Report generated on 07-Sep-2023 at 10:41:11 by pytest-html v3.2.0
13 tests ran in 46.37 seconds.
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13 passed, 0 skipped, 0 failed, 0 errors, 0 expected failures, 0 unexpected passes| Result | Test | Duration | Links |
|---|---|---|---|
| No results found. Try to check the filters | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_alphafold.py::TestAlphaFold::test_alphafold | 0.48 | |
|
------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:25,715 [MainThread ] [INFO ] Executing biobb_io.api.alphafold Version: 4.1.0 2023-09-07 10:40:25,715 [MainThread ] [INFO ] Downloading P00489 from: https://alphafold.ebi.ac.uk/files/AF-P00489-F1-model_v3.pdb 2023-09-07 10:40:25,818 [MainThread ] [INFO ] Writting pdb to: /tmp/biobb/unitests/alphafold/output_pdb_path.pdb Checking if empty file: /tmp/biobb/unitests/alphafold/output_pdb_path.pdb Checking RMSD between: PDB_A: /tmp/biobb/unitests/alphafold/output_pdb_path.pdb PDB_B: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/output_alphafold.pdb Ignoring HETAMT in RMSD Ignoring Hydrogen atoms in RMSD Atoms ALIGNED in PDB_A: 6860 Atoms ALIGNED in PDB_B: 6860 RMS: 9.343211792654216e-15 RMS_CUTOFF: 1 -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/alphafold/alphafold_log.out:file_utils.py:390 Executing biobb_io.api.alphafold Version: 4.1.0 INFO /tmp/biobb/unitests/alphafold/alphafold_log.out:file_utils.py:390 Downloading P00489 from: https://alphafold.ebi.ac.uk/files/AF-P00489-F1-model_v3.pdb INFO /tmp/biobb/unitests/alphafold/alphafold_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests/alphafold/output_pdb_path.pdb ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_api_binding_site.py::TestApiBindingSite::test_api_binding_site | 0.31 | |
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------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:26,218 [MainThread ] [INFO ] Executing biobb_io.api.api_binding_site Version: 4.1.0 2023-09-07 10:40:26,219 [MainThread ] [INFO ] Getting binding sites from: https://www.ebi.ac.uk/pdbe/api/pdb/entry/binding_sites/4i23 2023-09-07 10:40:26,513 [MainThread ] [INFO ] 1 binding sites found 2023-09-07 10:40:26,513 [MainThread ] [INFO ] Writting json to: /tmp/biobb/unitests/api_binding_site/output_json_path.json Checking if empty file: /tmp/biobb/unitests/api_binding_site/output_json_path.json Comparing: File_A: /tmp/biobb/unitests/api_binding_site/output_json_path.json File_B: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/output_binding_site.json File_A hash: b'\x8f\x13:\xb8\x9a\xa3\xd4\xc7w\x00|v\xa4\xb9\xef\x96X\xa5`#\x87P)\xa8[\xe9\x0b[\xe0D\xcc\x06' File_B hash: b'\x8f\x13:\xb8\x9a\xa3\xd4\xc7w\x00|v\xa4\xb9\xef\x96X\xa5`#\x87P)\xa8[\xe9\x0b[\xe0D\xcc\x06' -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/api_binding_site/api_binding_site_log.out:file_utils.py:390 Executing biobb_io.api.api_binding_site Version: 4.1.0 INFO /tmp/biobb/unitests/api_binding_site/api_binding_site_log.out:file_utils.py:390 Getting binding sites from: https://www.ebi.ac.uk/pdbe/api/pdb/entry/binding_sites/4i23 INFO /tmp/biobb/unitests/api_binding_site/api_binding_site_log.out:file_utils.py:390 1 binding sites found INFO /tmp/biobb/unitests/api_binding_site/api_binding_site_log.out:file_utils.py:390 Writting json to: /tmp/biobb/unitests/api_binding_site/output_json_path.json ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_canonical_fasta.py::TestCanonicalFasta::test_canonical_fasta | 5.30 | |
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------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:26,533 [MainThread ] [INFO ] Executing biobb_io.api.canonical_fasta Version: 4.1.0 2023-09-07 10:40:26,533 [MainThread ] [INFO ] Downloading 4i23 from: https://www.ebi.ac.uk/pdbe/entry/pdb/4i23/fasta 2023-09-07 10:40:31,788 [MainThread ] [INFO ] Writting FASTA to: /tmp/biobb/unitests/canonical_fasta/output_fasta_path.fasta Checking if empty file: /tmp/biobb/unitests/canonical_fasta/output_fasta_path.fasta Comparing: File_A: /tmp/biobb/unitests/canonical_fasta/output_fasta_path.fasta File_B: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/canonical_fasta.fasta File_A hash: b'C9\xff\xac\xb0\xc3k\xadw\xda\xb6\xe7\x85\xc7\x96;m\xedzs\xf7\x17\xd6\xf0h\xa1\xc8P\x94S\x1d\x16' File_B hash: b'C9\xff\xac\xb0\xc3k\xadw\xda\xb6\xe7\x85\xc7\x96;m\xedzs\xf7\x17\xd6\xf0h\xa1\xc8P\x94S\x1d\x16' -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/canonical_fasta/canonical_fasta_log.out:file_utils.py:390 Executing biobb_io.api.canonical_fasta Version: 4.1.0 INFO /tmp/biobb/unitests/canonical_fasta/canonical_fasta_log.out:file_utils.py:390 Downloading 4i23 from: https://www.ebi.ac.uk/pdbe/entry/pdb/4i23/fasta INFO /tmp/biobb/unitests/canonical_fasta/canonical_fasta_log.out:file_utils.py:390 Writting FASTA to: /tmp/biobb/unitests/canonical_fasta/output_fasta_path.fasta ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_drugbank.py::TestDrugbank::test_drugbank | 0.47 | |
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------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:31,841 [MainThread ] [INFO ] Executing biobb_io.api.drugbank Version: 4.1.0 2023-09-07 10:40:31,841 [MainThread ] [INFO ] Downloading db00530 from: https://www.drugbank.ca/structures/small_molecule_drugs/db00530.sdf?type=3d 2023-09-07 10:40:32,299 [MainThread ] [INFO ] Writting sdf to: /tmp/biobb/unitests/drugbank/output_sdf_path.sdf Checking if empty file: /tmp/biobb/unitests/drugbank/output_sdf_path.sdf Comparing: File_A: /tmp/biobb/unitests/drugbank/output_sdf_path.sdf File_B: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/output_drugbank.sdf File_A hash: b'\x92F\xda=\xd2\xce\xddwH\x0eX\xc9\xcaNI|y\x1d\x82\n\xdb\xff\x95u}W\xe1\xd0\xb7\xf1\x13\xd0' File_B hash: b'\x92F\xda=\xd2\xce\xddwH\x0eX\xc9\xcaNI|y\x1d\x82\n\xdb\xff\x95u}W\xe1\xd0\xb7\xf1\x13\xd0' -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/drugbank/drugbank_log.out:file_utils.py:390 Executing biobb_io.api.drugbank Version: 4.1.0 INFO /tmp/biobb/unitests/drugbank/drugbank_log.out:file_utils.py:390 Downloading db00530 from: https://www.drugbank.ca/structures/small_molecule_drugs/db00530.sdf?type=3d INFO /tmp/biobb/unitests/drugbank/drugbank_log.out:file_utils.py:390 Writting sdf to: /tmp/biobb/unitests/drugbank/output_sdf_path.sdf ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_ideal_sdf.py::TestIdealSdf::test_ideal_sdf | 0.44 | |
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------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:32,320 [MainThread ] [INFO ] Executing biobb_io.api.ideal_sdf Version: 4.1.0 2023-09-07 10:40:32,746 [MainThread ] [INFO ] Downloading HYZ from: ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/H/HYZ/HYZ_ideal.sdf 2023-09-07 10:40:32,747 [MainThread ] [INFO ] Writting sdf to: /tmp/biobb/unitests/ideal_sdf/output_sdf_path.sdf Checking if empty file: /tmp/biobb/unitests/ideal_sdf/output_sdf_path.sdf Comparing: File_A: /tmp/biobb/unitests/ideal_sdf/output_sdf_path.sdf File_B: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/ref_output.sdf File_A hash: b"\xd9g\xfb\xc4\x027\x8fV\x02\xc1l\xc0\xa4\x1b'\x07\xb1?^\xc1\xa2\x8d>\xc2+\xf5\xd2\xdfB\xd6v\xce" File_B hash: b"\xd9g\xfb\xc4\x027\x8fV\x02\xc1l\xc0\xa4\x1b'\x07\xb1?^\xc1\xa2\x8d>\xc2+\xf5\xd2\xdfB\xd6v\xce" -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/ideal_sdf/ideal_sdf_log.out:file_utils.py:390 Executing biobb_io.api.ideal_sdf Version: 4.1.0 INFO /tmp/biobb/unitests/ideal_sdf/ideal_sdf_log.out:file_utils.py:390 Downloading HYZ from: ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/H/HYZ/HYZ_ideal.sdf INFO /tmp/biobb/unitests/ideal_sdf/ideal_sdf_log.out:file_utils.py:390 Writting sdf to: /tmp/biobb/unitests/ideal_sdf/output_sdf_path.sdf ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_ligand.py::TestLigand::test_ligand | 0.43 | |
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------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:32,767 [MainThread ] [INFO ] Executing biobb_io.api.ligand Version: 4.1.0 2023-09-07 10:40:33,186 [MainThread ] [INFO ] Downloading ibp from: ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/I/IBP/IBP_ideal.pdb 2023-09-07 10:40:33,186 [MainThread ] [INFO ] Writting pdb to: /tmp/biobb/unitests/ligand/output_pdb_path.pdb Checking if empty file: /tmp/biobb/unitests/ligand/output_pdb_path.pdb Comparing: File_A: /tmp/biobb/unitests/ligand/output_pdb_path.pdb File_B: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/output_ligand.pdb File_A hash: b'\x90\xfb^O\x99&L\xd9RH$\xb8R\xcf\xbb[\\\x10\xa9\xa9\x1f2\n[Rsf\xb2\xee\xdd\x127' File_B hash: b'\x90\xfb^O\x99&L\xd9RH$\xb8R\xcf\xbb[\\\x10\xa9\xa9\x1f2\n[Rsf\xb2\xee\xdd\x127' -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/ligand/ligand_log.out:file_utils.py:390 Executing biobb_io.api.ligand Version: 4.1.0 INFO /tmp/biobb/unitests/ligand/ligand_log.out:file_utils.py:390 Downloading ibp from: ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/I/IBP/IBP_ideal.pdb INFO /tmp/biobb/unitests/ligand/ligand_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests/ligand/output_pdb_path.pdb ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_memprotmd_sim.py::TestMemProtMDSim::test_memprotmd_sim | 1.28 | |
|
------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:33,206 [MainThread ] [INFO ] Executing biobb_io.api.memprotmd_sim Version: 4.1.0 2023-09-07 10:40:33,206 [MainThread ] [INFO ] Getting simulation file from pdb code 1hzx 2023-09-07 10:40:34,469 [MainThread ] [INFO ] Saving output /tmp/biobb/unitests/memprotmd_sim/output_simulation.zip file Checking if empty file: /tmp/biobb/unitests/memprotmd_sim/output_simulation.zip -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/memprotmd_sim/memprotmd_sim_log.out:file_utils.py:390 Executing biobb_io.api.memprotmd_sim Version: 4.1.0 INFO /tmp/biobb/unitests/memprotmd_sim/memprotmd_sim_log.out:file_utils.py:390 Getting simulation file from pdb code 1hzx INFO /tmp/biobb/unitests/memprotmd_sim/memprotmd_sim_log.out:file_utils.py:390 Saving output /tmp/biobb/unitests/memprotmd_sim/output_simulation.zip file ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_memprotmd_sim_search.py::TestMemProtMDSimSearch::test_memprotmd_sim_search | 0.22 | |
|
------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:34,489 [MainThread ] [INFO ] Executing biobb_io.api.memprotmd_sim_search Version: 4.1.0 2023-09-07 10:40:34,489 [MainThread ] [INFO ] Getting search results from the MemProtMD REST API. Collection name: refs, keyword: porin 2023-09-07 10:40:34,698 [MainThread ] [INFO ] Total number of simulations: 251 2023-09-07 10:40:34,698 [MainThread ] [INFO ] Writting json to: /tmp/biobb/unitests/memprotmd_sim_search/output_simulations.json Checking if empty file: /tmp/biobb/unitests/memprotmd_sim_search/output_simulations.json Comparing: File_A: /tmp/biobb/unitests/memprotmd_sim_search/output_simulations.json File_B: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/output_sim_search.json File_A hash: b'5\x08\x00W\xfe\x15\xc9^!|\xe0\xc1\xd1\xf01\x80\xc3\xbaG\xe4\xc0\x02GN\x12Y\x08I\x86|\x85\xed' File_B hash: b'5\x08\x00W\xfe\x15\xc9^!|\xe0\xc1\xd1\xf01\x80\xc3\xbaG\xe4\xc0\x02GN\x12Y\x08I\x86|\x85\xed' -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/memprotmd_sim_search/memprotmd_sim_search_log.out:file_utils.py:390 Executing biobb_io.api.memprotmd_sim_search Version: 4.1.0 INFO /tmp/biobb/unitests/memprotmd_sim_search/memprotmd_sim_search_log.out:file_utils.py:390 Getting search results from the MemProtMD REST API. Collection name: refs, keyword: porin INFO /tmp/biobb/unitests/memprotmd_sim_search/memprotmd_sim_search_log.out:file_utils.py:390 Total number of simulations: 251 INFO /tmp/biobb/unitests/memprotmd_sim_search/memprotmd_sim_search_log.out:file_utils.py:390 Writting json to: /tmp/biobb/unitests/memprotmd_sim_search/output_simulations.json ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_mmcif.py::TestMmcif::test_mmcif | 5.90 | |
|
------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:34,718 [MainThread ] [INFO ] Executing biobb_io.api.mmcif Version: 4.1.0 2023-09-07 10:40:34,719 [MainThread ] [INFO ] Downloading 2vgb from: https://www.ebi.ac.uk/pdbe/entry-files/download/2vgb.cif 2023-09-07 10:40:40,592 [MainThread ] [INFO ] Writting mmcif to: /tmp/biobb/unitests/mmcif/output_mmcif_path.mmcif Checking if empty file: /tmp/biobb/unitests/mmcif/output_mmcif_path.mmcif Comparing: File_A: /tmp/biobb/unitests/mmcif/output_mmcif_path.mmcif File_B: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/ref_output.mmcif File_A hash: b"\x98\xd6\x15-|\xdb\xe30\xef\xe1#Y\xa4\xf9C\xbb+\x8e9';\x87\x05\xcc\xb8\x0f\xa6\xf5\xca4\xf3\x83" File_B hash: b"\x98\xd6\x15-|\xdb\xe30\xef\xe1#Y\xa4\xf9C\xbb+\x8e9';\x87\x05\xcc\xb8\x0f\xa6\xf5\xca4\xf3\x83" -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/mmcif/mmcif_log.out:file_utils.py:390 Executing biobb_io.api.mmcif Version: 4.1.0 INFO /tmp/biobb/unitests/mmcif/mmcif_log.out:file_utils.py:390 Downloading 2vgb from: https://www.ebi.ac.uk/pdbe/entry-files/download/2vgb.cif INFO /tmp/biobb/unitests/mmcif/mmcif_log.out:file_utils.py:390 Writting mmcif to: /tmp/biobb/unitests/mmcif/output_mmcif_path.mmcif ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_pdb.py::TestPdb::test_pdb | 1.08 | |
|
------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:40,623 [MainThread ] [INFO ] Executing biobb_io.api.pdb Version: 4.1.0 2023-09-07 10:40:40,623 [MainThread ] [INFO ] Downloading 2vgb from: https://mmb.irbbarcelona.org/api/pdb/2vgb/coords/? 2023-09-07 10:40:40,802 [MainThread ] [INFO ] Writting pdb to: /tmp/biobb/unitests/pdb/output_pdb_path.pdb 2023-09-07 10:40:40,802 [MainThread ] [INFO ] Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM'] Checking if empty file: /tmp/biobb/unitests/pdb/output_pdb_path.pdb Checking RMSD between: PDB_A: /tmp/biobb/unitests/pdb/output_pdb_path.pdb PDB_B: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/output_pdb.pdb Ignoring HETAMT in RMSD Ignoring Hydrogen atoms in RMSD Atoms ALIGNED in PDB_A: 15488 Atoms ALIGNED in PDB_B: 15488 RMS: 1.871093208699659e-14 RMS_CUTOFF: 1 -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/pdb/pdb_log.out:file_utils.py:390 Executing biobb_io.api.pdb Version: 4.1.0 INFO /tmp/biobb/unitests/pdb/pdb_log.out:file_utils.py:390 Downloading 2vgb from: https://mmb.irbbarcelona.org/api/pdb/2vgb/coords/? INFO /tmp/biobb/unitests/pdb/pdb_log.out:file_utils.py:390 Writting pdb to: /tmp/biobb/unitests/pdb/output_pdb_path.pdb INFO /tmp/biobb/unitests/pdb/pdb_log.out:file_utils.py:390 Filtering lines NOT starting with one of these words: ['ATOM', 'HETATM'] ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_pdb_cluster_zip.py::TestPdbClusterZip::test_pdb_cluster_zip | 19.64 | |
|
------------------------------Captured stdout call------------------------------ 2023-09-07 10:40:41,706 [MainThread ] [INFO ] Executing biobb_io.api.pdb_cluster_zip Version: 4.1.0 2023-09-07 10:40:46,709 [MainThread ] [INFO ] Cluster: 90 of pdb_code: 2vgb List: {'2vgb', '4ima', '2vgf', '2vgi', '2vgg', '4ip7'} 2023-09-07 10:40:46,709 [MainThread ] [INFO ] Downloading 2vgb from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2vgb.ent 2023-09-07 10:40:47,432 [MainThread ] [INFO ] Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgb.pdb 2023-09-07 10:40:47,432 [MainThread ] [INFO ] Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] 2023-09-07 10:40:47,448 [MainThread ] [INFO ] Downloading 4ima from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4ima.ent 2023-09-07 10:40:48,187 [MainThread ] [INFO ] Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/4ima.pdb 2023-09-07 10:40:48,187 [MainThread ] [INFO ] Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] 2023-09-07 10:40:48,204 [MainThread ] [INFO ] Downloading 2vgf from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2vgf.ent 2023-09-07 10:40:48,871 [MainThread ] [INFO ] Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgf.pdb 2023-09-07 10:40:48,872 [MainThread ] [INFO ] Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] 2023-09-07 10:40:48,888 [MainThread ] [INFO ] Downloading 2vgi from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2vgi.ent 2023-09-07 10:40:49,567 [MainThread ] [INFO ] Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgi.pdb 2023-09-07 10:40:49,568 [MainThread ] [INFO ] Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] 2023-09-07 10:40:49,584 [MainThread ] [INFO ] Downloading 2vgg from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2vgg.ent 2023-09-07 10:40:55,327 [MainThread ] [INFO ] Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgg.pdb 2023-09-07 10:40:55,328 [MainThread ] [INFO ] Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] 2023-09-07 10:40:55,346 [MainThread ] [INFO ] Downloading 4ip7 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4ip7.ent 2023-09-07 10:40:56,170 [MainThread ] [INFO ] Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/4ip7.pdb 2023-09-07 10:40:56,170 [MainThread ] [INFO ] Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] 2023-09-07 10:40:56,214 [MainThread ] [INFO ] Adding: 2023-09-07 10:40:56,214 [MainThread ] [INFO ] ['/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgb.pdb', '/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgf.pdb', '/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgg.pdb', '/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgi.pdb', '/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/4ima.pdb', '/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/4ip7.pdb'] 2023-09-07 10:40:56,215 [MainThread ] [INFO ] to: /tmp/biobb/unitests/pdb_cluster_zip/output_pdb_zip_path.zip 2023-09-07 10:40:56,216 [MainThread ] [INFO ] Removed: ['5923f390-c8f6-4fb5-9009-1f1f5bfa3535'] Checking if empty file: /tmp/biobb/unitests/pdb_cluster_zip/output_pdb_zip_path.zip This is a ZIP comparison! Unzipping: Creating a unique_dir for: /tmp/biobb/unitests/pdb_cluster_zip/output_pdb_zip_path.zip Creating a unique_dir for: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/output_pdb_cluster.zip Checking RMSD between: PDB_A: ae9c945a-e201-4bfb-9db9-965ad372dc63/2vgb.pdb PDB_B: 648901cb-cf7e-4582-b721-4583b5138aef/2vgb.pdb Ignoring HETAMT in RMSD Ignoring Hydrogen atoms in RMSD Atoms ALIGNED in PDB_A: 15423 Atoms ALIGNED in PDB_B: 15423 RMS: 8.991193166475726e-15 RMS_CUTOFF: 1 Checking RMSD between: PDB_A: ae9c945a-e201-4bfb-9db9-965ad372dc63/2vgf.pdb PDB_B: 648901cb-cf7e-4582-b721-4583b5138aef/2vgf.pdb Ignoring HETAMT in RMSD Ignoring Hydrogen atoms in RMSD Atoms ALIGNED in PDB_A: 15426 Atoms ALIGNED in PDB_B: 15426 RMS: 1.438935308919575e-14 RMS_CUTOFF: 1 Checking RMSD between: PDB_A: ae9c945a-e201-4bfb-9db9-965ad372dc63/2vgg.pdb PDB_B: 648901cb-cf7e-4582-b721-4583b5138aef/2vgg.pdb Ignoring HETAMT in RMSD Ignoring Hydrogen atoms in RMSD Atoms ALIGNED in PDB_A: 15181 Atoms ALIGNED in PDB_B: 15181 RMS: 2.850965768274829e-14 RMS_CUTOFF: 1 Checking RMSD between: PDB_A: ae9c945a-e201-4bfb-9db9-965ad372dc63/2vgi.pdb PDB_B: 648901cb-cf7e-4582-b721-4583b5138aef/2vgi.pdb Ignoring HETAMT in RMSD Ignoring Hydrogen atoms in RMSD Atoms ALIGNED in PDB_A: 15218 Atoms ALIGNED in PDB_B: 15218 RMS: 1.862757598492494e-14 RMS_CUTOFF: 1 Checking RMSD between: PDB_A: ae9c945a-e201-4bfb-9db9-965ad372dc63/4ima.pdb PDB_B: 648901cb-cf7e-4582-b721-4583b5138aef/4ima.pdb Ignoring HETAMT in RMSD Ignoring Hydrogen atoms in RMSD Atoms ALIGNED in PDB_A: 15095 Atoms ALIGNED in PDB_B: 15095 RMS: 1.4574209792358166e-14 RMS_CUTOFF: 1 Checking RMSD between: PDB_A: ae9c945a-e201-4bfb-9db9-965ad372dc63/4ip7.pdb PDB_B: 648901cb-cf7e-4582-b721-4583b5138aef/4ip7.pdb Ignoring HETAMT in RMSD Ignoring Hydrogen atoms in RMSD Atoms ALIGNED in PDB_A: 15291 Atoms ALIGNED in PDB_B: 15291 RMS: 1.3193904618819586e-14 RMS_CUTOFF: 1 -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Executing biobb_io.api.pdb_cluster_zip Version: 4.1.0 INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:common.py:245 Cluster: 90 of pdb_code: 2vgb List: {'2vgb', '4ima', '2vgf', '2vgi', '2vgg', '4ip7'} INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Downloading 2vgb from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2vgb.ent INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgb.pdb INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Downloading 4ima from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4ima.ent INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/4ima.pdb INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Downloading 2vgf from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2vgf.ent INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgf.pdb INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Downloading 2vgi from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2vgi.ent INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgi.pdb INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Downloading 2vgg from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb2vgg.ent INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgg.pdb INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Downloading 4ip7 from: https://www.ebi.ac.uk/pdbe/entry-files/download/pdb4ip7.ent INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Writting pdb to: 5923f390-c8f6-4fb5-9009-1f1f5bfa3535/4ip7.pdb INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Filtering lines NOT starting with one of these words: ['ATOM', 'MODEL', 'ENDMDL'] INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:147 Adding: INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:148 ['/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgb.pdb', '/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgf.pdb', '/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgg.pdb', '/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/2vgi.pdb', '/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/4ima.pdb', '/tmp/biobb/unitests/pdb_cluster_zip/5923f390-c8f6-4fb5-9009-1f1f5bfa3535/4ip7.pdb'] INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:149 to: /tmp/biobb/unitests/pdb_cluster_zip/output_pdb_zip_path.zip INFO /tmp/biobb/unitests/pdb_cluster_zip/pdb_cluster_zip_log.out:file_utils.py:390 Removed: ['5923f390-c8f6-4fb5-9009-1f1f5bfa3535'] ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_pdb_variants.py::TestMmbPdbVariants::test_get_pdb_zip | 1.64 | |
|
------------------------------Captured stdout call------------------------------ 2023-09-07 10:41:01,352 [MainThread ] [INFO ] Executing biobb_io.api.pdb_variants Version: 4.1.0 2023-09-07 10:41:01,423 [MainThread ] [INFO ] PDB code: 2vgb correspond to uniprot id: P30613 2023-09-07 10:41:01,424 [MainThread ] [INFO ] Fetching variants for uniprot_id: P30613 and pdb_code: 2vgb 2023-09-07 10:41:02,982 [MainThread ] [INFO ] Found: 102 variants for uniprot id: P30613 2023-09-07 10:41:02,984 [MainThread ] [INFO ] Found 399 mutations mapped to PDB: 2vgb 2023-09-07 10:41:02,984 [MainThread ] [INFO ] Writting mutations to: /tmp/biobb/unitests/pdb_variants/output_mutations_list_txt.txt Checking if empty file: /tmp/biobb/unitests/pdb_variants/output_mutations_list_txt.txt -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/pdb_variants/pdb_variants_log.out:file_utils.py:390 Executing biobb_io.api.pdb_variants Version: 4.1.0 INFO /tmp/biobb/unitests/pdb_variants/pdb_variants_log.out:common.py:262 PDB code: 2vgb correspond to uniprot id: P30613 INFO /tmp/biobb/unitests/pdb_variants/pdb_variants_log.out:file_utils.py:390 Fetching variants for uniprot_id: P30613 and pdb_code: 2vgb INFO /tmp/biobb/unitests/pdb_variants/pdb_variants_log.out:file_utils.py:390 Found: 102 variants for uniprot id: P30613 INFO /tmp/biobb/unitests/pdb_variants/pdb_variants_log.out:file_utils.py:390 Found 399 mutations mapped to PDB: 2vgb INFO /tmp/biobb/unitests/pdb_variants/pdb_variants_log.out:file_utils.py:390 Writting mutations to: /tmp/biobb/unitests/pdb_variants/output_mutations_list_txt.txt ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||
| Passed | biobb_io/test/unitests/test_mmb_api/test_structure_info.py::TestStructureInfo::test_structure_info | 8.54 | |
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------------------------------Captured stdout call------------------------------ 2023-09-07 10:41:03,003 [MainThread ] [INFO ] Executing biobb_io.api.structure_info Version: 4.1.0 2023-09-07 10:41:03,003 [MainThread ] [INFO ] Getting structure info from: http://mmb.irbbarcelona.org/api/pdb/2vgb.json 2023-09-07 10:41:11,516 [MainThread ] [INFO ] Writting json to: /tmp/biobb/unitests/structure_info/output_json_path.json Checking if empty file: /tmp/biobb/unitests/structure_info/output_json_path.json Comparing: File_A: /tmp/biobb/unitests/structure_info/output_json_path.json File_B: /home/user/actions-runner/_work/biobb_io/biobb_io/biobb_io/test/reference/api/ref_str_info.json File_A hash: b'1\x8c\x9e\xcd[\xf1\xa3|\x1a\xbf\xd2\x9a\x900\xc2\xfe\x12%w\xca\xfd\x85630\x96\x04\xc4w@\xb5\xdb' File_B hash: b'1\x8c\x9e\xcd[\xf1\xa3|\x1a\xbf\xd2\x9a\x900\xc2\xfe\x12%w\xca\xfd\x85630\x96\x04\xc4w@\xb5\xdb' -------------------------------Captured log call-------------------------------- INFO /tmp/biobb/unitests/structure_info/structure_info_log.out:file_utils.py:390 Executing biobb_io.api.structure_info Version: 4.1.0 INFO /tmp/biobb/unitests/structure_info/structure_info_log.out:file_utils.py:390 Getting structure info from: http://mmb.irbbarcelona.org/api/pdb/2vgb.json INFO /tmp/biobb/unitests/structure_info/structure_info_log.out:file_utils.py:390 Writting json to: /tmp/biobb/unitests/structure_info/output_json_path.json ----------------------------Captured stdout teardown---------------------------- Removing: /tmp/biobb/unitests | |||