15:45:04,499 copying pele_platform/Examples/clustering/summary.csv -> build/lib/pele_platform/Examples/clustering 2021-07-14T15:45:04,503 creating build/lib/pele_platform/Examples/clustering/0 2021-07-14T15:45:04,504 copying pele_platform/Examples/clustering/0/report_1 -> build/lib/pele_platform/Examples/clustering/0 2021-07-14T15:45:04,507 copying pele_platform/Examples/clustering/0/report_2 -> build/lib/pele_platform/Examples/clustering/0 2021-07-14T15:45:04,511 copying pele_platform/Examples/clustering/0/report_3 -> build/lib/pele_platform/Examples/clustering/0 2021-07-14T15:45:04,514 copying pele_platform/Examples/clustering/0/report_4 -> build/lib/pele_platform/Examples/clustering/0 2021-07-14T15:45:04,517 copying pele_platform/Examples/clustering/0/topologyMapping.txt -> build/lib/pele_platform/Examples/clustering/0 2021-07-14T15:45:04,520 copying pele_platform/Examples/clustering/0/trajectory_1.pdb -> build/lib/pele_platform/Examples/clustering/0 2021-07-14T15:45:04,552 copying pele_platform/Examples/clustering/0/trajectory_2.pdb -> build/lib/pele_platform/Examples/clustering/0 2021-07-14T15:45:04,570 copying pele_platform/Examples/clustering/0/trajectory_3.pdb -> build/lib/pele_platform/Examples/clustering/0 2021-07-14T15:45:04,604 copying pele_platform/Examples/clustering/0/trajectory_4.pdb -> build/lib/pele_platform/Examples/clustering/0 2021-07-14T15:45:04,636 creating build/lib/pele_platform/Examples/clustering/0/clustering 2021-07-14T15:45:04,638 copying pele_platform/Examples/clustering/0/clustering/object.pkl -> build/lib/pele_platform/Examples/clustering/0/clustering 2021-07-14T15:45:04,743 copying pele_platform/Examples/clustering/0/clustering/summary.txt -> build/lib/pele_platform/Examples/clustering/0/clustering 2021-07-14T15:45:04,746 creating build/lib/pele_platform/Examples/clustering_xtc 2021-07-14T15:45:04,748 copying pele_platform/Examples/clustering_xtc/water_clustering.yaml -> build/lib/pele_platform/Examples/clustering_xtc 2021-07-14T15:45:04,754 creating build/lib/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:04,756 copying pele_platform/Examples/clustering_xtc/0/report_1 -> build/lib/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:04,762 copying pele_platform/Examples/clustering_xtc/0/report_2 -> build/lib/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:04,768 copying pele_platform/Examples/clustering_xtc/0/report_3 -> build/lib/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:04,773 copying pele_platform/Examples/clustering_xtc/0/report_4 -> build/lib/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:04,777 copying pele_platform/Examples/clustering_xtc/0/topology.pdb -> build/lib/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:04,796 copying pele_platform/Examples/clustering_xtc/0/trajectory_1.xtc -> build/lib/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:04,801 copying pele_platform/Examples/clustering_xtc/0/trajectory_2.xtc -> build/lib/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:04,806 copying pele_platform/Examples/clustering_xtc/0/trajectory_3.xtc -> build/lib/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:04,812 copying pele_platform/Examples/clustering_xtc/0/trajectory_4.xtc -> build/lib/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:04,820 creating build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:04,822 copying pele_platform/Examples/constraints/1zop.pdb -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:04,840 copying pele_platform/Examples/constraints/4l3a_prep.pdb -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:04,867 copying pele_platform/Examples/constraints/4qnr_prep.pdb -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:04,895 copying pele_platform/Examples/constraints/4w4o_prep.pdb -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:04,912 copying pele_platform/Examples/constraints/4w5i_prep.pdb -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:04,933 copying pele_platform/Examples/constraints/4zu9_prep.pdb -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:04,989 copying pele_platform/Examples/constraints/ca_constraints.pdb -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,025 copying pele_platform/Examples/constraints/complex_smiles_error.pdb -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,045 copying pele_platform/Examples/constraints/fail_input_permissive_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,049 copying pele_platform/Examples/constraints/input_all_metal_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,053 copying pele_platform/Examples/constraints/input_ca_noppp.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,057 copying pele_platform/Examples/constraints/input_ca_ppp.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,062 copying pele_platform/Examples/constraints/input_constrain_smarts.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,069 copying pele_platform/Examples/constraints/input_constrain_smiles.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,075 copying pele_platform/Examples/constraints/input_external_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,081 copying pele_platform/Examples/constraints/input_ignore.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,085 copying pele_platform/Examples/constraints/input_k.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,089 copying pele_platform/Examples/constraints/input_metals.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,093 copying pele_platform/Examples/constraints/input_no_metal_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,097 copying pele_platform/Examples/constraints/input_permissive_exception.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,101 copying pele_platform/Examples/constraints/input_smiles_error.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,105 copying pele_platform/Examples/constraints/input_square_planar.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,109 copying pele_platform/Examples/constraints/input_square_planar_polarisation.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,113 copying pele_platform/Examples/constraints/input_tetrahedral.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,116 copying pele_platform/Examples/constraints/no_connects.pdb -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,120 copying pele_platform/Examples/constraints/pass_input_permissive_constraints.yaml -> build/lib/pele_platform/Examples/constraints 2021-07-14T15:45:05,124 creating build/lib/pele_platform/Examples/covalent_docking 2021-07-14T15:45:05,126 copying pele_platform/Examples/covalent_docking/5XXD_prepared.pdb -> build/lib/pele_platform/Examples/covalent_docking 2021-07-14T15:45:05,155 copying pele_platform/Examples/covalent_docking/6M06_prepared.pdb -> build/lib/pele_platform/Examples/covalent_docking 2021-07-14T15:45:05,183 copying pele_platform/Examples/covalent_docking/6P0M_prepared.pdb -> build/lib/pele_platform/Examples/covalent_docking 2021-07-14T15:45:05,201 copying pele_platform/Examples/covalent_docking/input1.yaml -> build/lib/pele_platform/Examples/covalent_docking 2021-07-14T15:45:05,207 copying pele_platform/Examples/covalent_docking/input2.yaml -> build/lib/pele_platform/Examples/covalent_docking 2021-07-14T15:45:05,211 copying pele_platform/Examples/covalent_docking/input3.yaml -> build/lib/pele_platform/Examples/covalent_docking 2021-07-14T15:45:05,214 copying pele_platform/Examples/covalent_docking/input_defaults.yaml -> build/lib/pele_platform/Examples/covalent_docking 2021-07-14T15:45:05,217 copying pele_platform/Examples/covalent_docking/input_defaults_refinement.yaml -> build/lib/pele_platform/Examples/covalent_docking 2021-07-14T15:45:05,221 creating build/lib/pele_platform/Examples/enzyme_engineering 2021-07-14T15:45:05,222 copying pele_platform/Examples/enzyme_engineering/restart_saturated_mutagenesis.yaml -> build/lib/pele_platform/Examples/enzyme_engineering 2021-07-14T15:45:05,228 copying pele_platform/Examples/enzyme_engineering/saturated_mutagenesis.yaml -> build/lib/pele_platform/Examples/enzyme_engineering 2021-07-14T15:45:05,233 copying pele_platform/Examples/enzyme_engineering/wrong_cpus.yaml -> build/lib/pele_platform/Examples/enzyme_engineering 2021-07-14T15:45:05,238 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart 2021-07-14T15:45:05,240 copying pele_platform/Examples/enzyme_engineering/directory_to_restart/completed_mutations.log -> build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart 2021-07-14T15:45:05,244 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2021-07-14T15:45:05,246 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 2021-07-14T15:45:05,249 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 2021-07-14T15:45:05,253 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 2021-07-14T15:45:05,257 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 2021-07-14T15:45:05,260 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal 2021-07-14T15:45:05,261 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs 2021-07-14T15:45:05,262 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 2021-07-14T15:45:05,266 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates 2021-07-14T15:45:05,267 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005 2021-07-14T15:45:05,268 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms 2021-07-14T15:45:05,269 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 2021-07-14T15:45:05,273 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2021-07-14T15:45:05,275 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 2021-07-14T15:45:05,304 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 2021-07-14T15:45:05,337 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 2021-07-14T15:45:05,367 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 2021-07-14T15:45:05,396 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 2021-07-14T15:45:05,399 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 2021-07-14T15:45:05,432 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output 2021-07-14T15:45:05,434 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 2021-07-14T15:45:05,437 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0 2021-07-14T15:45:05,439 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 2021-07-14T15:45:05,442 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering 2021-07-14T15:45:05,444 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 2021-07-14T15:45:05,449 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 2021-07-14T15:45:05,454 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2021-07-14T15:45:05,456 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 2021-07-14T15:45:05,462 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 2021-07-14T15:45:05,467 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 2021-07-14T15:45:05,521 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 2021-07-14T15:45:05,579 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2021-07-14T15:45:05,581 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 2021-07-14T15:45:05,584 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 2021-07-14T15:45:05,587 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 2021-07-14T15:45:05,647 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 2021-07-14T15:45:05,703 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization 2021-07-14T15:45:05,706 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 2021-07-14T15:45:05,711 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2021-07-14T15:45:05,713 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 2021-07-14T15:45:05,763 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 2021-07-14T15:45:05,792 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 2021-07-14T15:45:05,821 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2021-07-14T15:45:05,822 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 2021-07-14T15:45:05,827 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 2021-07-14T15:45:05,856 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 2021-07-14T15:45:05,884 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2021-07-14T15:45:05,886 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 2021-07-14T15:45:05,890 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 2021-07-14T15:45:05,893 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 2021-07-14T15:45:05,896 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 2021-07-14T15:45:05,900 creating build/lib/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2021-07-14T15:45:05,901 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 2021-07-14T15:45:05,931 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 2021-07-14T15:45:05,961 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 2021-07-14T15:45:05,965 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 2021-07-14T15:45:05,995 creating build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2021-07-14T15:45:05,996 copying pele_platform/Examples/enzyme_engineering/pdb_files/T454A.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2021-07-14T15:45:06,026 copying pele_platform/Examples/enzyme_engineering/pdb_files/T454D.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2021-07-14T15:45:06,055 copying pele_platform/Examples/enzyme_engineering/pdb_files/T454E.pdb -> build/lib/pele_platform/Examples/enzyme_engineering/pdb_files 2021-07-14T15:45:06,085 creating build/lib/pele_platform/Examples/exit 2021-07-14T15:45:06,087 copying pele_platform/Examples/exit/input.yaml -> build/lib/pele_platform/Examples/exit 2021-07-14T15:45:06,093 copying pele_platform/Examples/exit/input_defaults.yaml -> build/lib/pele_platform/Examples/exit 2021-07-14T15:45:06,099 creating build/lib/pele_platform/Examples/exit_soft 2021-07-14T15:45:06,101 copying pele_platform/Examples/exit_soft/input.yaml -> build/lib/pele_platform/Examples/exit_soft 2021-07-14T15:45:06,105 copying pele_platform/Examples/exit_soft/input_defaults.yaml -> build/lib/pele_platform/Examples/exit_soft 2021-07-14T15:45:06,108 creating build/lib/pele_platform/Examples/flags 2021-07-14T15:45:06,110 copying pele_platform/Examples/flags/input.yaml -> build/lib/pele_platform/Examples/flags 2021-07-14T15:45:06,113 creating build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,115 copying pele_platform/Examples/frag/1dyi_no_waters.pdb -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,127 copying pele_platform/Examples/frag/1dyi_waters.pdb -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,140 copying pele_platform/Examples/frag/1w7h_preparation_structure_2w.pdb -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,164 copying pele_platform/Examples/frag/1w7h_preparation_structure_2w_processed.pdb -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,192 copying pele_platform/Examples/frag/amino.pdb -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,195 copying pele_platform/Examples/frag/core.pdb -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,199 copying pele_platform/Examples/frag/flags.conf -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,202 copying pele_platform/Examples/frag/input_ai.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,205 copying pele_platform/Examples/frag/input_core.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,208 copying pele_platform/Examples/frag/input_core_sdf.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,211 copying pele_platform/Examples/frag/input_flags.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,215 copying pele_platform/Examples/frag/input_frag_waters.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,218 copying pele_platform/Examples/frag/input_fragment_atom.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,221 copying pele_platform/Examples/frag/input_lib_pdb.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,224 copying pele_platform/Examples/frag/input_lib_sdf.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,228 copying pele_platform/Examples/frag/input_point_analysis.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,231 copying pele_platform/Examples/frag/input_sim.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,235 copying pele_platform/Examples/frag/input_sim_xtc.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,239 copying pele_platform/Examples/frag/input_symmetry.yaml -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,243 copying pele_platform/Examples/frag/ligands.sdf -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,246 copying pele_platform/Examples/frag/ligands_water.sdf -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,250 copying pele_platform/Examples/frag/sequential.conf -> build/lib/pele_platform/Examples/frag 2021-07-14T15:45:06,253 creating build/lib/pele_platform/Examples/frag/analysis_data 2021-07-14T15:45:06,254 creating build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_mol1C3-H2C1-H1 2021-07-14T15:45:06,255 creating build/lib/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_mol1C3-H2C1-H1/top_result 2021-07-14T15:45:06,257 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 2021-07-14T15:45:06,281 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 2021-07-14T15:45:06,304 creating build/lib/pele_platform/Examples/frag/checker 2021-07-14T15:45:06,305 copying pele_platform/Examples/frag/checker/4RFM_proc.pdb -> build/lib/pele_platform/Examples/frag/checker 2021-07-14T15:45:06,309 copying pele_platform/Examples/frag/checker/4RFM_series.sdf -> build/lib/pele_platform/Examples/frag/checker 2021-07-14T15:45:06,313 copying pele_platform/Examples/frag/checker/receptor.sdf -> build/lib/pele_platform/Examples/frag/checker 2021-07-14T15:45:06,327 creating build/lib/pele_platform/Examples/frag/pdb_test_lib 2021-07-14T15:45:06,329 copying pele_platform/Examples/frag/pdb_test_lib/mol1.pdb -> build/lib/pele_platform/Examples/frag/pdb_test_lib 2021-07-14T15:45:06,332 copying pele_platform/Examples/frag/pdb_test_lib/mol2.pdb -> build/lib/pele_platform/Examples/frag/pdb_test_lib 2021-07-14T15:45:06,336 creating build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,337 copying pele_platform/Examples/frag/sdf_joiner/13_serie.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,344 copying pele_platform/Examples/frag/sdf_joiner/4RFM_core_sc.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,367 copying pele_platform/Examples/frag/sdf_joiner/4RFM_proc.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,392 copying pele_platform/Examples/frag/sdf_joiner/4RFM_series.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,396 copying pele_platform/Examples/frag/sdf_joiner/core2.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,415 copying pele_platform/Examples/frag/sdf_joiner/core3.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,424 copying pele_platform/Examples/frag/sdf_joiner/frag.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,428 copying pele_platform/Examples/frag/sdf_joiner/frag.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,432 copying pele_platform/Examples/frag/sdf_joiner/frag2.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,437 copying pele_platform/Examples/frag/sdf_joiner/frag2.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,441 copying pele_platform/Examples/frag/sdf_joiner/frag3.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,446 copying pele_platform/Examples/frag/sdf_joiner/frag3.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,449 copying pele_platform/Examples/frag/sdf_joiner/frag31.sdf -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,455 copying pele_platform/Examples/frag/sdf_joiner/frag4.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,458 copying pele_platform/Examples/frag/sdf_joiner/frag5.yml -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,461 copying pele_platform/Examples/frag/sdf_joiner/glide-dockSARS_core.pdb -> build/lib/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:06,497 creating build/lib/pele_platform/Examples/frag/sdf_test_lib 2021-07-14T15:45:06,499 copying pele_platform/Examples/frag/sdf_test_lib/test_library.sdf -> build/lib/pele_platform/Examples/frag/sdf_test_lib 2021-07-14T15:45:06,502 creating build/lib/pele_platform/Examples/global 2021-07-14T15:45:06,503 copying pele_platform/Examples/global/input.yaml -> build/lib/pele_platform/Examples/global 2021-07-14T15:45:06,507 copying pele_platform/Examples/global/input_defaults.yaml -> build/lib/pele_platform/Examples/global 2021-07-14T15:45:06,510 copying pele_platform/Examples/global/input_inputs.yaml -> build/lib/pele_platform/Examples/global 2021-07-14T15:45:06,513 copying pele_platform/Examples/global/input_inputs_asterisc.yaml -> build/lib/pele_platform/Examples/global 2021-07-14T15:45:06,516 creating build/lib/pele_platform/Examples/gpcr 2021-07-14T15:45:06,517 copying pele_platform/Examples/gpcr/complex.pdb -> build/lib/pele_platform/Examples/gpcr 2021-07-14T15:45:06,538 copying pele_platform/Examples/gpcr/complex_processed.pdb -> build/lib/pele_platform/Examples/gpcr 2021-07-14T15:45:06,558 copying pele_platform/Examples/gpcr/input.yaml -> build/lib/pele_platform/Examples/gpcr 2021-07-14T15:45:06,561 copying pele_platform/Examples/gpcr/input_atom_error.yaml -> build/lib/pele_platform/Examples/gpcr 2021-07-14T15:45:06,565 copying pele_platform/Examples/gpcr/input_defaults.yaml -> build/lib/pele_platform/Examples/gpcr 2021-07-14T15:45:06,568 copying pele_platform/Examples/gpcr/input_defaults2.yaml -> build/lib/pele_platform/Examples/gpcr 2021-07-14T15:45:06,571 creating build/lib/pele_platform/Examples/induced_fit 2021-07-14T15:45:06,572 copying pele_platform/Examples/induced_fit/input_exhaustive.yaml -> build/lib/pele_platform/Examples/induced_fit 2021-07-14T15:45:06,576 copying pele_platform/Examples/induced_fit/input_exhaustive_defaults.yaml -> build/lib/pele_platform/Examples/induced_fit 2021-07-14T15:45:06,579 copying pele_platform/Examples/induced_fit/input_fast.yaml -> build/lib/pele_platform/Examples/induced_fit 2021-07-14T15:45:06,582 copying pele_platform/Examples/induced_fit/input_fast_defaults.yaml -> build/lib/pele_platform/Examples/induced_fit 2021-07-14T15:45:06,585 copying pele_platform/Examples/induced_fit/input_mae.yaml -> build/lib/pele_platform/Examples/induced_fit 2021-07-14T15:45:06,588 creating build/lib/pele_platform/Examples/inputs 2021-07-14T15:45:06,590 copying pele_platform/Examples/inputs/input.yaml -> build/lib/pele_platform/Examples/inputs 2021-07-14T15:45:06,593 copying pele_platform/Examples/inputs/mn4.sl -> build/lib/pele_platform/Examples/inputs 2021-07-14T15:45:06,596 copying pele_platform/Examples/inputs/nord3.sge -> build/lib/pele_platform/Examples/inputs 2021-07-14T15:45:06,599 creating build/lib/pele_platform/Examples/interaction_restrictions 2021-07-14T15:45:06,600 copying pele_platform/Examples/interaction_restrictions/complex.pdb -> build/lib/pele_platform/Examples/interaction_restrictions 2021-07-14T15:45:06,631 copying pele_platform/Examples/interaction_restrictions/input.yaml -> build/lib/pele_platform/Examples/interaction_restrictions 2021-07-14T15:45:06,634 copying pele_platform/Examples/interaction_restrictions/input_error.yaml -> build/lib/pele_platform/Examples/interaction_restrictions 2021-07-14T15:45:06,637 copying pele_platform/Examples/interaction_restrictions/input_error_2.yaml -> build/lib/pele_platform/Examples/interaction_restrictions 2021-07-14T15:45:06,641 creating build/lib/pele_platform/Examples/interaction_restrictions/out 2021-07-14T15:45:06,642 copying pele_platform/Examples/interaction_restrictions/out/expected_conditions.txt -> build/lib/pele_platform/Examples/interaction_restrictions/out 2021-07-14T15:45:06,645 copying pele_platform/Examples/interaction_restrictions/out/expected_metrics.txt -> build/lib/pele_platform/Examples/interaction_restrictions/out 2021-07-14T15:45:06,648 creating build/lib/pele_platform/Examples/ligand_conformations 2021-07-14T15:45:06,650 copying pele_platform/Examples/ligand_conformations/1.pdb -> build/lib/pele_platform/Examples/ligand_conformations 2021-07-14T15:45:06,653 copying pele_platform/Examples/ligand_conformations/2.pdb -> build/lib/pele_platform/Examples/ligand_conformations 2021-07-14T15:45:06,657 copying pele_platform/Examples/ligand_conformations/3.pdb -> build/lib/pele_platform/Examples/ligand_conformations 2021-07-14T15:45:06,660 copying pele_platform/Examples/ligand_conformations/input.yaml -> build/lib/pele_platform/Examples/ligand_conformations 2021-07-14T15:45:06,663 creating build/lib/pele_platform/Examples/minimum_steps 2021-07-14T15:45:06,664 copying pele_platform/Examples/minimum_steps/complex.pdb -> build/lib/pele_platform/Examples/minimum_steps 2021-07-14T15:45:06,697 copying pele_platform/Examples/minimum_steps/input.yaml -> build/lib/pele_platform/Examples/minimum_steps 2021-07-14T15:45:06,702 creating build/lib/pele_platform/Examples/out_in 2021-07-14T15:45:06,704 copying pele_platform/Examples/out_in/1_3ZON_complex.pdb -> build/lib/pele_platform/Examples/out_in 2021-07-14T15:45:06,726 copying pele_platform/Examples/out_in/input.yaml -> build/lib/pele_platform/Examples/out_in 2021-07-14T15:45:06,729 copying pele_platform/Examples/out_in/input_box_center.yaml -> build/lib/pele_platform/Examples/out_in 2021-07-14T15:45:06,732 copying pele_platform/Examples/out_in/input_default.yaml -> build/lib/pele_platform/Examples/out_in 2021-07-14T15:45:06,735 copying pele_platform/Examples/out_in/input_flag_error.yaml -> build/lib/pele_platform/Examples/out_in 2021-07-14T15:45:06,738 creating build/lib/pele_platform/Examples/pca 2021-07-14T15:45:06,740 copying pele_platform/Examples/pca/1.pdb -> build/lib/pele_platform/Examples/pca 2021-07-14T15:45:06,760 copying pele_platform/Examples/pca/2.pdb -> build/lib/pele_platform/Examples/pca 2021-07-14T15:45:06,780 copying pele_platform/Examples/pca/3.pdb -> build/lib/pele_platform/Examples/pca 2021-07-14T15:45:06,800 copying pele_platform/Examples/pca/input.yaml -> build/lib/pele_platform/Examples/pca 2021-07-14T15:45:06,803 copying pele_platform/Examples/pca/input_str.yaml -> build/lib/pele_platform/Examples/pca 2021-07-14T15:45:06,806 creating build/lib/pele_platform/Examples/preparation 2021-07-14T15:45:06,808 copying pele_platform/Examples/preparation/6qmk_correct.pdb -> build/lib/pele_platform/Examples/preparation 2021-07-14T15:45:06,831 copying pele_platform/Examples/preparation/6qmk_repeated.pdb -> build/lib/pele_platform/Examples/preparation 2021-07-14T15:45:06,857 copying pele_platform/Examples/preparation/complex.pdb -> build/lib/pele_platform/Examples/preparation 2021-07-14T15:45:06,876 copying pele_platform/Examples/preparation/complex_2.pdb -> build/lib/pele_platform/Examples/preparation 2021-07-14T15:45:06,905 copying pele_platform/Examples/preparation/input.yaml -> build/lib/pele_platform/Examples/preparation 2021-07-14T15:45:06,908 copying pele_platform/Examples/preparation/input_nonstandard.yaml -> build/lib/pele_platform/Examples/preparation 2021-07-14T15:45:06,912 copying pele_platform/Examples/preparation/input_space.yaml -> build/lib/pele_platform/Examples/preparation 2021-07-14T15:45:06,917 copying pele_platform/Examples/preparation/parametrization_flags.yaml -> build/lib/pele_platform/Examples/preparation 2021-07-14T15:45:06,921 creating build/lib/pele_platform/Examples/production 2021-07-14T15:45:06,923 copying pele_platform/Examples/production/input.sl -> build/lib/pele_platform/Examples/production 2021-07-14T15:45:06,926 copying pele_platform/Examples/production/input_mae.yaml -> build/lib/pele_platform/Examples/production 2021-07-14T15:45:06,930 creating build/lib/pele_platform/Examples/rescoring 2021-07-14T15:45:06,931 copying pele_platform/Examples/rescoring/input.yaml -> build/lib/pele_platform/Examples/rescoring 2021-07-14T15:45:06,935 copying pele_platform/Examples/rescoring/input_defaults.yaml -> build/lib/pele_platform/Examples/rescoring 2021-07-14T15:45:06,939 creating build/lib/pele_platform/Examples/restart 2021-07-14T15:45:06,941 copying pele_platform/Examples/restart/restart.yaml -> build/lib/pele_platform/Examples/restart 2021-07-14T15:45:06,945 creating build/lib/pele_platform/Examples/singularity 2021-07-14T15:45:06,946 copying pele_platform/Examples/singularity/input_adaptive.yaml -> build/lib/pele_platform/Examples/singularity 2021-07-14T15:45:06,949 copying pele_platform/Examples/singularity/input_frag.yaml -> build/lib/pele_platform/Examples/singularity 2021-07-14T15:45:06,952 creating build/lib/pele_platform/Examples/site_finder 2021-07-14T15:45:06,954 copying pele_platform/Examples/site_finder/complex.pdb -> build/lib/pele_platform/Examples/site_finder 2021-07-14T15:45:06,976 copying pele_platform/Examples/site_finder/global.yaml -> build/lib/pele_platform/Examples/site_finder 2021-07-14T15:45:06,979 copying pele_platform/Examples/site_finder/input_folder.yaml -> build/lib/pele_platform/Examples/site_finder 2021-07-14T15:45:06,982 copying pele_platform/Examples/site_finder/input_global.yaml -> build/lib/pele_platform/Examples/site_finder 2021-07-14T15:45:06,985 copying pele_platform/Examples/site_finder/input_global_xtc.yaml -> build/lib/pele_platform/Examples/site_finder 2021-07-14T15:45:06,988 copying pele_platform/Examples/site_finder/input_restart.yaml -> build/lib/pele_platform/Examples/site_finder 2021-07-14T15:45:06,991 copying pele_platform/Examples/site_finder/input_skipref.yaml -> build/lib/pele_platform/Examples/site_finder 2021-07-14T15:45:06,994 copying pele_platform/Examples/site_finder/local.yaml -> build/lib/pele_platform/Examples/site_finder 2021-07-14T15:45:06,997 creating build/lib/pele_platform/Examples/tutorials 2021-07-14T15:45:06,998 creating build/lib/pele_platform/Examples/tutorials/gpcr 2021-07-14T15:45:06,1000 copying pele_platform/Examples/tutorials/gpcr/complex.pdb -> build/lib/pele_platform/Examples/tutorials/gpcr 2021-07-14T15:45:07,020 copying pele_platform/Examples/tutorials/gpcr/input.yaml -> build/lib/pele_platform/Examples/tutorials/gpcr 2021-07-14T15:45:07,023 creating build/lib/pele_platform/Examples/tutorials/induced_fit 2021-07-14T15:45:07,024 copying pele_platform/Examples/tutorials/induced_fit/docking.pdb -> build/lib/pele_platform/Examples/tutorials/induced_fit 2021-07-14T15:45:07,056 copying pele_platform/Examples/tutorials/induced_fit/input.yaml -> build/lib/pele_platform/Examples/tutorials/induced_fit 2021-07-14T15:45:07,059 creating build/lib/pele_platform/Examples/tutorials/ppi 2021-07-14T15:45:07,060 copying pele_platform/Examples/tutorials/ppi/4yy6_ligand.pdb -> build/lib/pele_platform/Examples/tutorials/ppi 2021-07-14T15:45:07,064 copying pele_platform/Examples/tutorials/ppi/4yy6_prep.pdb -> build/lib/pele_platform/Examples/tutorials/ppi 2021-07-14T15:45:07,077 copying pele_platform/Examples/tutorials/ppi/input.yaml -> build/lib/pele_platform/Examples/tutorials/ppi 2021-07-14T15:45:07,081 creating build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,083 copying pele_platform/Examples/water/complex_induced.pdb -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,096 copying pele_platform/Examples/water/complex_ref_LESSH2O.pdb -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,120 copying pele_platform/Examples/water/input_all.yaml -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,123 copying pele_platform/Examples/water/input_bs.yaml -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,127 copying pele_platform/Examples/water/input_bs_defaults.yaml -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,130 copying pele_platform/Examples/water/input_induced.yaml -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,133 copying pele_platform/Examples/water/input_lig.yaml -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,136 copying pele_platform/Examples/water/input_lig_defaults.yaml -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,139 copying pele_platform/Examples/water/input_nwaters.yaml -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,143 copying pele_platform/Examples/water/input_previous_water.yaml -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,146 copying pele_platform/Examples/water/water2_pele.conf -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,149 copying pele_platform/Examples/water/water_pele.conf -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,153 copying pele_platform/Examples/water/water_processed.pdb -> build/lib/pele_platform/Examples/water 2021-07-14T15:45:07,177 creating build/lib/pele_platform/Templates 2021-07-14T15:45:07,179 copying pele_platform/Templates/pele_template.conf -> build/lib/pele_platform/Templates 2021-07-14T15:45:07,183 copying pele_platform/Templates/solventParamsHCTOBC.txt -> build/lib/pele_platform/Templates 2021-07-14T15:45:07,193 copying pele_platform/Templates/template_adaptive.conf -> build/lib/pele_platform/Templates 2021-07-14T15:45:07,232 UPDATING build/lib/pele_platform/_version.py 2021-07-14T15:45:07,234 set build/lib/pele_platform/_version.py to '1.6.0rc1' 2021-07-14T15:45:07,240 installing to build/bdist.linux-armv7l/wheel 2021-07-14T15:45:07,240 running install 2021-07-14T15:45:07,242 running install_lib 2021-07-14T15:45:07,248 creating build/bdist.linux-armv7l 2021-07-14T15:45:07,249 creating build/bdist.linux-armv7l/wheel 2021-07-14T15:45:07,251 creating build/bdist.linux-armv7l/wheel/pele_platform 2021-07-14T15:45:07,254 creating build/bdist.linux-armv7l/wheel/pele_platform/out_in 2021-07-14T15:45:07,255 copying build/lib/pele_platform/out_in/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/out_in 2021-07-14T15:45:07,258 copying build/lib/pele_platform/out_in/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/out_in 2021-07-14T15:45:07,261 copying build/lib/pele_platform/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform 2021-07-14T15:45:07,264 creating build/bdist.linux-armv7l/wheel/pele_platform/enzyme_engineering 2021-07-14T15:45:07,265 copying build/lib/pele_platform/enzyme_engineering/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/enzyme_engineering 2021-07-14T15:45:07,268 copying build/lib/pele_platform/enzyme_engineering/saturated_mutagenesis.py -> build/bdist.linux-armv7l/wheel/pele_platform/enzyme_engineering 2021-07-14T15:45:07,272 creating build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-07-14T15:45:07,273 copying build/lib/pele_platform/Frag/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-07-14T15:45:07,277 creating build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-07-14T15:45:07,278 copying build/lib/pele_platform/Frag/parameters/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-07-14T15:45:07,281 copying build/lib/pele_platform/Frag/parameters/files.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-07-14T15:45:07,284 copying build/lib/pele_platform/Frag/parameters/water.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-07-14T15:45:07,286 copying build/lib/pele_platform/Frag/parameters/optional.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-07-14T15:45:07,289 copying build/lib/pele_platform/Frag/parameters/metrics.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-07-14T15:45:07,292 copying build/lib/pele_platform/Frag/parameters/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag/parameters 2021-07-14T15:45:07,295 copying build/lib/pele_platform/Frag/checker.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-07-14T15:45:07,297 copying build/lib/pele_platform/Frag/analysis.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-07-14T15:45:07,301 copying build/lib/pele_platform/Frag/generative_model.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-07-14T15:45:07,304 copying build/lib/pele_platform/Frag/fragments.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-07-14T15:45:07,306 copying build/lib/pele_platform/Frag/helpers.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-07-14T15:45:07,310 copying build/lib/pele_platform/Frag/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-07-14T15:45:07,313 copying build/lib/pele_platform/Frag/libraries.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-07-14T15:45:07,317 copying build/lib/pele_platform/Frag/atoms.py -> build/bdist.linux-armv7l/wheel/pele_platform/Frag 2021-07-14T15:45:07,320 creating build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-07-14T15:45:07,322 copying build/lib/pele_platform/analysis/data.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-07-14T15:45:07,327 copying build/lib/pele_platform/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-07-14T15:45:07,329 copying build/lib/pele_platform/analysis/plot.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-07-14T15:45:07,333 copying build/lib/pele_platform/analysis/pdf_report.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-07-14T15:45:07,335 copying build/lib/pele_platform/analysis/analysis.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-07-14T15:45:07,341 copying build/lib/pele_platform/analysis/interactive_plot.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-07-14T15:45:07,347 copying build/lib/pele_platform/analysis/clustering.py -> build/bdist.linux-armv7l/wheel/pele_platform/analysis 2021-07-14T15:45:07,353 creating build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-07-14T15:45:07,355 copying build/lib/pele_platform/Checker/valid_flags.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-07-14T15:45:07,361 copying build/lib/pele_platform/Checker/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-07-14T15:45:07,364 copying build/lib/pele_platform/Checker/environment_variables.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-07-14T15:45:07,367 copying build/lib/pele_platform/Checker/executable.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-07-14T15:45:07,370 copying build/lib/pele_platform/Checker/python_version.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-07-14T15:45:07,372 copying build/lib/pele_platform/Checker/pdb_checker.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-07-14T15:45:07,375 copying build/lib/pele_platform/Checker/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/Checker 2021-07-14T15:45:07,379 creating build/bdist.linux-armv7l/wheel/pele_platform/site_finder 2021-07-14T15:45:07,381 copying build/lib/pele_platform/site_finder/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/site_finder 2021-07-14T15:45:07,383 copying build/lib/pele_platform/site_finder/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/site_finder 2021-07-14T15:45:07,387 creating build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-07-14T15:45:07,388 copying build/lib/pele_platform/PPI/preparation.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-07-14T15:45:07,391 copying build/lib/pele_platform/PPI/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-07-14T15:45:07,393 copying build/lib/pele_platform/PPI/cluster.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-07-14T15:45:07,396 copying build/lib/pele_platform/PPI/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-07-14T15:45:07,399 copying build/lib/pele_platform/PPI/simulation_launcher.py -> build/bdist.linux-armv7l/wheel/pele_platform/PPI 2021-07-14T15:45:07,403 creating build/bdist.linux-armv7l/wheel/pele_platform/constants 2021-07-14T15:45:07,404 copying build/lib/pele_platform/constants/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/constants 2021-07-14T15:45:07,407 copying build/lib/pele_platform/constants/pele_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/constants 2021-07-14T15:45:07,413 copying build/lib/pele_platform/constants/constants.py -> build/bdist.linux-armv7l/wheel/pele_platform/constants 2021-07-14T15:45:07,419 creating build/bdist.linux-armv7l/wheel/pele_platform/Templates 2021-07-14T15:45:07,421 copying build/lib/pele_platform/Templates/pele_template.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Templates 2021-07-14T15:45:07,426 copying build/lib/pele_platform/Templates/template_adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Templates 2021-07-14T15:45:07,429 copying build/lib/pele_platform/Templates/solventParamsHCTOBC.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Templates 2021-07-14T15:45:07,436 creating build/bdist.linux-armv7l/wheel/pele_platform/covalent_docking 2021-07-14T15:45:07,437 copying build/lib/pele_platform/covalent_docking/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/covalent_docking 2021-07-14T15:45:07,439 copying build/lib/pele_platform/covalent_docking/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/covalent_docking 2021-07-14T15:45:07,443 creating build/bdist.linux-armv7l/wheel/pele_platform/gpcr 2021-07-14T15:45:07,445 copying build/lib/pele_platform/gpcr/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/gpcr 2021-07-14T15:45:07,449 copying build/lib/pele_platform/gpcr/main.py -> build/bdist.linux-armv7l/wheel/pele_platform/gpcr 2021-07-14T15:45:07,454 creating build/bdist.linux-armv7l/wheel/pele_platform/Errors 2021-07-14T15:45:07,456 copying build/lib/pele_platform/Errors/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Errors 2021-07-14T15:45:07,460 copying build/lib/pele_platform/Errors/custom_errors.py -> build/bdist.linux-armv7l/wheel/pele_platform/Errors 2021-07-14T15:45:07,466 creating build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-07-14T15:45:07,467 copying build/lib/pele_platform/Adaptive/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-07-14T15:45:07,470 copying build/lib/pele_platform/Adaptive/pca.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-07-14T15:45:07,473 copying build/lib/pele_platform/Adaptive/parametrizer.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-07-14T15:45:07,478 copying build/lib/pele_platform/Adaptive/plop_solvent.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-07-14T15:45:07,481 copying build/lib/pele_platform/Adaptive/plop_ligand_parametrization.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-07-14T15:45:07,483 copying build/lib/pele_platform/Adaptive/interaction_restrictions.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-07-14T15:45:07,487 copying build/lib/pele_platform/Adaptive/box.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-07-14T15:45:07,492 copying build/lib/pele_platform/Adaptive/metrics.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-07-14T15:45:07,497 copying build/lib/pele_platform/Adaptive/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Adaptive 2021-07-14T15:45:07,503 copying build/lib/pele_platform/main.py -> build/bdist.linux-armv7l/wheel/pele_platform 2021-07-14T15:45:07,508 creating build/bdist.linux-armv7l/wheel/pele_platform/features 2021-07-14T15:45:07,509 copying build/lib/pele_platform/features/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/features 2021-07-14T15:45:07,512 copying build/lib/pele_platform/features/frag.py -> build/bdist.linux-armv7l/wheel/pele_platform/features 2021-07-14T15:45:07,514 copying build/lib/pele_platform/features/adaptive.py -> build/bdist.linux-armv7l/wheel/pele_platform/features 2021-07-14T15:45:07,519 creating build/bdist.linux-armv7l/wheel/pele_platform/RNA 2021-07-14T15:45:07,520 copying build/lib/pele_platform/RNA/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/RNA 2021-07-14T15:45:07,522 copying build/lib/pele_platform/RNA/prep.py -> build/bdist.linux-armv7l/wheel/pele_platform/RNA 2021-07-14T15:45:07,527 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples 2021-07-14T15:45:07,529 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,531 copying build/lib/pele_platform/Examples/constraints/input_square_planar.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,533 copying build/lib/pele_platform/Examples/constraints/input_tetrahedral.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,536 copying build/lib/pele_platform/Examples/constraints/input_constrain_smiles.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,539 copying build/lib/pele_platform/Examples/constraints/input_metals.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,542 copying build/lib/pele_platform/Examples/constraints/ca_constraints.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,572 copying build/lib/pele_platform/Examples/constraints/no_connects.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,575 copying build/lib/pele_platform/Examples/constraints/input_square_planar_polarisation.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,578 copying build/lib/pele_platform/Examples/constraints/input_ignore.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,581 copying build/lib/pele_platform/Examples/constraints/input_all_metal_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,583 copying build/lib/pele_platform/Examples/constraints/input_no_metal_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,586 copying build/lib/pele_platform/Examples/constraints/input_permissive_exception.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,589 copying build/lib/pele_platform/Examples/constraints/4zu9_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,640 copying build/lib/pele_platform/Examples/constraints/input_smiles_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,643 copying build/lib/pele_platform/Examples/constraints/4w4o_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,658 copying build/lib/pele_platform/Examples/constraints/fail_input_permissive_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,661 copying build/lib/pele_platform/Examples/constraints/complex_smiles_error.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,680 copying build/lib/pele_platform/Examples/constraints/4l3a_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,705 copying build/lib/pele_platform/Examples/constraints/input_k.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,708 copying build/lib/pele_platform/Examples/constraints/input_ca_noppp.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,710 copying build/lib/pele_platform/Examples/constraints/4w5i_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,726 copying build/lib/pele_platform/Examples/constraints/pass_input_permissive_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,729 copying build/lib/pele_platform/Examples/constraints/input_constrain_smarts.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,731 copying build/lib/pele_platform/Examples/constraints/4qnr_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,755 copying build/lib/pele_platform/Examples/constraints/input_ca_ppp.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,758 copying build/lib/pele_platform/Examples/constraints/1zop.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,772 copying build/lib/pele_platform/Examples/constraints/input_external_constraints.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/constraints 2021-07-14T15:45:07,776 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-07-14T15:45:07,777 copying build/lib/pele_platform/Examples/out_in/input_box_center.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-07-14T15:45:07,780 copying build/lib/pele_platform/Examples/out_in/input_default.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-07-14T15:45:07,782 copying build/lib/pele_platform/Examples/out_in/1_3ZON_complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-07-14T15:45:07,801 copying build/lib/pele_platform/Examples/out_in/input_flag_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-07-14T15:45:07,804 copying build/lib/pele_platform/Examples/out_in/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/out_in 2021-07-14T15:45:07,807 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2021-07-14T15:45:07,808 copying build/lib/pele_platform/Examples/enzyme_engineering/restart_saturated_mutagenesis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2021-07-14T15:45:07,812 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart 2021-07-14T15:45:07,814 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2 2021-07-14T15:45:07,816 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 2021-07-14T15:45:07,819 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 2021-07-14T15:45:07,822 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 2021-07-14T15:45:07,825 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_2/input 2021-07-14T15:45:07,827 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 2021-07-14T15:45:07,855 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 2021-07-14T15:45:07,858 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 2021-07-14T15:45:07,887 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 2021-07-14T15:45:07,916 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 2021-07-14T15:45:07,920 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1 2021-07-14T15:45:07,922 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output 2021-07-14T15:45:07,924 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0 2021-07-14T15:45:07,926 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/0/clustering 2021-07-14T15:45:07,928 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 2021-07-14T15:45:07,931 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 2021-07-14T15:45:07,934 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 2021-07-14T15:45:07,937 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/topologies 2021-07-14T15:45:07,938 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 2021-07-14T15:45:07,967 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 2021-07-14T15:45:08,016 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 2021-07-14T15:45:08,045 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/synchronization 2021-07-14T15:45:08,047 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 2021-07-14T15:45:08,050 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 2021-07-14T15:45:08,053 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454D 2021-07-14T15:45:08,054 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 2021-07-14T15:45:08,108 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 2021-07-14T15:45:08,111 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 2021-07-14T15:45:08,164 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 2021-07-14T15:45:08,168 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/output/T454A 2021-07-14T15:45:08,169 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 2021-07-14T15:45:08,223 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 2021-07-14T15:45:08,276 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 2021-07-14T15:45:08,279 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 2021-07-14T15:45:08,282 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 2021-07-14T15:45:08,286 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 2021-07-14T15:45:08,289 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal 2021-07-14T15:45:08,291 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates 2021-07-14T15:45:08,294 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005 2021-07-14T15:45:08,296 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/Templates/OPLS2005/HeteroAtoms 2021-07-14T15:45:08,298 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 2021-07-14T15:45:08,302 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/DataLocal/LigandRotamerLibs 2021-07-14T15:45:08,303 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 2021-07-14T15:45:08,306 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 2021-07-14T15:45:08,310 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/input 2021-07-14T15:45:08,311 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 2021-07-14T15:45:08,340 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 2021-07-14T15:45:08,345 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 2021-07-14T15:45:08,379 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 2021-07-14T15:45:08,407 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 2021-07-14T15:45:08,436 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 2021-07-14T15:45:08,464 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 2021-07-14T15:45:08,468 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/directory_to_restart/Subset_1/tmp_output 2021-07-14T15:45:08,469 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 2021-07-14T15:45:08,498 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 2021-07-14T15:45:08,526 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 2021-07-14T15:45:08,530 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 2021-07-14T15:45:08,533 copying build/lib/pele_platform/Examples/enzyme_engineering/saturated_mutagenesis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2021-07-14T15:45:08,536 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2021-07-14T15:45:08,537 copying build/lib/pele_platform/Examples/enzyme_engineering/pdb_files/T454D.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2021-07-14T15:45:08,566 copying build/lib/pele_platform/Examples/enzyme_engineering/pdb_files/T454E.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2021-07-14T15:45:08,595 copying build/lib/pele_platform/Examples/enzyme_engineering/pdb_files/T454A.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering/pdb_files 2021-07-14T15:45:08,624 copying build/lib/pele_platform/Examples/enzyme_engineering/wrong_cpus.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/enzyme_engineering 2021-07-14T15:45:08,628 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/minimum_steps 2021-07-14T15:45:08,629 copying build/lib/pele_platform/Examples/minimum_steps/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/minimum_steps 2021-07-14T15:45:08,632 copying build/lib/pele_platform/Examples/minimum_steps/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/minimum_steps 2021-07-14T15:45:08,666 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/bias 2021-07-14T15:45:08,667 copying build/lib/pele_platform/Examples/bias/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/bias 2021-07-14T15:45:08,685 copying build/lib/pele_platform/Examples/bias/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/bias 2021-07-14T15:45:08,688 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering 2021-07-14T15:45:08,691 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-07-14T15:45:08,693 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0/clustering 2021-07-14T15:45:08,694 copying build/lib/pele_platform/Examples/clustering/0/clustering/object.pkl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0/clustering 2021-07-14T15:45:08,799 copying build/lib/pele_platform/Examples/clustering/0/clustering/summary.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0/clustering 2021-07-14T15:45:08,802 copying build/lib/pele_platform/Examples/clustering/0/trajectory_1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-07-14T15:45:08,834 copying build/lib/pele_platform/Examples/clustering/0/trajectory_4.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-07-14T15:45:08,866 copying build/lib/pele_platform/Examples/clustering/0/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-07-14T15:45:08,868 copying build/lib/pele_platform/Examples/clustering/0/trajectory_3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-07-14T15:45:08,900 copying build/lib/pele_platform/Examples/clustering/0/topologyMapping.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-07-14T15:45:08,903 copying build/lib/pele_platform/Examples/clustering/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-07-14T15:45:08,906 copying build/lib/pele_platform/Examples/clustering/0/trajectory_2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-07-14T15:45:08,924 copying build/lib/pele_platform/Examples/clustering/0/report_3 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-07-14T15:45:08,927 copying build/lib/pele_platform/Examples/clustering/0/report_4 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering/0 2021-07-14T15:45:08,929 copying build/lib/pele_platform/Examples/clustering/summary.csv -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering 2021-07-14T15:45:08,933 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2021-07-14T15:45:08,934 copying build/lib/pele_platform/Examples/analysis/input_xtc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2021-07-14T15:45:08,938 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:08,941 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output 2021-07-14T15:45:08,943 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0 2021-07-14T15:45:08,945 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0/clustering 2021-07-14T15:45:08,947 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 2021-07-14T15:45:08,966 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 2021-07-14T15:45:08,969 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 2021-07-14T15:45:08,986 copying build/lib/pele_platform/Examples/analysis/data/output/0/topologyMapping.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0 2021-07-14T15:45:08,989 copying build/lib/pele_platform/Examples/analysis/data/output/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/0 2021-07-14T15:45:08,993 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/topologies 2021-07-14T15:45:08,994 copying build/lib/pele_platform/Examples/analysis/data/output/topologies/topologies.pkl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/topologies 2021-07-14T15:45:09,011 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 2021-07-14T15:45:09,030 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/synchronization 2021-07-14T15:45:09,031 copying build/lib/pele_platform/Examples/analysis/data/output/synchronization/syncFile.lock -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output/synchronization 2021-07-14T15:45:09,034 copying build/lib/pele_platform/Examples/analysis/data/output/originalControlFile.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/output 2021-07-14T15:45:09,037 copying build/lib/pele_platform/Examples/analysis/data/pele.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:09,041 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc 2021-07-14T15:45:09,043 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2021-07-14T15:45:09,045 copying build/lib/pele_platform/Examples/analysis/data/xtc/0/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2021-07-14T15:45:09,048 copying build/lib/pele_platform/Examples/analysis/data/xtc/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/0 2021-07-14T15:45:09,051 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 2021-07-14T15:45:09,054 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 2021-07-14T15:45:09,059 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc/topologies 2021-07-14T15:45:09,060 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 2021-07-14T15:45:09,068 copying build/lib/pele_platform/Examples/analysis/data/xtc/summary.csv -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/xtc 2021-07-14T15:45:09,071 copying build/lib/pele_platform/Examples/analysis/data/mgz -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:09,073 copying build/lib/pele_platform/Examples/analysis/data/STR.rot.assign -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:09,076 copying build/lib/pele_platform/Examples/analysis/data/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:09,079 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output 2021-07-14T15:45:09,081 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:09,083 copying build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:09,103 copying build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:09,106 copying build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0/topologyMapping.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:09,109 copying build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:09,112 copying build/lib/pele_platform/Examples/analysis/data/empty_reports_output/0/trajectory_2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/empty_reports_output/0 2021-07-14T15:45:09,165 copying build/lib/pele_platform/Examples/analysis/data/MG.rot.assign -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:09,167 copying build/lib/pele_platform/Examples/analysis/data/input_mae.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:09,171 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2021-07-14T15:45:09,172 copying build/lib/pele_platform/Examples/analysis/data/inputs/input2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2021-07-14T15:45:09,191 copying build/lib/pele_platform/Examples/analysis/data/inputs/input3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2021-07-14T15:45:09,209 copying build/lib/pele_platform/Examples/analysis/data/inputs/input1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data/inputs 2021-07-14T15:45:09,228 copying build/lib/pele_platform/Examples/analysis/data/adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:09,230 copying build/lib/pele_platform/Examples/analysis/data/input_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:09,233 copying build/lib/pele_platform/Examples/analysis/data/strz -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:09,235 copying build/lib/pele_platform/Examples/analysis/data/input_flags0.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis/data 2021-07-14T15:45:09,238 copying build/lib/pele_platform/Examples/analysis/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2021-07-14T15:45:09,242 copying build/lib/pele_platform/Examples/analysis/input_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2021-07-14T15:45:09,246 copying build/lib/pele_platform/Examples/analysis/input_flags0.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/analysis 2021-07-14T15:45:09,250 copying build/lib/pele_platform/Examples/test.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples 2021-07-14T15:45:09,256 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit 2021-07-14T15:45:09,258 copying build/lib/pele_platform/Examples/exit/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit 2021-07-14T15:45:09,262 copying build/lib/pele_platform/Examples/exit/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit 2021-07-14T15:45:09,265 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-07-14T15:45:09,266 copying build/lib/pele_platform/Examples/site_finder/input_restart.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-07-14T15:45:09,269 copying build/lib/pele_platform/Examples/site_finder/local.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-07-14T15:45:09,272 copying build/lib/pele_platform/Examples/site_finder/input_global.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-07-14T15:45:09,275 copying build/lib/pele_platform/Examples/site_finder/input_skipref.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-07-14T15:45:09,277 copying build/lib/pele_platform/Examples/site_finder/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-07-14T15:45:09,299 copying build/lib/pele_platform/Examples/site_finder/global.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-07-14T15:45:09,301 copying build/lib/pele_platform/Examples/site_finder/input_global_xtc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-07-14T15:45:09,304 copying build/lib/pele_platform/Examples/site_finder/input_folder.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/site_finder 2021-07-14T15:45:09,308 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-07-14T15:45:09,309 copying build/lib/pele_platform/Examples/PPI/1tnf_ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-07-14T15:45:09,313 copying build/lib/pele_platform/Examples/PPI/1tnf_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-07-14T15:45:09,341 copying build/lib/pele_platform/Examples/PPI/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-07-14T15:45:09,344 copying build/lib/pele_platform/Examples/PPI/input_skipref.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-07-14T15:45:09,347 copying build/lib/pele_platform/Examples/PPI/1f47_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-07-14T15:45:09,358 copying build/lib/pele_platform/Examples/PPI/1f47_ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-07-14T15:45:09,362 copying build/lib/pele_platform/Examples/PPI/input_folder.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/PPI 2021-07-14T15:45:09,367 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/box 2021-07-14T15:45:09,370 copying build/lib/pele_platform/Examples/box/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/box 2021-07-14T15:45:09,376 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials 2021-07-14T15:45:09,380 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2021-07-14T15:45:09,382 copying build/lib/pele_platform/Examples/tutorials/ppi/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2021-07-14T15:45:09,386 copying build/lib/pele_platform/Examples/tutorials/ppi/4yy6_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2021-07-14T15:45:09,398 copying build/lib/pele_platform/Examples/tutorials/ppi/4yy6_ligand.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/ppi 2021-07-14T15:45:09,402 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/gpcr 2021-07-14T15:45:09,404 copying build/lib/pele_platform/Examples/tutorials/gpcr/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/gpcr 2021-07-14T15:45:09,407 copying build/lib/pele_platform/Examples/tutorials/gpcr/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/gpcr 2021-07-14T15:45:09,427 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/induced_fit 2021-07-14T15:45:09,429 copying build/lib/pele_platform/Examples/tutorials/induced_fit/docking.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/induced_fit 2021-07-14T15:45:09,460 copying build/lib/pele_platform/Examples/tutorials/induced_fit/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/tutorials/induced_fit 2021-07-14T15:45:09,463 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/singularity 2021-07-14T15:45:09,464 copying build/lib/pele_platform/Examples/singularity/input_adaptive.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/singularity 2021-07-14T15:45:09,467 copying build/lib/pele_platform/Examples/singularity/input_frag.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/singularity 2021-07-14T15:45:09,471 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2021-07-14T15:45:09,472 copying build/lib/pele_platform/Examples/interaction_restrictions/input_error_2.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2021-07-14T15:45:09,476 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions/out 2021-07-14T15:45:09,477 copying build/lib/pele_platform/Examples/interaction_restrictions/out/expected_conditions.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions/out 2021-07-14T15:45:09,480 copying build/lib/pele_platform/Examples/interaction_restrictions/out/expected_metrics.txt -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions/out 2021-07-14T15:45:09,483 copying build/lib/pele_platform/Examples/interaction_restrictions/input_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2021-07-14T15:45:09,486 copying build/lib/pele_platform/Examples/interaction_restrictions/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2021-07-14T15:45:09,489 copying build/lib/pele_platform/Examples/interaction_restrictions/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/interaction_restrictions 2021-07-14T15:45:09,521 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2021-07-14T15:45:09,522 copying build/lib/pele_platform/Examples/covalent_docking/input_defaults_refinement.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2021-07-14T15:45:09,525 copying build/lib/pele_platform/Examples/covalent_docking/input2.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2021-07-14T15:45:09,528 copying build/lib/pele_platform/Examples/covalent_docking/input1.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2021-07-14T15:45:09,531 copying build/lib/pele_platform/Examples/covalent_docking/6P0M_prepared.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2021-07-14T15:45:09,549 copying build/lib/pele_platform/Examples/covalent_docking/input3.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2021-07-14T15:45:09,551 copying build/lib/pele_platform/Examples/covalent_docking/5XXD_prepared.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2021-07-14T15:45:09,579 copying build/lib/pele_platform/Examples/covalent_docking/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2021-07-14T15:45:09,582 copying build/lib/pele_platform/Examples/covalent_docking/6M06_prepared.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/covalent_docking 2021-07-14T15:45:09,607 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-07-14T15:45:09,609 copying build/lib/pele_platform/Examples/pca/input_str.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-07-14T15:45:09,613 copying build/lib/pele_platform/Examples/pca/2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-07-14T15:45:09,633 copying build/lib/pele_platform/Examples/pca/1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-07-14T15:45:09,654 copying build/lib/pele_platform/Examples/pca/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-07-14T15:45:09,657 copying build/lib/pele_platform/Examples/pca/3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/pca 2021-07-14T15:45:09,679 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/rescoring 2021-07-14T15:45:09,681 copying build/lib/pele_platform/Examples/rescoring/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/rescoring 2021-07-14T15:45:09,685 copying build/lib/pele_platform/Examples/rescoring/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/rescoring 2021-07-14T15:45:09,692 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-07-14T15:45:09,696 copying build/lib/pele_platform/Examples/gpcr/input_defaults2.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-07-14T15:45:09,702 copying build/lib/pele_platform/Examples/gpcr/complex_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-07-14T15:45:09,726 copying build/lib/pele_platform/Examples/gpcr/input_atom_error.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-07-14T15:45:09,731 copying build/lib/pele_platform/Examples/gpcr/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-07-14T15:45:09,737 copying build/lib/pele_platform/Examples/gpcr/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-07-14T15:45:09,763 copying build/lib/pele_platform/Examples/gpcr/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/gpcr 2021-07-14T15:45:09,767 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/ligand_conformations 2021-07-14T15:45:09,770 copying build/lib/pele_platform/Examples/ligand_conformations/2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/ligand_conformations 2021-07-14T15:45:09,776 copying build/lib/pele_platform/Examples/ligand_conformations/1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/ligand_conformations 2021-07-14T15:45:09,783 copying build/lib/pele_platform/Examples/ligand_conformations/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/ligand_conformations 2021-07-14T15:45:09,788 copying build/lib/pele_platform/Examples/ligand_conformations/3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/ligand_conformations 2021-07-14T15:45:09,794 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-07-14T15:45:09,796 copying build/lib/pele_platform/Examples/Adaptive/test.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-07-14T15:45:09,800 copying build/lib/pele_platform/Examples/Adaptive/STR.rot.assign -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-07-14T15:45:09,804 copying build/lib/pele_platform/Examples/Adaptive/adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-07-14T15:45:09,808 copying build/lib/pele_platform/Examples/Adaptive/strz -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-07-14T15:45:09,814 copying build/lib/pele_platform/Examples/Adaptive/pele_file_4Adaptive.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Adaptive 2021-07-14T15:45:09,819 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit_soft 2021-07-14T15:45:09,821 copying build/lib/pele_platform/Examples/exit_soft/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit_soft 2021-07-14T15:45:09,825 copying build/lib/pele_platform/Examples/exit_soft/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/exit_soft 2021-07-14T15:45:09,829 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/production 2021-07-14T15:45:09,831 copying build/lib/pele_platform/Examples/production/input.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/production 2021-07-14T15:45:09,835 copying build/lib/pele_platform/Examples/production/input_mae.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/production 2021-07-14T15:45:09,839 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-07-14T15:45:09,842 copying build/lib/pele_platform/Examples/RNA/5C45_prep.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-07-14T15:45:09,863 copying build/lib/pele_platform/Examples/RNA/2l94.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-07-14T15:45:09,866 copying build/lib/pele_platform/Examples/RNA/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-07-14T15:45:09,870 copying build/lib/pele_platform/Examples/RNA/input_induced.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-07-14T15:45:09,875 copying build/lib/pele_platform/Examples/RNA/5C45_prep_proc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/RNA 2021-07-14T15:45:09,900 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:09,902 copying build/lib/pele_platform/Examples/checker/incompatible_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:09,905 copying build/lib/pele_platform/Examples/checker/mapping_complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:09,939 copying build/lib/pele_platform/Examples/checker/complex_unk.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:09,976 copying build/lib/pele_platform/Examples/checker/complex2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:09,990 copying build/lib/pele_platform/Examples/checker/input_pele_exec.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:09,993 copying build/lib/pele_platform/Examples/checker/input_map_atom_str.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:09,998 copying build/lib/pele_platform/Examples/checker/input_tab.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,004 copying build/lib/pele_platform/Examples/checker/negative_residues.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,010 copying build/lib/pele_platform/Examples/checker/input_atom_string.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,016 copying build/lib/pele_platform/Examples/checker/input_underscore.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,019 copying build/lib/pele_platform/Examples/checker/input_template.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,025 copying build/lib/pele_platform/Examples/checker/input_space.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,029 copying build/lib/pele_platform/Examples/checker/ligand2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,034 copying build/lib/pele_platform/Examples/checker/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,037 copying build/lib/pele_platform/Examples/checker/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,062 copying build/lib/pele_platform/Examples/checker/multiple_simulations.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,067 copying build/lib/pele_platform/Examples/checker/input_rotamer.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,074 copying build/lib/pele_platform/Examples/checker/input_map_atom_num.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,079 copying build/lib/pele_platform/Examples/checker/input_unk.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,082 copying build/lib/pele_platform/Examples/checker/input_env.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/checker 2021-07-14T15:45:10,086 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-07-14T15:45:10,089 copying build/lib/pele_platform/Examples/preparation/6qmk_repeated.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-07-14T15:45:10,115 copying build/lib/pele_platform/Examples/preparation/input_space.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-07-14T15:45:10,118 copying build/lib/pele_platform/Examples/preparation/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-07-14T15:45:10,122 copying build/lib/pele_platform/Examples/preparation/complex.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-07-14T15:45:10,142 copying build/lib/pele_platform/Examples/preparation/6qmk_correct.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-07-14T15:45:10,169 copying build/lib/pele_platform/Examples/preparation/input_nonstandard.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-07-14T15:45:10,173 copying build/lib/pele_platform/Examples/preparation/complex_2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-07-14T15:45:10,206 copying build/lib/pele_platform/Examples/preparation/parametrization_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/preparation 2021-07-14T15:45:10,211 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc 2021-07-14T15:45:10,214 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:10,216 copying build/lib/pele_platform/Examples/clustering_xtc/0/trajectory_3.xtc -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:10,222 copying build/lib/pele_platform/Examples/clustering_xtc/0/trajectory_4.xtc -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:10,227 copying build/lib/pele_platform/Examples/clustering_xtc/0/report_2 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:10,231 copying build/lib/pele_platform/Examples/clustering_xtc/0/topology.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:10,250 copying build/lib/pele_platform/Examples/clustering_xtc/0/report_1 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:10,253 copying build/lib/pele_platform/Examples/clustering_xtc/0/report_3 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:10,257 copying build/lib/pele_platform/Examples/clustering_xtc/0/report_4 -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:10,263 copying build/lib/pele_platform/Examples/clustering_xtc/0/trajectory_1.xtc -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:10,273 copying build/lib/pele_platform/Examples/clustering_xtc/0/trajectory_2.xtc -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc/0 2021-07-14T15:45:10,281 copying build/lib/pele_platform/Examples/clustering_xtc/water_clustering.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/clustering_xtc 2021-07-14T15:45:10,285 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2021-07-14T15:45:10,286 copying build/lib/pele_platform/Examples/inputs/mn4.sl -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2021-07-14T15:45:10,289 copying build/lib/pele_platform/Examples/inputs/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2021-07-14T15:45:10,292 copying build/lib/pele_platform/Examples/inputs/nord3.sge -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/inputs 2021-07-14T15:45:10,296 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/flags 2021-07-14T15:45:10,297 copying build/lib/pele_platform/Examples/flags/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/flags 2021-07-14T15:45:10,302 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-07-14T15:45:10,303 copying build/lib/pele_platform/Examples/Msm/PR_AS4.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-07-14T15:45:10,321 copying build/lib/pele_platform/Examples/Msm/PR_1A28_xray_-_minimized.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-07-14T15:45:10,339 copying build/lib/pele_platform/Examples/Msm/PR_1A28_protein.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-07-14T15:45:10,357 copying build/lib/pele_platform/Examples/Msm/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-07-14T15:45:10,361 copying build/lib/pele_platform/Examples/Msm/AS4_INIT.mae -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-07-14T15:45:10,365 copying build/lib/pele_platform/Examples/Msm/PR_1A28_xray_-_minimized_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/Msm 2021-07-14T15:45:10,383 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2021-07-14T15:45:10,385 copying build/lib/pele_platform/Examples/global/input_inputs_asterisc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2021-07-14T15:45:10,388 copying build/lib/pele_platform/Examples/global/input.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2021-07-14T15:45:10,391 copying build/lib/pele_platform/Examples/global/input_inputs.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2021-07-14T15:45:10,394 copying build/lib/pele_platform/Examples/global/input_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/global 2021-07-14T15:45:10,398 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,399 copying build/lib/pele_platform/Examples/water/complex_ref_LESSH2O.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,421 copying build/lib/pele_platform/Examples/water/input_lig.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,424 copying build/lib/pele_platform/Examples/water/input_previous_water.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,427 copying build/lib/pele_platform/Examples/water/water2_pele.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,430 copying build/lib/pele_platform/Examples/water/input_bs_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,433 copying build/lib/pele_platform/Examples/water/water_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,456 copying build/lib/pele_platform/Examples/water/input_lig_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,459 copying build/lib/pele_platform/Examples/water/input_nwaters.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,461 copying build/lib/pele_platform/Examples/water/input_all.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,464 copying build/lib/pele_platform/Examples/water/water_pele.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,468 copying build/lib/pele_platform/Examples/water/input_induced.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,471 copying build/lib/pele_platform/Examples/water/input_bs.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,474 copying build/lib/pele_platform/Examples/water/complex_induced.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/water 2021-07-14T15:45:10,485 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,486 copying build/lib/pele_platform/Examples/frag/input_core_sdf.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,490 copying build/lib/pele_platform/Examples/frag/input_core.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,493 copying build/lib/pele_platform/Examples/frag/input_ai.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,495 copying build/lib/pele_platform/Examples/frag/input_sim_xtc.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,498 copying build/lib/pele_platform/Examples/frag/flags.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,501 copying build/lib/pele_platform/Examples/frag/sequential.conf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,504 copying build/lib/pele_platform/Examples/frag/input_frag_waters.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,507 copying build/lib/pele_platform/Examples/frag/input_fragment_atom.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,510 copying build/lib/pele_platform/Examples/frag/input_lib_pdb.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,512 copying build/lib/pele_platform/Examples/frag/1dyi_no_waters.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,525 copying build/lib/pele_platform/Examples/frag/1w7h_preparation_structure_2w.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,548 copying build/lib/pele_platform/Examples/frag/input_point_analysis.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,552 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_test_lib 2021-07-14T15:45:10,553 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 2021-07-14T15:45:10,557 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/pdb_test_lib 2021-07-14T15:45:10,559 copying build/lib/pele_platform/Examples/frag/pdb_test_lib/mol1.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/pdb_test_lib 2021-07-14T15:45:10,562 copying build/lib/pele_platform/Examples/frag/pdb_test_lib/mol2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/pdb_test_lib 2021-07-14T15:45:10,565 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2021-07-14T15:45:10,567 copying build/lib/pele_platform/Examples/frag/checker/receptor.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2021-07-14T15:45:10,581 copying build/lib/pele_platform/Examples/frag/checker/4RFM_series.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2021-07-14T15:45:10,585 copying build/lib/pele_platform/Examples/frag/checker/4RFM_proc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/checker 2021-07-14T15:45:10,587 copying build/lib/pele_platform/Examples/frag/amino.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,590 copying build/lib/pele_platform/Examples/frag/ligands.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,594 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,595 copying build/lib/pele_platform/Examples/frag/sdf_joiner/core2.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,614 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag3.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,619 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag2.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,621 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag4.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,624 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,627 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag5.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,630 copying build/lib/pele_platform/Examples/frag/sdf_joiner/13_serie.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,636 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag3.yml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,639 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag31.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,644 copying build/lib/pele_platform/Examples/frag/sdf_joiner/4RFM_series.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,648 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag2.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,653 copying build/lib/pele_platform/Examples/frag/sdf_joiner/frag.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,658 copying build/lib/pele_platform/Examples/frag/sdf_joiner/glide-dockSARS_core.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,696 copying build/lib/pele_platform/Examples/frag/sdf_joiner/core3.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,707 copying build/lib/pele_platform/Examples/frag/sdf_joiner/4RFM_proc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,731 copying build/lib/pele_platform/Examples/frag/sdf_joiner/4RFM_core_sc.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/sdf_joiner 2021-07-14T15:45:10,755 copying build/lib/pele_platform/Examples/frag/ligands_water.sdf -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,759 copying build/lib/pele_platform/Examples/frag/1w7h_preparation_structure_2w_processed.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,782 copying build/lib/pele_platform/Examples/frag/input_symmetry.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,785 copying build/lib/pele_platform/Examples/frag/input_sim.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,789 copying build/lib/pele_platform/Examples/frag/1dyi_waters.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,802 copying build/lib/pele_platform/Examples/frag/input_lib_sdf.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,806 copying build/lib/pele_platform/Examples/frag/input_flags.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,808 copying build/lib/pele_platform/Examples/frag/core.pdb -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag 2021-07-14T15:45:10,812 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data 2021-07-14T15:45:10,814 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_mol1C3-H2C1-H1 2021-07-14T15:45:10,817 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/frag/analysis_data/1w7h_preparation_structure_2w_processed_mol1C3-H2C1-H1/top_result 2021-07-14T15:45:10,819 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 2021-07-14T15:45:10,843 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 2021-07-14T15:45:10,867 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/restart 2021-07-14T15:45:10,868 copying build/lib/pele_platform/Examples/restart/restart.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/restart 2021-07-14T15:45:10,872 creating build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-07-14T15:45:10,873 copying build/lib/pele_platform/Examples/induced_fit/input_fast.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-07-14T15:45:10,876 copying build/lib/pele_platform/Examples/induced_fit/input_fast_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-07-14T15:45:10,879 copying build/lib/pele_platform/Examples/induced_fit/input_exhaustive.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-07-14T15:45:10,882 copying build/lib/pele_platform/Examples/induced_fit/input_exhaustive_defaults.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-07-14T15:45:10,885 copying build/lib/pele_platform/Examples/induced_fit/input_mae.yaml -> build/bdist.linux-armv7l/wheel/pele_platform/Examples/induced_fit 2021-07-14T15:45:10,888 copying build/lib/pele_platform/_version.py -> build/bdist.linux-armv7l/wheel/pele_platform 2021-07-14T15:45:10,891 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities 2021-07-14T15:45:10,892 copying build/lib/pele_platform/Utilities/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities 2021-07-14T15:45:10,896 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters 2021-07-14T15:45:10,897 copying build/lib/pele_platform/Utilities/Parameters/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters 2021-07-14T15:45:10,901 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams 2021-07-14T15:45:10,903 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-07-14T15:45:10,905 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-07-14T15:45:10,907 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/InOutParams/inout_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/InOutParams 2021-07-14T15:45:10,910 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams 2021-07-14T15:45:10,913 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-07-14T15:45:10,914 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-07-14T15:45:10,917 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PCA/pca.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PCA 2021-07-14T15:45:10,921 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2021-07-14T15:45:10,922 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/site_finder/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/site_finder 2021-07-14T15:45:10,924 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 2021-07-14T15:45:10,928 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-07-14T15:45:10,929 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-07-14T15:45:10,932 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/PPI/ppi.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/PPI 2021-07-14T15:45:10,935 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/simulation_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams 2021-07-14T15:45:10,940 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-07-14T15:45:10,941 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-07-14T15:45:10,944 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/GlideParams/glide_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/GlideParams 2021-07-14T15:45:10,947 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-07-14T15:45:10,949 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-07-14T15:45:10,951 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/MSMParams/msm_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/MSMParams 2021-07-14T15:45:10,955 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-07-14T15:45:10,956 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-07-14T15:45:10,959 copying build/lib/pele_platform/Utilities/Parameters/SimulationParams/BiasParams/bias_params.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationParams/BiasParams 2021-07-14T15:45:10,962 copying build/lib/pele_platform/Utilities/Parameters/parameters.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters 2021-07-14T15:45:10,966 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationFolders 2021-07-14T15:45:10,967 copying build/lib/pele_platform/Utilities/Parameters/SimulationFolders/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationFolders 2021-07-14T15:45:10,970 copying build/lib/pele_platform/Utilities/Parameters/SimulationFolders/simulation_folders.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Parameters/SimulationFolders 2021-07-14T15:45:10,974 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:10,976 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2021-07-14T15:45:10,978 copying build/lib/pele_platform/Utilities/Helpers/constraints/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2021-07-14T15:45:10,980 copying build/lib/pele_platform/Utilities/Helpers/constraints/alpha_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2021-07-14T15:45:10,984 copying build/lib/pele_platform/Utilities/Helpers/constraints/smiles_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/constraints 2021-07-14T15:45:10,988 copying build/lib/pele_platform/Utilities/Helpers/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:10,990 copying build/lib/pele_platform/Utilities/Helpers/launcher.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:10,993 copying build/lib/pele_platform/Utilities/Helpers/system_prep.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:10,997 copying build/lib/pele_platform/Utilities/Helpers/map_atoms.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,000 copying build/lib/pele_platform/Utilities/Helpers/solventOBCParamsGenerator.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,004 copying build/lib/pele_platform/Utilities/Helpers/conda_deployment.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,007 copying build/lib/pele_platform/Utilities/Helpers/water.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,011 copying build/lib/pele_platform/Utilities/Helpers/template_builder.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,013 copying build/lib/pele_platform/Utilities/Helpers/missing_residues.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,016 copying build/lib/pele_platform/Utilities/Helpers/ligand_conformations.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,019 copying build/lib/pele_platform/Utilities/Helpers/helpers.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,023 copying build/lib/pele_platform/Utilities/Helpers/plop_launcher.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,026 copying build/lib/pele_platform/Utilities/Helpers/bestStructs.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,029 copying build/lib/pele_platform/Utilities/Helpers/randomize.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,033 copying build/lib/pele_platform/Utilities/Helpers/interaction_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,036 creating build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2021-07-14T15:45:11,038 copying build/lib/pele_platform/Utilities/Helpers/Metals/__init__.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2021-07-14T15:45:11,040 copying build/lib/pele_platform/Utilities/Helpers/Metals/metal_polarisation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2021-07-14T15:45:11,043 copying build/lib/pele_platform/Utilities/Helpers/Metals/metal_constraints.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers/Metals 2021-07-14T15:45:11,047 copying build/lib/pele_platform/Utilities/Helpers/yaml_parser.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,051 copying build/lib/pele_platform/Utilities/Helpers/calculatePCA4PELE.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,055 copying build/lib/pele_platform/Utilities/Helpers/simulation.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,059 copying build/lib/pele_platform/Utilities/Helpers/protein_wizard.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,062 copying build/lib/pele_platform/Utilities/Helpers/center_of_mass.py -> build/bdist.linux-armv7l/wheel/pele_platform/Utilities/Helpers 2021-07-14T15:45:11,064 running install_egg_info 2021-07-14T15:45:11,079 Copying pele_platform.egg-info to build/bdist.linux-armv7l/wheel/pele_platform-1.6.0rc1-py3.5.egg-info 2021-07-14T15:45:11,096 running install_scripts 2021-07-14T15:45:11,292 creating build/bdist.linux-armv7l/wheel/pele_platform-1.6.0rc1.dist-info/WHEEL 2021-07-14T15:45:24,747 Building wheel for pele-platform (setup.py): finished with status 'done' 2021-07-14T15:45:24,910 Created wheel for pele-platform: filename=pele_platform-1.6.0rc1-py3-none-any.whl size=11408459 sha256=f17628f12454edfa542ff6dd8b1597e6dbe27366006582efa2b65537a009272d 2021-07-14T15:45:24,911 Stored in directory: /tmp/pip-ephem-wheel-cache-ai8xuh7r/wheels/4e/3b/f0/4bc45669a1a764ddc6b976bf71723ab8b52c73a733caa7f6e8 2021-07-14T15:45:24,964 Successfully built pele-platform 2021-07-14T15:45:28,222 Removed build tracker: '/tmp/pip-req-tracker-g5s86_lb'