2025-12-19T11:01:15,206 Created temporary directory: /tmp/pip-ephem-wheel-cache-nriiou06
2025-12-19T11:01:15,208 Created temporary directory: /tmp/pip-build-tracker-jit8kq7b
2025-12-19T11:01:15,209 Initialized build tracking at /tmp/pip-build-tracker-jit8kq7b
2025-12-19T11:01:15,209 Created build tracker: /tmp/pip-build-tracker-jit8kq7b
2025-12-19T11:01:15,210 Entered build tracker: /tmp/pip-build-tracker-jit8kq7b
2025-12-19T11:01:15,211 Created temporary directory: /tmp/pip-wheel-_sis9spi
2025-12-19T11:01:15,213 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2025-12-19T11:01:15,216 Created temporary directory: /tmp/pip-ephem-wheel-cache-gmeuccqb
2025-12-19T11:01:15,238 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-12-19T11:01:15,242 2 location(s) to search for versions of pmx-biobb:
2025-12-19T11:01:15,242 * https://pypi.org/simple/pmx-biobb/
2025-12-19T11:01:15,242 * https://www.piwheels.org/simple/pmx-biobb/
2025-12-19T11:01:15,243 Fetching project page and analyzing links: https://pypi.org/simple/pmx-biobb/
2025-12-19T11:01:15,244 Getting page https://pypi.org/simple/pmx-biobb/
2025-12-19T11:01:15,245 Found index url https://pypi.org/simple
2025-12-19T11:01:15,458 Fetched page https://pypi.org/simple/pmx-biobb/ as application/vnd.pypi.simple.v1+json
2025-12-19T11:01:15,464   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/ea/0e/652070bd7d0ca56047ee9da48bdce6ad248973b822b5fe7d931c07a93625/pmx_biobb-1.0.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2025-12-19T11:01:15,465   Link requires a different Python (3.11.2 not in: '==3.7.*'): https://files.pythonhosted.org/packages/c3/e5/f2e9751452ed944cd072d3cde0ec9523f4b3bfbde758a1b325d3d0ee42cf/pmx_biobb-1.0.0.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2025-12-19T11:01:15,465   Skipping link: 1.0.0 Requires-Python ==3.7.*: https://files.pythonhosted.org/packages/c3/e5/f2e9751452ed944cd072d3cde0ec9523f4b3bfbde758a1b325d3d0ee42cf/pmx_biobb-1.0.0.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2025-12-19T11:01:15,466   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/88/5b/2f2f6e34ed256b51485f1313f89aeb9647a2df056fad635dc6c69354a142/pmx_biobb-1.0.1-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2025-12-19T11:01:15,467   Link requires a different Python (3.11.2 not in: '==3.7.*'): https://files.pythonhosted.org/packages/44/5e/69dc9d443dcb657ec4849d483f4e759b6e40192def9d15d46fb85f2e8ba2/pmx_biobb-1.0.1.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2025-12-19T11:01:15,468   Skipping link: 1.0.1 Requires-Python ==3.7.*: https://files.pythonhosted.org/packages/44/5e/69dc9d443dcb657ec4849d483f4e759b6e40192def9d15d46fb85f2e8ba2/pmx_biobb-1.0.1.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2025-12-19T11:01:15,468   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/dc/26/88efc470b39ed04650850696ca8d4c1777e1f1788960a41b063c4f9f64cc/pmx_biobb-2.0.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,469   Found link https://files.pythonhosted.org/packages/32/7c/dd656cd2d785a7b9815e0ca54fb9bec35c258cdc058d9450726e65bc201c/pmx_biobb-2.0.0.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 2.0.0
2025-12-19T11:01:15,470   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/73/a2/51564515b8b81b725a8aa81b962e040e66d59ce4637be894cf02315fc403/pmx_biobb-3.0.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,471   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/e7/93/4fac73a6fe156e0940953662d457f0424e847a9546db1c10a7bbad5d3642/pmx_biobb-3.0.1-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,472   Found link https://files.pythonhosted.org/packages/3c/b8/7dcc8b482f02b8ff26aa1a9819fd389f9cc01087954d968e156a073ea4ac/pmx_biobb-3.0.1.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 3.0.1
2025-12-19T11:01:15,472   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/c4/2a/c00053a2535945c6900b99621be5c40437e939c64f36ea7d14e3bb5febbe/pmx_biobb-3.0.2-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,473   Found link https://files.pythonhosted.org/packages/8a/0b/e7b469ecf2b337e713cafe136f826f79709c9940a4d3a1eb00a669657af0/pmx_biobb-3.0.2.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 3.0.2
2025-12-19T11:01:15,474   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/8a/70/3744fd3fd4d13d0fcd04c50740aa9584ba6c5b7eb43e1a4dd65a7c223cf2/pmx_biobb-3.0.3-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,474   Found link https://files.pythonhosted.org/packages/6f/b2/61607c93aa5d3c34838e44ed7df748137d3b266a06a32b6d521a19ddedb4/pmx_biobb-3.0.3.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 3.0.3
2025-12-19T11:01:15,475   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/34/3e/e0a91c21ec82ca2108ec1f20c6f9fb0feb3e83b1d9277b2b521b43e77067/pmx_biobb-4.0.0-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,476   Found link https://files.pythonhosted.org/packages/d3/ee/61a98e8a9a4a1d5ab8ea32a2712cc1dfb3d7326a8404fcbd3347b28fab4d/pmx_biobb-4.0.0.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 4.0.0
2025-12-19T11:01:15,477   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/cf/d3/2cac189bd5b21c71cb79a57bf2f38121a2ecc930294758e3565302de7d21/pmx_biobb-4.0.1-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,478   Found link https://files.pythonhosted.org/packages/b9/64/0a7b31944dfae299db2a1da0949f82c4843cbc8ee4abb2f2b3f716d38640/pmx_biobb-4.0.1.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 4.0.1
2025-12-19T11:01:15,478   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/88/6d/c32f57cf60dce3b6835df798488a8e6980ca6e2865723f9e1c9551a8bff3/pmx_biobb-4.0.2-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,479   Found link https://files.pythonhosted.org/packages/1e/f1/377ebcaabe3ae496f4e58c434464cc6899d7a1a6287abea0ac19c9a84f38/pmx_biobb-4.0.2.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 4.0.2
2025-12-19T11:01:15,480   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/21/d8/92f5da41c0ccee7807122989b44711b075159e3129707c40a469a5333825/pmx_biobb-4.1.2-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,481   Found link https://files.pythonhosted.org/packages/de/e6/7e0419f8305191fb52c09e3f36db33fa8e37e029e6e2d0c361cb384cfefa/pmx_biobb-4.1.2.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 4.1.2
2025-12-19T11:01:15,482   Skipping link: No binaries permitted for pmx-biobb: https://files.pythonhosted.org/packages/8f/b7/67894a846ff237417e009dd532d744eff5fd675e98ccb50e27fda4c145e1/pmx_biobb-4.1.3-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,483   Found link https://files.pythonhosted.org/packages/ff/3a/d6a0cec96cc00189a683995a26e729c9d09e503129b35192923c46bd93ed/pmx_biobb-4.1.3.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.7), version: 4.1.3
2025-12-19T11:01:15,484   Found link https://files.pythonhosted.org/packages/a8/4e/25bd821ca79c5cf26558617be7b519e15d7a160d0bb3d9b9d6e5e826975e/pmx_biobb-5.2.0.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.10), version: 5.2.0
2025-12-19T11:01:15,485   Found link https://files.pythonhosted.org/packages/ba/96/4bd005ce3d4c0c715be9a91cb98c0af6f871d0303415cdd3a5a79e27946f/pmx_biobb-5.2.1.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.10), version: 5.2.1
2025-12-19T11:01:15,486   Found link https://files.pythonhosted.org/packages/5c/16/f53c3ff55706adfb58410ae04da0c8b1f59f2daa379ef6cd7853d770c00c/pmx_biobb-5.2.2.tar.gz (from https://pypi.org/simple/pmx-biobb/) (requires-python:>=3.9), version: 5.2.2
2025-12-19T11:01:15,486 Fetching project page and analyzing links: https://www.piwheels.org/simple/pmx-biobb/
2025-12-19T11:01:15,487 Getting page https://www.piwheels.org/simple/pmx-biobb/
2025-12-19T11:01:15,488 Found index url https://www.piwheels.org/simple
2025-12-19T11:01:15,644 Fetched page https://www.piwheels.org/simple/pmx-biobb/ as text/html
2025-12-19T11:01:15,660   Skipping link: No binaries permitted for pmx-biobb: https://www.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.1-cp311-cp311-linux_armv6l.whl#sha256=2a0d3dadcb1b00cce1cf39fe332a083a145f0c142d06c67b49cb5f0ae09e0cac (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2025-12-19T11:01:15,661   Skipping link: No binaries permitted for pmx-biobb: https://www.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.1-cp311-cp311-linux_armv7l.whl#sha256=2a0d3dadcb1b00cce1cf39fe332a083a145f0c142d06c67b49cb5f0ae09e0cac (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2025-12-19T11:01:15,662   Skipping link: No binaries permitted for pmx-biobb: https://www.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.1-cp313-cp313-linux_armv6l.whl#sha256=90a801512df6c5c518f5664ee26983ceb1f4991b01ac289edff33dbdc5b3911d (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2025-12-19T11:01:15,663   Skipping link: No binaries permitted for pmx-biobb: https://www.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.1-cp313-cp313-linux_armv7l.whl#sha256=90a801512df6c5c518f5664ee26983ceb1f4991b01ac289edff33dbdc5b3911d (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2025-12-19T11:01:15,663   Skipping link: No binaries permitted for pmx-biobb: https://www.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.0-cp311-cp311-linux_armv6l.whl#sha256=674c314199bb33edcf62c2e5acef5e2852ac4be5aa1d93b4aa13b6db7b4c6674 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2025-12-19T11:01:15,664   Skipping link: No binaries permitted for pmx-biobb: https://www.piwheels.org/simple/pmx-biobb/pmx_biobb-5.2.0-cp311-cp311-linux_armv7l.whl#sha256=674c314199bb33edcf62c2e5acef5e2852ac4be5aa1d93b4aa13b6db7b4c6674 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.10)
2025-12-19T11:01:15,664   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp37-cp37m-linux_armv6l.whl#sha256=49e6d6e858b81a9cb06fd1e8dfb1a6813af3e81f6f471e1473a782a4063ca3eb (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,665   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp37-cp37m-linux_armv7l.whl#sha256=49e6d6e858b81a9cb06fd1e8dfb1a6813af3e81f6f471e1473a782a4063ca3eb (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,666   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp39-cp39-linux_armv6l.whl#sha256=53bd7ffc22fe4dae9200c2f72b9650e77d4ab7809ecb0219685e7429222e7b43 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,666   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp39-cp39-linux_armv7l.whl#sha256=53bd7ffc22fe4dae9200c2f72b9650e77d4ab7809ecb0219685e7429222e7b43 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,667   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp311-cp311-linux_armv6l.whl#sha256=c8756d69d71e4ca7d72f84df02cf29e97e8b7ed8f41949404774e3ba7accb428 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,668   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.3-cp311-cp311-linux_armv7l.whl#sha256=c8756d69d71e4ca7d72f84df02cf29e97e8b7ed8f41949404774e3ba7accb428 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,668   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.2-cp37-cp37m-linux_armv6l.whl#sha256=c9442c9129d171b9470330209ab7822af7bdaeaaae306c2c891597b1267bfec5 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,669   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.2-cp37-cp37m-linux_armv7l.whl#sha256=c9442c9129d171b9470330209ab7822af7bdaeaaae306c2c891597b1267bfec5 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,669   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.2-cp39-cp39-linux_armv6l.whl#sha256=5cfda4f30e6f90d0f14fdd9d401fec01a00d3b528b9cd88614bc3161a158087a (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,670   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.1.2-cp39-cp39-linux_armv7l.whl#sha256=5cfda4f30e6f90d0f14fdd9d401fec01a00d3b528b9cd88614bc3161a158087a (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,670   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.2-cp37-cp37m-linux_armv6l.whl#sha256=dff92724f2cf8b25319328fe3e99d42581794b289ae551733a6615c659395b84 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,671   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.2-cp37-cp37m-linux_armv7l.whl#sha256=dff92724f2cf8b25319328fe3e99d42581794b289ae551733a6615c659395b84 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,672   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.2-cp39-cp39-linux_armv6l.whl#sha256=47ab27371c794d3c80f75be7a95551af23c6e6a52f55acc0bf15aca71c443d0b (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,672   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.2-cp39-cp39-linux_armv7l.whl#sha256=47ab27371c794d3c80f75be7a95551af23c6e6a52f55acc0bf15aca71c443d0b (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,673   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp37-cp37m-linux_armv6l.whl#sha256=4cba66df7056ed44e240f4e96c0a53a26e29aed4edb814b23de779fbc2de2b6e (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,674   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp37-cp37m-linux_armv7l.whl#sha256=4cba66df7056ed44e240f4e96c0a53a26e29aed4edb814b23de779fbc2de2b6e (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,674   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp39-cp39-linux_armv6l.whl#sha256=bd751f2807a45f17c0e9676ccda12b6edbbebf475c170e3ec27044838f1d5b82 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,675   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp39-cp39-linux_armv7l.whl#sha256=bd751f2807a45f17c0e9676ccda12b6edbbebf475c170e3ec27044838f1d5b82 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,676   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp311-cp311-linux_armv6l.whl#sha256=b0398fae5229f8915a467bfa70ecf4855a9df4be5b25b6846c503634fd819011 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,676   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.1-cp311-cp311-linux_armv7l.whl#sha256=b0398fae5229f8915a467bfa70ecf4855a9df4be5b25b6846c503634fd819011 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,677   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp37-cp37m-linux_armv6l.whl#sha256=a27ba6f102f456ee697a94e3336dc27b59746723f1054ffdd4229bc85b007dd1 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,677   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp37-cp37m-linux_armv7l.whl#sha256=a27ba6f102f456ee697a94e3336dc27b59746723f1054ffdd4229bc85b007dd1 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,677   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp39-cp39-linux_armv6l.whl#sha256=62a965b247bcd5d3d8de872fe3c431c183e1e627d6e3103ae0fde87ff9df3ca3 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,678   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp39-cp39-linux_armv7l.whl#sha256=62a965b247bcd5d3d8de872fe3c431c183e1e627d6e3103ae0fde87ff9df3ca3 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,679   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp311-cp311-linux_armv6l.whl#sha256=bef6e7259c029c9892522e445c7f1205d39811f71f9a90bf16770566dea86f31 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,679   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-4.0.0-cp311-cp311-linux_armv7l.whl#sha256=bef6e7259c029c9892522e445c7f1205d39811f71f9a90bf16770566dea86f31 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,680   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp37-cp37m-linux_armv6l.whl#sha256=fc8fbd57b0cb8610bb25bffb894b86ccd8e7585d21e9449ddd6574a630f9b239 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,680   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp37-cp37m-linux_armv7l.whl#sha256=fc8fbd57b0cb8610bb25bffb894b86ccd8e7585d21e9449ddd6574a630f9b239 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,681   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp39-cp39-linux_armv6l.whl#sha256=40a70608dd4bf4f418963f9f6cea5d67ebf81a1a19341a6326b8df270f390f13 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,681   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp39-cp39-linux_armv7l.whl#sha256=40a70608dd4bf4f418963f9f6cea5d67ebf81a1a19341a6326b8df270f390f13 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,682   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp311-cp311-linux_armv6l.whl#sha256=7e73de5f2261d43b7ce076f78698fe893948d8d7cc9c88c7ee3def9a035a4e68 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,682   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.3-cp311-cp311-linux_armv7l.whl#sha256=7e73de5f2261d43b7ce076f78698fe893948d8d7cc9c88c7ee3def9a035a4e68 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,683   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.2-cp37-cp37m-linux_armv6l.whl#sha256=d9a0e387d6642853c6a15e0775ee01c0d16b83bc10043722ce37d48e97775ea0 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,683   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.2-cp37-cp37m-linux_armv7l.whl#sha256=d9a0e387d6642853c6a15e0775ee01c0d16b83bc10043722ce37d48e97775ea0 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,684   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.2-cp39-cp39-linux_armv6l.whl#sha256=74fd458e035071ba11d9e1399e02fc5bb4eb6423558ebf830a74400b03b09d21 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,684   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.2-cp39-cp39-linux_armv7l.whl#sha256=74fd458e035071ba11d9e1399e02fc5bb4eb6423558ebf830a74400b03b09d21 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,685   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp37-cp37m-linux_armv6l.whl#sha256=07b4c88db1007c2b4048164c399202c430d8a7a8cc06ba72b508c989771d479d (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,686   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp37-cp37m-linux_armv7l.whl#sha256=07b4c88db1007c2b4048164c399202c430d8a7a8cc06ba72b508c989771d479d (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,686   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp39-cp39-linux_armv6l.whl#sha256=ee00c4200b2d58c9f38a7fd4e90bf138cd1a944485cce1bdbcb00cff45c8a842 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,687   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp39-cp39-linux_armv7l.whl#sha256=ee00c4200b2d58c9f38a7fd4e90bf138cd1a944485cce1bdbcb00cff45c8a842 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,687   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp311-cp311-linux_armv6l.whl#sha256=c2f9b6cb2cb584c68d74d0ee760d79c627644692dc8371d1189026b09a9dc068 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,688   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-3.0.1-cp311-cp311-linux_armv7l.whl#sha256=c2f9b6cb2cb584c68d74d0ee760d79c627644692dc8371d1189026b09a9dc068 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,688   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-2.0.0-cp37-cp37m-linux_armv6l.whl#sha256=7ed553f6de880f8fb39de2e8b4d6ea35ed8208bf52b08e62d1bcabe12bce2581 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,689   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-2.0.0-cp37-cp37m-linux_armv7l.whl#sha256=7ed553f6de880f8fb39de2e8b4d6ea35ed8208bf52b08e62d1bcabe12bce2581 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,689   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-2.0.0-cp39-cp39-linux_armv6l.whl#sha256=49cc38d8b7531ef391784e7e40fe37f1e923ef8df1e325feb77291ce2ebbf2f9 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,690   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-2.0.0-cp39-cp39-linux_armv7l.whl#sha256=49cc38d8b7531ef391784e7e40fe37f1e923ef8df1e325feb77291ce2ebbf2f9 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:>=3.7)
2025-12-19T11:01:15,690   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-1.0.1-cp37-cp37m-linux_armv6l.whl#sha256=06669bc75e212029d4eb66faec74a5eea1198968e9440e0b77c050a0ae585625 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2025-12-19T11:01:15,691   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-1.0.1-cp37-cp37m-linux_armv7l.whl#sha256=06669bc75e212029d4eb66faec74a5eea1198968e9440e0b77c050a0ae585625 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2025-12-19T11:01:15,691   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-1.0.0-cp37-cp37m-linux_armv6l.whl#sha256=6658576cd352d7f064666a210bfcbbf197410e312cbbdba101d4f6e4f6e9f868 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2025-12-19T11:01:15,692   Skipping link: No binaries permitted for pmx-biobb: https://archive1.piwheels.org/simple/pmx-biobb/pmx_biobb-1.0.0-cp37-cp37m-linux_armv7l.whl#sha256=6658576cd352d7f064666a210bfcbbf197410e312cbbdba101d4f6e4f6e9f868 (from https://www.piwheels.org/simple/pmx-biobb/) (requires-python:==3.7.*)
2025-12-19T11:01:15,692 Skipping link: not a file: https://www.piwheels.org/simple/pmx-biobb/
2025-12-19T11:01:15,693 Skipping link: not a file: https://pypi.org/simple/pmx-biobb/
2025-12-19T11:01:15,714 Given no hashes to check 1 links for project 'pmx-biobb': discarding no candidates
2025-12-19T11:01:15,732 Collecting pmx-biobb==5.2.2
2025-12-19T11:01:15,734   Created temporary directory: /tmp/pip-unpack-ljqan8mt
2025-12-19T11:01:15,865   Downloading pmx_biobb-5.2.2.tar.gz (5.2 MB)
2025-12-19T11:01:18,258   Added pmx-biobb==5.2.2 from https://files.pythonhosted.org/packages/5c/16/f53c3ff55706adfb58410ae04da0c8b1f59f2daa379ef6cd7853d770c00c/pmx_biobb-5.2.2.tar.gz to build tracker '/tmp/pip-build-tracker-jit8kq7b'
2025-12-19T11:01:18,259   Running setup.py (path:/tmp/pip-wheel-_sis9spi/pmx-biobb_7848368f761842c88d063026a1d35eb9/setup.py) egg_info for package pmx-biobb
2025-12-19T11:01:18,260   Created temporary directory: /tmp/pip-pip-egg-info-avm0b1_g
2025-12-19T11:01:18,261   Preparing metadata (setup.py): started
2025-12-19T11:01:18,262   Running command python setup.py egg_info
2025-12-19T11:01:18,836   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
2025-12-19T11:01:18,836     warnings.warn(msg)
2025-12-19T11:01:19,160   running egg_info
2025-12-19T11:01:19,188   creating /tmp/pip-pip-egg-info-avm0b1_g/pmx_biobb.egg-info
2025-12-19T11:01:19,189   writing /tmp/pip-pip-egg-info-avm0b1_g/pmx_biobb.egg-info/PKG-INFO
2025-12-19T11:01:19,193   writing dependency_links to /tmp/pip-pip-egg-info-avm0b1_g/pmx_biobb.egg-info/dependency_links.txt
2025-12-19T11:01:19,194   writing entry points to /tmp/pip-pip-egg-info-avm0b1_g/pmx_biobb.egg-info/entry_points.txt
2025-12-19T11:01:19,195   writing requirements to /tmp/pip-pip-egg-info-avm0b1_g/pmx_biobb.egg-info/requires.txt
2025-12-19T11:01:19,196   writing top-level names to /tmp/pip-pip-egg-info-avm0b1_g/pmx_biobb.egg-info/top_level.txt
2025-12-19T11:01:19,198   writing manifest file '/tmp/pip-pip-egg-info-avm0b1_g/pmx_biobb.egg-info/SOURCES.txt'
2025-12-19T11:01:19,283   reading manifest file '/tmp/pip-pip-egg-info-avm0b1_g/pmx_biobb.egg-info/SOURCES.txt'
2025-12-19T11:01:19,284   reading manifest template 'MANIFEST.in'
2025-12-19T11:01:19,315   adding license file 'LICENSE'
2025-12-19T11:01:19,330   writing manifest file '/tmp/pip-pip-egg-info-avm0b1_g/pmx_biobb.egg-info/SOURCES.txt'
2025-12-19T11:01:19,439   Preparing metadata (setup.py): finished with status 'done'
2025-12-19T11:01:19,443   Source in /tmp/pip-wheel-_sis9spi/pmx-biobb_7848368f761842c88d063026a1d35eb9 has version 5.2.2, which satisfies requirement pmx-biobb==5.2.2 from https://files.pythonhosted.org/packages/5c/16/f53c3ff55706adfb58410ae04da0c8b1f59f2daa379ef6cd7853d770c00c/pmx_biobb-5.2.2.tar.gz
2025-12-19T11:01:19,444   Removed pmx-biobb==5.2.2 from https://files.pythonhosted.org/packages/5c/16/f53c3ff55706adfb58410ae04da0c8b1f59f2daa379ef6cd7853d770c00c/pmx_biobb-5.2.2.tar.gz from build tracker '/tmp/pip-build-tracker-jit8kq7b'
2025-12-19T11:01:19,450 Created temporary directory: /tmp/pip-unpack-cmhqc3hy
2025-12-19T11:01:19,451 Building wheels for collected packages: pmx-biobb
2025-12-19T11:01:19,455   Created temporary directory: /tmp/pip-wheel-2vxz_wbd
2025-12-19T11:01:19,456   Building wheel for pmx-biobb (setup.py): started
2025-12-19T11:01:19,457   Destination directory: /tmp/pip-wheel-2vxz_wbd
2025-12-19T11:01:19,457   Running command python setup.py bdist_wheel
2025-12-19T11:01:20,009   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
2025-12-19T11:01:20,009     warnings.warn(msg)
2025-12-19T11:01:20,308   running bdist_wheel
2025-12-19T11:01:20,439   running build
2025-12-19T11:01:20,440   running build_py
2025-12-19T11:01:20,444   creating build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,446   copying src/pmx/utils.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,449   copying src/pmx/mutdb.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,451   copying src/pmx/jobscript.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,454   copying src/pmx/forcefield.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,458   copying src/pmx/_version.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,460   copying src/pmx/rosetta.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,463   copying src/pmx/analysis.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,465   copying src/pmx/library.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,470   copying src/pmx/model.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,474   copying src/pmx/geometry.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,476   copying src/pmx/xdrfile.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,478   copying src/pmx/summary.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,481   copying src/pmx/ffparser.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,484   copying src/pmx/ligand_alchemy.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,488   copying src/pmx/options.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,491   copying src/pmx/parser.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,493   copying src/pmx/__init__.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,495   copying src/pmx/alchemy.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,499   copying src/pmx/gmx.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,501   copying src/pmx/AbsRestraints.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,504   copying src/pmx/ndx.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,506   copying src/pmx/resselection.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,508   copying src/pmx/rosetta_analyze.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,511   copying src/pmx/rotamer.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,513   copying src/pmx/molecule.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,516   copying src/pmx/chain.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,519   copying src/pmx/estimators.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,521   copying src/pmx/atomselection.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,524   copying src/pmx/builder.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,526   copying src/pmx/atom.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,529   copying src/pmx/xtc.py -> build/lib.linux-armv7l-cpython-311/pmx
2025-12-19T11:01:20,530   running egg_info
2025-12-19T11:01:20,557   writing src/pmx_biobb.egg-info/PKG-INFO
2025-12-19T11:01:20,560   writing dependency_links to src/pmx_biobb.egg-info/dependency_links.txt
2025-12-19T11:01:20,561   writing entry points to src/pmx_biobb.egg-info/entry_points.txt
2025-12-19T11:01:20,563   writing requirements to src/pmx_biobb.egg-info/requires.txt
2025-12-19T11:01:20,564   writing top-level names to src/pmx_biobb.egg-info/top_level.txt
2025-12-19T11:01:20,596   reading manifest file 'src/pmx_biobb.egg-info/SOURCES.txt'
2025-12-19T11:01:20,616   reading manifest template 'MANIFEST.in'
2025-12-19T11:01:20,632   adding license file 'LICENSE'
2025-12-19T11:01:20,648   writing manifest file 'src/pmx_biobb.egg-info/SOURCES.txt'
2025-12-19T11:01:20,651   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pmx.data' is absent from the `packages` configuration.
2025-12-19T11:01:20,652   !!

2025-12-19T11:01:20,653           ********************************************************************************
2025-12-19T11:01:20,654           ############################
2025-12-19T11:01:20,654           # Package would be ignored #
2025-12-19T11:01:20,655           ############################
2025-12-19T11:01:20,655           Python recognizes 'pmx.data' as an importable package[^1],
2025-12-19T11:01:20,656           but it is absent from setuptools' `packages` configuration.

2025-12-19T11:01:20,657           This leads to an ambiguous overall configuration. If you want to distribute this
2025-12-19T11:01:20,657           package, please make sure that 'pmx.data' is explicitly added
2025-12-19T11:01:20,658           to the `packages` configuration field.

2025-12-19T11:01:20,659           Alternatively, you can also rely on setuptools' discovery methods
2025-12-19T11:01:20,659           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-12-19T11:01:20,660           instead of `find_packages(...)`/`find:`).

2025-12-19T11:01:20,661           You can read more about "package discovery" on setuptools documentation page:

2025-12-19T11:01:20,662           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-12-19T11:01:20,663           If you don't want 'pmx.data' to be distributed and are
2025-12-19T11:01:20,664           already explicitly excluding 'pmx.data' via
2025-12-19T11:01:20,665           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-12-19T11:01:20,665           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-12-19T11:01:20,666           combination with a more fine grained `package-data` configuration.

2025-12-19T11:01:20,667           You can read more about "package data files" on setuptools documentation page:

2025-12-19T11:01:20,668           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-12-19T11:01:20,669           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-12-19T11:01:20,669                 even if it does not contain any `.py` files.
2025-12-19T11:01:20,670                 On the other hand, currently there is no concept of package data
2025-12-19T11:01:20,670                 directory, all directories are treated like packages.
2025-12-19T11:01:20,671           ********************************************************************************

2025-12-19T11:01:20,671   !!
2025-12-19T11:01:20,672     check.warn(importable)
2025-12-19T11:01:20,672   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pmx.data.mutff' is absent from the `packages` configuration.
2025-12-19T11:01:20,673   !!

2025-12-19T11:01:20,674           ********************************************************************************
2025-12-19T11:01:20,674           ############################
2025-12-19T11:01:20,674           # Package would be ignored #
2025-12-19T11:01:20,675           ############################
2025-12-19T11:01:20,675           Python recognizes 'pmx.data.mutff' as an importable package[^1],
2025-12-19T11:01:20,676           but it is absent from setuptools' `packages` configuration.

2025-12-19T11:01:20,677           This leads to an ambiguous overall configuration. If you want to distribute this
2025-12-19T11:01:20,678           package, please make sure that 'pmx.data.mutff' is explicitly added
2025-12-19T11:01:20,678           to the `packages` configuration field.

2025-12-19T11:01:20,679           Alternatively, you can also rely on setuptools' discovery methods
2025-12-19T11:01:20,680           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-12-19T11:01:20,681           instead of `find_packages(...)`/`find:`).

2025-12-19T11:01:20,682           You can read more about "package discovery" on setuptools documentation page:

2025-12-19T11:01:20,683           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-12-19T11:01:20,684           If you don't want 'pmx.data.mutff' to be distributed and are
2025-12-19T11:01:20,684           already explicitly excluding 'pmx.data.mutff' via
2025-12-19T11:01:20,685           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-12-19T11:01:20,685           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-12-19T11:01:20,686           combination with a more fine grained `package-data` configuration.

2025-12-19T11:01:20,687           You can read more about "package data files" on setuptools documentation page:

2025-12-19T11:01:20,688           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-12-19T11:01:20,690           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-12-19T11:01:20,690                 even if it does not contain any `.py` files.
2025-12-19T11:01:20,691                 On the other hand, currently there is no concept of package data
2025-12-19T11:01:20,691                 directory, all directories are treated like packages.
2025-12-19T11:01:20,692           ********************************************************************************

2025-12-19T11:01:20,693   !!
2025-12-19T11:01:20,693     check.warn(importable)
2025-12-19T11:01:20,694   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pmx.extensions.pmx' is absent from the `packages` configuration.
2025-12-19T11:01:20,695   !!

2025-12-19T11:01:20,696           ********************************************************************************
2025-12-19T11:01:20,697           ############################
2025-12-19T11:01:20,698           # Package would be ignored #
2025-12-19T11:01:20,698           ############################
2025-12-19T11:01:20,699           Python recognizes 'pmx.extensions.pmx' as an importable package[^1],
2025-12-19T11:01:20,699           but it is absent from setuptools' `packages` configuration.

2025-12-19T11:01:20,701           This leads to an ambiguous overall configuration. If you want to distribute this
2025-12-19T11:01:20,701           package, please make sure that 'pmx.extensions.pmx' is explicitly added
2025-12-19T11:01:20,702           to the `packages` configuration field.

2025-12-19T11:01:20,703           Alternatively, you can also rely on setuptools' discovery methods
2025-12-19T11:01:20,704           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-12-19T11:01:20,704           instead of `find_packages(...)`/`find:`).

2025-12-19T11:01:20,705           You can read more about "package discovery" on setuptools documentation page:

2025-12-19T11:01:20,706           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-12-19T11:01:20,707           If you don't want 'pmx.extensions.pmx' to be distributed and are
2025-12-19T11:01:20,708           already explicitly excluding 'pmx.extensions.pmx' via
2025-12-19T11:01:20,708           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-12-19T11:01:20,709           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-12-19T11:01:20,709           combination with a more fine grained `package-data` configuration.

2025-12-19T11:01:20,710           You can read more about "package data files" on setuptools documentation page:

2025-12-19T11:01:20,711           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-12-19T11:01:20,713           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-12-19T11:01:20,714                 even if it does not contain any `.py` files.
2025-12-19T11:01:20,715                 On the other hand, currently there is no concept of package data
2025-12-19T11:01:20,716                 directory, all directories are treated like packages.
2025-12-19T11:01:20,716           ********************************************************************************

2025-12-19T11:01:20,717   !!
2025-12-19T11:01:20,718     check.warn(importable)
2025-12-19T11:01:20,719   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pmx.extensions.xdr' is absent from the `packages` configuration.
2025-12-19T11:01:20,719   !!

2025-12-19T11:01:20,721           ********************************************************************************
2025-12-19T11:01:20,721           ############################
2025-12-19T11:01:20,722           # Package would be ignored #
2025-12-19T11:01:20,723           ############################
2025-12-19T11:01:20,723           Python recognizes 'pmx.extensions.xdr' as an importable package[^1],
2025-12-19T11:01:20,724           but it is absent from setuptools' `packages` configuration.

2025-12-19T11:01:20,725           This leads to an ambiguous overall configuration. If you want to distribute this
2025-12-19T11:01:20,726           package, please make sure that 'pmx.extensions.xdr' is explicitly added
2025-12-19T11:01:20,726           to the `packages` configuration field.

2025-12-19T11:01:20,727           Alternatively, you can also rely on setuptools' discovery methods
2025-12-19T11:01:20,728           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-12-19T11:01:20,729           instead of `find_packages(...)`/`find:`).

2025-12-19T11:01:20,730           You can read more about "package discovery" on setuptools documentation page:

2025-12-19T11:01:20,731           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-12-19T11:01:20,733           If you don't want 'pmx.extensions.xdr' to be distributed and are
2025-12-19T11:01:20,733           already explicitly excluding 'pmx.extensions.xdr' via
2025-12-19T11:01:20,734           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-12-19T11:01:20,735           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-12-19T11:01:20,735           combination with a more fine grained `package-data` configuration.

2025-12-19T11:01:20,736           You can read more about "package data files" on setuptools documentation page:

2025-12-19T11:01:20,737           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-12-19T11:01:20,738           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-12-19T11:01:20,739                 even if it does not contain any `.py` files.
2025-12-19T11:01:20,739                 On the other hand, currently there is no concept of package data
2025-12-19T11:01:20,740                 directory, all directories are treated like packages.
2025-12-19T11:01:20,740           ********************************************************************************

2025-12-19T11:01:20,741   !!
2025-12-19T11:01:20,742     check.warn(importable)
2025-12-19T11:01:20,742   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pmx.rosetta_example' is absent from the `packages` configuration.
2025-12-19T11:01:20,743   !!

2025-12-19T11:01:20,744           ********************************************************************************
2025-12-19T11:01:20,744           ############################
2025-12-19T11:01:20,745           # Package would be ignored #
2025-12-19T11:01:20,745           ############################
2025-12-19T11:01:20,746           Python recognizes 'pmx.rosetta_example' as an importable package[^1],
2025-12-19T11:01:20,746           but it is absent from setuptools' `packages` configuration.

2025-12-19T11:01:20,748           This leads to an ambiguous overall configuration. If you want to distribute this
2025-12-19T11:01:20,748           package, please make sure that 'pmx.rosetta_example' is explicitly added
2025-12-19T11:01:20,749           to the `packages` configuration field.

2025-12-19T11:01:20,750           Alternatively, you can also rely on setuptools' discovery methods
2025-12-19T11:01:20,751           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-12-19T11:01:20,752           instead of `find_packages(...)`/`find:`).

2025-12-19T11:01:20,753           You can read more about "package discovery" on setuptools documentation page:

2025-12-19T11:01:20,754           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-12-19T11:01:20,755           If you don't want 'pmx.rosetta_example' to be distributed and are
2025-12-19T11:01:20,756           already explicitly excluding 'pmx.rosetta_example' via
2025-12-19T11:01:20,756           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-12-19T11:01:20,757           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-12-19T11:01:20,757           combination with a more fine grained `package-data` configuration.

2025-12-19T11:01:20,759           You can read more about "package data files" on setuptools documentation page:

2025-12-19T11:01:20,760           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-12-19T11:01:20,761           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-12-19T11:01:20,762                 even if it does not contain any `.py` files.
2025-12-19T11:01:20,763                 On the other hand, currently there is no concept of package data
2025-12-19T11:01:20,763                 directory, all directories are treated like packages.
2025-12-19T11:01:20,764           ********************************************************************************

2025-12-19T11:01:20,765   !!
2025-12-19T11:01:20,766     check.warn(importable)
2025-12-19T11:01:20,766   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pmx.scripts' is absent from the `packages` configuration.
2025-12-19T11:01:20,767   !!

2025-12-19T11:01:20,769           ********************************************************************************
2025-12-19T11:01:20,769           ############################
2025-12-19T11:01:20,770           # Package would be ignored #
2025-12-19T11:01:20,770           ############################
2025-12-19T11:01:20,770           Python recognizes 'pmx.scripts' as an importable package[^1],
2025-12-19T11:01:20,771           but it is absent from setuptools' `packages` configuration.

2025-12-19T11:01:20,772           This leads to an ambiguous overall configuration. If you want to distribute this
2025-12-19T11:01:20,772           package, please make sure that 'pmx.scripts' is explicitly added
2025-12-19T11:01:20,773           to the `packages` configuration field.

2025-12-19T11:01:20,774           Alternatively, you can also rely on setuptools' discovery methods
2025-12-19T11:01:20,774           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-12-19T11:01:20,775           instead of `find_packages(...)`/`find:`).

2025-12-19T11:01:20,776           You can read more about "package discovery" on setuptools documentation page:

2025-12-19T11:01:20,777           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-12-19T11:01:20,777           If you don't want 'pmx.scripts' to be distributed and are
2025-12-19T11:01:20,778           already explicitly excluding 'pmx.scripts' via
2025-12-19T11:01:20,778           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-12-19T11:01:20,779           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-12-19T11:01:20,779           combination with a more fine grained `package-data` configuration.

2025-12-19T11:01:20,781           You can read more about "package data files" on setuptools documentation page:

2025-12-19T11:01:20,782           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-12-19T11:01:20,784           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-12-19T11:01:20,785                 even if it does not contain any `.py` files.
2025-12-19T11:01:20,785                 On the other hand, currently there is no concept of package data
2025-12-19T11:01:20,786                 directory, all directories are treated like packages.
2025-12-19T11:01:20,787           ********************************************************************************

2025-12-19T11:01:20,788   !!
2025-12-19T11:01:20,789     check.warn(importable)
2025-12-19T11:01:20,789   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pmx.scripts.icolos_entrypoints' is absent from the `packages` configuration.
2025-12-19T11:01:20,790   !!

2025-12-19T11:01:20,791           ********************************************************************************
2025-12-19T11:01:20,792           ############################
2025-12-19T11:01:20,793           # Package would be ignored #
2025-12-19T11:01:20,793           ############################
2025-12-19T11:01:20,794           Python recognizes 'pmx.scripts.icolos_entrypoints' as an importable package[^1],
2025-12-19T11:01:20,794           but it is absent from setuptools' `packages` configuration.

2025-12-19T11:01:20,795           This leads to an ambiguous overall configuration. If you want to distribute this
2025-12-19T11:01:20,815           package, please make sure that 'pmx.scripts.icolos_entrypoints' is explicitly added
2025-12-19T11:01:20,821           to the `packages` configuration field.

2025-12-19T11:01:20,826           Alternatively, you can also rely on setuptools' discovery methods
2025-12-19T11:01:20,830           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-12-19T11:01:20,837           instead of `find_packages(...)`/`find:`).

2025-12-19T11:01:20,909           You can read more about "package discovery" on setuptools documentation page:

2025-12-19T11:01:20,932           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-12-19T11:01:20,957           If you don't want 'pmx.scripts.icolos_entrypoints' to be distributed and are
2025-12-19T11:01:20,973           already explicitly excluding 'pmx.scripts.icolos_entrypoints' via
2025-12-19T11:01:20,974           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-12-19T11:01:20,974           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-12-19T11:01:20,974           combination with a more fine grained `package-data` configuration.

2025-12-19T11:01:20,975           You can read more about "package data files" on setuptools documentation page:

2025-12-19T11:01:20,976           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-12-19T11:01:20,977           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-12-19T11:01:20,977                 even if it does not contain any `.py` files.
2025-12-19T11:01:20,977                 On the other hand, currently there is no concept of package data
2025-12-19T11:01:20,978                 directory, all directories are treated like packages.
2025-12-19T11:01:20,978           ********************************************************************************

2025-12-19T11:01:20,979   !!
2025-12-19T11:01:20,979     check.warn(importable)
2025-12-19T11:01:20,980   creating build/lib.linux-armv7l-cpython-311/pmx/data
2025-12-19T11:01:20,980   copying src/pmx/data/aminoacids.pkl -> build/lib.linux-armv7l-cpython-311/pmx/data
2025-12-19T11:01:20,981   copying src/pmx/data/bbdep.pkl -> build/lib.linux-armv7l-cpython-311/pmx/data
2025-12-19T11:01:20,982   copying src/pmx/data/blosum62_new.mat -> build/lib.linux-armv7l-cpython-311/pmx/data
2025-12-19T11:01:20,984   copying src/pmx/data/bp.pkl -> build/lib.linux-armv7l-cpython-311/pmx/data
2025-12-19T11:01:20,988   copying src/pmx/data/bp_amber.pkl -> build/lib.linux-armv7l-cpython-311/pmx/data
2025-12-19T11:01:20,993   copying src/pmx/data/bp_charmm.pkl -> build/lib.linux-armv7l-cpython-311/pmx/data
2025-12-19T11:01:20,998   copying src/pmx/data/rna.pkl -> build/lib.linux-armv7l-cpython-311/pmx/data
2025-12-19T11:01:21,001   creating build/lib.linux-armv7l-cpython-311/pmx/data/mutff
2025-12-19T11:01:21,002   copying src/pmx/data/mutff/atommass.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff
2025-12-19T11:01:21,005   copying src/pmx/data/mutff/elements.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff
2025-12-19T11:01:21,007   copying src/pmx/data/mutff/residuetypes.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff
2025-12-19T11:01:21,009   copying src/pmx/data/mutff/spc216.gro -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff
2025-12-19T11:01:21,012   copying src/pmx/data/mutff/specbond.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff
2025-12-19T11:01:21,015   copying src/pmx/data/mutff/vdwradii.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff
2025-12-19T11:01:21,017   copying src/pmx/data/mutff/xlateat.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff
2025-12-19T11:01:21,019   creating build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,020   copying src/pmx/data/mutff/amber14sbmut.ff/Makefile.am -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,022   copying src/pmx/data/mutff/amber14sbmut.ff/Makefile.in -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,025   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,028   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.c.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,030   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,033   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.n.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,035   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,037   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,041   copying src/pmx/data/mutff/amber14sbmut.ff/aminoacids.vsd -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,044   copying src/pmx/data/mutff/amber14sbmut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,046   copying src/pmx/data/mutff/amber14sbmut.ff/dna.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,048   copying src/pmx/data/mutff/amber14sbmut.ff/dna.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,050   copying src/pmx/data/mutff/amber14sbmut.ff/dna.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,052   copying src/pmx/data/mutff/amber14sbmut.ff/dna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,055   copying src/pmx/data/mutff/amber14sbmut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,059   copying src/pmx/data/mutff/amber14sbmut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,061   copying src/pmx/data/mutff/amber14sbmut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,063   copying src/pmx/data/mutff/amber14sbmut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,066   copying src/pmx/data/mutff/amber14sbmut.ff/gbsa.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,068   copying src/pmx/data/mutff/amber14sbmut.ff/ions.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,070   copying src/pmx/data/mutff/amber14sbmut.ff/mutres.mtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,116   copying src/pmx/data/mutff/amber14sbmut.ff/mutres.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,137   copying src/pmx/data/mutff/amber14sbmut.ff/rna.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,140   copying src/pmx/data/mutff/amber14sbmut.ff/rna.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,142   copying src/pmx/data/mutff/amber14sbmut.ff/rna.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,144   copying src/pmx/data/mutff/amber14sbmut.ff/rna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,147   copying src/pmx/data/mutff/amber14sbmut.ff/spc.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,149   copying src/pmx/data/mutff/amber14sbmut.ff/spce.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,152   copying src/pmx/data/mutff/amber14sbmut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,154   copying src/pmx/data/mutff/amber14sbmut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,156   copying src/pmx/data/mutff/amber14sbmut.ff/tip4pew.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,158   copying src/pmx/data/mutff/amber14sbmut.ff/tip5p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,160   copying src/pmx/data/mutff/amber14sbmut.ff/urea.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,162   copying src/pmx/data/mutff/amber14sbmut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:21,165   creating build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,165   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,168   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn_backup -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,170   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.c.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,172   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,175   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.n.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,177   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,179   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,183   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.vsd -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,186   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,188   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_ffbonded_for_ildn_test.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,191   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_mutres -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,211   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/correct_ffbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,214   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,217   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,219   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,221   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,224   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffberger.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,227   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,231   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,233   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,235   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,237   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/gbsa.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,239   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ions.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,242   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.mtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,249   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,253   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,256   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer_posre.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,259   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,262   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,264   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,266   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,269   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spc.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,272   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spce.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,274   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,276   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,278   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4pew.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,281   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip5p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,283   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/urea.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,285   copying src/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:21,287   creating build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,288   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,291   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.c.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,293   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,295   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.n.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,297   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,299   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,304   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.vsd -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,307   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,309   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_ffbonded_for_ildn_test.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,312   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_mutres -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,333   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/correct_ffbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,337   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,339   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,341   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,343   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,347   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffberger.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,349   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,352   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,355   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,357   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,359   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/gbsa.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,361   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ions.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,364   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.mtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,371   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,376   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,379   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer_posre.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,382   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,384   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,386   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,388   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,391   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spc.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,393   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spce.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,395   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,397   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,399   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4pew.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,401   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip5p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,404   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/urea.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,406   copying src/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:21,408   creating build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,409   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,412   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.c.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,414   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,416   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.n.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,419   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,421   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,425   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.vsd -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,428   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,430   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,433   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,436   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,438   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,441   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,444   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,446   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,449   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,451   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/gbsa.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,453   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ions.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,455   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.mtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,507   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,533   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,535   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,538   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,540   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,543   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/spc.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,545   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/spce.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,547   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,549   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,551   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4pew.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,554   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip5p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,556   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/urea.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,558   copying src/pmx/data/mutff/amber99sb-star-ildn-mut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:21,560   creating build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,561   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,564   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.c.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,566   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,569   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.n.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,571   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,573   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,576   copying src/pmx/data/mutff/charmm22star-mut.ff/aminoacids.vsd -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,579   copying src/pmx/data/mutff/charmm22star-mut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,581   copying src/pmx/data/mutff/charmm22star-mut.ff/cmap.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,585   copying src/pmx/data/mutff/charmm22star-mut.ff/dna.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,587   copying src/pmx/data/mutff/charmm22star-mut.ff/dna.c.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,589   copying src/pmx/data/mutff/charmm22star-mut.ff/dna.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,591   copying src/pmx/data/mutff/charmm22star-mut.ff/dna.n.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,593   copying src/pmx/data/mutff/charmm22star-mut.ff/dna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,596   copying src/pmx/data/mutff/charmm22star-mut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,600   copying src/pmx/data/mutff/charmm22star-mut.ff/ffnabonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,604   copying src/pmx/data/mutff/charmm22star-mut.ff/ffnanonbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,607   copying src/pmx/data/mutff/charmm22star-mut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,614   copying src/pmx/data/mutff/charmm22star-mut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,616   copying src/pmx/data/mutff/charmm22star-mut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,619   copying src/pmx/data/mutff/charmm22star-mut.ff/gb.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,621   copying src/pmx/data/mutff/charmm22star-mut.ff/ions.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,623   copying src/pmx/data/mutff/charmm22star-mut.ff/lipids.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,625   copying src/pmx/data/mutff/charmm22star-mut.ff/lipids.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,629   copying src/pmx/data/mutff/charmm22star-mut.ff/mutres.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,631   copying src/pmx/data/mutff/charmm22star-mut.ff/mutres.mtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,684   copying src/pmx/data/mutff/charmm22star-mut.ff/mutres.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,712   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,715   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.c.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,717   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,720   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.n.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,723   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,725   copying src/pmx/data/mutff/charmm22star-mut.ff/rna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,728   copying src/pmx/data/mutff/charmm22star-mut.ff/spc.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,731   copying src/pmx/data/mutff/charmm22star-mut.ff/spce.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,734   copying src/pmx/data/mutff/charmm22star-mut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,736   copying src/pmx/data/mutff/charmm22star-mut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,739   copying src/pmx/data/mutff/charmm22star-mut.ff/tip4pew.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,742   copying src/pmx/data/mutff/charmm22star-mut.ff/tip5p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,745   copying src/pmx/data/mutff/charmm22star-mut.ff/tips3p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,747   copying src/pmx/data/mutff/charmm22star-mut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:21,750   creating build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,751   copying src/pmx/data/mutff/charmm36m-mut.ff/atomtypes.atp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,755   copying src/pmx/data/mutff/charmm36m-mut.ff/cmap.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,760   copying src/pmx/data/mutff/charmm36m-mut.ff/ffbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,787   copying src/pmx/data/mutff/charmm36m-mut.ff/ffnonbonded.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,830   copying src/pmx/data/mutff/charmm36m-mut.ff/forcefield.doc -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,834   copying src/pmx/data/mutff/charmm36m-mut.ff/forcefield.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,837   copying src/pmx/data/mutff/charmm36m-mut.ff/gb.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,839   copying src/pmx/data/mutff/charmm36m-mut.ff/ions.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,842   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,845   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.c.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,848   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.hdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,851   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.n.tdb -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,854   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.r2b -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,857   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,883   copying src/pmx/data/mutff/charmm36m-mut.ff/merged.vsd -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,886   copying src/pmx/data/mutff/charmm36m-mut.ff/mutres.arn -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,888   copying src/pmx/data/mutff/charmm36m-mut.ff/mutres.mtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,943   copying src/pmx/data/mutff/charmm36m-mut.ff/mutres.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,964   copying src/pmx/data/mutff/charmm36m-mut.ff/mutres_dna.mtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,973   copying src/pmx/data/mutff/charmm36m-mut.ff/mutres_dna.rtp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,977   copying src/pmx/data/mutff/charmm36m-mut.ff/nbfix.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,980   copying src/pmx/data/mutff/charmm36m-mut.ff/spc.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,982   copying src/pmx/data/mutff/charmm36m-mut.ff/spce.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,984   copying src/pmx/data/mutff/charmm36m-mut.ff/tip3p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,987   copying src/pmx/data/mutff/charmm36m-mut.ff/tip4p.itp -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,990   copying src/pmx/data/mutff/charmm36m-mut.ff/watermodels.dat -> build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:21,992   creating build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx
2025-12-19T11:01:21,993   copying src/pmx/extensions/pmx/Energy.c -> build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx
2025-12-19T11:01:21,997   copying src/pmx/extensions/pmx/Geometry.c -> build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx
2025-12-19T11:01:22,000   copying src/pmx/extensions/pmx/Geometry.h -> build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx
2025-12-19T11:01:22,003   copying src/pmx/extensions/pmx/cpp_test.cpp -> build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx
2025-12-19T11:01:22,006   copying src/pmx/extensions/pmx/init.c -> build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx
2025-12-19T11:01:22,008   copying src/pmx/extensions/pmx/pmx.h -> build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx
2025-12-19T11:01:22,011   copying src/pmx/extensions/pmx/wrap_Geometry.c -> build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx
2025-12-19T11:01:22,015   creating build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr
2025-12-19T11:01:22,016   copying src/pmx/extensions/xdr/trr2xtc.c -> build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr
2025-12-19T11:01:22,019   copying src/pmx/extensions/xdr/xdrfile.c -> build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr
2025-12-19T11:01:22,023   copying src/pmx/extensions/xdr/xdrfile.h -> build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr
2025-12-19T11:01:22,026   copying src/pmx/extensions/xdr/xdrfile_c_test.c -> build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr
2025-12-19T11:01:22,029   copying src/pmx/extensions/xdr/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr
2025-12-19T11:01:22,033   copying src/pmx/extensions/xdr/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr
2025-12-19T11:01:22,035   copying src/pmx/extensions/xdr/xdrfile_xtc.c -> build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr
2025-12-19T11:01:22,038   copying src/pmx/extensions/xdr/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr
2025-12-19T11:01:22,041   creating build/lib.linux-armv7l-cpython-311/pmx/rosetta_example
2025-12-19T11:01:22,042   copying src/pmx/rosetta_example/README -> build/lib.linux-armv7l-cpython-311/pmx/rosetta_example
2025-12-19T11:01:22,045   copying src/pmx/rosetta_example/analyze.py -> build/lib.linux-armv7l-cpython-311/pmx/rosetta_example
2025-12-19T11:01:22,047   copying src/pmx/rosetta_example/mut.dat -> build/lib.linux-armv7l-cpython-311/pmx/rosetta_example
2025-12-19T11:01:22,049   copying src/pmx/rosetta_example/plot_results.ipynb -> build/lib.linux-armv7l-cpython-311/pmx/rosetta_example
2025-12-19T11:01:22,056   copying src/pmx/rosetta_example/prot_zn.pdb -> build/lib.linux-armv7l-cpython-311/pmx/rosetta_example
2025-12-19T11:01:22,066   copying src/pmx/rosetta_example/rosetta_prepare.ipynb -> build/lib.linux-armv7l-cpython-311/pmx/rosetta_example
2025-12-19T11:01:22,069   copying src/pmx/rosetta_example/submit_jobscripts.py -> build/lib.linux-armv7l-cpython-311/pmx/rosetta_example
2025-12-19T11:01:22,071   creating build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,072   copying src/pmx/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,075   copying src/pmx/scripts/analyze_dhdl.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,078   copying src/pmx/scripts/atomMapping.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,081   copying src/pmx/scripts/build_cyclic_top.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,084   copying src/pmx/scripts/cli.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,087   copying src/pmx/scripts/fill_cgenff_itp.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,090   copying src/pmx/scripts/fix_residue_names.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,094   copying src/pmx/scripts/gen_abs_restraints.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,096   copying src/pmx/scripts/generate_hybrid_residue.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,101   copying src/pmx/scripts/generate_hybrid_topology.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,104   copying src/pmx/scripts/hydrogen_atom_renaming.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,107   copying src/pmx/scripts/ligandHybrid.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,110   copying src/pmx/scripts/make_double_box.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,113   copying src/pmx/scripts/md_setup.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,116   copying src/pmx/scripts/mutate.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,119   copying src/pmx/scripts/parameterize_ligands.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,123   copying src/pmx/scripts/prepare_crooks_runs.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,126   copying src/pmx/scripts/repartition_mass.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,129   copying src/pmx/scripts/set_gmxlib.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,132   copying src/pmx/scripts/setup_abfe.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts
2025-12-19T11:01:22,135   creating build/lib.linux-armv7l-cpython-311/pmx/scripts/icolos_entrypoints
2025-12-19T11:01:22,136   copying src/pmx/scripts/icolos_entrypoints/__init__.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts/icolos_entrypoints
2025-12-19T11:01:22,139   copying src/pmx/scripts/icolos_entrypoints/assemble_systems.py -> build/lib.linux-armv7l-cpython-311/pmx/scripts/icolos_entrypoints
2025-12-19T11:01:22,144   UPDATING build/lib.linux-armv7l-cpython-311/pmx/_version.py
2025-12-19T11:01:22,145   set build/lib.linux-armv7l-cpython-311/pmx/_version.py to '5.2.2'
2025-12-19T11:01:22,146   running build_ext
2025-12-19T11:01:22,781   building 'pmx._pmx' extension
2025-12-19T11:01:22,782   creating build/temp.linux-armv7l-cpython-311/src/pmx/extensions/pmx
2025-12-19T11:01:22,786   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pmx/extensions/pmx -I/usr/include/python3.11 -c src/pmx/extensions/pmx/Energy.c -o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/pmx/Energy.o
2025-12-19T11:01:23,889   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pmx/extensions/pmx -I/usr/include/python3.11 -c src/pmx/extensions/pmx/Geometry.c -o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/pmx/Geometry.o
2025-12-19T11:01:24,286   src/pmx/extensions/pmx/Geometry.c: In function ‘spread_atoms_on_grid’:
2025-12-19T11:01:24,286   src/pmx/extensions/pmx/Geometry.c:527:15: warning: variable ‘nz’ set but not used [-Wunused-but-set-variable]
2025-12-19T11:01:24,287     527 |   int nx, ny, nz;
2025-12-19T11:01:24,287         |               ^~
2025-12-19T11:01:24,288   src/pmx/extensions/pmx/Geometry.c: In function ‘search_neighbors’:
2025-12-19T11:01:24,289   src/pmx/extensions/pmx/Geometry.c:586:15: warning: variable ‘nz’ set but not used [-Wunused-but-set-variable]
2025-12-19T11:01:24,289     586 |   int nx, ny, nz;
2025-12-19T11:01:24,291         |               ^~
2025-12-19T11:01:26,172   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pmx/extensions/pmx -I/usr/include/python3.11 -c src/pmx/extensions/pmx/init.c -o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/pmx/init.o
2025-12-19T11:01:26,575   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pmx/extensions/pmx -I/usr/include/python3.11 -c src/pmx/extensions/pmx/wrap_Geometry.c -o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/pmx/wrap_Geometry.o
2025-12-19T11:01:28,148   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/src/pmx/extensions/pmx/Energy.o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/pmx/Geometry.o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/pmx/init.o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/pmx/wrap_Geometry.o -L/usr/lib/arm-linux-gnueabihf -lm -o build/lib.linux-armv7l-cpython-311/pmx/_pmx.cpython-311-arm-linux-gnueabihf.so
2025-12-19T11:01:28,273   building 'pmx._xdrio' extension
2025-12-19T11:01:28,274   creating build/temp.linux-armv7l-cpython-311/src/pmx/extensions/xdr
2025-12-19T11:01:28,275   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pmx/extensions/xdr -I/usr/include/python3.11 -c src/pmx/extensions/xdr/xdrfile.c -o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/xdr/xdrfile.o
2025-12-19T11:01:28,318   src/pmx/extensions/xdr/xdrfile.c:5:2: warning: "/*" within comment [-Wcomment]
2025-12-19T11:01:28,319       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2025-12-19T11:01:28,320         |
2025-12-19T11:01:28,410   In file included from src/pmx/extensions/xdr/xdrfile.c:60:
2025-12-19T11:01:28,411   src/pmx/extensions/xdr/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2025-12-19T11:01:28,411       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2025-12-19T11:01:28,412         |
2025-12-19T11:01:28,419   src/pmx/extensions/xdr/xdrfile.c: In function ‘sizeofint’:
2025-12-19T11:01:28,420   src/pmx/extensions/xdr/xdrfile.c:499:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2025-12-19T11:01:28,420     499 |     while (size >= num && num_of_bits < 32)
2025-12-19T11:01:28,421         |                 ^~
2025-12-19T11:01:28,422   src/pmx/extensions/xdr/xdrfile.c: In function ‘sizeofints’:
2025-12-19T11:01:28,423   src/pmx/extensions/xdr/xdrfile.c:545:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2025-12-19T11:01:28,423     545 |     while (bytes[num_of_bytes] >= num)
2025-12-19T11:01:28,423         |                                ^~
2025-12-19T11:01:28,424   src/pmx/extensions/xdr/xdrfile.c: In function ‘encodeints’:
2025-12-19T11:01:28,424   src/pmx/extensions/xdr/xdrfile.c:654:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2025-12-19T11:01:28,425     654 |     if (num_of_bits >= num_of_bytes * 8)
2025-12-19T11:01:28,425         |                     ^~
2025-12-19T11:01:28,426   src/pmx/extensions/xdr/xdrfile.c:656:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2025-12-19T11:01:28,426     656 |                 for (i = 0; i < num_of_bytes; i++)
2025-12-19T11:01:28,427         |                               ^
2025-12-19T11:01:28,428   src/pmx/extensions/xdr/xdrfile.c:664:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2025-12-19T11:01:28,428     664 |                 for (i = 0; i < num_of_bytes-1; i++)
2025-12-19T11:01:28,429         |                               ^
2025-12-19T11:01:28,429   src/pmx/extensions/xdr/xdrfile.c: In function ‘decodebits’:
2025-12-19T11:01:28,430   src/pmx/extensions/xdr/xdrfile.c:704:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2025-12-19T11:01:28,430     704 |                 if (lastbits < num_of_bits)
2025-12-19T11:01:28,431         |                              ^
2025-12-19T11:01:28,431   src/pmx/extensions/xdr/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
2025-12-19T11:01:28,432   src/pmx/extensions/xdr/xdrfile.c:814:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2025-12-19T11:01:28,433     814 |         if(size3>xfp->buf1size)
2025-12-19T11:01:28,433         |                 ^
2025-12-19T11:01:28,434   src/pmx/extensions/xdr/xdrfile.c:866:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2025-12-19T11:01:28,435     866 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2025-12-19T11:01:28,435         |                          ^
2025-12-19T11:01:28,436   src/pmx/extensions/xdr/xdrfile.c:866:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2025-12-19T11:01:28,436     866 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2025-12-19T11:01:28,437         |                                            ^~~
2025-12-19T11:01:28,438   src/pmx/extensions/xdr/xdrfile.c:792:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2025-12-19T11:01:28,438     792 |         int smallnum, smaller, larger, i, is_smaller, run;
2025-12-19T11:01:28,439         |                                ^~~~~~
2025-12-19T11:01:28,440   src/pmx/extensions/xdr/xdrfile.c:789:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2025-12-19T11:01:28,440     789 |         int smallidx, minidx, maxidx;
2025-12-19T11:01:28,441         |                       ^~~~~~
2025-12-19T11:01:28,442   src/pmx/extensions/xdr/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
2025-12-19T11:01:28,442   src/pmx/extensions/xdr/xdrfile.c:1010:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2025-12-19T11:01:28,443    1010 |         if(size3>xfp->buf1size)
2025-12-19T11:01:28,444         |                 ^
2025-12-19T11:01:28,445   src/pmx/extensions/xdr/xdrfile.c:1133:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2025-12-19T11:01:28,446    1133 |         while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
2025-12-19T11:01:28,447         |                         ^
2025-12-19T11:01:28,447   src/pmx/extensions/xdr/xdrfile.c:1139:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2025-12-19T11:01:28,448    1139 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2025-12-19T11:01:28,448         |                          ^
2025-12-19T11:01:28,449   src/pmx/extensions/xdr/xdrfile.c:1139:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2025-12-19T11:01:28,449    1139 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2025-12-19T11:01:28,450         |                                            ^~~
2025-12-19T11:01:28,453   src/pmx/extensions/xdr/xdrfile.c:1271:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2025-12-19T11:01:28,453    1271 |         if(tmp==(unsigned int)buf2[0])
2025-12-19T11:01:28,454         |               ^~
2025-12-19T11:01:28,454   src/pmx/extensions/xdr/xdrfile.c:999:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2025-12-19T11:01:28,455     999 |         int errval=1;
2025-12-19T11:01:28,455         |             ^~~~~~
2025-12-19T11:01:28,456   src/pmx/extensions/xdr/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
2025-12-19T11:01:28,456   src/pmx/extensions/xdr/xdrfile.c:1311:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2025-12-19T11:01:28,457    1311 |         if(size3>xfp->buf1size)
2025-12-19T11:01:28,458         |                 ^
2025-12-19T11:01:28,460   src/pmx/extensions/xdr/xdrfile.c:1366:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2025-12-19T11:01:28,461    1366 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2025-12-19T11:01:28,461         |                          ^
2025-12-19T11:01:28,462   src/pmx/extensions/xdr/xdrfile.c:1366:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2025-12-19T11:01:28,463    1366 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2025-12-19T11:01:28,464         |                                            ^~~
2025-12-19T11:01:28,466   src/pmx/extensions/xdr/xdrfile.c:1288:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2025-12-19T11:01:28,467    1288 |         int smallnum, smaller, larger, i, is_smaller, run;
2025-12-19T11:01:28,467         |                                ^~~~~~
2025-12-19T11:01:28,468   src/pmx/extensions/xdr/xdrfile.c:1285:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2025-12-19T11:01:28,468    1285 |         int smallidx, minidx, maxidx;
2025-12-19T11:01:28,469         |                       ^~~~~~
2025-12-19T11:01:28,469   src/pmx/extensions/xdr/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
2025-12-19T11:01:28,470   src/pmx/extensions/xdr/xdrfile.c:1502:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2025-12-19T11:01:28,471    1502 |         if(size3>xfp->buf1size) {
2025-12-19T11:01:28,471         |                 ^
2025-12-19T11:01:28,478   src/pmx/extensions/xdr/xdrfile.c:1617:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2025-12-19T11:01:28,478    1617 |         while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
2025-12-19T11:01:28,479         |                         ^
2025-12-19T11:01:28,480   src/pmx/extensions/xdr/xdrfile.c:1622:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2025-12-19T11:01:28,480    1622 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2025-12-19T11:01:28,481         |                          ^
2025-12-19T11:01:28,482   src/pmx/extensions/xdr/xdrfile.c:1622:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2025-12-19T11:01:28,482    1622 |         maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2025-12-19T11:01:28,483         |                                            ^~~
2025-12-19T11:01:28,486   src/pmx/extensions/xdr/xdrfile.c:1732:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2025-12-19T11:01:28,486    1732 |         if(tmp==(unsigned int)buf2[0])
2025-12-19T11:01:28,487         |               ^~
2025-12-19T11:01:28,487   src/pmx/extensions/xdr/xdrfile.c:1492:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2025-12-19T11:01:28,488    1492 |         int errval=1;
2025-12-19T11:01:28,488         |             ^~~~~~
2025-12-19T11:01:31,068   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pmx/extensions/xdr -I/usr/include/python3.11 -c src/pmx/extensions/xdr/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/xdr/xdrfile_trr.o
2025-12-19T11:01:31,110   src/pmx/extensions/xdr/xdrfile_trr.c:5:2: warning: "/*" within comment [-Wcomment]
2025-12-19T11:01:31,110       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2025-12-19T11:01:31,111         |
2025-12-19T11:01:31,151   In file included from src/pmx/extensions/xdr/xdrfile_trr.c:41:
2025-12-19T11:01:31,151   src/pmx/extensions/xdr/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2025-12-19T11:01:31,152       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2025-12-19T11:01:31,153         |
2025-12-19T11:01:31,153   In file included from src/pmx/extensions/xdr/xdrfile_trr.c:42:
2025-12-19T11:01:31,154   src/pmx/extensions/xdr/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
2025-12-19T11:01:31,155       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2025-12-19T11:01:31,155         |
2025-12-19T11:01:31,156   src/pmx/extensions/xdr/xdrfile_trr.c: In function ‘do_trnheader’:
2025-12-19T11:01:31,157   src/pmx/extensions/xdr/xdrfile_trr.c:108:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2025-12-19T11:01:31,157     108 |         if (slen != strlen(version)+1)
2025-12-19T11:01:31,158         |                  ^~
2025-12-19T11:01:31,159   src/pmx/extensions/xdr/xdrfile_trr.c:118:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2025-12-19T11:01:31,159     118 |         if (xdrfile_write_string(version,xd) != (strlen(version)+1) )
2025-12-19T11:01:31,160         |                                              ^~
2025-12-19T11:01:31,832   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pmx/extensions/xdr -I/usr/include/python3.11 -c src/pmx/extensions/xdr/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/xdr/xdrfile_xtc.o
2025-12-19T11:01:31,906   In file included from src/pmx/extensions/xdr/xdrfile_xtc.c:31:
2025-12-19T11:01:31,907   src/pmx/extensions/xdr/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2025-12-19T11:01:31,908       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2025-12-19T11:01:31,908         |
2025-12-19T11:01:31,909   In file included from src/pmx/extensions/xdr/xdrfile_xtc.c:32:
2025-12-19T11:01:31,910   src/pmx/extensions/xdr/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
2025-12-19T11:01:31,910       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2025-12-19T11:01:31,911         |
2025-12-19T11:01:31,911   src/pmx/extensions/xdr/xdrfile_xtc.c: In function ‘xtc_coord’:
2025-12-19T11:01:31,912   src/pmx/extensions/xdr/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable]
2025-12-19T11:01:31,913      66 |         int i,j,result;
2025-12-19T11:01:31,914         |               ^
2025-12-19T11:01:31,914   src/pmx/extensions/xdr/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable]
2025-12-19T11:01:31,915      66 |         int i,j,result;
2025-12-19T11:01:31,915         |             ^
2025-12-19T11:01:32,028   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/src/pmx/extensions/xdr/xdrfile.o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/xdr/xdrfile_trr.o build/temp.linux-armv7l-cpython-311/src/pmx/extensions/xdr/xdrfile_xtc.o -L/usr/lib/arm-linux-gnueabihf -lm -o build/lib.linux-armv7l-cpython-311/pmx/_xdrio.cpython-311-arm-linux-gnueabihf.so
2025-12-19T11:01:32,164   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-12-19T11:01:32,164   !!

2025-12-19T11:01:32,165           ********************************************************************************
2025-12-19T11:01:32,166           Please avoid running ``setup.py`` directly.
2025-12-19T11:01:32,166           Instead, use pypa/build, pypa/installer or other
2025-12-19T11:01:32,167           standards-based tools.

2025-12-19T11:01:32,168           This deprecation is overdue, please update your project and remove deprecated
2025-12-19T11:01:32,168           calls to avoid build errors in the future.

2025-12-19T11:01:32,169           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-12-19T11:01:32,170           ********************************************************************************

2025-12-19T11:01:32,171   !!
2025-12-19T11:01:32,172     self.initialize_options()
2025-12-19T11:01:32,193   installing to build/bdist.linux-armv7l/wheel
2025-12-19T11:01:32,194   running install
2025-12-19T11:01:32,217   running install_lib
2025-12-19T11:01:32,245   creating build/bdist.linux-armv7l/wheel
2025-12-19T11:01:32,248   creating build/bdist.linux-armv7l/wheel/pmx
2025-12-19T11:01:32,249   copying build/lib.linux-armv7l-cpython-311/pmx/utils.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:32,252   copying build/lib.linux-armv7l-cpython-311/pmx/mutdb.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:32,254   copying build/lib.linux-armv7l-cpython-311/pmx/jobscript.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:32,257   creating build/bdist.linux-armv7l/wheel/pmx/data
2025-12-19T11:01:32,258   copying build/lib.linux-armv7l-cpython-311/pmx/data/aminoacids.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2025-12-19T11:01:32,267   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff
2025-12-19T11:01:32,269   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,270   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/dna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,273   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/aminoacids.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,275   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/tip5p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,277   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/dna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,279   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/mutres.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,343   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/gbsa.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,346   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,348   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,350   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,352   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/aminoacids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,355   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/urea.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,357   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/aminoacids.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,359   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,362   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,364   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/Makefile.in -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,366   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,369   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/aminoacids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,373   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/Makefile.am -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,375   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/rna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,377   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/dna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,379   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/aminoacids.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,382   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,384   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/rna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,387   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,389   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/mutres.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,417   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/aminoacids.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,420   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/rna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,422   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,424   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/aminoacids.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,426   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/rna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,428   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,431   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,433   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,435   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber14sbmut.ff/tip4pew.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber14sbmut.ff
2025-12-19T11:01:32,437   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/spc216.gro -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2025-12-19T11:01:32,440   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,441   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,444   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,446   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip5p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,448   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,451   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,503   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/gbsa.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,505   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,508   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,510   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,513   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,516   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/urea.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,519   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,521   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,525   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,528   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,531   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,536   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,539   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,541   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,543   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,545   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,549   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,551   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,589   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,592   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,595   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,597   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,599   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,602   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,606   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,608   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,609   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4pew.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-mut.ff
2025-12-19T11:01:32,611   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/specbond.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2025-12-19T11:01:32,614   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,615   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,617   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,619   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip5p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,621   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_mutres -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,644   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,646   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/gbsa.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,648   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,650   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,652   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,654   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,656   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/urea.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,658   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,660   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_ffbonded_for_ildn_test.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,663   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,666   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,669   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,670   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,675   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffberger.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,678   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,681   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,682   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,685   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,686   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,688   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,691   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,693   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,696   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn_backup -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,698   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,700   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,702   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,703   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,710   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer_posre.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,713   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,715   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,718   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,720   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,722   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4pew.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,724   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/correct_ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,727   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff
2025-12-19T11:01:32,731   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/elements.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2025-12-19T11:01:32,733   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/xlateat.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2025-12-19T11:01:32,736   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,737   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/merged.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,739   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/merged.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,741   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/mutres.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,788   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/mutres.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,789   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,792   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,794   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,795   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/gb.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,798   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/merged.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,799   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/merged.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,802   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,833   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/merged.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,851   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,854   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/cmap.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,858   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,860   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/merged.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,862   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/nbfix.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,864   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,866   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/mutres.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,891   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,893   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/merged.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,895   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/mutres_dna.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,902   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,922   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,924   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,925   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm36m-mut.ff/mutres_dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm36m-mut.ff
2025-12-19T11:01:32,929   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/residuetypes.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2025-12-19T11:01:32,932   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/atommass.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2025-12-19T11:01:32,934   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,935   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,937   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,939   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip5p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,941   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_mutres -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,960   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,962   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/gbsa.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,963   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,966   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,967   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,969   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,971   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/urea.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,973   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,975   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_ffbonded_for_ildn_test.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,978   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,981   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,983   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,984   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,988   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffberger.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,990   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,993   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,994   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,996   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:32,998   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,000   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,002   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,004   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,006   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,008   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,009   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,011   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,018   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer_posre.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,021   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,023   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,025   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,027   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,029   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4pew.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,030   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/correct_ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,033   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff
2025-12-19T11:01:33,038   creating build/bdist.linux-armv7l/wheel/pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,039   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/dna.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,041   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/dna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,043   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/aminoacids.vsd -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,045   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/tip5p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,046   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/ffnanonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,050   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/mutres.mtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,102   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/mutres.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,104   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/atomtypes.atp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,106   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/watermodels.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,108   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/spce.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,110   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/gb.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,111   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/ffnabonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,115   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/aminoacids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,117   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/aminoacids.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,119   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/rna.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,121   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/dna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,123   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/ffnonbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,129   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/forcefield.doc -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,131   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/aminoacids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,134   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/tips3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,136   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/rna.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,137   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/lipids.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,141   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/dna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,142   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/aminoacids.r2b -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,144   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/cmap.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,148   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/rna.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,149   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/ions.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,151   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/rna.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,154   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/tip3p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,156   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/mutres.rtp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,188   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/aminoacids.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,190   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/rna.arn -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,192   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/spc.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,194   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/dna.n.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,196   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/lipids.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,198   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/aminoacids.c.tdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,200   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/rna.hdb -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,203   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/ffbonded.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,207   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/tip4p.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,209   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/forcefield.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,211   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/charmm22star-mut.ff/tip4pew.itp -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff/charmm22star-mut.ff
2025-12-19T11:01:33,213   copying build/lib.linux-armv7l-cpython-311/pmx/data/mutff/vdwradii.dat -> build/bdist.linux-armv7l/wheel/./pmx/data/mutff
2025-12-19T11:01:33,215   copying build/lib.linux-armv7l-cpython-311/pmx/data/bp_amber.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2025-12-19T11:01:33,221   copying build/lib.linux-armv7l-cpython-311/pmx/data/bp_charmm.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2025-12-19T11:01:33,225   copying build/lib.linux-armv7l-cpython-311/pmx/data/bp.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2025-12-19T11:01:33,230   copying build/lib.linux-armv7l-cpython-311/pmx/data/rna.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2025-12-19T11:01:33,234   copying build/lib.linux-armv7l-cpython-311/pmx/data/blosum62_new.mat -> build/bdist.linux-armv7l/wheel/./pmx/data
2025-12-19T11:01:33,236   copying build/lib.linux-armv7l-cpython-311/pmx/data/bbdep.pkl -> build/bdist.linux-armv7l/wheel/./pmx/data
2025-12-19T11:01:33,532   copying build/lib.linux-armv7l-cpython-311/pmx/forcefield.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,536   copying build/lib.linux-armv7l-cpython-311/pmx/_version.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,538   copying build/lib.linux-armv7l-cpython-311/pmx/rosetta.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,541   copying build/lib.linux-armv7l-cpython-311/pmx/analysis.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,544   creating build/bdist.linux-armv7l/wheel/pmx/rosetta_example
2025-12-19T11:01:33,545   copying build/lib.linux-armv7l-cpython-311/pmx/rosetta_example/README -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2025-12-19T11:01:33,547   copying build/lib.linux-armv7l-cpython-311/pmx/rosetta_example/prot_zn.pdb -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2025-12-19T11:01:33,557   copying build/lib.linux-armv7l-cpython-311/pmx/rosetta_example/mut.dat -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2025-12-19T11:01:33,560   copying build/lib.linux-armv7l-cpython-311/pmx/rosetta_example/analyze.py -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2025-12-19T11:01:33,563   copying build/lib.linux-armv7l-cpython-311/pmx/rosetta_example/rosetta_prepare.ipynb -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2025-12-19T11:01:33,565   copying build/lib.linux-armv7l-cpython-311/pmx/rosetta_example/submit_jobscripts.py -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2025-12-19T11:01:33,567   copying build/lib.linux-armv7l-cpython-311/pmx/rosetta_example/plot_results.ipynb -> build/bdist.linux-armv7l/wheel/./pmx/rosetta_example
2025-12-19T11:01:33,573   copying build/lib.linux-armv7l-cpython-311/pmx/library.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,577   copying build/lib.linux-armv7l-cpython-311/pmx/model.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,581   copying build/lib.linux-armv7l-cpython-311/pmx/geometry.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,583   copying build/lib.linux-armv7l-cpython-311/pmx/xdrfile.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,586   copying build/lib.linux-armv7l-cpython-311/pmx/summary.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,589   copying build/lib.linux-armv7l-cpython-311/pmx/ffparser.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,592   copying build/lib.linux-armv7l-cpython-311/pmx/ligand_alchemy.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,596   copying build/lib.linux-armv7l-cpython-311/pmx/options.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,599   copying build/lib.linux-armv7l-cpython-311/pmx/parser.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,602   creating build/bdist.linux-armv7l/wheel/pmx/scripts
2025-12-19T11:01:33,604   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/parameterize_ligands.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,607   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/ligandHybrid.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,610   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/atomMapping.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,613   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/make_double_box.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,615   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,617   creating build/bdist.linux-armv7l/wheel/pmx/scripts/icolos_entrypoints
2025-12-19T11:01:33,619   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/icolos_entrypoints/__init__.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts/icolos_entrypoints
2025-12-19T11:01:33,621   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/icolos_entrypoints/assemble_systems.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts/icolos_entrypoints
2025-12-19T11:01:33,623   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/gen_abs_restraints.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,626   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/build_cyclic_top.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,628   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/hydrogen_atom_renaming.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,631   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/setup_abfe.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,634   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/prepare_crooks_runs.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,636   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/generate_hybrid_topology.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,639   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/fill_cgenff_itp.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,642   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/generate_hybrid_residue.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,646   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/md_setup.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,649   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/repartition_mass.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,651   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/set_gmxlib.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,653   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/mutate.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,656   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/analyze_dhdl.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,659   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/cli.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,662   copying build/lib.linux-armv7l-cpython-311/pmx/scripts/fix_residue_names.py -> build/bdist.linux-armv7l/wheel/./pmx/scripts
2025-12-19T11:01:33,664   copying build/lib.linux-armv7l-cpython-311/pmx/__init__.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,667   copying build/lib.linux-armv7l-cpython-311/pmx/_xdrio.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,672   copying build/lib.linux-armv7l-cpython-311/pmx/alchemy.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,677   copying build/lib.linux-armv7l-cpython-311/pmx/gmx.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,679   copying build/lib.linux-armv7l-cpython-311/pmx/AbsRestraints.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,682   copying build/lib.linux-armv7l-cpython-311/pmx/ndx.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,685   copying build/lib.linux-armv7l-cpython-311/pmx/resselection.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,688   copying build/lib.linux-armv7l-cpython-311/pmx/rosetta_analyze.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,691   copying build/lib.linux-armv7l-cpython-311/pmx/rotamer.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,693   copying build/lib.linux-armv7l-cpython-311/pmx/molecule.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,696   copying build/lib.linux-armv7l-cpython-311/pmx/_pmx.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,703   copying build/lib.linux-armv7l-cpython-311/pmx/chain.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,706   copying build/lib.linux-armv7l-cpython-311/pmx/estimators.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,709   copying build/lib.linux-armv7l-cpython-311/pmx/atomselection.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,713   creating build/bdist.linux-armv7l/wheel/pmx/extensions
2025-12-19T11:01:33,715   creating build/bdist.linux-armv7l/wheel/pmx/extensions/pmx
2025-12-19T11:01:33,717   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx/cpp_test.cpp -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2025-12-19T11:01:33,719   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx/init.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2025-12-19T11:01:33,721   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx/pmx.h -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2025-12-19T11:01:33,724   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx/Energy.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2025-12-19T11:01:33,727   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx/wrap_Geometry.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2025-12-19T11:01:33,730   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx/Geometry.h -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2025-12-19T11:01:33,732   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/pmx/Geometry.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/pmx
2025-12-19T11:01:33,736   creating build/bdist.linux-armv7l/wheel/pmx/extensions/xdr
2025-12-19T11:01:33,737   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr/xdrfile_c_test.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2025-12-19T11:01:33,740   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr/xdrfile_xtc.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2025-12-19T11:01:33,742   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr/xdrfile.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2025-12-19T11:01:33,746   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2025-12-19T11:01:33,748   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2025-12-19T11:01:33,750   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2025-12-19T11:01:33,752   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr/trr2xtc.c -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2025-12-19T11:01:33,755   copying build/lib.linux-armv7l-cpython-311/pmx/extensions/xdr/xdrfile.h -> build/bdist.linux-armv7l/wheel/./pmx/extensions/xdr
2025-12-19T11:01:33,758   copying build/lib.linux-armv7l-cpython-311/pmx/builder.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,761   copying build/lib.linux-armv7l-cpython-311/pmx/atom.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,764   copying build/lib.linux-armv7l-cpython-311/pmx/xtc.py -> build/bdist.linux-armv7l/wheel/./pmx
2025-12-19T11:01:33,766   running install_egg_info
2025-12-19T11:01:33,800   Copying src/pmx_biobb.egg-info to build/bdist.linux-armv7l/wheel/./pmx_biobb-5.2.2-py3.11.egg-info
2025-12-19T11:01:33,815   running install_scripts
2025-12-19T11:01:33,868   creating build/bdist.linux-armv7l/wheel/pmx_biobb-5.2.2.dist-info/WHEEL
2025-12-19T11:01:33,871   creating '/tmp/pip-wheel-2vxz_wbd/pmx_biobb-5.2.2-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-12-19T11:01:33,876   adding 'pmx/AbsRestraints.py'
2025-12-19T11:01:33,878   adding 'pmx/__init__.py'
2025-12-19T11:01:33,913   adding 'pmx/_pmx.cpython-311-arm-linux-gnueabihf.so'
2025-12-19T11:01:33,915   adding 'pmx/_version.py'
2025-12-19T11:01:33,938   adding 'pmx/_xdrio.cpython-311-arm-linux-gnueabihf.so'
2025-12-19T11:01:33,946   adding 'pmx/alchemy.py'
2025-12-19T11:01:33,949   adding 'pmx/analysis.py'
2025-12-19T11:01:33,952   adding 'pmx/atom.py'
2025-12-19T11:01:33,955   adding 'pmx/atomselection.py'
2025-12-19T11:01:33,958   adding 'pmx/builder.py'
2025-12-19T11:01:33,961   adding 'pmx/chain.py'
2025-12-19T11:01:33,965   adding 'pmx/estimators.py'
2025-12-19T11:01:33,969   adding 'pmx/ffparser.py'
2025-12-19T11:01:33,979   adding 'pmx/forcefield.py'
2025-12-19T11:01:33,981   adding 'pmx/geometry.py'
2025-12-19T11:01:33,984   adding 'pmx/gmx.py'
2025-12-19T11:01:33,986   adding 'pmx/jobscript.py'
2025-12-19T11:01:33,995   adding 'pmx/library.py'
2025-12-19T11:01:34,008   adding 'pmx/ligand_alchemy.py'
2025-12-19T11:01:34,014   adding 'pmx/model.py'
2025-12-19T11:01:34,018   adding 'pmx/molecule.py'
2025-12-19T11:01:34,020   adding 'pmx/mutdb.py'
2025-12-19T11:01:34,023   adding 'pmx/ndx.py'
2025-12-19T11:01:34,025   adding 'pmx/options.py'
2025-12-19T11:01:34,027   adding 'pmx/parser.py'
2025-12-19T11:01:34,029   adding 'pmx/resselection.py'
2025-12-19T11:01:34,033   adding 'pmx/rosetta.py'
2025-12-19T11:01:34,036   adding 'pmx/rosetta_analyze.py'
2025-12-19T11:01:34,038   adding 'pmx/rotamer.py'
2025-12-19T11:01:34,041   adding 'pmx/summary.py'
2025-12-19T11:01:34,044   adding 'pmx/utils.py'
2025-12-19T11:01:34,046   adding 'pmx/xdrfile.py'
2025-12-19T11:01:34,048   adding 'pmx/xtc.py'
2025-12-19T11:01:34,074   adding 'pmx/data/aminoacids.pkl'
2025-12-19T11:01:35,886   adding 'pmx/data/bbdep.pkl'
2025-12-19T11:01:35,996   adding 'pmx/data/blosum62_new.mat'
2025-12-19T11:01:36,011   adding 'pmx/data/bp.pkl'
2025-12-19T11:01:36,031   adding 'pmx/data/bp_amber.pkl'
2025-12-19T11:01:36,052   adding 'pmx/data/bp_charmm.pkl'
2025-12-19T11:01:36,062   adding 'pmx/data/rna.pkl'
2025-12-19T11:01:36,065   adding 'pmx/data/mutff/atommass.dat'
2025-12-19T11:01:36,067   adding 'pmx/data/mutff/elements.dat'
2025-12-19T11:01:36,069   adding 'pmx/data/mutff/residuetypes.dat'
2025-12-19T11:01:36,076   adding 'pmx/data/mutff/spc216.gro'
2025-12-19T11:01:36,078   adding 'pmx/data/mutff/specbond.dat'
2025-12-19T11:01:36,079   adding 'pmx/data/mutff/vdwradii.dat'
2025-12-19T11:01:36,081   adding 'pmx/data/mutff/xlateat.dat'
2025-12-19T11:01:36,084   adding 'pmx/data/mutff/amber14sbmut.ff/Makefile.am'
2025-12-19T11:01:36,086   adding 'pmx/data/mutff/amber14sbmut.ff/Makefile.in'
2025-12-19T11:01:36,089   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.arn'
2025-12-19T11:01:36,091   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.c.tdb'
2025-12-19T11:01:36,092   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.hdb'
2025-12-19T11:01:36,094   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.n.tdb'
2025-12-19T11:01:36,096   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.r2b'
2025-12-19T11:01:36,103   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.rtp'
2025-12-19T11:01:36,105   adding 'pmx/data/mutff/amber14sbmut.ff/aminoacids.vsd'
2025-12-19T11:01:36,107   adding 'pmx/data/mutff/amber14sbmut.ff/atomtypes.atp'
2025-12-19T11:01:36,109   adding 'pmx/data/mutff/amber14sbmut.ff/dna.arn'
2025-12-19T11:01:36,111   adding 'pmx/data/mutff/amber14sbmut.ff/dna.hdb'
2025-12-19T11:01:36,112   adding 'pmx/data/mutff/amber14sbmut.ff/dna.r2b'
2025-12-19T11:01:36,115   adding 'pmx/data/mutff/amber14sbmut.ff/dna.rtp'
2025-12-19T11:01:36,123   adding 'pmx/data/mutff/amber14sbmut.ff/ffbonded.itp'
2025-12-19T11:01:36,125   adding 'pmx/data/mutff/amber14sbmut.ff/ffnonbonded.itp'
2025-12-19T11:01:36,127   adding 'pmx/data/mutff/amber14sbmut.ff/forcefield.doc'
2025-12-19T11:01:36,128   adding 'pmx/data/mutff/amber14sbmut.ff/forcefield.itp'
2025-12-19T11:01:36,130   adding 'pmx/data/mutff/amber14sbmut.ff/gbsa.itp'
2025-12-19T11:01:36,132   adding 'pmx/data/mutff/amber14sbmut.ff/ions.itp'
2025-12-19T11:01:36,310   adding 'pmx/data/mutff/amber14sbmut.ff/mutres.mtp'
2025-12-19T11:01:36,395   adding 'pmx/data/mutff/amber14sbmut.ff/mutres.rtp'
2025-12-19T11:01:36,404   adding 'pmx/data/mutff/amber14sbmut.ff/rna.arn'
2025-12-19T11:01:36,406   adding 'pmx/data/mutff/amber14sbmut.ff/rna.hdb'
2025-12-19T11:01:36,408   adding 'pmx/data/mutff/amber14sbmut.ff/rna.r2b'
2025-12-19T11:01:36,411   adding 'pmx/data/mutff/amber14sbmut.ff/rna.rtp'
2025-12-19T11:01:36,413   adding 'pmx/data/mutff/amber14sbmut.ff/spc.itp'
2025-12-19T11:01:36,414   adding 'pmx/data/mutff/amber14sbmut.ff/spce.itp'
2025-12-19T11:01:36,416   adding 'pmx/data/mutff/amber14sbmut.ff/tip3p.itp'
2025-12-19T11:01:36,418   adding 'pmx/data/mutff/amber14sbmut.ff/tip4p.itp'
2025-12-19T11:01:36,419   adding 'pmx/data/mutff/amber14sbmut.ff/tip4pew.itp'
2025-12-19T11:01:36,421   adding 'pmx/data/mutff/amber14sbmut.ff/tip5p.itp'
2025-12-19T11:01:36,423   adding 'pmx/data/mutff/amber14sbmut.ff/urea.itp'
2025-12-19T11:01:36,425   adding 'pmx/data/mutff/amber14sbmut.ff/watermodels.dat'
2025-12-19T11:01:36,429   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn'
2025-12-19T11:01:36,431   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.arn_backup'
2025-12-19T11:01:36,433   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.c.tdb'
2025-12-19T11:01:36,435   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.hdb'
2025-12-19T11:01:36,436   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.n.tdb'
2025-12-19T11:01:36,438   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.r2b'
2025-12-19T11:01:36,447   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.rtp'
2025-12-19T11:01:36,449   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/aminoacids.vsd'
2025-12-19T11:01:36,452   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/atomtypes.atp'
2025-12-19T11:01:36,456   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_ffbonded_for_ildn_test.itp'
2025-12-19T11:01:36,517   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/backup_mutres'
2025-12-19T11:01:36,529   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/correct_ffbonded.itp'
2025-12-19T11:01:36,531   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.arn'
2025-12-19T11:01:36,532   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.hdb'
2025-12-19T11:01:36,534   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.r2b'
2025-12-19T11:01:36,537   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/dna.rtp'
2025-12-19T11:01:36,539   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffberger.itp'
2025-12-19T11:01:36,544   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffbonded.itp'
2025-12-19T11:01:36,546   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ffnonbonded.itp'
2025-12-19T11:01:36,548   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.doc'
2025-12-19T11:01:36,549   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/forcefield.itp'
2025-12-19T11:01:36,551   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/gbsa.itp'
2025-12-19T11:01:36,553   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/ions.itp'
2025-12-19T11:01:36,571   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.mtp'
2025-12-19T11:01:36,581   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/mutres_dna.rtp'
2025-12-19T11:01:36,584   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer.itp'
2025-12-19T11:01:36,586   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/popc_AmbBer_posre.itp'
2025-12-19T11:01:36,587   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.arn'
2025-12-19T11:01:36,589   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.hdb'
2025-12-19T11:01:36,590   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.r2b'
2025-12-19T11:01:36,593   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/rna.rtp'
2025-12-19T11:01:36,594   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spc.itp'
2025-12-19T11:01:36,595   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/spce.itp'
2025-12-19T11:01:36,596   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip3p.itp'
2025-12-19T11:01:36,598   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4p.itp'
2025-12-19T11:01:36,599   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip4pew.itp'
2025-12-19T11:01:36,601   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/tip5p.itp'
2025-12-19T11:01:36,602   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/urea.itp'
2025-12-19T11:01:36,603   adding 'pmx/data/mutff/amber99sb-star-ildn-bsc1-mut.ff/watermodels.dat'
2025-12-19T11:01:36,605   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.arn'
2025-12-19T11:01:36,606   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.c.tdb'
2025-12-19T11:01:36,608   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.hdb'
2025-12-19T11:01:36,609   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.n.tdb'
2025-12-19T11:01:36,611   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.r2b'
2025-12-19T11:01:36,619   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.rtp'
2025-12-19T11:01:36,621   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/aminoacids.vsd'
2025-12-19T11:01:36,623   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/atomtypes.atp'
2025-12-19T11:01:36,626   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_ffbonded_for_ildn_test.itp'
2025-12-19T11:01:36,688   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/backup_mutres'
2025-12-19T11:01:36,699   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/correct_ffbonded.itp'
2025-12-19T11:01:36,700   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.arn'
2025-12-19T11:01:36,702   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.hdb'
2025-12-19T11:01:36,703   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.r2b'
2025-12-19T11:01:36,705   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/dna.rtp'
2025-12-19T11:01:36,707   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffberger.itp'
2025-12-19T11:01:36,711   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffbonded.itp'
2025-12-19T11:01:36,713   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ffnonbonded.itp'
2025-12-19T11:01:36,714   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.doc'
2025-12-19T11:01:36,715   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/forcefield.itp'
2025-12-19T11:01:36,717   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/gbsa.itp'
2025-12-19T11:01:36,718   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/ions.itp'
2025-12-19T11:01:36,736   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.mtp'
2025-12-19T11:01:36,745   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/mutres_dna.rtp'
2025-12-19T11:01:36,748   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer.itp'
2025-12-19T11:01:36,751   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/popc_AmbBer_posre.itp'
2025-12-19T11:01:36,752   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.arn'
2025-12-19T11:01:36,753   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.hdb'
2025-12-19T11:01:36,754   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.r2b'
2025-12-19T11:01:36,757   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/rna.rtp'
2025-12-19T11:01:36,758   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spc.itp'
2025-12-19T11:01:36,759   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/spce.itp'
2025-12-19T11:01:36,760   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip3p.itp'
2025-12-19T11:01:36,761   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4p.itp'
2025-12-19T11:01:36,762   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip4pew.itp'
2025-12-19T11:01:36,764   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/tip5p.itp'
2025-12-19T11:01:36,765   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/urea.itp'
2025-12-19T11:01:36,766   adding 'pmx/data/mutff/amber99sb-star-ildn-dna-mut.ff/watermodels.dat'
2025-12-19T11:01:36,769   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.arn'
2025-12-19T11:01:36,770   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.c.tdb'
2025-12-19T11:01:36,771   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.hdb'
2025-12-19T11:01:36,772   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.n.tdb'
2025-12-19T11:01:36,774   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.r2b'
2025-12-19T11:01:36,782   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.rtp'
2025-12-19T11:01:36,785   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/aminoacids.vsd'
2025-12-19T11:01:36,786   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/atomtypes.atp'
2025-12-19T11:01:36,787   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.arn'
2025-12-19T11:01:36,788   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.hdb'
2025-12-19T11:01:36,790   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.r2b'
2025-12-19T11:01:36,792   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/dna.rtp'
2025-12-19T11:01:36,796   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffbonded.itp'
2025-12-19T11:01:36,798   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/ffnonbonded.itp'
2025-12-19T11:01:36,799   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.doc'
2025-12-19T11:01:36,800   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/forcefield.itp'
2025-12-19T11:01:36,801   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/gbsa.itp'
2025-12-19T11:01:36,803   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/ions.itp'
2025-12-19T11:01:36,993   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.mtp'
2025-12-19T11:01:37,084   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/mutres.rtp'
2025-12-19T11:01:37,094   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.arn'
2025-12-19T11:01:37,095   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.hdb'
2025-12-19T11:01:37,096   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.r2b'
2025-12-19T11:01:37,099   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/rna.rtp'
2025-12-19T11:01:37,100   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/spc.itp'
2025-12-19T11:01:37,102   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/spce.itp'
2025-12-19T11:01:37,103   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip3p.itp'
2025-12-19T11:01:37,104   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4p.itp'
2025-12-19T11:01:37,105   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip4pew.itp'
2025-12-19T11:01:37,107   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/tip5p.itp'
2025-12-19T11:01:37,108   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/urea.itp'
2025-12-19T11:01:37,109   adding 'pmx/data/mutff/amber99sb-star-ildn-mut.ff/watermodels.dat'
2025-12-19T11:01:37,111   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.arn'
2025-12-19T11:01:37,113   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.c.tdb'
2025-12-19T11:01:37,114   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.hdb'
2025-12-19T11:01:37,115   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.n.tdb'
2025-12-19T11:01:37,116   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.r2b'
2025-12-19T11:01:37,120   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.rtp'
2025-12-19T11:01:37,122   adding 'pmx/data/mutff/charmm22star-mut.ff/aminoacids.vsd'
2025-12-19T11:01:37,124   adding 'pmx/data/mutff/charmm22star-mut.ff/atomtypes.atp'
2025-12-19T11:01:37,128   adding 'pmx/data/mutff/charmm22star-mut.ff/cmap.itp'
2025-12-19T11:01:37,130   adding 'pmx/data/mutff/charmm22star-mut.ff/dna.arn'
2025-12-19T11:01:37,131   adding 'pmx/data/mutff/charmm22star-mut.ff/dna.c.tdb'
2025-12-19T11:01:37,132   adding 'pmx/data/mutff/charmm22star-mut.ff/dna.hdb'
2025-12-19T11:01:37,133   adding 'pmx/data/mutff/charmm22star-mut.ff/dna.n.tdb'
2025-12-19T11:01:37,135   adding 'pmx/data/mutff/charmm22star-mut.ff/dna.rtp'
2025-12-19T11:01:37,143   adding 'pmx/data/mutff/charmm22star-mut.ff/ffbonded.itp'
2025-12-19T11:01:37,150   adding 'pmx/data/mutff/charmm22star-mut.ff/ffnabonded.itp'
2025-12-19T11:01:37,154   adding 'pmx/data/mutff/charmm22star-mut.ff/ffnanonbonded.itp'
2025-12-19T11:01:37,166   adding 'pmx/data/mutff/charmm22star-mut.ff/ffnonbonded.itp'
2025-12-19T11:01:37,168   adding 'pmx/data/mutff/charmm22star-mut.ff/forcefield.doc'
2025-12-19T11:01:37,170   adding 'pmx/data/mutff/charmm22star-mut.ff/forcefield.itp'
2025-12-19T11:01:37,171   adding 'pmx/data/mutff/charmm22star-mut.ff/gb.itp'
2025-12-19T11:01:37,172   adding 'pmx/data/mutff/charmm22star-mut.ff/ions.itp'
2025-12-19T11:01:37,173   adding 'pmx/data/mutff/charmm22star-mut.ff/lipids.hdb'
2025-12-19T11:01:37,177   adding 'pmx/data/mutff/charmm22star-mut.ff/lipids.rtp'
2025-12-19T11:01:37,179   adding 'pmx/data/mutff/charmm22star-mut.ff/mutres.arn'
2025-12-19T11:01:37,329   adding 'pmx/data/mutff/charmm22star-mut.ff/mutres.mtp'
2025-12-19T11:01:37,404   adding 'pmx/data/mutff/charmm22star-mut.ff/mutres.rtp'
2025-12-19T11:01:37,413   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.arn'
2025-12-19T11:01:37,414   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.c.tdb'
2025-12-19T11:01:37,415   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.hdb'
2025-12-19T11:01:37,416   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.n.tdb'
2025-12-19T11:01:37,417   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.r2b'
2025-12-19T11:01:37,419   adding 'pmx/data/mutff/charmm22star-mut.ff/rna.rtp'
2025-12-19T11:01:37,421   adding 'pmx/data/mutff/charmm22star-mut.ff/spc.itp'
2025-12-19T11:01:37,422   adding 'pmx/data/mutff/charmm22star-mut.ff/spce.itp'
2025-12-19T11:01:37,423   adding 'pmx/data/mutff/charmm22star-mut.ff/tip3p.itp'
2025-12-19T11:01:37,425   adding 'pmx/data/mutff/charmm22star-mut.ff/tip4p.itp'
2025-12-19T11:01:37,426   adding 'pmx/data/mutff/charmm22star-mut.ff/tip4pew.itp'
2025-12-19T11:01:37,427   adding 'pmx/data/mutff/charmm22star-mut.ff/tip5p.itp'
2025-12-19T11:01:37,429   adding 'pmx/data/mutff/charmm22star-mut.ff/tips3p.itp'
2025-12-19T11:01:37,430   adding 'pmx/data/mutff/charmm22star-mut.ff/watermodels.dat'
2025-12-19T11:01:37,434   adding 'pmx/data/mutff/charmm36m-mut.ff/atomtypes.atp'
2025-12-19T11:01:37,446   adding 'pmx/data/mutff/charmm36m-mut.ff/cmap.itp'
2025-12-19T11:01:37,529   adding 'pmx/data/mutff/charmm36m-mut.ff/ffbonded.itp'
2025-12-19T11:01:37,655   adding 'pmx/data/mutff/charmm36m-mut.ff/ffnonbonded.itp'
2025-12-19T11:01:37,666   adding 'pmx/data/mutff/charmm36m-mut.ff/forcefield.doc'
2025-12-19T11:01:37,668   adding 'pmx/data/mutff/charmm36m-mut.ff/forcefield.itp'
2025-12-19T11:01:37,669   adding 'pmx/data/mutff/charmm36m-mut.ff/gb.itp'
2025-12-19T11:01:37,671   adding 'pmx/data/mutff/charmm36m-mut.ff/ions.itp'
2025-12-19T11:01:37,672   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.arn'
2025-12-19T11:01:37,673   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.c.tdb'
2025-12-19T11:01:37,675   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.hdb'
2025-12-19T11:01:37,676   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.n.tdb'
2025-12-19T11:01:37,677   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.r2b'
2025-12-19T11:01:37,813   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.rtp'
2025-12-19T11:01:37,822   adding 'pmx/data/mutff/charmm36m-mut.ff/merged.vsd'
2025-12-19T11:01:37,823   adding 'pmx/data/mutff/charmm36m-mut.ff/mutres.arn'
2025-12-19T11:01:37,987   adding 'pmx/data/mutff/charmm36m-mut.ff/mutres.mtp'
2025-12-19T11:01:38,070   adding 'pmx/data/mutff/charmm36m-mut.ff/mutres.rtp'
2025-12-19T11:01:38,096   adding 'pmx/data/mutff/charmm36m-mut.ff/mutres_dna.mtp'
2025-12-19T11:01:38,106   adding 'pmx/data/mutff/charmm36m-mut.ff/mutres_dna.rtp'
2025-12-19T11:01:38,107   adding 'pmx/data/mutff/charmm36m-mut.ff/nbfix.itp'
2025-12-19T11:01:38,109   adding 'pmx/data/mutff/charmm36m-mut.ff/spc.itp'
2025-12-19T11:01:38,110   adding 'pmx/data/mutff/charmm36m-mut.ff/spce.itp'
2025-12-19T11:01:38,111   adding 'pmx/data/mutff/charmm36m-mut.ff/tip3p.itp'
2025-12-19T11:01:38,112   adding 'pmx/data/mutff/charmm36m-mut.ff/tip4p.itp'
2025-12-19T11:01:38,113   adding 'pmx/data/mutff/charmm36m-mut.ff/watermodels.dat'
2025-12-19T11:01:38,116   adding 'pmx/extensions/pmx/Energy.c'
2025-12-19T11:01:38,118   adding 'pmx/extensions/pmx/Geometry.c'
2025-12-19T11:01:38,121   adding 'pmx/extensions/pmx/Geometry.h'
2025-12-19T11:01:38,122   adding 'pmx/extensions/pmx/cpp_test.cpp'
2025-12-19T11:01:38,124   adding 'pmx/extensions/pmx/init.c'
2025-12-19T11:01:38,125   adding 'pmx/extensions/pmx/pmx.h'
2025-12-19T11:01:38,127   adding 'pmx/extensions/pmx/wrap_Geometry.c'
2025-12-19T11:01:38,129   adding 'pmx/extensions/xdr/trr2xtc.c'
2025-12-19T11:01:38,136   adding 'pmx/extensions/xdr/xdrfile.c'
2025-12-19T11:01:38,140   adding 'pmx/extensions/xdr/xdrfile.h'
2025-12-19T11:01:38,142   adding 'pmx/extensions/xdr/xdrfile_c_test.c'
2025-12-19T11:01:38,144   adding 'pmx/extensions/xdr/xdrfile_trr.c'
2025-12-19T11:01:38,146   adding 'pmx/extensions/xdr/xdrfile_trr.h'
2025-12-19T11:01:38,147   adding 'pmx/extensions/xdr/xdrfile_xtc.c'
2025-12-19T11:01:38,149   adding 'pmx/extensions/xdr/xdrfile_xtc.h'
2025-12-19T11:01:38,150   adding 'pmx/rosetta_example/README'
2025-12-19T11:01:38,152   adding 'pmx/rosetta_example/analyze.py'
2025-12-19T11:01:38,153   adding 'pmx/rosetta_example/mut.dat'
2025-12-19T11:01:38,182   adding 'pmx/rosetta_example/plot_results.ipynb'
2025-12-19T11:01:38,274   adding 'pmx/rosetta_example/prot_zn.pdb'
2025-12-19T11:01:38,279   adding 'pmx/rosetta_example/rosetta_prepare.ipynb'
2025-12-19T11:01:38,280   adding 'pmx/rosetta_example/submit_jobscripts.py'
2025-12-19T11:01:38,282   adding 'pmx/scripts/__init__.py'
2025-12-19T11:01:38,285   adding 'pmx/scripts/analyze_dhdl.py'
2025-12-19T11:01:38,288   adding 'pmx/scripts/atomMapping.py'
2025-12-19T11:01:38,290   adding 'pmx/scripts/build_cyclic_top.py'
2025-12-19T11:01:38,291   adding 'pmx/scripts/cli.py'
2025-12-19T11:01:38,294   adding 'pmx/scripts/fill_cgenff_itp.py'
2025-12-19T11:01:38,296   adding 'pmx/scripts/fix_residue_names.py'
2025-12-19T11:01:38,298   adding 'pmx/scripts/gen_abs_restraints.py'
2025-12-19T11:01:38,305   adding 'pmx/scripts/generate_hybrid_residue.py'
2025-12-19T11:01:38,307   adding 'pmx/scripts/generate_hybrid_topology.py'
2025-12-19T11:01:38,308   adding 'pmx/scripts/hydrogen_atom_renaming.py'
2025-12-19T11:01:38,310   adding 'pmx/scripts/ligandHybrid.py'
2025-12-19T11:01:38,312   adding 'pmx/scripts/make_double_box.py'
2025-12-19T11:01:38,314   adding 'pmx/scripts/md_setup.py'
2025-12-19T11:01:38,317   adding 'pmx/scripts/mutate.py'
2025-12-19T11:01:38,322   adding 'pmx/scripts/parameterize_ligands.py'
2025-12-19T11:01:38,323   adding 'pmx/scripts/prepare_crooks_runs.py'
2025-12-19T11:01:38,325   adding 'pmx/scripts/repartition_mass.py'
2025-12-19T11:01:38,326   adding 'pmx/scripts/set_gmxlib.py'
2025-12-19T11:01:38,328   adding 'pmx/scripts/setup_abfe.py'
2025-12-19T11:01:38,330   adding 'pmx/scripts/icolos_entrypoints/__init__.py'
2025-12-19T11:01:38,332   adding 'pmx/scripts/icolos_entrypoints/assemble_systems.py'
2025-12-19T11:01:38,335   adding 'pmx_biobb-5.2.2.dist-info/licenses/LICENSE'
2025-12-19T11:01:38,336   adding 'pmx_biobb-5.2.2.dist-info/METADATA'
2025-12-19T11:01:38,337   adding 'pmx_biobb-5.2.2.dist-info/WHEEL'
2025-12-19T11:01:38,338   adding 'pmx_biobb-5.2.2.dist-info/entry_points.txt'
2025-12-19T11:01:38,339   adding 'pmx_biobb-5.2.2.dist-info/top_level.txt'
2025-12-19T11:01:38,343   adding 'pmx_biobb-5.2.2.dist-info/RECORD'
2025-12-19T11:01:38,414   removing build/bdist.linux-armv7l/wheel
2025-12-19T11:01:38,653   Building wheel for pmx-biobb (setup.py): finished with status 'done'
2025-12-19T11:01:38,779   Created wheel for pmx-biobb: filename=pmx_biobb-5.2.2-cp311-cp311-linux_armv7l.whl size=5730903 sha256=f1ddfc034712fd5bf794f676e9d34b3dd905c15bc3d03a8412587dc4748ec89a
2025-12-19T11:01:38,781   Stored in directory: /tmp/pip-ephem-wheel-cache-gmeuccqb/wheels/87/16/9c/838dbb4541fc518cf383be1cf614411d803c3b6a4945689986
2025-12-19T11:01:38,802 Successfully built pmx-biobb
2025-12-19T11:01:38,944 Removed build tracker: '/tmp/pip-build-tracker-jit8kq7b'