diff options
Diffstat (limited to 'plip/test/test_literature_validated.py')
| -rw-r--r-- | plip/test/test_literature_validated.py | 264 |
1 files changed, 141 insertions, 123 deletions
diff --git a/plip/test/test_literature_validated.py b/plip/test/test_literature_validated.py index f3f7cbc..d49dba5 100644 --- a/plip/test/test_literature_validated.py +++ b/plip/test/test_literature_validated.py @@ -21,10 +21,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Chakrabarti et al. Geometry of nonbonded interactions involving planar groups in proteins. (2007) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1eve.pdb') - bsid = 'E20:A:2001' + tmpmol.load_pdb("./pdb/1eve.pdb") + bsid = "E20:A:2001" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Aromatic stacking with Trp84 and Trp279 @@ -39,10 +39,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Chakrabarti et al. Geometry of nonbonded interactions involving planar groups in proteins. (2007) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1h2t.pdb') - bsid = 'GDP:Z:1151' + tmpmol.load_pdb("./pdb/1h2t.pdb") + bsid = "GDP:Z:1151" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Sandwiched pi-stacking involving Tyr20 and Tyr43 @@ -60,10 +60,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Betzi et al. Discovery of a potential allosteric ligand binding site in CDK2 (2012) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/3pxf.pdb') - bsids = ['2AN:A:305', '2AN:A:304'] + tmpmol.load_pdb("./pdb/3pxf.pdb") + bsids = ["2AN:A:305", "2AN:A:304"] for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) in bsids: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) in bsids: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsids[0]] # 2AN:A:305 @@ -91,10 +91,10 @@ class LiteratureValidatedTest(unittest.TestCase): from Sinorhizobium meliloti in the liganded and unliganded-closed states. (2008) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/2reg.pdb') - bsid = 'CHT:A:1' + tmpmol.load_pdb("./pdb/2reg.pdb") + bsid = "CHT:A:1" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Cation-pi interactions with Trp43, Trp90, Trp205, and Tyr119 @@ -109,10 +109,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Bird et al. Crystal structures of Varicella Zoster Virus Thyrimidine Kinase. (2003) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1osn.pdb') - bsid = 'BVP:A:500' + tmpmol.load_pdb("./pdb/1osn.pdb") + bsid = "BVP:A:500" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Sandwiched pi-stacking involving Phe93 and Phe139 @@ -128,10 +128,10 @@ class LiteratureValidatedTest(unittest.TestCase): has implications for antiviral therapy (2008) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/2w0s.pdb') - bsid = 'BVP:B:1207' # Complex of BVDU with Magnesium Cofactor + tmpmol.load_pdb("./pdb/2w0s.pdb") + bsid = "BVP:B:1207" # Complex of BVDU with Magnesium Cofactor for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonding of Tyr101 and Arg72 @@ -152,10 +152,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Li et al. Identification of a potent and selective non-basic cathepsin K inhibitor. (2006) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1vsn.pdb') - bsid = 'NFT:A:283' + tmpmol.load_pdb("./pdb/1vsn.pdb") + bsid = "NFT:A:283" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonding to Gly66 @@ -167,10 +167,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: De Moliner et al. Alternative binding modes of an inhibitor to two different kinases. (2003) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1p5e.pdb') - bsid = 'TBS:A:301' + tmpmol.load_pdb("./pdb/1p5e.pdb") + bsid = "TBS:A:301" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Halogen Bonding of Ile10 and Leu83 @@ -183,10 +183,10 @@ class LiteratureValidatedTest(unittest.TestCase): acetylcholinesterase.. (1993) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1acj.pdb') - bsid = 'THA:A:999' + tmpmol.load_pdb("./pdb/1acj.pdb") + bsid = "THA:A:999" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # pi-stacking interaction with Phe330 and Trp84 @@ -199,10 +199,10 @@ class LiteratureValidatedTest(unittest.TestCase): glutamicum CgmR in Complex with Inducers and with an Operator. (2010) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/2zoz.pdb') - bsid = 'ET:B:184' + tmpmol.load_pdb("./pdb/2zoz.pdb") + bsid = "ET:B:184" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # pi-stacking interaction with Trp63 and Phe147 @@ -219,10 +219,10 @@ class LiteratureValidatedTest(unittest.TestCase): RNA editing ligase 1. (2004) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1xdn.pdb') - bsid = 'ATP:A:501' + tmpmol.load_pdb("./pdb/1xdn.pdb") + bsid = "ATP:A:501" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Arg111, Ile61 (backbone), Asn92, Val88, Lys87 and Glu86# @@ -241,10 +241,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Peisach et al. Interaction of a Peptidomimetic Aminimide Inhibitor with Elastase. (1995) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1bma.pdb') - bsid = '0QH:A:256' + tmpmol.load_pdb("./pdb/1bma.pdb") + bsid = "0QH:A:256" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to val224 and Gln200 @@ -265,14 +265,16 @@ class LiteratureValidatedTest(unittest.TestCase): and Their Prodrugs As Antimalarial Agents (2004) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/4rao.pdb') - bsid = '3L7:B:301' + tmpmol.load_pdb("./pdb/4rao.pdb") + bsid = "3L7:B:301" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Val187, Lys165, Thr141, Lys140, Gly139, Thr138, Asp137 - hbonds = {hbond.resnr for hbond in s.hbonds_pdon} # res nr 100, 68, 69 and 199 in alternative conformation, + hbonds = { + hbond.resnr for hbond in s.hbonds_pdon + } # res nr 100, 68, 69 and 199 in alternative conformation, self.assertTrue({137, 138, 139, 140, 141, 165, 187}.issubset(hbonds)) # Water bridges to Asp137, Thr141, Met142, Arg199 and Gly139 # res nr 199 and 142 in alternative conformation @@ -286,10 +288,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Bhattacharya et al. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6(2014) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/4qnb.pdb') - bsid = '1B0:A:301' + tmpmol.load_pdb("./pdb/4qnb.pdb") + bsid = "1B0:A:301" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Asn57 and Lys70 @@ -304,10 +306,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Zaware et al. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6(2014) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/4kya.pdb') - bsid = '1UG:E:702' + tmpmol.load_pdb("./pdb/4kya.pdb") + bsid = "1UG:E:702" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Ala609 @@ -329,10 +331,10 @@ class LiteratureValidatedTest(unittest.TestCase): implications for ligand binding and specificity(2002) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1n7g.pdb') - bsid = 'NDP:A:701' + tmpmol.load_pdb("./pdb/1n7g.pdb") + bsid = "NDP:A:701" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Thr37, Gly38, Gln39, Asp40, Arg60, Leu92, Asp91, Ser63, Leu92, Ala115, Ser117, @@ -340,7 +342,9 @@ class LiteratureValidatedTest(unittest.TestCase): # Publication give the Prediction for Asp91 as hydrogen bond, when this contains two acceptor atoms. hbonds = {hbond.resnr for hbond in s.hbonds_pdon} # #@todo Hbond to 128 not detected - self.assertTrue({37, 38, 39, 40, 92, 63, 92, 115, 117, 185, 189, 215, 220}.issubset(hbonds)) + self.assertTrue( + {37, 38, 39, 40, 92, 63, 92, 115, 117, 185, 189, 215, 220}.issubset(hbonds) + ) # Water bridges to Gly35, Thr37, Gly38, Asp40, Arg60, Arg61, Ser63, Asn66, Ser117, Tyr128, Lys189, Arg220 waterbridges = {wb.resnr for wb in s.water_bridges} # Hydrogen bonds to 35, 37, 38, 40, 63, 117, 128, 189, 220 not detected due to prioritization @@ -358,10 +362,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Tsuhako et al. The design, synthesis, and biological evaluation of PIM kinase inhibitors.(2012) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/4alw.pdb') - bsid = 'HY7:A:1308' + tmpmol.load_pdb("./pdb/4alw.pdb") + bsid = "HY7:A:1308" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Asp186 @@ -377,10 +381,10 @@ class LiteratureValidatedTest(unittest.TestCase): for TMAO.(2013) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/3o1h.pdb') - bsid = 'TMO:B:1' + tmpmol.load_pdb("./pdb/3o1h.pdb") + bsid = "TMO:B:1" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Trp45 @@ -396,10 +400,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Shikha et al. Mechanism of mismatch recognition revealed by human MutSĪ² bound to unpaired DNA loops.(2012) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/3thy.pdb') - bsid = 'ADP:A:935' + tmpmol.load_pdb("./pdb/3thy.pdb") + bsid = "ADP:A:935" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Saltbridge to His295 and Lys675 @@ -414,10 +418,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Ash et al. The structure of an N11A mutant of the G-protein domain of FeoB.(2011) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/3tah.pdb') - bsid = 'BGO:A:300' + tmpmol.load_pdb("./pdb/3tah.pdb") + bsid = "BGO:A:300" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Ala11, Lys14, Thr15, Ser16, Asp113, Met114, Ala143 and Asp113 @@ -434,10 +438,10 @@ class LiteratureValidatedTest(unittest.TestCase): kinase CK2 inhibitors in clinical trials for the treatment of cancer (2011). """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/3r0t.pdb') - bsid = 'FU9:A:338' + tmpmol.load_pdb("./pdb/3r0t.pdb") + bsid = "FU9:A:338" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Val116 @@ -462,10 +466,10 @@ class LiteratureValidatedTest(unittest.TestCase): Redox Potentials of DesulfoVibrio Vulgaris Flavodoxin.(2002) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1aku.pdb') - bsid = 'FMN:A:150' + tmpmol.load_pdb("./pdb/1aku.pdb") + bsid = "FMN:A:150" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Thr59 @@ -488,10 +492,10 @@ class LiteratureValidatedTest(unittest.TestCase): 673, a potent inhibitor derived from dihydropyridophthalazinone.(2014) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/4pjt.pdb') - bsid = '2YQ:D:1104' + tmpmol.load_pdb("./pdb/4pjt.pdb") + bsid = "2YQ:D:1104" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Gly863 @@ -506,15 +510,15 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Presnell et al. Oxyanion-Mediated Inhibition of Serine Proteases.(1998) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1bju.pdb') - bsid = 'GP6:A:910' + tmpmol.load_pdb("./pdb/1bju.pdb") + bsid = "GP6:A:910" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] - #@todo Publication show hydrogen bond interactions for Gly219 + # @todo Publication show hydrogen bond interactions for Gly219 # Hydrogen bonds to Ser190, Ser195, Gly219 and Asp189 - hbonds = {hbond.resnr for hbond in s.hbonds_pdon+s.hbonds_ldon} + hbonds = {hbond.resnr for hbond in s.hbonds_pdon + s.hbonds_ldon} self.assertTrue({189, 190, 195}.issubset(hbonds)) # Water bridges to Ser190 and Val227 # Water bridge to 190 not detected due to prioritization @@ -532,10 +536,10 @@ class LiteratureValidatedTest(unittest.TestCase): Reference: Wilcken et al. Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant p53.(2012) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/4agl.pdb') - bsid = 'P84:A:400' + tmpmol.load_pdb("./pdb/4agl.pdb") + bsid = "P84:A:400" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Water bridges to Val147 @@ -554,10 +558,10 @@ class LiteratureValidatedTest(unittest.TestCase): Pathway.(2007) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/2efj.pdb') - bsid = '37T:A:502' + tmpmol.load_pdb("./pdb/2efj.pdb") + bsid = "37T:A:502" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bond to Ser237 @@ -573,10 +577,10 @@ class LiteratureValidatedTest(unittest.TestCase): inhibitor.(2006) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/2iuz.pdb') - bsid = 'D1H:A:1440' + tmpmol.load_pdb("./pdb/2iuz.pdb") + bsid = "D1H:A:1440" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Trp137 @@ -597,10 +601,10 @@ class LiteratureValidatedTest(unittest.TestCase): phosphodiesterase type 5 (PDE5) inhibitors.(2011) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/3shy.pdb') - bsid = '5FO:A:1' + tmpmol.load_pdb("./pdb/3shy.pdb") + bsid = "5FO:A:1" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Gln817 @@ -622,10 +626,10 @@ class LiteratureValidatedTest(unittest.TestCase): substrate recognition site constructed by rearrangement of hydrogen bond network..(1998) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1ay8.pdb') - bsid = 'PLP:A:413' + tmpmol.load_pdb("./pdb/1ay8.pdb") + bsid = "PLP:A:413" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds to Gly108, Thr109, Asn194 and Ser257 @@ -644,10 +648,10 @@ class LiteratureValidatedTest(unittest.TestCase): evolutionary path selected by the Lewis epitope..(2014) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/4rdl.pdb') - bsid = 'FUC:A:601' + tmpmol.load_pdb("./pdb/4rdl.pdb") + bsid = "FUC:A:601" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Instead of FUC-A-604 (sugar representative) # Water bridges to Asn395 @@ -670,18 +674,22 @@ class LiteratureValidatedTest(unittest.TestCase): with CGP 53820, a novel pseudosymmetric inhibitor (1995) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1hii.pdb') - bsid = 'C20:B:101' + tmpmol.load_pdb("./pdb/1hii.pdb") + bsid = "C20:B:101" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Water bridges - waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges} - self.assertTrue({'50A', '50B'}.issubset(waterbridges)) # Bridging Ile-B50 and Ile-A50 with ligand + waterbridges = {str(wb.resnr) + wb.reschain for wb in s.water_bridges} + self.assertTrue( + {"50A", "50B"}.issubset(waterbridges) + ) # Bridging Ile-B50 and Ile-A50 with ligand # Hydrogen bonds - hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon} - self.assertTrue({'27A', '27B', '29A', '48A', '48B'}.issubset(hbonds)) + hbonds = { + str(hbond.resnr) + hbond.reschain for hbond in s.hbonds_pdon + s.hbonds_ldon + } + self.assertTrue({"27A", "27B", "29A", "48A", "48B"}.issubset(hbonds)) # #@todo Publication mentions additional possible hydrogen bond with Asp28B # Hydrogen bonds with Asp-A25 are reported as a salt bridge as both partners have (potential) charges @@ -691,22 +699,28 @@ class LiteratureValidatedTest(unittest.TestCase): Diol Inhibitors of HIV-1 Protease (1994) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1hvi.pdb') - bsid = 'A77:A:800' + tmpmol.load_pdb("./pdb/1hvi.pdb") + bsid = "A77:A:800" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Water bridges - waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges} + waterbridges = {str(wb.resnr) + wb.reschain for wb in s.water_bridges} # #@todo Water bridge with 50B not detected - self.assertTrue({'50A'}.issubset(waterbridges)) # Bridging Ile-B50 and Ile-A50 with ligand + self.assertTrue( + {"50A"}.issubset(waterbridges) + ) # Bridging Ile-B50 and Ile-A50 with ligand # pi-cation Interactions picat = {pication.resnr for pication in s.pication_laro} - self.assertEqual({8}, picat) # Described as weakly polar contact/stacking in paper + self.assertEqual( + {8}, picat + ) # Described as weakly polar contact/stacking in paper # Hydrogen bonds - hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon} - self.assertTrue({'25B', '27A', '27B', '48A', '48B'}.issubset(hbonds)) + hbonds = { + str(hbond.resnr) + hbond.reschain for hbond in s.hbonds_pdon + s.hbonds_ldon + } + self.assertTrue({"25B", "27A", "27B", "48A", "48B"}.issubset(hbonds)) # #@todo Paper describes additional hydrogen bond with Asp25A def test_3o7g(self): @@ -715,16 +729,18 @@ class LiteratureValidatedTest(unittest.TestCase): melanoma (2010) """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/3og7.pdb') - bsid = '032:A:1' + tmpmol.load_pdb("./pdb/3og7.pdb") + bsid = "032:A:1" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrogen bonds - hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon} + hbonds = { + str(hbond.resnr) + hbond.reschain for hbond in s.hbonds_pdon + s.hbonds_ldon + } # Additional hydrogen bond to residue 530A reported - self.assertTrue({'594A'}.issubset(hbonds)) + self.assertTrue({"594A"}.issubset(hbonds)) def test_1hpx(self): """ @@ -735,20 +751,22 @@ class LiteratureValidatedTest(unittest.TestCase): For residues in the B chain, the offset is -100 (e.g. Ile 50B in the PDB structure is Ile 150 in the paper). """ tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1hpx.pdb') - bsid = 'KNI:B:900' + tmpmol.load_pdb("./pdb/1hpx.pdb") + bsid = "KNI:B:900" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] # Hydrophobic contacts to Val82, Ile84, Ile150 as part of flap (S1, S1' sites) - hydroph = {str(hyd.resnr)+hyd.reschain for hyd in s.all_hydrophobic_contacts} - self.assertTrue({'82A', '84A', '50B'}.issubset(hydroph)) + hydroph = {str(hyd.resnr) + hyd.reschain for hyd in s.all_hydrophobic_contacts} + self.assertTrue({"82A", "84A", "50B"}.issubset(hydroph)) # Hydrogen bonds - hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_ldon+s.hbonds_pdon} + hbonds = { + str(hbond.resnr) + hbond.reschain for hbond in s.hbonds_ldon + s.hbonds_pdon + } # Additional hbond to 25B not detected (low angle?) - self.assertTrue({'29B', '48B', '27B', '25A'}.issubset(hbonds)) + self.assertTrue({"29B", "48B", "27B", "25A"}.issubset(hbonds)) # Water bridges - waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges} + waterbridges = {str(wb.resnr) + wb.reschain for wb in s.water_bridges} # Waterbridge with Gly27 is detected instead of Ala28/Asp29 - self.assertTrue({'50A', '50B', '29A'}.issubset(waterbridges)) + self.assertTrue({"50A", "50B", "29A"}.issubset(waterbridges)) |