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             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.3">coverage.py v7.6.3</a>,
-            created at 2024-10-17 14:08 +0000
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+            created at 2024-10-17 14:25 +0000
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             &nbsp; &nbsp; &nbsp;
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+            created at 2024-10-17 14:25 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -289,7 +289,7 @@ <h2>
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+            created at 2024-10-17 14:25 +0000
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 <head>
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-    <title>Coverage for biobb_cmip/cmip/common.py: 44%</title>
+    <title>Coverage for biobb_cmip/cmip/common.py: 45%</title>
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             &nbsp; &nbsp; &nbsp;
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+            created at 2024-10-17 14:25 +0000
         </p>
         <aside class="hidden">
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+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">    <span class="key">while</span> <span class="key">True</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
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@@ -702,7 +702,7 @@ <h2>
             <a class="nav" href="z_edf6e6b2d5ce0b2c___init___py.html">&#xbb; next</a>
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+            created at 2024-10-17 14:25 +0000
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+            created at 2024-10-17 14:25 +0000
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+            created at 2024-10-17 14:25 +0000
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diff --git a/flake8/index.html b/flake8/index.html
index 33fc9ea..eae2332 100644
--- a/flake8/index.html
+++ b/flake8/index.html
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       <div id="page">
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+         <p id="versions">Generated on 2024-10-17 14:25
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index c0f2ee2..575d650 100644
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+++ b/junit/junit.xml
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-    <p>Report generated on 17-Oct-2024 at 14:08:47 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 17-Oct-2024 at 14:25:50 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
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backbone --add_caps none; fixside --fix All; add_hydrogen --add_mode auto --add_charges CMIP&amp;#x27;\n\n2024-10-17 14:08:21,599 [MainThread  ] [INFO ]  Executing: check_structure -v -i /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7...\n2024-10-17 14:08:21,599 [MainThread  ] [INFO ]  Exit code: 0\n2024-10-17 14:08:21,600 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7bd9-49eb-88c9-6eebf1bc4a36/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\n\nStep 1: water --remove yes\nRunning water. Options: --remove yes\nDetected 78 Water molecules\nRemoved 78 Water molecules\n\nStep 2:  backbone --add_caps none\nRunning backbone. Options: --add_caps none\nFound No residues with missing backbone atoms\nNo backbone breaks\nNo unexpected backbone links\nCapping terminal ends\nTrue terminal residues: A1,A129\nNothing to do\nNo caps added\n\nStep 3:  fixside --fix All\nRunning fixside. Options: --fix All\nFound no residues with missing or unknown side chain atoms\n\nStep 4:  add_hydrogen --add_mode auto --add_charges CMIP\nRunning add_hydrogen. Options: --add_mode auto --add_charges CMIP\nFound 38 Residues requiring selection on adding H atoms\n CYS A6,A30,A64,A76,A80,A94,A115,A127\n ASP A18,A48,A52,A66,A87,A101,A119\n GLU A7,A35\n HIS A15\n LYS A1,A13,A33,A96,A97,A116\n ARG A5,A14,A21,A45,A61,A68,A73,A112,A114,A125,A128\n TYR A20,A23,A53\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A15 by HIE\nUpdating partial charges and atom types\nTotal assigned charge:       8.00\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  129\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 129 (total 967 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1968\nStructure saved on /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7bd9-49eb-88c9-6eebf1bc4a36/1aki_cmip.pdb\n\n2024-10-17 14:08:21,600 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7bd9-49eb-88c9-6eebf1bc4a36&amp;#x27;]\n2024-10-17 14:08:21,601 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_31/cmip_prepare_pdb/1aki_cmip.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_31/cmip_prepare_pdb/1aki_cmip.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/1aki_cmip.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 1001\n     Atoms ALIGNED in PDB_B: 1001\n     RMS: 1.4828848083881487e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_prepare_pdb Version: 4.2.0\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:82 /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7bd9-49eb-88c9-6eebf1bc4a36 directory successfully created\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/1aki.pdb to /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7bd9-49eb-88c9-6eebf1bc4a36\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:63 check_structure -v -i /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7bd9-49eb-88c9-6eebf1bc4a36/1aki.pdb -o /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7bd9-49eb-88c9-6eebf1bc4a36/1aki_cmip.pdb --output_format cmip --non_interactive command_list --list &amp;#x27;water --remove yes; backbone --add_caps none; fixside --fix All; add_hydrogen --add_mode auto --add_charges CMIP&amp;#x27;\n\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:36 Executing: check_structure -v -i /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7...\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7bd9-49eb-88c9-6eebf1bc4a36/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\n\nStep 1: water --remove yes\nRunning water. Options: --remove yes\nDetected 78 Water molecules\nRemoved 78 Water molecules\n\nStep 2:  backbone --add_caps none\nRunning backbone. Options: --add_caps none\nFound No residues with missing backbone atoms\nNo backbone breaks\nNo unexpected backbone links\nCapping terminal ends\nTrue terminal residues: A1,A129\nNothing to do\nNo caps added\n\nStep 3:  fixside --fix All\nRunning fixside. Options: --fix All\nFound no residues with missing or unknown side chain atoms\n\nStep 4:  add_hydrogen --add_mode auto --add_charges CMIP\nRunning add_hydrogen. Options: --add_mode auto --add_charges CMIP\nFound 38 Residues requiring selection on adding H atoms\n CYS A6,A30,A64,A76,A80,A94,A115,A127\n ASP A18,A48,A52,A66,A87,A101,A119\n GLU A7,A35\n HIS A15\n LYS A1,A13,A33,A96,A97,A116\n ARG A5,A14,A21,A45,A61,A68,A73,A112,A114,A125,A128\n TYR A20,A23,A53\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A15 by HIE\nUpdating partial charges and atom types\nTotal assigned charge:       8.00\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  129\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 129 (total 967 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1968\nStructure saved on /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7bd9-49eb-88c9-6eebf1bc4a36/1aki_cmip.pdb\n\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_dfe66409-7bd9-49eb-88c9-6eebf1bc4a36&amp;#x27;]\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_31\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&#34;, &#34;duration&#34;: &#34;00:00:08&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:08&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-10-17 14:08:21,806 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_prepare_structure Version: 4.2.0\n2024-10-17 14:08:21,810 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\n2024-10-17 14:08:21,810 [MainThread  ] [INFO ]  to:\n2024-10-17 14:08:21,810 [MainThread  ] [INFO ]  [&amp;#x27;967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_p2g.top&amp;#x27;, &amp;#x27;967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_posre.itp&amp;#x27;]\n2024-10-17 14:08:21,810 [MainThread  ] [INFO ]  Unzipping: \n2024-10-17 14:08:21,810 [MainThread  ] [INFO ]  /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\n2024-10-17 14:08:21,810 [MainThread  ] [INFO ]  To: \n2024-10-17 14:08:21,810 [MainThread  ] [INFO ]  967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_p2g.top\n2024-10-17 14:08:21,810 [MainThread  ] [INFO ]  967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_posre.itp\n2024-10-17 14:08:21,811 [MainThread  ] [INFO ]  Reading: 967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_p2g.top to extract charges\n2024-10-17 14:08:25,323 [MainThread  ] [INFO ]  Reading: 967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_p2g.top to extract elements\n2024-10-17 14:08:29,201 [MainThread  ] [INFO ]  Removed: [&amp;#x27;967f6306-3058-4dc0-a872-6ff2da46d617&amp;#x27;]\n2024-10-17 14:08:29,201 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_31/cmip_prepare_structure_topology/prepare_structure_topology_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_31/cmip_prepare_structure_topology/prepare_structure_topology_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/egfr_cmip.pdb\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2872\n     Atoms ALIGNED in PDB_B: 2872\n     RMS: 1.1126217417895259e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_prepare_structure Version: 4.2.0\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:174 [&amp;#x27;967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_p2g.top&amp;#x27;, &amp;#x27;967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_posre.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:256 967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_p2g.top\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:256 967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_posre.itp\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Reading: 967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_p2g.top to extract charges\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Reading: 967f6306-3058-4dc0-a872-6ff2da46d617/pdb2gmx_p2g.top to extract elements\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Removed: [&amp;#x27;967f6306-3058-4dc0-a872-6ff2da46d617&amp;#x27;]\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_31\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&#34;, &#34;duration&#34;: &#34;00:00:18&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:18&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-10-17 14:08:29,521 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_run Version: 4.2.0\n2024-10-17 14:08:29,521 [MainThread  ] [INFO ]  /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8 directory successfully created\n2024-10-17 14:08:29,522 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.hACE2.cmip.pdb to /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8\n2024-10-17 14:08:29,523 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.RBD.cmip.pdb to /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8\n2024-10-17 14:08:29,523 [MainThread  ] [INFO ]  Copy: /home/user/micromamba/envs/test_environment/share/cmip/dat/vdwprm to /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8\n2024-10-17 14:08:29,523 [MainThread  ] [INFO ]  Copy: 2809ad07-4d51-433b-a5b5-82ca499b0c52/params to /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8\n2024-10-17 14:08:29,523 [MainThread  ] [INFO ]  cmip -i /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/params -vdw /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/vdwprm -hs /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/RBD-hACE2.hACE2.cmip.pdb -pr /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/RBD-hACE2.RBD.cmip.pdb -byat /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/output_byat.out\n\n2024-10-17 14:08:47,240 [MainThread  ] [INFO ]  Executing: cmip -i /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e08981...\n2024-10-17 14:08:47,240 [MainThread  ] [INFO ]  Exit code: 0\n2024-10-17 14:08:47,240 [MainThread  ] [INFO ]   =================================================\n =                                               =\n =                C M I P  (2.7.0)               =\n =          J. Ll. Gelpi, A. Morreale,           =\n =            F. J. Luque, M.Orozco              =\n =      Dept. Biochemistry. Univ. Barcelona      =\n =                  1999-2021                    =\n =================================================\n\n  Code for ASA calculation by Juan F. Recio       \n\n#T Run started at   14: 8:29 h on 17-10-2024\n SIZES\n -----\n MAXTIP:           100\n MAXATH:            80000\n MAXATP x MAXCONF: 100000\n\n INPUT FILES\n -----------\n    Calc. settings: /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/params                                                                   \n VdW Parameters:      /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/vdwprm                                                                   \n PDB Host:            /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/RBD-hACE2.hACE2.cmip.pdb                                                 \n PDB Guest:           /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/RBD-hACE2.RBD.cmip.pdb                                                   \n Conf. energies:      energies                                                                                                                                              \n\n OUTPUT FILES\n ------------\n LOG file:            output                                                                                                                                                \n Grid Out:            gridout                                                                                                                                               \n Output PDB coords:          outpdb                                                                                                                                                \n\n Parameters\n ----------\nDocking Interaction energy calculation. PB electrostatics                       \n&amp;amp;cntrl                                                                          \n tipcalc = 3                                                                    \n calcgrid = 1                                                                   \n irest = 0                                                                      \n orest = 0                                                                      \n coorfmt = 2                                                                    \n fvdw = 0.8                                                                     \n pbelec = 1                                                                     \n pbinic = 2                                                                     \n wgp = 0                                                                        \n ebyatom = 1                                                                    \n readgrid = 2                                                                   \n CENX=0.0,CENY=0.0,CENZ=0.0                                                     \n DIMX=64,DIMY=64,DIMZ=64                                                        \n INTX0=1.5,INTY0=1.5,INTZ0=1.5                                                  \n readgrid0 = 2                                                                  \n perfill0 = 0.6                                                                 \n pbfocus = 1                                                                    \n IREST = 0                                                                      \n&amp;amp;end                                                                            \n\n 18 VdW parameters loaded successfully\n\n Host:      9519 atoms loaded, charge   -27.000\n\n TYPE OF CALCULATION: DOCKING\n Single point\n\n Guest: 3000 atom(s), charge -11.145,    1 conformation(s) loaded\n\n PB Focussing requested\n AUTOMATIC OUTER GRID\n --------------------\n Fill:    0.600\nAutomatic Outer Grid                                                                                                                \n Grid Size:      96.000 138.000 108.000  90.000  90.000  90.000\n Grid density:    64   92   72\n Grid units:      1.500   1.500   1.500\n Grid origin:    23.610  -1.245   2.315\n Grid center:    71.610  67.755  56.315\n     441285 Grid points\n\n AUTOMATIC GRID\n --------------\n Fill:    0.800\nAutomatic Grid                                                                                                                      \n Grid Size:      72.000 103.000  81.500  90.000  90.000  90.000\n Grid density:   144  206  163\n Grid units:      0.500   0.500   0.500\n Grid origin:    35.610  16.255  15.565\n Grid center:    71.610  67.755  56.315\n    4922460 Grid points\n\n All input data read succesfully\n\n Warning: Dielectric grid computed at double density\n Mapping host molecule to outer grid\n   Total charge            :   -27.0000248    \n   Low diel. grid points   :                230941 (   97428.2344     A3)\n   High diel. grid points  :               3229484\n   I Str=0 grid points     :                441285\n   Boundary grid points    :                 57064\n Mapping host molecule to grid\n   Total charge            :   -27.0000019    \n   Low diel. grid points   :               5855067 (   91485.4219      A3)\n   High diel. grid points  :              33174672\n   I Str=0 grid points     :               4922460\n   Boundary grid points    :                550671\n\n CLHOST=           0\n EXTERNAL CUTOFF=   999999.000    \n Checking potentials to calculate...\n - Vdw: C   \n - Vdw: N   \n - Vdw: S   \n - Vdw: HO  \n - Vdw: HN  \n - Vdw: H   \n - Vdw: O   \n - Electrostatic \n     Dielectric type    :            0\n     Dielectric constant:    2.00000000    \n Vdw energies:\n  -C    -2.15     0.254E+21\n  -N    -2.73     0.266E+21\n  -S    -3.82     0.557E+21\n  -HO    0.00      0.00    \n  -HN  -0.344     0.116E+18\n  -H   -0.860     0.268E+20\n  -O    -2.87     0.169E+21\n     Poisson-Boltzmann calculation requested\n     Focussing          :            1\n     Initial potentials :            2\n     Solute  Dielectric :    2.00000000    \n     Solvent Dielectric :    79.8000031    \n     Solvent radius     :    1.39999998    \n     Convergence crit.  :    9.99999975E-05\n     Ionic strength     :    0.00000000    \n Outer grid\n          20  0.147574857       14.6699677    \n          40   2.98345201E-02   3.29004049    \n          60   6.40256703E-03  0.731274426    \n          80   1.45485543E-03  0.142998144    \n         100   3.42993939E-04   1.78021304E-02\n         120   8.23287264E-05   2.51317094E-03\n         140   1.94953154E-05   8.38404230E-04\n Converged at   158 iterations (Mean:       0.499E-05, Max:      0.923E-04)\n Potentials:   -145.994   169.029\n Inner Grid limits\n Potentials:   -128.467   156.689\n          20  0.879424870       44.1415825    \n          40  0.403403550       18.3190784    \n          60  0.196925759       11.3940735    \n          80   9.77351591E-02   6.85034132    \n         100   4.82290052E-02   3.02071881    \n         120   2.38220431E-02   1.71308899    \n         140   1.16539253E-02  0.880087018    \n         160   5.68585889E-03  0.497510761    \n         180   2.73818849E-03  0.352287740    \n         200   1.29186665E-03  0.225940496    \n         220   5.93950623E-04  0.123246640    \n         240   2.69010896E-04   4.76482585E-02\n         260   1.19791985E-04   1.82344895E-02\n         280   5.35966064E-05   5.74939372E-03\n         300   2.40469999E-05   2.51911697E-03\n         320   1.08288414E-05   9.81772551E-04\n         340   4.89419563E-06   3.82507715E-04\n         360   2.25630197E-06   1.72914923E-04\n Converged at   376 iterations (Mean:       0.125E-05, Max:      0.967E-04)\n Potentials:   -739.519  1051.831\n Internal:        4.20389539E-42  kcal/mol\n Van der Waals:         Infinity  kcal/mol\n Electrostatic:   90.0758438     kcal/mol\n Total Energy :         Infinity kcal/mol\n\n#T Run finished at  14: 8:47 h on 17-10-2024\n\n#T       T I M I N G S \n#T       ---------------\n#T         Input:     0.250 s,   1.42%\n#T         Setup:     2.250 s,  12.77%\n#T         Grids:    15.125 s,  85.82%\n#T        Energy:     0.000 s,   0.00%\n#T        Output:     0.000 s,   0.00%\n ----------------------------------\n#T         TOTAL:    17.625 s ( 0.00 h)\n\n2024-10-17 14:08:47,241 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8&amp;#x27;, &amp;#x27;2809ad07-4d51-433b-a5b5-82ca499b0c52&amp;#x27;]\n2024-10-17 14:08:47,242 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_31/cmip_run/output_byat.out\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_run Version: 4.2.0\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:82 /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8 directory successfully created\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.hACE2.cmip.pdb to /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.RBD.cmip.pdb to /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/micromamba/envs/test_environment/share/cmip/dat/vdwprm to /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: 2809ad07-4d51-433b-a5b5-82ca499b0c52/params to /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:cmd_wrapper.py:63 cmip -i /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/params -vdw /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/vdwprm -hs /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/RBD-hACE2.hACE2.cmip.pdb -pr /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/RBD-hACE2.RBD.cmip.pdb -byat /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/output_byat.out\n\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:cmd_wrapper.py:36 Executing: cmip -i /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e08981...\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:cmd_wrapper.py:41  =================================================\n =                                               =\n =                C M I P  (2.7.0)               =\n =          J. Ll. Gelpi, A. Morreale,           =\n =            F. J. Luque, M.Orozco              =\n =      Dept. Biochemistry. Univ. Barcelona      =\n =                  1999-2021                    =\n =================================================\n\n  Code for ASA calculation by Juan F. Recio       \n\n#T Run started at   14: 8:29 h on 17-10-2024\n SIZES\n -----\n MAXTIP:           100\n MAXATH:            80000\n MAXATP x MAXCONF: 100000\n\n INPUT FILES\n -----------\n    Calc. settings: /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/params                                                                   \n VdW Parameters:      /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/vdwprm                                                                   \n PDB Host:            /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/RBD-hACE2.hACE2.cmip.pdb                                                 \n PDB Guest:           /tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8/RBD-hACE2.RBD.cmip.pdb                                                   \n Conf. energies:      energies                                                                                                                                              \n\n OUTPUT FILES\n ------------\n LOG file:            output                                                                                                                                                \n Grid Out:            gridout                                                                                                                                               \n Output PDB coords:          outpdb                                                                                                                                                \n\n Parameters\n ----------\nDocking Interaction energy calculation. PB electrostatics                       \n&amp;amp;cntrl                                                                          \n tipcalc = 3                                                                    \n calcgrid = 1                                                                   \n irest = 0                                                                      \n orest = 0                                                                      \n coorfmt = 2                                                                    \n fvdw = 0.8                                                                     \n pbelec = 1                                                                     \n pbinic = 2                                                                     \n wgp = 0                                                                        \n ebyatom = 1                                                                    \n readgrid = 2                                                                   \n CENX=0.0,CENY=0.0,CENZ=0.0                                                     \n DIMX=64,DIMY=64,DIMZ=64                                                        \n INTX0=1.5,INTY0=1.5,INTZ0=1.5                                                  \n readgrid0 = 2                                                                  \n perfill0 = 0.6                                                                 \n pbfocus = 1                                                                    \n IREST = 0                                                                      \n&amp;amp;end                                                                            \n\n 18 VdW parameters loaded successfully\n\n Host:      9519 atoms loaded, charge   -27.000\n\n TYPE OF CALCULATION: DOCKING\n Single point\n\n Guest: 3000 atom(s), charge -11.145,    1 conformation(s) loaded\n\n PB Focussing requested\n AUTOMATIC OUTER GRID\n --------------------\n Fill:    0.600\nAutomatic Outer Grid                                                                                                                \n Grid Size:      96.000 138.000 108.000  90.000  90.000  90.000\n Grid density:    64   92   72\n Grid units:      1.500   1.500   1.500\n Grid origin:    23.610  -1.245   2.315\n Grid center:    71.610  67.755  56.315\n     441285 Grid points\n\n AUTOMATIC GRID\n --------------\n Fill:    0.800\nAutomatic Grid                                                                                                                      \n Grid Size:      72.000 103.000  81.500  90.000  90.000  90.000\n Grid density:   144  206  163\n Grid units:      0.500   0.500   0.500\n Grid origin:    35.610  16.255  15.565\n Grid center:    71.610  67.755  56.315\n    4922460 Grid points\n\n All input data read succesfully\n\n Warning: Dielectric grid computed at double density\n Mapping host molecule to outer grid\n   Total charge            :   -27.0000248    \n   Low diel. grid points   :                230941 (   97428.2344     A3)\n   High diel. grid points  :               3229484\n   I Str=0 grid points     :                441285\n   Boundary grid points    :                 57064\n Mapping host molecule to grid\n   Total charge            :   -27.0000019    \n   Low diel. grid points   :               5855067 (   91485.4219      A3)\n   High diel. grid points  :              33174672\n   I Str=0 grid points     :               4922460\n   Boundary grid points    :                550671\n\n CLHOST=           0\n EXTERNAL CUTOFF=   999999.000    \n Checking potentials to calculate...\n - Vdw: C   \n - Vdw: N   \n - Vdw: S   \n - Vdw: HO  \n - Vdw: HN  \n - Vdw: H   \n - Vdw: O   \n - Electrostatic \n     Dielectric type    :            0\n     Dielectric constant:    2.00000000    \n Vdw energies:\n  -C    -2.15     0.254E+21\n  -N    -2.73     0.266E+21\n  -S    -3.82     0.557E+21\n  -HO    0.00      0.00    \n  -HN  -0.344     0.116E+18\n  -H   -0.860     0.268E+20\n  -O    -2.87     0.169E+21\n     Poisson-Boltzmann calculation requested\n     Focussing          :            1\n     Initial potentials :            2\n     Solute  Dielectric :    2.00000000    \n     Solvent Dielectric :    79.8000031    \n     Solvent radius     :    1.39999998    \n     Convergence crit.  :    9.99999975E-05\n     Ionic strength     :    0.00000000    \n Outer grid\n          20  0.147574857       14.6699677    \n          40   2.98345201E-02   3.29004049    \n          60   6.40256703E-03  0.731274426    \n          80   1.45485543E-03  0.142998144    \n         100   3.42993939E-04   1.78021304E-02\n         120   8.23287264E-05   2.51317094E-03\n         140   1.94953154E-05   8.38404230E-04\n Converged at   158 iterations (Mean:       0.499E-05, Max:      0.923E-04)\n Potentials:   -145.994   169.029\n Inner Grid limits\n Potentials:   -128.467   156.689\n          20  0.879424870       44.1415825    \n          40  0.403403550       18.3190784    \n          60  0.196925759       11.3940735    \n          80   9.77351591E-02   6.85034132    \n         100   4.82290052E-02   3.02071881    \n         120   2.38220431E-02   1.71308899    \n         140   1.16539253E-02  0.880087018    \n         160   5.68585889E-03  0.497510761    \n         180   2.73818849E-03  0.352287740    \n         200   1.29186665E-03  0.225940496    \n         220   5.93950623E-04  0.123246640    \n         240   2.69010896E-04   4.76482585E-02\n         260   1.19791985E-04   1.82344895E-02\n         280   5.35966064E-05   5.74939372E-03\n         300   2.40469999E-05   2.51911697E-03\n         320   1.08288414E-05   9.81772551E-04\n         340   4.89419563E-06   3.82507715E-04\n         360   2.25630197E-06   1.72914923E-04\n Converged at   376 iterations (Mean:       0.125E-05, Max:      0.967E-04)\n Potentials:   -739.519  1051.831\n Internal:        4.20389539E-42  kcal/mol\n Van der Waals:         Infinity  kcal/mol\n Electrostatic:   90.0758438     kcal/mol\n Total Energy :         Infinity kcal/mol\n\n#T Run finished at  14: 8:47 h on 17-10-2024\n\n#T       T I M I N G S \n#T       ---------------\n#T         Input:     0.250 s,   1.42%\n#T         Setup:     2.250 s,  12.77%\n#T         Grids:    15.125 s,  85.82%\n#T        Energy:     0.000 s,   0.00%\n#T        Output:     0.000 s,   0.00%\n ----------------------------------\n#T         TOTAL:    17.625 s ( 0.00 h)\n\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_31/cmip_run/sandbox_aced85c1-f2be-4074-9e5e-a5e0898190c8&amp;#x27;, &amp;#x27;2809ad07-4d51-433b-a5b5-82ca499b0c52&amp;#x27;]\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_31\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.10.15&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-190-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.3&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py::TestCmipIgnoreResidues::test_cmip_ignore_residues&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py::TestCmipIgnoreResidues::test_cmip_ignore_residues&#34;, &#34;duration&#34;: &#34;316 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py::TestCmipIgnoreResidues::test_cmip_ignore_residues&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;316 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-10-17 14:25:23,081 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_ignore_residues Version: 5.0.0\n2024-10-17 14:25:23,082 [MainThread  ] [INFO ]  Residue list: [&amp;#x27;:3&amp;#x27;]\n2024-10-17 14:25:23,108 [MainThread  ] [INFO ]  17 residues have been marked\n2024-10-17 14:25:23,108 [MainThread  ] [INFO ]  Removed: []\n2024-10-17 14:25:23,109 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_31/cmip_ignore_residues/ignore_residues_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_31/cmip_ignore_residues/ignore_residues_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/ignore_res_gln3.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3173\n     Atoms ALIGNED in PDB_B: 3173\n     RMS: 1.0024822746830985e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_31/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_ignore_residues Version: 5.0.0\nINFO     /tmp/biobb/unitests_31/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 Residue list: [&amp;#x27;:3&amp;#x27;]\nINFO     /tmp/biobb/unitests_31/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 17 residues have been marked\nINFO     /tmp/biobb/unitests_31/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 Removed: []\nINFO     /tmp/biobb/unitests_31/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_31\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py::TestCmipPreparePDB::test_cmip_prepare_pdb&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py::TestCmipPreparePDB::test_cmip_prepare_pdb&#34;, &#34;duration&#34;: &#34;834 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py::TestCmipPreparePDB::test_cmip_prepare_pdb&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;834 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-10-17 14:25:23,408 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_prepare_pdb Version: 5.0.0\n2024-10-17 14:25:23,408 [MainThread  ] [INFO ]  /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1 directory successfully created\n2024-10-17 14:25:23,408 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/1aki.pdb to /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1\n2024-10-17 14:25:23,409 [MainThread  ] [INFO ]  check_structure -v -i /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1/1aki.pdb -o /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1/1aki_cmip.pdb --output_format cmip --non_interactive command_list --list &amp;#x27;water --remove yes; backbone --add_caps none; fixside --fix All; add_hydrogen --add_mode auto --add_charges CMIP&amp;#x27;\n\n2024-10-17 14:25:24,071 [MainThread  ] [INFO ]  Executing: check_structure -v -i /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8...\n2024-10-17 14:25:24,071 [MainThread  ] [INFO ]  Exit code: 0\n2024-10-17 14:25:24,071 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\n\nStep 1: water --remove yes\nRunning water. Options: --remove yes\nDetected 78 Water molecules\nRemoved 78 Water molecules\n\nStep 2:  backbone --add_caps none\nRunning backbone. Options: --add_caps none\nFound No residues with missing backbone atoms\nNo backbone breaks\nNo unexpected backbone links\nCapping terminal ends\nTrue terminal residues: A1,A129\nNothing to do\nNo caps added\n\nStep 3:  fixside --fix All\nRunning fixside. Options: --fix All\nFound no residues with missing or unknown side chain atoms\n\nStep 4:  add_hydrogen --add_mode auto --add_charges CMIP\nRunning add_hydrogen. Options: --add_mode auto --add_charges CMIP\nFound 38 Residues requiring selection on adding H atoms\n CYS A6,A30,A64,A76,A80,A94,A115,A127\n ASP A18,A48,A52,A66,A87,A101,A119\n GLU A7,A35\n HIS A15\n LYS A1,A13,A33,A96,A97,A116\n ARG A5,A14,A21,A45,A61,A68,A73,A112,A114,A125,A128\n TYR A20,A23,A53\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A15 by HIE\nUpdating partial charges and atom types\nTotal assigned charge:       8.00\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  129\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 129 (total 967 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1968\nStructure saved on /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1/1aki_cmip.pdb\n\n2024-10-17 14:25:24,072 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1&amp;#x27;]\n2024-10-17 14:25:24,072 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_31/cmip_prepare_pdb/1aki_cmip.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_31/cmip_prepare_pdb/1aki_cmip.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/1aki_cmip.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 1001\n     Atoms ALIGNED in PDB_B: 1001\n     RMS: 1.4828848083881487e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_prepare_pdb Version: 5.0.0\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:82 /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1 directory successfully created\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/1aki.pdb to /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:63 check_structure -v -i /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1/1aki.pdb -o /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1/1aki_cmip.pdb --output_format cmip --non_interactive command_list --list &amp;#x27;water --remove yes; backbone --add_caps none; fixside --fix All; add_hydrogen --add_mode auto --add_charges CMIP&amp;#x27;\n\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:36 Executing: check_structure -v -i /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8...\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\n\nStep 1: water --remove yes\nRunning water. Options: --remove yes\nDetected 78 Water molecules\nRemoved 78 Water molecules\n\nStep 2:  backbone --add_caps none\nRunning backbone. Options: --add_caps none\nFound No residues with missing backbone atoms\nNo backbone breaks\nNo unexpected backbone links\nCapping terminal ends\nTrue terminal residues: A1,A129\nNothing to do\nNo caps added\n\nStep 3:  fixside --fix All\nRunning fixside. Options: --fix All\nFound no residues with missing or unknown side chain atoms\n\nStep 4:  add_hydrogen --add_mode auto --add_charges CMIP\nRunning add_hydrogen. Options: --add_mode auto --add_charges CMIP\nFound 38 Residues requiring selection on adding H atoms\n CYS A6,A30,A64,A76,A80,A94,A115,A127\n ASP A18,A48,A52,A66,A87,A101,A119\n GLU A7,A35\n HIS A15\n LYS A1,A13,A33,A96,A97,A116\n ARG A5,A14,A21,A45,A61,A68,A73,A112,A114,A125,A128\n TYR A20,A23,A53\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A15 by HIE\nUpdating partial charges and atom types\nTotal assigned charge:       8.00\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  129\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 129 (total 967 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1968\nStructure saved on /tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1/1aki_cmip.pdb\n\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_31/cmip_prepare_pdb/sandbox_092e356c-8cc2-4570-b64d-860cdfe0d3a1&amp;#x27;]\nINFO     /tmp/biobb/unitests_31/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_31\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&#34;, &#34;duration&#34;: &#34;00:00:08&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:08&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-10-17 14:25:24,243 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_prepare_structure Version: 5.0.0\n2024-10-17 14:25:24,246 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\n2024-10-17 14:25:24,246 [MainThread  ] [INFO ]  to:\n2024-10-17 14:25:24,246 [MainThread  ] [INFO ]  [&amp;#x27;b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_p2g.top&amp;#x27;, &amp;#x27;b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_posre.itp&amp;#x27;]\n2024-10-17 14:25:24,247 [MainThread  ] [INFO ]  Unzipping: \n2024-10-17 14:25:24,247 [MainThread  ] [INFO ]  /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\n2024-10-17 14:25:24,247 [MainThread  ] [INFO ]  To: \n2024-10-17 14:25:24,247 [MainThread  ] [INFO ]  b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_p2g.top\n2024-10-17 14:25:24,247 [MainThread  ] [INFO ]  b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_posre.itp\n2024-10-17 14:25:24,247 [MainThread  ] [INFO ]  Reading: b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_p2g.top to extract charges\n2024-10-17 14:25:27,797 [MainThread  ] [INFO ]  Reading: b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_p2g.top to extract elements\n2024-10-17 14:25:31,989 [MainThread  ] [INFO ]  Removed: [&amp;#x27;b7d2fd50-6194-49e1-a6f7-487bdc4f2971&amp;#x27;]\n2024-10-17 14:25:31,989 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_31/cmip_prepare_structure_topology/prepare_structure_topology_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_31/cmip_prepare_structure_topology/prepare_structure_topology_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/egfr_cmip.pdb\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2872\n     Atoms ALIGNED in PDB_B: 2872\n     RMS: 1.1126217417895259e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_prepare_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:174 [&amp;#x27;b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_p2g.top&amp;#x27;, &amp;#x27;b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_posre.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:256 b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_p2g.top\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:256 b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_posre.itp\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Reading: b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_p2g.top to extract charges\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Reading: b7d2fd50-6194-49e1-a6f7-487bdc4f2971/pdb2gmx_p2g.top to extract elements\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Removed: [&amp;#x27;b7d2fd50-6194-49e1-a6f7-487bdc4f2971&amp;#x27;]\nINFO     /tmp/biobb/unitests_31/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_31\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&#34;, &#34;duration&#34;: &#34;00:00:18&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:18&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-10-17 14:25:32,253 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_run Version: 5.0.0\n2024-10-17 14:25:32,253 [MainThread  ] [INFO ]  /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41 directory successfully created\n2024-10-17 14:25:32,254 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.hACE2.cmip.pdb to /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41\n2024-10-17 14:25:32,255 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.RBD.cmip.pdb to /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41\n2024-10-17 14:25:32,255 [MainThread  ] [INFO ]  Copy: /home/user/micromamba/envs/test_environment/share/cmip/dat/vdwprm to /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41\n2024-10-17 14:25:32,255 [MainThread  ] [INFO ]  Copy: 0fbd2f25-ffcb-4b65-88fe-5013f7591445/params to /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41\n2024-10-17 14:25:32,255 [MainThread  ] [INFO ]  cmip -i /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/params -vdw /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/vdwprm -hs /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/RBD-hACE2.hACE2.cmip.pdb -pr /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/RBD-hACE2.RBD.cmip.pdb -byat /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/output_byat.out\n\n2024-10-17 14:25:50,168 [MainThread  ] [INFO ]  Executing: cmip -i /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b95...\n2024-10-17 14:25:50,169 [MainThread  ] [INFO ]  Exit code: 0\n2024-10-17 14:25:50,169 [MainThread  ] [INFO ]   =================================================\n =                                               =\n =                C M I P  (2.7.0)               =\n =          J. Ll. Gelpi, A. Morreale,           =\n =            F. J. Luque, M.Orozco              =\n =      Dept. Biochemistry. Univ. Barcelona      =\n =                  1999-2021                    =\n =================================================\n\n  Code for ASA calculation by Juan F. Recio       \n\n#T Run started at   14:25:32 h on 17-10-2024\n SIZES\n -----\n MAXTIP:           100\n MAXATH:            80000\n MAXATP x MAXCONF: 100000\n\n INPUT FILES\n -----------\n    Calc. settings: /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/params                                                                   \n VdW Parameters:      /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/vdwprm                                                                   \n PDB Host:            /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/RBD-hACE2.hACE2.cmip.pdb                                                 \n PDB Guest:           /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/RBD-hACE2.RBD.cmip.pdb                                                   \n Conf. energies:      energies                                                                                                                                              \n\n OUTPUT FILES\n ------------\n LOG file:            output                                                                                                                                                \n Grid Out:            gridout                                                                                                                                               \n Output PDB coords:          outpdb                                                                                                                                                \n\n Parameters\n ----------\nDocking Interaction energy calculation. PB electrostatics                       \n&amp;amp;cntrl                                                                          \n tipcalc = 3                                                                    \n calcgrid = 1                                                                   \n irest = 0                                                                      \n orest = 0                                                                      \n coorfmt = 2                                                                    \n fvdw = 0.8                                                                     \n pbelec = 1                                                                     \n pbinic = 2                                                                     \n wgp = 0                                                                        \n ebyatom = 1                                                                    \n readgrid = 2                                                                   \n CENX=0.0,CENY=0.0,CENZ=0.0                                                     \n DIMX=64,DIMY=64,DIMZ=64                                                        \n INTX0=1.5,INTY0=1.5,INTZ0=1.5                                                  \n readgrid0 = 2                                                                  \n perfill0 = 0.6                                                                 \n pbfocus = 1                                                                    \n IREST = 0                                                                      \n&amp;amp;end                                                                            \n\n 18 VdW parameters loaded successfully\n\n Host:      9519 atoms loaded, charge   -27.000\n\n TYPE OF CALCULATION: DOCKING\n Single point\n\n Guest: 3000 atom(s), charge -11.145,    1 conformation(s) loaded\n\n PB Focussing requested\n AUTOMATIC OUTER GRID\n --------------------\n Fill:    0.600\nAutomatic Outer Grid                                                                                                                \n Grid Size:      96.000 138.000 108.000  90.000  90.000  90.000\n Grid density:    64   92   72\n Grid units:      1.500   1.500   1.500\n Grid origin:    23.610  -1.245   2.315\n Grid center:    71.610  67.755  56.315\n     441285 Grid points\n\n AUTOMATIC GRID\n --------------\n Fill:    0.800\nAutomatic Grid                                                                                                                      \n Grid Size:      72.000 103.000  81.500  90.000  90.000  90.000\n Grid density:   144  206  163\n Grid units:      0.500   0.500   0.500\n Grid origin:    35.610  16.255  15.565\n Grid center:    71.610  67.755  56.315\n    4922460 Grid points\n\n All input data read succesfully\n\n Warning: Dielectric grid computed at double density\n Mapping host molecule to outer grid\n   Total charge            :   -27.0000248    \n   Low diel. grid points   :                230941 (   97428.2344     A3)\n   High diel. grid points  :               3229484\n   I Str=0 grid points     :                441285\n   Boundary grid points    :                 57064\n Mapping host molecule to grid\n   Total charge            :   -27.0000019    \n   Low diel. grid points   :               5855067 (   91485.4219      A3)\n   High diel. grid points  :              33174672\n   I Str=0 grid points     :               4922460\n   Boundary grid points    :                550671\n\n CLHOST=           0\n EXTERNAL CUTOFF=   999999.000    \n Checking potentials to calculate...\n - Vdw: C   \n - Vdw: N   \n - Vdw: S   \n - Vdw: HO  \n - Vdw: HN  \n - Vdw: H   \n - Vdw: O   \n - Electrostatic \n     Dielectric type    :            0\n     Dielectric constant:    2.00000000    \n Vdw energies:\n  -C    -2.15     0.254E+21\n  -N    -2.73     0.266E+21\n  -S    -3.82     0.557E+21\n  -HO    0.00      0.00    \n  -HN  -0.344     0.116E+18\n  -H   -0.860     0.268E+20\n  -O    -2.87     0.169E+21\n     Poisson-Boltzmann calculation requested\n     Focussing          :            1\n     Initial potentials :            2\n     Solute  Dielectric :    2.00000000    \n     Solvent Dielectric :    79.8000031    \n     Solvent radius     :    1.39999998    \n     Convergence crit.  :    9.99999975E-05\n     Ionic strength     :    0.00000000    \n Outer grid\n          20  0.147574857       14.6699677    \n          40   2.98345201E-02   3.29004049    \n          60   6.40256703E-03  0.731274426    \n          80   1.45485543E-03  0.142998144    \n         100   3.42993939E-04   1.78021304E-02\n         120   8.23287264E-05   2.51317094E-03\n         140   1.94953154E-05   8.38404230E-04\n Converged at   158 iterations (Mean:       0.498E-05, Max:      0.923E-04)\n Potentials:   -145.994   169.029\n Inner Grid limits\n Potentials:   -128.467   156.689\n          20  0.879424989       44.1415825    \n          40  0.403403580       18.3190784    \n          60  0.196925759       11.3940735    \n          80   9.77351665E-02   6.85034132    \n         100   4.82290089E-02   3.02071881    \n         120   2.38220431E-02   1.71308899    \n         140   1.16539253E-02  0.880087018    \n         160   5.68585889E-03  0.497510761    \n         180   2.73818872E-03  0.352287740    \n         200   1.29186665E-03  0.225940481    \n         220   5.93950739E-04  0.123246640    \n         240   2.69010925E-04   4.76482585E-02\n         260   1.19791970E-04   1.82344913E-02\n         280   5.35966064E-05   5.74939372E-03\n         300   2.40470035E-05   2.51911674E-03\n         320   1.08288432E-05   9.81772435E-04\n         340   4.89419654E-06   3.82507744E-04\n         360   2.25630242E-06   1.72914923E-04\n Converged at   376 iterations (Mean:       0.125E-05, Max:      0.967E-04)\n Potentials:   -739.519  1051.831\n Internal:        4.20389539E-42  kcal/mol\n Van der Waals:         Infinity  kcal/mol\n Electrostatic:   90.0758286     kcal/mol\n Total Energy :         Infinity kcal/mol\n\n#T Run finished at  14:25:50 h on 17-10-2024\n\n#T       T I M I N G S \n#T       ---------------\n#T         Input:     0.250 s,   1.40%\n#T         Setup:     2.250 s,  12.59%\n#T         Grids:    15.375 s,  86.01%\n#T        Energy:     0.000 s,   0.00%\n#T        Output:     0.000 s,   0.00%\n ----------------------------------\n#T         TOTAL:    17.875 s ( 0.00 h)\n\n2024-10-17 14:25:50,170 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41&amp;#x27;, &amp;#x27;0fbd2f25-ffcb-4b65-88fe-5013f7591445&amp;#x27;]\n2024-10-17 14:25:50,170 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_31/cmip_run/output_byat.out\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_run Version: 5.0.0\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:82 /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41 directory successfully created\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.hACE2.cmip.pdb to /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.RBD.cmip.pdb to /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/micromamba/envs/test_environment/share/cmip/dat/vdwprm to /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: 0fbd2f25-ffcb-4b65-88fe-5013f7591445/params to /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:cmd_wrapper.py:63 cmip -i /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/params -vdw /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/vdwprm -hs /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/RBD-hACE2.hACE2.cmip.pdb -pr /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/RBD-hACE2.RBD.cmip.pdb -byat /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/output_byat.out\n\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:cmd_wrapper.py:36 Executing: cmip -i /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b95...\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:cmd_wrapper.py:41  =================================================\n =                                               =\n =                C M I P  (2.7.0)               =\n =          J. Ll. Gelpi, A. Morreale,           =\n =            F. J. Luque, M.Orozco              =\n =      Dept. Biochemistry. Univ. Barcelona      =\n =                  1999-2021                    =\n =================================================\n\n  Code for ASA calculation by Juan F. Recio       \n\n#T Run started at   14:25:32 h on 17-10-2024\n SIZES\n -----\n MAXTIP:           100\n MAXATH:            80000\n MAXATP x MAXCONF: 100000\n\n INPUT FILES\n -----------\n    Calc. settings: /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/params                                                                   \n VdW Parameters:      /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/vdwprm                                                                   \n PDB Host:            /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/RBD-hACE2.hACE2.cmip.pdb                                                 \n PDB Guest:           /tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41/RBD-hACE2.RBD.cmip.pdb                                                   \n Conf. energies:      energies                                                                                                                                              \n\n OUTPUT FILES\n ------------\n LOG file:            output                                                                                                                                                \n Grid Out:            gridout                                                                                                                                               \n Output PDB coords:          outpdb                                                                                                                                                \n\n Parameters\n ----------\nDocking Interaction energy calculation. PB electrostatics                       \n&amp;amp;cntrl                                                                          \n tipcalc = 3                                                                    \n calcgrid = 1                                                                   \n irest = 0                                                                      \n orest = 0                                                                      \n coorfmt = 2                                                                    \n fvdw = 0.8                                                                     \n pbelec = 1                                                                     \n pbinic = 2                                                                     \n wgp = 0                                                                        \n ebyatom = 1                                                                    \n readgrid = 2                                                                   \n CENX=0.0,CENY=0.0,CENZ=0.0                                                     \n DIMX=64,DIMY=64,DIMZ=64                                                        \n INTX0=1.5,INTY0=1.5,INTZ0=1.5                                                  \n readgrid0 = 2                                                                  \n perfill0 = 0.6                                                                 \n pbfocus = 1                                                                    \n IREST = 0                                                                      \n&amp;amp;end                                                                            \n\n 18 VdW parameters loaded successfully\n\n Host:      9519 atoms loaded, charge   -27.000\n\n TYPE OF CALCULATION: DOCKING\n Single point\n\n Guest: 3000 atom(s), charge -11.145,    1 conformation(s) loaded\n\n PB Focussing requested\n AUTOMATIC OUTER GRID\n --------------------\n Fill:    0.600\nAutomatic Outer Grid                                                                                                                \n Grid Size:      96.000 138.000 108.000  90.000  90.000  90.000\n Grid density:    64   92   72\n Grid units:      1.500   1.500   1.500\n Grid origin:    23.610  -1.245   2.315\n Grid center:    71.610  67.755  56.315\n     441285 Grid points\n\n AUTOMATIC GRID\n --------------\n Fill:    0.800\nAutomatic Grid                                                                                                                      \n Grid Size:      72.000 103.000  81.500  90.000  90.000  90.000\n Grid density:   144  206  163\n Grid units:      0.500   0.500   0.500\n Grid origin:    35.610  16.255  15.565\n Grid center:    71.610  67.755  56.315\n    4922460 Grid points\n\n All input data read succesfully\n\n Warning: Dielectric grid computed at double density\n Mapping host molecule to outer grid\n   Total charge            :   -27.0000248    \n   Low diel. grid points   :                230941 (   97428.2344     A3)\n   High diel. grid points  :               3229484\n   I Str=0 grid points     :                441285\n   Boundary grid points    :                 57064\n Mapping host molecule to grid\n   Total charge            :   -27.0000019    \n   Low diel. grid points   :               5855067 (   91485.4219      A3)\n   High diel. grid points  :              33174672\n   I Str=0 grid points     :               4922460\n   Boundary grid points    :                550671\n\n CLHOST=           0\n EXTERNAL CUTOFF=   999999.000    \n Checking potentials to calculate...\n - Vdw: C   \n - Vdw: N   \n - Vdw: S   \n - Vdw: HO  \n - Vdw: HN  \n - Vdw: H   \n - Vdw: O   \n - Electrostatic \n     Dielectric type    :            0\n     Dielectric constant:    2.00000000    \n Vdw energies:\n  -C    -2.15     0.254E+21\n  -N    -2.73     0.266E+21\n  -S    -3.82     0.557E+21\n  -HO    0.00      0.00    \n  -HN  -0.344     0.116E+18\n  -H   -0.860     0.268E+20\n  -O    -2.87     0.169E+21\n     Poisson-Boltzmann calculation requested\n     Focussing          :            1\n     Initial potentials :            2\n     Solute  Dielectric :    2.00000000    \n     Solvent Dielectric :    79.8000031    \n     Solvent radius     :    1.39999998    \n     Convergence crit.  :    9.99999975E-05\n     Ionic strength     :    0.00000000    \n Outer grid\n          20  0.147574857       14.6699677    \n          40   2.98345201E-02   3.29004049    \n          60   6.40256703E-03  0.731274426    \n          80   1.45485543E-03  0.142998144    \n         100   3.42993939E-04   1.78021304E-02\n         120   8.23287264E-05   2.51317094E-03\n         140   1.94953154E-05   8.38404230E-04\n Converged at   158 iterations (Mean:       0.498E-05, Max:      0.923E-04)\n Potentials:   -145.994   169.029\n Inner Grid limits\n Potentials:   -128.467   156.689\n          20  0.879424989       44.1415825    \n          40  0.403403580       18.3190784    \n          60  0.196925759       11.3940735    \n          80   9.77351665E-02   6.85034132    \n         100   4.82290089E-02   3.02071881    \n         120   2.38220431E-02   1.71308899    \n         140   1.16539253E-02  0.880087018    \n         160   5.68585889E-03  0.497510761    \n         180   2.73818872E-03  0.352287740    \n         200   1.29186665E-03  0.225940481    \n         220   5.93950739E-04  0.123246640    \n         240   2.69010925E-04   4.76482585E-02\n         260   1.19791970E-04   1.82344913E-02\n         280   5.35966064E-05   5.74939372E-03\n         300   2.40470035E-05   2.51911674E-03\n         320   1.08288432E-05   9.81772435E-04\n         340   4.89419654E-06   3.82507744E-04\n         360   2.25630242E-06   1.72914923E-04\n Converged at   376 iterations (Mean:       0.125E-05, Max:      0.967E-04)\n Potentials:   -739.519  1051.831\n Internal:        4.20389539E-42  kcal/mol\n Van der Waals:         Infinity  kcal/mol\n Electrostatic:   90.0758286     kcal/mol\n Total Energy :         Infinity kcal/mol\n\n#T Run finished at  14:25:50 h on 17-10-2024\n\n#T       T I M I N G S \n#T       ---------------\n#T         Input:     0.250 s,   1.40%\n#T         Setup:     2.250 s,  12.59%\n#T         Grids:    15.375 s,  86.01%\n#T        Energy:     0.000 s,   0.00%\n#T        Output:     0.000 s,   0.00%\n ----------------------------------\n#T         TOTAL:    17.875 s ( 0.00 h)\n\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_31/cmip_run/sandbox_2f1654a0-3e66-44b1-ac28-426e5b959b41&amp;#x27;, &amp;#x27;0fbd2f25-ffcb-4b65-88fe-5013f7591445&amp;#x27;]\nINFO     /tmp/biobb/unitests_31/cmip_run/cmip_run_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_31\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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