diff options
| -rw-r--r-- | plip/basic/config.py | 606 | ||||
| -rw-r--r-- | plip/exchange/report.py | 788 | ||||
| -rw-r--r-- | plip/plipcmd.py | 410 | ||||
| -rw-r--r-- | plip/structure/preparation.py | 1823 | ||||
| -rw-r--r-- | plip/test/test_command_line.py | 31 | ||||
| -rw-r--r-- | plip/test/test_hydrogen_bonds.py | 18 |
6 files changed, 2775 insertions, 901 deletions
diff --git a/plip/basic/config.py b/plip/basic/config.py index 4eee215..91103fa 100644 --- a/plip/basic/config.py +++ b/plip/basic/config.py @@ -1,5 +1,5 @@ -__version__ = '2.1.3' -__maintainer__ = 'PharmAI GmbH (2020) - www.pharm.ai - hello@pharm.ai' +__version__ = "2.1.3" +__maintainer__ = "PharmAI GmbH (2020) - www.pharm.ai - hello@pharm.ai" import logging @@ -14,8 +14,8 @@ PICS = False PYMOL = False STDOUT = False RAWSTRING = False # use raw strings for input / output -OUTPATH = './' -BASEPATH = './' +OUTPATH = "./" +BASEPATH = "./" BREAKCOMPOSITE = False # Break up composite ligands with covalent bonds ALTLOC = False # Consider alternate locations PLUGIN_MODE = False # Special mode for PLIP in Plugins (e.g. PyMOL) @@ -34,27 +34,45 @@ NOHYDRO = False # Do not add hydrogen bonds (in case already present in the str # Thresholds for detection (global variables) BS_DIST = 7.5 # Determines maximum distance to include binding site residues -AROMATIC_PLANARITY = 5.0 # Determines allowed deviation from planarity in aromatic rings +AROMATIC_PLANARITY = ( + 5.0 # Determines allowed deviation from planarity in aromatic rings +) MIN_DIST = 0.5 # Minimum distance for all distance thresholds # Some distance thresholds were extended (max. 1.0A) if too restrictive too account for low-quality structures HYDROPH_DIST_MAX = 4.0 # Distance cutoff for detection of hydrophobic contacts HBOND_DIST_MAX = 4.1 # Max. distance between hydrogen bond donor and acceptor (Hubbard & Haider, 2001) + 0.6 A -HBOND_DON_ANGLE_MIN = 100 # Min. angle at the hydrogen bond donor (Hubbard & Haider, 2001) + 10 -PISTACK_DIST_MAX = 5.5 # Max. distance for parallel or offset pistacking (McGaughey, 1998) -PISTACK_ANG_DEV = 30 # Max. Deviation from parallel or perpendicular orientation (in degrees) +HBOND_DON_ANGLE_MIN = ( + 100 # Min. angle at the hydrogen bond donor (Hubbard & Haider, 2001) + 10 +) +PISTACK_DIST_MAX = ( + 5.5 # Max. distance for parallel or offset pistacking (McGaughey, 1998) +) +PISTACK_ANG_DEV = ( + 30 # Max. Deviation from parallel or perpendicular orientation (in degrees) +) PISTACK_OFFSET_MAX = 2.0 # Maximum offset of the two rings (corresponds to the radius of benzene + 0.5 A) PICATION_DIST_MAX = 6.0 # Max. distance between charged atom and aromatic ring center (Gallivan and Dougherty, 1999) SALTBRIDGE_DIST_MAX = 5.5 # Max. distance between centers of charge for salt bridges (Barlow and Thornton, 1983) + 1.5 HALOGEN_DIST_MAX = 4.0 # Max. distance between oxy. and halogen (Halogen bonds in biological molecules., Auffinger)+0.5 -HALOGEN_ACC_ANGLE = 120 # Optimal acceptor angle (Halogen bonds in biological molecules., Auffinger) -HALOGEN_DON_ANGLE = 165 # Optimal donor angle (Halogen bonds in biological molecules., Auffinger) +HALOGEN_ACC_ANGLE = ( + 120 # Optimal acceptor angle (Halogen bonds in biological molecules., Auffinger) +) +HALOGEN_DON_ANGLE = ( + 165 # Optimal donor angle (Halogen bonds in biological molecules., Auffinger) +) HALOGEN_ANGLE_DEV = 30 # Max. deviation from optimal angle -WATER_BRIDGE_MINDIST = 2.5 # Min. distance between water oxygen and polar atom (Jiang et al., 2005) -0.1 -WATER_BRIDGE_MAXDIST = 4.1 # Max. distance between water oxygen and polar atom (Jiang et al., 2005) +0.5 +WATER_BRIDGE_MINDIST = ( + 2.5 # Min. distance between water oxygen and polar atom (Jiang et al., 2005) -0.1 +) +WATER_BRIDGE_MAXDIST = ( + 4.1 # Max. distance between water oxygen and polar atom (Jiang et al., 2005) +0.5 +) WATER_BRIDGE_OMEGA_MIN = 71 # Min. angle between acceptor, water oxygen and donor hydrogen (Jiang et al., 2005) - 9 WATER_BRIDGE_OMEGA_MAX = 140 # Max. angle between acceptor, water oxygen and donor hydrogen (Jiang et al., 2005) WATER_BRIDGE_THETA_MIN = 100 # Min. angle between water oxygen, donor hydrogen and donor atom (Jiang et al., 2005) -METAL_DIST_MAX = 3.0 # Max. distance between metal ion and interacting atom (Harding, 2001) +METAL_DIST_MAX = ( + 3.0 # Max. distance between metal ion and interacting atom (Harding, 2001) +) # Other thresholds MAX_COMPOSITE_LENGTH = 200 # Filter out ligands with more than 200 fragments @@ -64,8 +82,8 @@ MAX_COMPOSITE_LENGTH = 200 # Filter out ligands with more than 200 fragments ######### # Names of RNA and DNA residues to be considered (detection by name) -RNA = ['U', 'A', 'C', 'G'] -DNA = ['DT', 'DA', 'DC', 'DG'] +RNA = ["U", "A", "C", "G"] +DNA = ["DT", "DA", "DC", "DG"] ############# # Whitelist # @@ -73,49 +91,535 @@ DNA = ['DT', 'DA', 'DC', 'DG'] # Metal cations which can be complexed -METAL_IONS = ['CA', 'CO', 'MG', 'MN', 'FE', 'CU', 'ZN', 'FE2', 'FE3', 'FE4', 'LI', 'NA', 'K', 'RB', 'SR', 'CS', 'BA', - 'CR', 'NI', 'FE1', 'NI', 'RU', 'RU1', 'RH', 'RH1', 'PD', 'AG', 'CD', 'LA', 'W', 'W1', 'OS', 'IR', 'PT', - 'PT1', 'AU', 'HG', 'CE', 'PR', 'SM', 'EU', 'GD', 'TB', 'YB', 'LU', 'AL', 'GA', 'IN', 'SB', 'TL', 'PB'] +METAL_IONS = [ + "CA", + "CO", + "MG", + "MN", + "FE", + "CU", + "ZN", + "FE2", + "FE3", + "FE4", + "LI", + "NA", + "K", + "RB", + "SR", + "CS", + "BA", + "CR", + "NI", + "FE1", + "NI", + "RU", + "RU1", + "RH", + "RH1", + "PD", + "AG", + "CD", + "LA", + "W", + "W1", + "OS", + "IR", + "PT", + "PT1", + "AU", + "HG", + "CE", + "PR", + "SM", + "EU", + "GD", + "TB", + "YB", + "LU", + "AL", + "GA", + "IN", + "SB", + "TL", + "PB", +] ############## # Blacklists # ############## # Other Ions/Atoms (not yet supported) -anions = ['CL', 'IOD', 'BR'] -other = ['MO', 'RE', 'HO'] +anions = ["CL", "IOD", "BR"] +other = ["MO", "RE", "HO"] UNSUPPORTED = anions + other # BioLiP list of suspicious ligands from http://zhanglab.ccmb.med.umich.edu/BioLiP/ligand_list (2014-07-10) # Add ligands here to get warnings for possible artifacts. -biolip_list = ['ACE', 'HEX', 'TMA', 'SOH', 'P25', 'CCN', 'PR', 'PTN', 'NO3', 'TCN', 'BU1', 'BCN', 'CB3', 'HCS', 'NBN', - 'SO2', 'MO6', 'MOH', 'CAC', 'MLT', 'KR', '6PH', 'MOS', 'UNL', 'MO3', 'SR', 'CD3', 'PB', 'ACM', 'LUT', - 'PMS', 'OF3', 'SCN', 'DHB', 'E4N', '13P', '3PG', 'CYC', 'NC', 'BEN', 'NAO', 'PHQ', 'EPE', 'BME', 'TB', - 'ETE', 'EU', 'OES', 'EAP', 'ETX', 'BEZ', '5AD', 'OC2', 'OLA', 'GD3', 'CIT', 'DVT', 'OC6', 'MW1', 'OC3', - 'SRT', 'LCO', 'BNZ', 'PPV', 'STE', 'PEG', 'RU', 'PGE', 'MPO', 'B3P', 'OGA', 'IPA', 'LU', 'EDO', 'MAC', - '9PE', 'IPH', 'MBN', 'C1O', '1PE', 'YF3', 'PEF', 'GD', '8PE', 'DKA', 'RB', 'YB', 'GGD', 'SE4', 'LHG', - 'SMO', 'DGD', 'CMO', 'MLI', 'MW2', 'DTT', 'DOD', '7PH', 'PBM', 'AU', 'FOR', 'PSC', 'TG1', 'KAI', '1PG', - 'DGA', 'IR', 'PE4', 'VO4', 'ACN', 'AG', 'MO4', 'OCL', '6UL', 'CHT', 'RHD', 'CPS', 'IR3', 'OC4', 'MTE', - 'HGC', 'CR', 'PC1', 'HC4', 'TEA', 'BOG', 'PEO', 'PE5', '144', 'IUM', 'LMG', 'SQU', 'MMC', 'GOL', 'NVP', - 'AU3', '3PH', 'PT4', 'PGO', 'ICT', 'OCM', 'BCR', 'PG4', 'L4P', 'OPC', 'OXM', 'SQD', 'PQ9', 'BAM', 'PI', - 'PL9', 'P6G', 'IRI', '15P', 'MAE', 'MBO', 'FMT', 'L1P', 'DUD', 'PGV', 'CD1', 'P33', 'DTU', 'XAT', 'CD', - 'THE', 'U1', 'NA', 'MW3', 'BHG', 'Y1', 'OCT', 'BET', 'MPD', 'HTO', 'IBM', 'D01', 'HAI', 'HED', 'CAD', - 'CUZ', 'TLA', 'SO4', 'OC5', 'ETF', 'MRD', 'PT', 'PHB', 'URE', 'MLA', 'TGL', 'PLM', 'NET', 'LAC', 'AUC', - 'UNX', 'GA', 'DMS', 'MO2', 'LA', 'NI', 'TE', 'THJ', 'NHE', 'HAE', 'MO1', 'DAO', '3PE', 'LMU', 'DHJ', - 'FLC', 'SAL', 'GAI', 'ORO', 'HEZ', 'TAM', 'TRA', 'NEX', 'CXS', 'LCP', 'HOH', 'OCN', 'PER', 'ACY', 'MH2', - 'ARS', '12P', 'L3P', 'PUT', 'IN', 'CS', 'NAW', 'SB', 'GUN', 'SX', 'CON', 'C2O', 'EMC', 'BO4', 'BNG', - 'MN5', '__O', 'K', 'CYN', 'H2S', 'MH3', 'YT3', 'P22', 'KO4', '1AG', 'CE', 'IPL', 'PG6', 'MO5', 'F09', - 'HO', 'AL', 'TRS', 'EOH', 'GCP', 'MSE', 'AKR', 'NCO', 'PO4', 'L2P', 'LDA', 'SIN', 'DMI', 'SM', 'DTD', - 'SGM', 'DIO', 'PPI', 'DDQ', 'DPO', 'HCA', 'CO5', 'PD', 'OS', 'OH', 'NA6', 'NAG', 'W', 'ENC', 'NA5', - 'LI1', 'P4C', 'GLV', 'DMF', 'ACT', 'BTB', '6PL', 'BGL', 'OF1', 'N8E', 'LMT', 'THM', 'EU3', 'PGR', 'NA2', - 'FOL', '543', '_CP', 'PEK', 'NSP', 'PEE', 'OCO', 'CHD', 'CO2', 'TBU', 'UMQ', 'MES', 'NH4', 'CD5', 'HTG', - 'DEP', 'OC1', 'KDO', '2PE', 'PE3', 'IOD', 'NDG', 'CL', 'HG', 'F', 'XE', 'TL', 'BA', 'LI', 'BR', 'TAU', - 'TCA', 'SPD', 'SPM', 'SAR', 'SUC', 'PAM', 'SPH', 'BE7', 'P4G', 'OLC', 'OLB', 'LFA', 'D10', 'D12', 'DD9', - 'HP6', 'R16', 'PX4', 'TRD', 'UND', 'FTT', 'MYR', 'RG1', 'IMD', 'DMN', 'KEN', 'C14', 'UPL', 'CMJ', 'ULI', - 'MYS', 'TWT', 'M2M', 'P15', 'PG0', 'PEU', 'AE3', 'TOE', 'ME2', 'PE8', '6JZ', '7PE', 'P3G', '7PG', 'PG5', - '16P', 'XPE', 'PGF', 'AE4', '7E8', '7E9', 'MVC', 'TAR', 'DMR', 'LMR', 'NER', '02U', 'NGZ', 'LXB', 'A2G', - 'BM3', 'NAA', 'NGA', 'LXZ', 'PX6', 'PA8', 'LPP', 'PX2', 'MYY', 'PX8', 'PD7', 'XP4', 'XPA', 'PEV', '6PE', - 'PEX', 'PEH', 'PTY', 'YB2', 'PGT', 'CN3', 'AGA', 'DGG', 'CD4', 'CN6', 'CDL', 'PG8', 'MGE', 'DTV', 'L44', - 'L2C', '4AG', 'B3H', '1EM', 'DDR', 'I42', 'CNS', 'PC7', 'HGP', 'PC8', 'HGX', 'LIO', 'PLD', 'PC2', 'PCF', - 'MC3', 'P1O', 'PLC', 'PC6', 'HSH', 'BXC', 'HSG', 'DPG', '2DP', 'POV', 'PCW', 'GVT', 'CE9', 'CXE', 'C10', - 'CE1', 'SPJ', 'SPZ', 'SPK', 'SPW', 'HT3', 'HTH', '2OP', '3NI', 'BO3', 'DET', 'D1D', 'SWE', 'SOG'] +biolip_list = [ + "ACE", + "HEX", + "TMA", + "SOH", + "P25", + "CCN", + "PR", + "PTN", + "NO3", + "TCN", + "BU1", + "BCN", + "CB3", + "HCS", + "NBN", + "SO2", + "MO6", + "MOH", + "CAC", + "MLT", + "KR", + "6PH", + "MOS", + "UNL", + "MO3", + "SR", + "CD3", + "PB", + "ACM", + "LUT", + "PMS", + "OF3", + "SCN", + "DHB", + "E4N", + "13P", + "3PG", + "CYC", + "NC", + "BEN", + "NAO", + "PHQ", + "EPE", + "BME", + "TB", + "ETE", + "EU", + "OES", + "EAP", + "ETX", + "BEZ", + "5AD", + "OC2", + "OLA", + "GD3", + "CIT", + "DVT", + "OC6", + "MW1", + "OC3", + "SRT", + "LCO", + "BNZ", + "PPV", + "STE", + "PEG", + "RU", + "PGE", + "MPO", + "B3P", + "OGA", + "IPA", + "LU", + "EDO", + "MAC", + "9PE", + "IPH", + "MBN", + "C1O", + "1PE", + "YF3", + "PEF", + "GD", + "8PE", + "DKA", + "RB", + "YB", + "GGD", + "SE4", + "LHG", + "SMO", + "DGD", + "CMO", + "MLI", + "MW2", + "DTT", + "DOD", + "7PH", + "PBM", + "AU", + "FOR", + "PSC", + "TG1", + "KAI", + "1PG", + "DGA", + "IR", + "PE4", + "VO4", + "ACN", + "AG", + "MO4", + "OCL", + "6UL", + "CHT", + "RHD", + "CPS", + "IR3", + "OC4", + "MTE", + "HGC", + "CR", + "PC1", + "HC4", + "TEA", + "BOG", + "PEO", + "PE5", + "144", + "IUM", + "LMG", + "SQU", + "MMC", + "GOL", + "NVP", + "AU3", + "3PH", + "PT4", + "PGO", + "ICT", + "OCM", + "BCR", + "PG4", + "L4P", + "OPC", + "OXM", + "SQD", + "PQ9", + "BAM", + "PI", + "PL9", + "P6G", + "IRI", + "15P", + "MAE", + "MBO", + "FMT", + "L1P", + "DUD", + "PGV", + "CD1", + "P33", + "DTU", + "XAT", + "CD", + "THE", + "U1", + "NA", + "MW3", + "BHG", + "Y1", + "OCT", + "BET", + "MPD", + "HTO", + "IBM", + "D01", + "HAI", + "HED", + "CAD", + "CUZ", + "TLA", + "SO4", + "OC5", + "ETF", + "MRD", + "PT", + "PHB", + "URE", + "MLA", + "TGL", + "PLM", + "NET", + "LAC", + "AUC", + "UNX", + "GA", + "DMS", + "MO2", + "LA", + "NI", + "TE", + "THJ", + "NHE", + "HAE", + "MO1", + "DAO", + "3PE", + "LMU", + "DHJ", + "FLC", + "SAL", + "GAI", + "ORO", + "HEZ", + "TAM", + "TRA", + "NEX", + "CXS", + "LCP", + "HOH", + "OCN", + "PER", + "ACY", + "MH2", + "ARS", + "12P", + "L3P", + "PUT", + "IN", + "CS", + "NAW", + "SB", + "GUN", + "SX", + "CON", + "C2O", + "EMC", + "BO4", + "BNG", + "MN5", + "__O", + "K", + "CYN", + "H2S", + "MH3", + "YT3", + "P22", + "KO4", + "1AG", + "CE", + "IPL", + "PG6", + "MO5", + "F09", + "HO", + "AL", + "TRS", + "EOH", + "GCP", + "MSE", + "AKR", + "NCO", + "PO4", + "L2P", + "LDA", + "SIN", + "DMI", + "SM", + "DTD", + "SGM", + "DIO", + "PPI", + "DDQ", + "DPO", + "HCA", + "CO5", + "PD", + "OS", + "OH", + "NA6", + "NAG", + "W", + "ENC", + "NA5", + "LI1", + "P4C", + "GLV", + "DMF", + "ACT", + "BTB", + "6PL", + "BGL", + "OF1", + "N8E", + "LMT", + "THM", + "EU3", + "PGR", + "NA2", + "FOL", + "543", + "_CP", + "PEK", + "NSP", + "PEE", + "OCO", + "CHD", + "CO2", + "TBU", + "UMQ", + "MES", + "NH4", + "CD5", + "HTG", + "DEP", + "OC1", + "KDO", + "2PE", + "PE3", + "IOD", + "NDG", + "CL", + "HG", + "F", + "XE", + "TL", + "BA", + "LI", + "BR", + "TAU", + "TCA", + "SPD", + "SPM", + "SAR", + "SUC", + "PAM", + "SPH", + "BE7", + "P4G", + "OLC", + "OLB", + "LFA", + "D10", + "D12", + "DD9", + "HP6", + "R16", + "PX4", + "TRD", + "UND", + "FTT", + "MYR", + "RG1", + "IMD", + "DMN", + "KEN", + "C14", + "UPL", + "CMJ", + "ULI", + "MYS", + "TWT", + "M2M", + "P15", + "PG0", + "PEU", + "AE3", + "TOE", + "ME2", + "PE8", + "6JZ", + "7PE", + "P3G", + "7PG", + "PG5", + "16P", + "XPE", + "PGF", + "AE4", + "7E8", + "7E9", + "MVC", + "TAR", + "DMR", + "LMR", + "NER", + "02U", + "NGZ", + "LXB", + "A2G", + "BM3", + "NAA", + "NGA", + "LXZ", + "PX6", + "PA8", + "LPP", + "PX2", + "MYY", + "PX8", + "PD7", + "XP4", + "XPA", + "PEV", + "6PE", + "PEX", + "PEH", + "PTY", + "YB2", + "PGT", + "CN3", + "AGA", + "DGG", + "CD4", + "CN6", + "CDL", + "PG8", + "MGE", + "DTV", + "L44", + "L2C", + "4AG", + "B3H", + "1EM", + "DDR", + "I42", + "CNS", + "PC7", + "HGP", + "PC8", + "HGX", + "LIO", + "PLD", + "PC2", + "PCF", + "MC3", + "P1O", + "PLC", + "PC6", + "HSH", + "BXC", + "HSG", + "DPG", + "2DP", + "POV", + "PCW", + "GVT", + "CE9", + "CXE", + "C10", + "CE1", + "SPJ", + "SPZ", + "SPK", + "SPW", + "HT3", + "HTH", + "2OP", + "3NI", + "BO3", + "DET", + "D1D", + "SWE", + "SOG", +] diff --git a/plip/exchange/report.py b/plip/exchange/report.py index 20f281e..8ea2130 100644 --- a/plip/exchange/report.py +++ b/plip/exchange/report.py @@ -11,7 +11,7 @@ from plip.structure.preparation import PDBComplex class StructureReport: """Creates reports (xml or txt) for one structure/""" - def __init__(self, mol: PDBComplex, outputprefix: str = 'report'): + def __init__(self, mol: PDBComplex, outputprefix: str = "report"): self.mol = mol self.excluded = self.mol.excluded self.xmlreport = self.construct_xml_tree() @@ -22,57 +22,75 @@ class StructureReport: def construct_xml_tree(self): """Construct the basic XML tree""" - report = et.Element('report') - plipversion = et.SubElement(report, 'plipversion') + report = et.Element("report") + plipversion = et.SubElement(report, "plipversion") plipversion.text = __version__ - date_of_creation = et.SubElement(report, 'date_of_creation') + date_of_creation = et.SubElement(report, "date_of_creation") date_of_creation.text = time.strftime("%Y/%m/%d") - citation_information = et.SubElement(report, 'citation_information') - citation_information.text = "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " \ - "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315" + citation_information = et.SubElement(report, "citation_information") + citation_information.text = ( + "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " + "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315" + ) - maintainer_information = et.SubElement(report, 'maintainer_information') + maintainer_information = et.SubElement(report, "maintainer_information") maintainer_information.text = config.__maintainer__ - mode = et.SubElement(report, 'mode') + mode = et.SubElement(report, "mode") if config.DNARECEPTOR: - mode.text = 'dna_receptor' + mode.text = "dna_receptor" else: - mode.text = 'default' - pdbid = et.SubElement(report, 'pdbid') + mode.text = "default" + pdbid = et.SubElement(report, "pdbid") pdbid.text = self.mol.pymol_name.upper() - filetype = et.SubElement(report, 'filetype') + filetype = et.SubElement(report, "filetype") filetype.text = self.mol.filetype.upper() - pdbfile = et.SubElement(report, 'pdbfile') - pdbfile.text = self.mol.sourcefiles['pdbcomplex'] - pdbfixes = et.SubElement(report, 'pdbfixes') - pdbfixes.text = str(self.mol.information['pdbfixes']) - filename = et.SubElement(report, 'filename') - filename.text = str(self.mol.sourcefiles.get('filename') or None) - exligs = et.SubElement(report, 'excluded_ligands') + pdbfile = et.SubElement(report, "pdbfile") + pdbfile.text = self.mol.sourcefiles["pdbcomplex"] + pdbfixes = et.SubElement(report, "pdbfixes") + pdbfixes.text = str(self.mol.information["pdbfixes"]) + filename = et.SubElement(report, "filename") + filename.text = str(self.mol.sourcefiles.get("filename") or None) + exligs = et.SubElement(report, "excluded_ligands") for i, exlig in enumerate(self.excluded): - e = et.SubElement(exligs, 'excluded_ligand', id=str(i + 1)) + e = et.SubElement(exligs, "excluded_ligand", id=str(i + 1)) e.text = exlig - covalent = et.SubElement(report, 'covlinkages') + covalent = et.SubElement(report, "covlinkages") for i, covlinkage in enumerate(self.mol.covalent): - e = et.SubElement(covalent, 'covlinkage', id=str(i + 1)) - f1 = et.SubElement(e, 'res1') - f2 = et.SubElement(e, 'res2') - f1.text = ":".join([covlinkage.id1, covlinkage.chain1, str(covlinkage.pos1)]) - f2.text = ":".join([covlinkage.id2, covlinkage.chain2, str(covlinkage.pos2)]) + e = et.SubElement(covalent, "covlinkage", id=str(i + 1)) + f1 = et.SubElement(e, "res1") + f2 = et.SubElement(e, "res2") + f1.text = ":".join( + [covlinkage.id1, covlinkage.chain1, str(covlinkage.pos1)] + ) + f2.text = ":".join( + [covlinkage.id2, covlinkage.chain2, str(covlinkage.pos2)] + ) return report def construct_txt_file(self): """Construct the header of the txt file""" - textlines = ['Prediction of noncovalent interactions for PDB structure %s' % self.mol.pymol_name.upper(), ] + textlines = [ + "Prediction of noncovalent interactions for PDB structure %s" + % self.mol.pymol_name.upper(), + ] textlines.append("=" * len(textlines[0])) - textlines.append('Created on %s using PLIP v%s\n' % (time.strftime("%Y/%m/%d"), __version__)) - textlines.append('If you are using PLIP in your work, please cite:') - textlines.append('Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.') - textlines.append('Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n') + textlines.append( + "Created on %s using PLIP v%s\n" % (time.strftime("%Y/%m/%d"), __version__) + ) + textlines.append("If you are using PLIP in your work, please cite:") + textlines.append( + "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler." + ) + textlines.append( + "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n" + ) if len(self.excluded) != 0: - textlines.append('Excluded molecules as ligands: %s\n' % ','.join([lig for lig in self.excluded])) + textlines.append( + "Excluded molecules as ligands: %s\n" + % ",".join([lig for lig in self.excluded]) + ) if config.DNARECEPTOR: - textlines.append('DNA/RNA in structure was chosen as the receptor part.\n') + textlines.append("DNA/RNA in structure was chosen as the receptor part.\n") return textlines def get_bindingsite_data(self): @@ -80,32 +98,35 @@ class StructureReport: for i, site in enumerate(sorted(self.mol.interaction_sets)): s = self.mol.interaction_sets[site] bindingsite = BindingSiteReport(s).generate_xml() - bindingsite.set('id', str(i + 1)) - bindingsite.set('has_interactions', 'False') + bindingsite.set("id", str(i + 1)) + bindingsite.set("has_interactions", "False") self.xmlreport.insert(i + 1, bindingsite) for itype in BindingSiteReport(s).generate_txt(): self.txtreport.append(itype) if not s.no_interactions: - bindingsite.set('has_interactions', 'True') + bindingsite.set("has_interactions", "True") else: - self.txtreport.append('No interactions detected.') + self.txtreport.append("No interactions detected.") def write_xml(self, as_string=False): """Write the XML report""" if not as_string: - et.ElementTree(self.xmlreport).write('{}/{}.xml'.format(self.outpath, self.outputprefix), pretty_print=True, - xml_declaration=True) + et.ElementTree(self.xmlreport).write( + "{}/{}.xml".format(self.outpath, self.outputprefix), + pretty_print=True, + xml_declaration=True, + ) else: output = et.tostring(self.xmlreport, pretty_print=True) - print(output.decode('utf8')) + print(output.decode("utf8")) def write_txt(self, as_string=False): """Write the TXT report""" if not as_string: - with open('{}/{}.txt'.format(self.outpath, self.outputprefix), 'w') as f: - [f.write(textline + '\n') for textline in self.txtreport] + with open("{}/{}.txt".format(self.outpath, self.outputprefix), "w") as f: + [f.write(textline + "\n") for textline in self.txtreport] else: - output = '\n'.join(self.txtreport) + output = "\n".join(self.txtreport) print(output) @@ -122,7 +143,9 @@ class BindingSiteReport: self.ligand = self.complex.ligand self.bindingsite = self.complex.bindingsite self.output_path = self.complex.output_path - self.bsid = ':'.join([self.ligand.hetid, self.ligand.chain, str(self.ligand.position)]) + self.bsid = ":".join( + [self.ligand.hetid, self.ligand.chain, str(self.ligand.position)] + ) self.longname = self.ligand.longname self.ligtype = self.ligand.type self.bs_res = self.bindingsite.bs_res @@ -137,163 +160,408 @@ class BindingSiteReport: ############################ self.hydrophobic_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'LIGCARBONIDX', - 'PROTCARBONIDX', 'LIGCOO', - 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "DIST", + "LIGCARBONIDX", + "PROTCARBONIDX", + "LIGCOO", + "PROTCOO", + ) self.hydrophobic_info = [] for hydroph in self.complex.hydrophobic_contacts: - self.hydrophobic_info.append((hydroph.resnr, hydroph.restype, hydroph.reschain, hydroph.resnr_l, - hydroph.restype_l, hydroph.reschain_l, '%.2f' % hydroph.distance, - hydroph.ligatom_orig_idx, hydroph.bsatom_orig_idx, hydroph.ligatom.coords, - hydroph.bsatom.coords)) + self.hydrophobic_info.append( + ( + hydroph.resnr, + hydroph.restype, + hydroph.reschain, + hydroph.resnr_l, + hydroph.restype_l, + hydroph.reschain_l, + "%.2f" % hydroph.distance, + hydroph.ligatom_orig_idx, + hydroph.bsatom_orig_idx, + hydroph.ligatom.coords, + hydroph.bsatom.coords, + ) + ) ################## # HYDROGEN BONDS # ################## self.hbond_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'SIDECHAIN', 'DIST_H-A', - 'DIST_D-A', - 'DON_ANGLE', - 'PROTISDON', 'DONORIDX', 'DONORTYPE', 'ACCEPTORIDX', 'ACCEPTORTYPE', 'LIGCOO', 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "SIDECHAIN", + "DIST_H-A", + "DIST_D-A", + "DON_ANGLE", + "PROTISDON", + "DONORIDX", + "DONORTYPE", + "ACCEPTORIDX", + "ACCEPTORTYPE", + "LIGCOO", + "PROTCOO", + ) self.hbond_info = [] for hbond in self.complex.hbonds_pdon + self.complex.hbonds_ldon: - ligatom, protatom = (hbond.a, hbond.d) if hbond.protisdon else (hbond.d, hbond.a) - self.hbond_info.append((hbond.resnr, hbond.restype, hbond.reschain, hbond.resnr_l, hbond.restype_l, - hbond.reschain_l, hbond.sidechain, - '%.2f' % hbond.distance_ah, '%.2f' % hbond.distance_ad, '%.2f' % hbond.angle, - hbond.protisdon, hbond.d_orig_idx, hbond.dtype, hbond.a_orig_idx, hbond.atype, - ligatom.coords, protatom.coords)) + ligatom, protatom = ( + (hbond.a, hbond.d) if hbond.protisdon else (hbond.d, hbond.a) + ) + self.hbond_info.append( + ( + hbond.resnr, + hbond.restype, + hbond.reschain, + hbond.resnr_l, + hbond.restype_l, + hbond.reschain_l, + hbond.sidechain, + "%.2f" % hbond.distance_ah, + "%.2f" % hbond.distance_ad, + "%.2f" % hbond.angle, + hbond.protisdon, + hbond.d_orig_idx, + hbond.dtype, + hbond.a_orig_idx, + hbond.atype, + ligatom.coords, + protatom.coords, + ) + ) ################# # WATER-BRIDGES # ################# self.waterbridge_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST_A-W', 'DIST_D-W', - 'DON_ANGLE', - 'WATER_ANGLE', - 'PROTISDON', 'DONOR_IDX', 'DONORTYPE', 'ACCEPTOR_IDX', 'ACCEPTORTYPE', 'WATER_IDX', - 'LIGCOO', 'PROTCOO', 'WATERCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "DIST_A-W", + "DIST_D-W", + "DON_ANGLE", + "WATER_ANGLE", + "PROTISDON", + "DONOR_IDX", + "DONORTYPE", + "ACCEPTOR_IDX", + "ACCEPTORTYPE", + "WATER_IDX", + "LIGCOO", + "PROTCOO", + "WATERCOO", + ) # The coordinate format is an exception here, since the interaction is not only between ligand and protein self.waterbridge_info = [] for wbridge in self.complex.water_bridges: - lig, prot = (wbridge.a, wbridge.d) if wbridge.protisdon else (wbridge.d, wbridge.a) - self.waterbridge_info.append((wbridge.resnr, wbridge.restype, wbridge.reschain, wbridge.resnr_l, - wbridge.restype_l, wbridge.reschain_l, - '%.2f' % wbridge.distance_aw, '%.2f' % wbridge.distance_dw, - '%.2f' % wbridge.d_angle, '%.2f' % wbridge.w_angle, wbridge.protisdon, - wbridge.d_orig_idx, wbridge.dtype, wbridge.a_orig_idx, wbridge.atype, - wbridge.water_orig_idx, lig.coords, prot.coords, wbridge.water.coords)) + lig, prot = ( + (wbridge.a, wbridge.d) if wbridge.protisdon else (wbridge.d, wbridge.a) + ) + self.waterbridge_info.append( + ( + wbridge.resnr, + wbridge.restype, + wbridge.reschain, + wbridge.resnr_l, + wbridge.restype_l, + wbridge.reschain_l, + "%.2f" % wbridge.distance_aw, + "%.2f" % wbridge.distance_dw, + "%.2f" % wbridge.d_angle, + "%.2f" % wbridge.w_angle, + wbridge.protisdon, + wbridge.d_orig_idx, + wbridge.dtype, + wbridge.a_orig_idx, + wbridge.atype, + wbridge.water_orig_idx, + lig.coords, + prot.coords, + wbridge.water.coords, + ) + ) ################ # SALT BRIDGES # ################ self.saltbridge_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'PROTISPOS', - 'LIG_GROUP', - 'LIG_IDX_LIST', - 'LIGCOO', 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "DIST", + "PROTISPOS", + "LIG_GROUP", + "LIG_IDX_LIST", + "LIGCOO", + "PROTCOO", + ) self.saltbridge_info = [] for sb in self.complex.saltbridge_lneg + self.complex.saltbridge_pneg: if sb.protispos: - group, ids = sb.negative.fgroup, [str(x) for x in sb.negative.atoms_orig_idx] - self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, sb.resnr_l, sb.restype_l, sb.reschain_l, - '%.2f' % sb.distance, sb.protispos, - group.capitalize(), ",".join(ids), - tuple(sb.negative.center), tuple(sb.positive.center))) + group, ids = ( + sb.negative.fgroup, + [str(x) for x in sb.negative.atoms_orig_idx], + ) + self.saltbridge_info.append( + ( + sb.resnr, + sb.restype, + sb.reschain, + sb.resnr_l, + sb.restype_l, + sb.reschain_l, + "%.2f" % sb.distance, + sb.protispos, + group.capitalize(), + ",".join(ids), + tuple(sb.negative.center), + tuple(sb.positive.center), + ) + ) else: - group, ids = sb.positive.fgroup, [str(x) for x in sb.positive.atoms_orig_idx] - self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, sb.resnr_l, sb.restype_l, sb.reschain_l, - '%.2f' % sb.distance, sb.protispos, - group.capitalize(), ",".join(ids), - tuple(sb.positive.center), tuple(sb.negative.center))) + group, ids = ( + sb.positive.fgroup, + [str(x) for x in sb.positive.atoms_orig_idx], + ) + self.saltbridge_info.append( + ( + sb.resnr, + sb.restype, + sb.reschain, + sb.resnr_l, + sb.restype_l, + sb.reschain_l, + "%.2f" % sb.distance, + sb.protispos, + group.capitalize(), + ",".join(ids), + tuple(sb.positive.center), + tuple(sb.negative.center), + ) + ) ############### # PI-STACKING # ############### self.pistacking_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'CENTDIST', 'ANGLE', 'OFFSET', - 'TYPE', - 'LIG_IDX_LIST', 'LIGCOO', 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "CENTDIST", + "ANGLE", + "OFFSET", + "TYPE", + "LIG_IDX_LIST", + "LIGCOO", + "PROTCOO", + ) self.pistacking_info = [] for stack in self.complex.pistacking: ids = [str(x) for x in stack.ligandring.atoms_orig_idx] - self.pistacking_info.append((stack.resnr, stack.restype, stack.reschain, stack.resnr_l, stack.restype_l, - stack.reschain_l, '%.2f' % stack.distance, - '%.2f' % stack.angle, '%.2f' % stack.offset, stack.type, ",".join(ids), - tuple(stack.ligandring.center), tuple(stack.proteinring.center))) + self.pistacking_info.append( + ( + stack.resnr, + stack.restype, + stack.reschain, + stack.resnr_l, + stack.restype_l, + stack.reschain_l, + "%.2f" % stack.distance, + "%.2f" % stack.angle, + "%.2f" % stack.offset, + stack.type, + ",".join(ids), + tuple(stack.ligandring.center), + tuple(stack.proteinring.center), + ) + ) ########################## # PI-CATION INTERACTIONS # ########################## self.pication_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'OFFSET', 'PROTCHARGED', - 'LIG_GROUP', - 'LIG_IDX_LIST', 'LIGCOO', 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "DIST", + "OFFSET", + "PROTCHARGED", + "LIG_GROUP", + "LIG_IDX_LIST", + "LIGCOO", + "PROTCOO", + ) self.pication_info = [] for picat in self.complex.pication_laro + self.complex.pication_paro: if picat.protcharged: ids = [str(x) for x in picat.ring.atoms_orig_idx] - group = 'Aromatic' - self.pication_info.append((picat.resnr, picat.restype, picat.reschain, picat.resnr_l, picat.restype_l, - picat.reschain_l, '%.2f' % picat.distance, - '%.2f' % picat.offset, picat.protcharged, group, ",".join(ids), - tuple(picat.ring.center), tuple(picat.charge.center))) + group = "Aromatic" + self.pication_info.append( + ( + picat.resnr, + picat.restype, + picat.reschain, + picat.resnr_l, + picat.restype_l, + picat.reschain_l, + "%.2f" % picat.distance, + "%.2f" % picat.offset, + picat.protcharged, + group, + ",".join(ids), + tuple(picat.ring.center), + tuple(picat.charge.center), + ) + ) else: ids = [str(x) for x in picat.charge.atoms_orig_idx] group = picat.charge.fgroup - self.pication_info.append((picat.resnr, picat.restype, picat.reschain, picat.resnr_l, picat.restype_l, - picat.reschain_l, '%.2f' % picat.distance, - '%.2f' % picat.offset, picat.protcharged, group, ",".join(ids), - tuple(picat.charge.center), tuple(picat.ring.center))) + self.pication_info.append( + ( + picat.resnr, + picat.restype, + picat.reschain, + picat.resnr_l, + picat.restype_l, + picat.reschain_l, + "%.2f" % picat.distance, + "%.2f" % picat.offset, + picat.protcharged, + group, + ",".join(ids), + tuple(picat.charge.center), + tuple(picat.ring.center), + ) + ) ################# # HALOGEN BONDS # ################# self.halogen_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'SIDECHAIN', 'DIST', - 'DON_ANGLE', - 'ACC_ANGLE', - 'DON_IDX', 'DONORTYPE', 'ACC_IDX', 'ACCEPTORTYPE', 'LIGCOO', 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "SIDECHAIN", + "DIST", + "DON_ANGLE", + "ACC_ANGLE", + "DON_IDX", + "DONORTYPE", + "ACC_IDX", + "ACCEPTORTYPE", + "LIGCOO", + "PROTCOO", + ) self.halogen_info = [] for halogen in self.complex.halogen_bonds: - self.halogen_info.append((halogen.resnr, halogen.restype, halogen.reschain, halogen.resnr_l, - halogen.restype_l, halogen.reschain_l, halogen.sidechain, - '%.2f' % halogen.distance, '%.2f' % halogen.don_angle, '%.2f' % halogen.acc_angle, - halogen.don_orig_idx, halogen.donortype, - halogen.acc_orig_idx, halogen.acctype, - halogen.acc.o.coords, halogen.don.x.coords)) + self.halogen_info.append( + ( + halogen.resnr, + halogen.restype, + halogen.reschain, + halogen.resnr_l, + halogen.restype_l, + halogen.reschain_l, + halogen.sidechain, + "%.2f" % halogen.distance, + "%.2f" % halogen.don_angle, + "%.2f" % halogen.acc_angle, + halogen.don_orig_idx, + halogen.donortype, + halogen.acc_orig_idx, + halogen.acctype, + halogen.acc.o.coords, + halogen.don.x.coords, + ) + ) ################### # METAL COMPLEXES # ################### self.metal_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'METAL_IDX', 'METAL_TYPE', - 'TARGET_IDX', 'TARGET_TYPE', - 'COORDINATION', 'DIST', 'LOCATION', 'RMS', 'GEOMETRY', 'COMPLEXNUM', 'METALCOO', - 'TARGETCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "METAL_IDX", + "METAL_TYPE", + "TARGET_IDX", + "TARGET_TYPE", + "COORDINATION", + "DIST", + "LOCATION", + "RMS", + "GEOMETRY", + "COMPLEXNUM", + "METALCOO", + "TARGETCOO", + ) self.metal_info = [] # Coordinate format here is non-standard since the interaction partner can be either ligand or protein for m in self.complex.metal_complexes: self.metal_info.append( - (m.resnr, m.restype, m.reschain, m.resnr_l, m.restype_l, m.reschain_l, m.metal_orig_idx, m.metal_type, - m.target_orig_idx, m.target_type, m.coordination_num, '%.2f' % m.distance, - m.location, '%.2f' % m.rms, m.geometry, str(m.complexnum), m.metal.coords, - m.target.atom.coords)) + ( + m.resnr, + m.restype, + m.reschain, + m.resnr_l, + m.restype_l, + m.reschain_l, + m.metal_orig_idx, + m.metal_type, + m.target_orig_idx, + m.target_type, + m.coordination_num, + "%.2f" % m.distance, + m.location, + "%.2f" % m.rms, + m.geometry, + str(m.complexnum), + m.metal.coords, + m.target.atom.coords, + ) + ) def write_section(self, name, features, info, f): """Provides formatting for one section (e.g. hydrogen bonds)""" if not len(info) == 0: - f.write('\n\n### %s ###\n' % name) - f.write('%s\n' % '\t'.join(features)) + f.write("\n\n### %s ###\n" % name) + f.write("%s\n" % "\t".join(features)) for line in info: - f.write('%s\n' % '\t'.join(map(str, line))) + f.write("%s\n" % "\t".join(map(str, line))) def rst_table(self, array): """Given an array, the function formats and returns and table in rST format.""" @@ -305,62 +573,77 @@ class BindingSiteReport: cell_dict[j] = [] cell_dict[j].append(val) for item in cell_dict: - cell_dict[item] = max([len(x) for x in cell_dict[item]]) + 1 # Contains adapted width for each column + cell_dict[item] = ( + max([len(x) for x in cell_dict[item]]) + 1 + ) # Contains adapted width for each column # Format top line num_cols = len(array[0]) - form = '+' + form = "+" for col in range(num_cols): - form += (cell_dict[col] + 1) * '-' - form += '+' - form += '\n' + form += (cell_dict[col] + 1) * "-" + form += "+" + form += "\n" # Format values for i, row in enumerate(array): - form += '| ' + form += "| " for j, val in enumerate(row): cell_width = cell_dict[j] - form += str(val) + (cell_width - len(val)) * ' ' + '| ' + form += str(val) + (cell_width - len(val)) * " " + "| " form.rstrip() - form += '\n' + form += "\n" # Seperation lines - form += '+' + form += "+" if i == 0: - sign = '=' + sign = "=" else: - sign = '-' + sign = "-" for col in range(num_cols): form += (cell_dict[col] + 1) * sign - form += '+' - form += '\n' + form += "+" + form += "\n" return form def generate_txt(self): """Generates an flat text report for a single binding site""" txt = [] - titletext = '%s (%s) - %s' % (self.bsid, self.longname, self.ligtype) + titletext = "%s (%s) - %s" % (self.bsid, self.longname, self.ligtype) txt.append(titletext) for i, member in enumerate(self.lig_members[1:]): - txt.append(' + %s' % ":".join(str(element) for element in member)) + txt.append(" + %s" % ":".join(str(element) for element in member)) txt.append("-" * len(titletext)) - txt.append("Interacting chain(s): %s\n" % ','.join([chain for chain in self.interacting_chains])) - for section in [['Hydrophobic Interactions', self.hydrophobic_features, self.hydrophobic_info], - ['Hydrogen Bonds', self.hbond_features, self.hbond_info], - ['Water Bridges', self.waterbridge_features, self.waterbridge_info], - ['Salt Bridges', self.saltbridge_features, self.saltbridge_info], - ['pi-Stacking', self.pistacking_features, self.pistacking_info], - ['pi-Cation Interactions', self.pication_features, self.pication_info], - ['Halogen Bonds', self.halogen_features, self.halogen_info], - ['Metal Complexes', self.metal_features, self.metal_info]]: + txt.append( + "Interacting chain(s): %s\n" + % ",".join([chain for chain in self.interacting_chains]) + ) + for section in [ + [ + "Hydrophobic Interactions", + self.hydrophobic_features, + self.hydrophobic_info, + ], + ["Hydrogen Bonds", self.hbond_features, self.hbond_info], + ["Water Bridges", self.waterbridge_features, self.waterbridge_info], + ["Salt Bridges", self.saltbridge_features, self.saltbridge_info], + ["pi-Stacking", self.pistacking_features, self.pistacking_info], + ["pi-Cation Interactions", self.pication_features, self.pication_info], + ["Halogen Bonds", self.halogen_features, self.halogen_info], + ["Metal Complexes", self.metal_features, self.metal_info], + ]: iname, features, interaction_information = section # Sort results first by res number, then by distance and finally ligand coordinates to get a unique order - interaction_information = sorted(interaction_information, key=itemgetter(0, 2, -2)) + interaction_information = sorted( + interaction_information, key=itemgetter(0, 2, -2) + ) if not len(interaction_information) == 0: - txt.append('\n**%s**' % iname) - table = [features, ] + txt.append("\n**%s**" % iname) + table = [ + features, + ] for single_contact in interaction_information: values = [] for x in single_contact: @@ -372,122 +655,185 @@ class BindingSiteReport: values.append(str(x)) table.append(values) txt.append(self.rst_table(table)) - txt.append('\n') + txt.append("\n") return txt def generate_xml(self): """Generates an XML-formatted report for a single binding site""" - report = et.Element('bindingsite') - identifiers = et.SubElement(report, 'identifiers') - longname = et.SubElement(identifiers, 'longname') - ligtype = et.SubElement(identifiers, 'ligtype') - hetid = et.SubElement(identifiers, 'hetid') - chain = et.SubElement(identifiers, 'chain') - position = et.SubElement(identifiers, 'position') - composite = et.SubElement(identifiers, 'composite') - members = et.SubElement(identifiers, 'members') - smiles = et.SubElement(identifiers, 'smiles') - inchikey = et.SubElement(identifiers, 'inchikey') + report = et.Element("bindingsite") + identifiers = et.SubElement(report, "identifiers") + longname = et.SubElement(identifiers, "longname") + ligtype = et.SubElement(identifiers, "ligtype") + hetid = et.SubElement(identifiers, "hetid") + chain = et.SubElement(identifiers, "chain") + position = et.SubElement(identifiers, "position") + composite = et.SubElement(identifiers, "composite") + members = et.SubElement(identifiers, "members") + smiles = et.SubElement(identifiers, "smiles") + inchikey = et.SubElement(identifiers, "inchikey") # Ligand properties. Number of (unpaired) functional atoms and rings. - lig_properties = et.SubElement(report, 'lig_properties') - num_heavy_atoms = et.SubElement(lig_properties, 'num_heavy_atoms') - num_hbd = et.SubElement(lig_properties, 'num_hbd') + lig_properties = et.SubElement(report, "lig_properties") + num_heavy_atoms = et.SubElement(lig_properties, "num_heavy_atoms") + num_hbd = et.SubElement(lig_properties, "num_hbd") num_hbd.text = str(self.ligand.num_hbd) - num_unpaired_hbd = et.SubElement(lig_properties, 'num_unpaired_hbd') + num_unpaired_hbd = et.SubElement(lig_properties, "num_unpaired_hbd") num_unpaired_hbd.text = str(self.complex.num_unpaired_hbd) - num_hba = et.SubElement(lig_properties, 'num_hba') + num_hba = et.SubElement(lig_properties, "num_hba") num_hba.text = str(self.ligand.num_hba) - num_unpaired_hba = et.SubElement(lig_properties, 'num_unpaired_hba') + num_unpaired_hba = et.SubElement(lig_properties, "num_unpaired_hba") num_unpaired_hba.text = str(self.complex.num_unpaired_hba) - num_hal = et.SubElement(lig_properties, 'num_hal') + num_hal = et.SubElement(lig_properties, "num_hal") num_hal.text = str(self.ligand.num_hal) - num_unpaired_hal = et.SubElement(lig_properties, 'num_unpaired_hal') + num_unpaired_hal = et.SubElement(lig_properties, "num_unpaired_hal") num_unpaired_hal.text = str(self.complex.num_unpaired_hal) - num_aromatic_rings = et.SubElement(lig_properties, 'num_aromatic_rings') + num_aromatic_rings = et.SubElement(lig_properties, "num_aromatic_rings") num_aromatic_rings.text = str(self.ligand.num_rings) - num_rot_bonds = et.SubElement(lig_properties, 'num_rotatable_bonds') + num_rot_bonds = et.SubElement(lig_properties, "num_rotatable_bonds") num_rot_bonds.text = str(self.ligand.num_rot_bonds) - molweight = et.SubElement(lig_properties, 'molweight') + molweight = et.SubElement(lig_properties, "molweight") molweight.text = str(self.ligand.molweight) - logp = et.SubElement(lig_properties, 'logp') + logp = et.SubElement(lig_properties, "logp") logp.text = str(self.ligand.logp) - ichains = et.SubElement(report, 'interacting_chains') - bsresidues = et.SubElement(report, 'bs_residues') + ichains = et.SubElement(report, "interacting_chains") + bsresidues = et.SubElement(report, "bs_residues") for i, ichain in enumerate(self.interacting_chains): - c = et.SubElement(ichains, 'interacting_chain', id=str(i + 1)) + c = et.SubElement(ichains, "interacting_chain", id=str(i + 1)) c.text = ichain for i, bsres in enumerate(self.bs_res): - contact = 'True' if bsres in self.bs_res_interacting else 'False' - distance = '%.1f' % self.min_dist[bsres][0] + contact = "True" if bsres in self.bs_res_interacting else "False" + distance = "%.1f" % self.min_dist[bsres][0] aatype = self.min_dist[bsres][1] - c = et.SubElement(bsresidues, 'bs_residue', id=str(i + 1), contact=contact, min_dist=distance, aa=aatype) + c = et.SubElement( + bsresidues, + "bs_residue", + id=str(i + 1), + contact=contact, + min_dist=distance, + aa=aatype, + ) c.text = bsres - hetid.text, chain.text, position.text = self.ligand.hetid, self.ligand.chain, str(self.ligand.position) - composite.text = 'True' if len(self.lig_members) > 1 else 'False' + hetid.text, chain.text, position.text = ( + self.ligand.hetid, + self.ligand.chain, + str(self.ligand.position), + ) + composite.text = "True" if len(self.lig_members) > 1 else "False" longname.text = self.longname ligtype.text = self.ligtype smiles.text = self.ligand.smiles inchikey.text = self.ligand.inchikey - num_heavy_atoms.text = str(self.ligand.heavy_atoms) # Number of heavy atoms in ligand + num_heavy_atoms.text = str( + self.ligand.heavy_atoms + ) # Number of heavy atoms in ligand for i, member in enumerate(self.lig_members): bsid = ":".join(str(element) for element in member) - m = et.SubElement(members, 'member', id=str(i + 1)) + m = et.SubElement(members, "member", id=str(i + 1)) m.text = bsid - interactions = et.SubElement(report, 'interactions') + interactions = et.SubElement(report, "interactions") def format_interactions(element_name, features, interaction_information): """Returns a formatted element with interaction information.""" interaction = et.Element(element_name) # Sort results first by res number, then by distance and finally ligand coordinates to get a unique order - interaction_information = sorted(interaction_information, key=itemgetter(0, 2, -2)) + interaction_information = sorted( + interaction_information, key=itemgetter(0, 2, -2) + ) for j, single_contact in enumerate(interaction_information): - if not element_name == 'metal_complexes': - new_contact = et.SubElement(interaction, element_name[:-1], id=str(j + 1)) + if not element_name == "metal_complexes": + new_contact = et.SubElement( + interaction, element_name[:-1], id=str(j + 1) + ) else: # Metal Complex[es] - new_contact = et.SubElement(interaction, element_name[:-2], id=str(j + 1)) + new_contact = et.SubElement( + interaction, element_name[:-2], id=str(j + 1) + ) for i, feature in enumerate(single_contact): # Just assign the value unless it's an atom list, use subelements in this case - if features[i] == 'LIG_IDX_LIST': + if features[i] == "LIG_IDX_LIST": feat = et.SubElement(new_contact, features[i].lower()) - for k, atm_idx in enumerate(feature.split(',')): - idx = et.SubElement(feat, 'idx', id=str(k + 1)) + for k, atm_idx in enumerate(feature.split(",")): + idx = et.SubElement(feat, "idx", id=str(k + 1)) idx.text = str(atm_idx) - elif features[i].endswith('COO'): + elif features[i].endswith("COO"): feat = et.SubElement(new_contact, features[i].lower()) xc, yc, zc = feature - xcoo = et.SubElement(feat, 'x') - xcoo.text = '%.3f' % xc - ycoo = et.SubElement(feat, 'y') - ycoo.text = '%.3f' % yc - zcoo = et.SubElement(feat, 'z') - zcoo.text = '%.3f' % zc + xcoo = et.SubElement(feat, "x") + xcoo.text = "%.3f" % xc + ycoo = et.SubElement(feat, "y") + ycoo.text = "%.3f" % yc + zcoo = et.SubElement(feat, "z") + zcoo.text = "%.3f" % zc else: feat = et.SubElement(new_contact, features[i].lower()) feat.text = str(feature) return interaction - interactions.append(format_interactions('hydrophobic_interactions', self.hydrophobic_features, - self.hydrophobic_info)) - interactions.append(format_interactions('hydrogen_bonds', self.hbond_features, self.hbond_info)) - interactions.append(format_interactions('water_bridges', self.waterbridge_features, self.waterbridge_info)) - interactions.append(format_interactions('salt_bridges', self.saltbridge_features, self.saltbridge_info)) - interactions.append(format_interactions('pi_stacks', self.pistacking_features, self.pistacking_info)) - interactions.append(format_interactions('pi_cation_interactions', self.pication_features, self.pication_info)) - interactions.append(format_interactions('halogen_bonds', self.halogen_features, self.halogen_info)) - interactions.append(format_interactions('metal_complexes', self.metal_features, self.metal_info)) + interactions.append( + format_interactions( + "hydrophobic_interactions", + self.hydrophobic_features, + self.hydrophobic_info, + ) + ) + interactions.append( + format_interactions("hydrogen_bonds", self.hbond_features, self.hbond_info) + ) + interactions.append( + format_interactions( + "water_bridges", self.waterbridge_features, self.waterbridge_info + ) + ) + interactions.append( + format_interactions( + "salt_bridges", self.saltbridge_features, self.saltbridge_info + ) + ) + interactions.append( + format_interactions( + "pi_stacks", self.pistacking_features, self.pistacking_info + ) + ) + interactions.append( + format_interactions( + "pi_cation_interactions", self.pication_features, self.pication_info + ) + ) + interactions.append( + format_interactions( + "halogen_bonds", self.halogen_features, self.halogen_info + ) + ) + interactions.append( + format_interactions("metal_complexes", self.metal_features, self.metal_info) + ) # Mappings - mappings = et.SubElement(report, 'mappings') - smiles_to_pdb = et.SubElement(mappings, 'smiles_to_pdb') # SMILES numbering to PDB file numbering (atoms) - bsid = ':'.join([self.ligand.hetid, self.ligand.chain, str(self.ligand.position)]) + mappings = et.SubElement(report, "mappings") + smiles_to_pdb = et.SubElement( + mappings, "smiles_to_pdb" + ) # SMILES numbering to PDB file numbering (atoms) + bsid = ":".join( + [self.ligand.hetid, self.ligand.chain, str(self.ligand.position)] + ) if self.ligand.atomorder is not None: - smiles_to_pdb_map = [(key, self.ligand.Mapper.mapid(self.ligand.can_to_pdb[key], - mtype='protein', bsid=bsid)) for key in - self.ligand.can_to_pdb] - smiles_to_pdb.text = ','.join([str(mapping[0]) + ':' + str(mapping[1]) for mapping in smiles_to_pdb_map]) + smiles_to_pdb_map = [ + ( + key, + self.ligand.Mapper.mapid( + self.ligand.can_to_pdb[key], mtype="protein", bsid=bsid + ), + ) + for key in self.ligand.can_to_pdb + ] + smiles_to_pdb.text = ",".join( + [ + str(mapping[0]) + ":" + str(mapping[1]) + for mapping in smiles_to_pdb_map + ] + ) else: - smiles_to_pdb.text = '' + smiles_to_pdb.text = "" return report diff --git a/plip/plipcmd.py b/plip/plipcmd.py index f7dffab..6b4a884 100644 --- a/plip/plipcmd.py +++ b/plip/plipcmd.py @@ -25,12 +25,14 @@ from plip.exchange.webservices import fetch_pdb from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid from plip.structure.preparation import tilde_expansion, PDBComplex -description = f"The Protein-Ligand Interaction Profiler (PLIP) {__version__}" \ - "is a command-line based tool to analyze interactions in a protein-ligand complex. " \ - "If you are using PLIP in your work, please cite: " \ - "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " \ - "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi:10.1093/nar/gkv315" \ - f"Supported and maintained by: {config.__maintainer__}" +description = ( + f"The Protein-Ligand Interaction Profiler (PLIP) {__version__}" + "is a command-line based tool to analyze interactions in a protein-ligand complex. " + "If you are using PLIP in your work, please cite: " + "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " + "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi:10.1093/nar/gkv315" + f"Supported and maintained by: {config.__maintainer__}" +) def threshold_limiter(aparser, arg): @@ -40,13 +42,13 @@ def threshold_limiter(aparser, arg): return arg -def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'): +def process_pdb(pdbfile, outpath, as_string=False, outputprefix="report"): """Analysis of a single PDB file. Can generate textual reports XML, PyMOL session files and images as output.""" if not as_string: - pdb_file_name = pdbfile.split('/')[-1] - startmessage = f'starting analysis of {pdb_file_name}' + pdb_file_name = pdbfile.split("/")[-1] + startmessage = f"starting analysis of {pdb_file_name}" else: - startmessage = 'starting analysis from STDIN' + startmessage = "starting analysis from STDIN" logger.info(startmessage) mol = PDBComplex() mol.output_path = outpath @@ -68,10 +70,16 @@ def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'): if config.PYMOL or config.PICS: from plip.visualization.visualize import visualize_in_pymol - complexes = [VisualizerData(mol, site) for site in sorted(mol.interaction_sets) - if not len(mol.interaction_sets[site].interacting_res) == 0] + + complexes = [ + VisualizerData(mol, site) + for site in sorted(mol.interaction_sets) + if not len(mol.interaction_sets[site].interacting_res) == 0 + ] if config.MAXTHREADS > 1: - logger.info(f'generating visualizations in parallel on {config.MAXTHREADS} cores') + logger.info( + f"generating visualizations in parallel on {config.MAXTHREADS} cores" + ) parfn = parallel_fn(visualize_in_pymol) parfn(complexes, processes=config.MAXTHREADS) else: @@ -89,19 +97,22 @@ def download_structure(inputpdbid): Checks for validity of ID and handles error while downloading. Returns the path of the downloaded file.""" try: - if len(inputpdbid) != 4 or extract_pdbid(inputpdbid.lower()) == 'UnknownProtein': - logger.error(f'invalid PDB-ID (wrong format): {inputpdbid}') + if ( + len(inputpdbid) != 4 + or extract_pdbid(inputpdbid.lower()) == "UnknownProtein" + ): + logger.error(f"invalid PDB-ID (wrong format): {inputpdbid}") sys.exit(1) pdbfile, pdbid = fetch_pdb(inputpdbid.lower()) - pdbpath = tilde_expansion('%s/%s.pdb' % (config.BASEPATH.rstrip('/'), pdbid)) + pdbpath = tilde_expansion("%s/%s.pdb" % (config.BASEPATH.rstrip("/"), pdbid)) create_folder_if_not_exists(config.BASEPATH) - with open(pdbpath, 'w') as g: + with open(pdbpath, "w") as g: g.write(pdbfile) - logger.info(f'file downloaded as {pdbpath}') + logger.info(f"file downloaded as {pdbpath}") return pdbpath, pdbid except ValueError: # Invalid PDB ID, cannot fetch from RCBS server - logger.error(f'PDB-ID does not exist: {inputpdbid}') + logger.error(f"PDB-ID does not exist: {inputpdbid}") sys.exit(1) @@ -111,9 +122,9 @@ def remove_duplicates(slist): unique = list(set(slist)) difference = len(slist) - len(unique) if difference == 1: - logger.info('removed one duplicate entry from input list') + logger.info("removed one duplicate entry from input list") if difference > 1: - logger.info(f'Removed {difference} duplicate entries from input list') + logger.info(f"Removed {difference} duplicate entries from input list") return unique @@ -122,9 +133,9 @@ def run_analysis(inputstructs, inputpdbids): pdbid, pdbpath = None, None # @todo For multiprocessing, implement better stacktracing for errors # Print title and version - logger.info(f'Protein-Ligand Interaction Profiler (PLIP) {__version__}') - logger.info(f'brought to you by: {config.__maintainer__}') - logger.info(f'please cite: https://www.doi.org/10.1093/nar/gkv315') + logger.info(f"Protein-Ligand Interaction Profiler (PLIP) {__version__}") + logger.info(f"brought to you by: {config.__maintainer__}") + logger.info(f"please cite: https://www.doi.org/10.1093/nar/gkv315") output_prefix = config.OUTPUTFILENAME if inputstructs is not None: # Process PDB file(s) @@ -132,114 +143,258 @@ def run_analysis(inputstructs, inputpdbids): inputstructs = remove_duplicates(inputstructs) read_from_stdin = False for inputstruct in inputstructs: - if inputstruct == '-': + if inputstruct == "-": inputstruct = sys.stdin.read() read_from_stdin = True if config.RAWSTRING: if sys.version_info < (3,): - inputstruct = bytes(inputstruct).decode('unicode_escape') + inputstruct = bytes(inputstruct).decode("unicode_escape") else: - inputstruct = bytes(inputstruct, 'utf8').decode('unicode_escape') + inputstruct = bytes(inputstruct, "utf8").decode( + "unicode_escape" + ) else: if os.path.getsize(inputstruct) == 0: - logger.error('empty PDB file') + logger.error("empty PDB file") sys.exit(1) if num_structures > 1: - basename = inputstruct.split('.')[-2].split('/')[-1] - config.OUTPATH = '/'.join([config.BASEPATH, basename]) - output_prefix = 'report' - process_pdb(inputstruct, config.OUTPATH, as_string=read_from_stdin, outputprefix=output_prefix) + basename = inputstruct.split(".")[-2].split("/")[-1] + config.OUTPATH = "/".join([config.BASEPATH, basename]) + output_prefix = "report" + process_pdb( + inputstruct, + config.OUTPATH, + as_string=read_from_stdin, + outputprefix=output_prefix, + ) else: # Try to fetch the current PDB structure(s) directly from the RCBS server num_pdbids = len(inputpdbids) inputpdbids = remove_duplicates(inputpdbids) for inputpdbid in inputpdbids: pdbpath, pdbid = download_structure(inputpdbid) if num_pdbids > 1: - config.OUTPATH = '/'.join([config.BASEPATH, pdbid[1:3].upper(), pdbid.upper()]) - output_prefix = 'report' + config.OUTPATH = "/".join( + [config.BASEPATH, pdbid[1:3].upper(), pdbid.upper()] + ) + output_prefix = "report" process_pdb(pdbpath, config.OUTPATH, outputprefix=output_prefix) if (pdbid is not None or inputstructs is not None) and config.BASEPATH is not None: - if config.BASEPATH in ['.', './']: - logger.info('finished analysis, find the result files in the working directory') + if config.BASEPATH in [".", "./"]: + logger.info( + "finished analysis, find the result files in the working directory" + ) else: - logger.info(f'finished analysis, find the result files in {config.BASEPATH}') + logger.info( + f"finished analysis, find the result files in {config.BASEPATH}" + ) def main(): """Parse command line arguments and start main script for analysis.""" parser = ArgumentParser(prog="PLIP", description=description) - pdbstructure = parser.add_mutually_exclusive_group(required=True) # Needs either PDB ID or file + pdbstructure = parser.add_mutually_exclusive_group( + required=True + ) # Needs either PDB ID or file # '-' as file name reads from stdin - pdbstructure.add_argument("-f", "--file", dest="input", nargs="+", help="Set input file, '-' reads from stdin") + pdbstructure.add_argument( + "-f", + "--file", + dest="input", + nargs="+", + help="Set input file, '-' reads from stdin", + ) pdbstructure.add_argument("-i", "--input", dest="pdbid", nargs="+") - outputgroup = parser.add_mutually_exclusive_group(required=False) # Needs either outpath or stdout + outputgroup = parser.add_mutually_exclusive_group( + required=False + ) # Needs either outpath or stdout outputgroup.add_argument("-o", "--out", dest="outpath", default="./") - outputgroup.add_argument("-O", "--stdout", dest="stdout", action="store_true", default=False, - help="Write to stdout instead of file") - parser.add_argument("--rawstring", dest="use_raw_string", default=False, action="store_true", - help="Use Python raw strings for stdin") - parser.add_argument("-v", "--verbose", dest="verbose", default=False, help="Turn on verbose mode", - action="store_true") - parser.add_argument("-q", "--quiet", dest="quiet", default=False, help="Turn on quiet mode", action="store_true") - parser.add_argument("-s", "--silent", dest="silent", default=False, help="Turn on silent mode", action="store_true") - parser.add_argument("-p", "--pics", dest="pics", default=False, help="Additional pictures", action="store_true") - parser.add_argument("-x", "--xml", dest="xml", default=False, help="Generate report file in XML format", - action="store_true") - parser.add_argument("-t", "--txt", dest="txt", default=False, help="Generate report file in TXT (RST) format", - action="store_true") - parser.add_argument("-y", "--pymol", dest="pymol", default=False, help="Additional PyMOL session files", - action="store_true") - parser.add_argument("--maxthreads", dest="maxthreads", default=multiprocessing.cpu_count(), - help="Set maximum number of main threads (number of binding sites processed simultaneously)." - "If not set, PLIP uses all available CPUs if possible.", - type=int) - parser.add_argument("--breakcomposite", dest="breakcomposite", default=False, - help="Don't combine ligand fragments with covalent bonds but treat them as single ligands for the analysis.", - action="store_true") - parser.add_argument("--altlocation", dest="altlocation", default=False, - help="Also consider alternate locations for atoms (e.g. alternate conformations).", - action="store_true") - parser.add_argument("--nofix", dest="nofix", default=False, - help="Turns off fixing of PDB files.", - action="store_true") - parser.add_argument("--nofixfile", dest="nofixfile", default=False, - help="Turns off writing files for fixed PDB files.", - action="store_true") - parser.add_argument("--nopdbcanmap", dest="nopdbcanmap", default=False, - help="Turns off calculation of mapping between canonical and PDB atom order for ligands.", - action="store_true") - parser.add_argument("--dnareceptor", dest="dnareceptor", default=False, - help="Uses the DNA instead of the protein as a receptor for interactions.", - action="store_true") - parser.add_argument("--name", dest="outputfilename", default="report", - help="Set a filename for the report TXT and XML files. Will only work when processing single structures.") - ligandtype = parser.add_mutually_exclusive_group() # Either peptide/inter or intra mode - ligandtype.add_argument("--peptides", "--inter", dest="peptides", default=[], - help="Allows to define one or multiple chains as peptide ligands or to detect inter-chain contacts", - nargs="+") - ligandtype.add_argument("--intra", dest="intra", help="Allows to define one chain to analyze intra-chain contacts.") - parser.add_argument("--keepmod", dest="keepmod", default=False, - help="Keep modified residues as ligands", - action="store_true") - parser.add_argument("--nohydro", dest="nohydro", default=False, - help="Do not add polar hydrogens in case your structure already contains hydrogens.", - action="store_true") + outputgroup.add_argument( + "-O", + "--stdout", + dest="stdout", + action="store_true", + default=False, + help="Write to stdout instead of file", + ) + parser.add_argument( + "--rawstring", + dest="use_raw_string", + default=False, + action="store_true", + help="Use Python raw strings for stdin", + ) + parser.add_argument( + "-v", + "--verbose", + dest="verbose", + default=False, + help="Turn on verbose mode", + action="store_true", + ) + parser.add_argument( + "-q", + "--quiet", + dest="quiet", + default=False, + help="Turn on quiet mode", + action="store_true", + ) + parser.add_argument( + "-s", + "--silent", + dest="silent", + default=False, + help="Turn on silent mode", + action="store_true", + ) + parser.add_argument( + "-p", + "--pics", + dest="pics", + default=False, + help="Additional pictures", + action="store_true", + ) + parser.add_argument( + "-x", + "--xml", + dest="xml", + default=False, + help="Generate report file in XML format", + action="store_true", + ) + parser.add_argument( + "-t", + "--txt", + dest="txt", + default=False, + help="Generate report file in TXT (RST) format", + action="store_true", + ) + parser.add_argument( + "-y", + "--pymol", + dest="pymol", + default=False, + help="Additional PyMOL session files", + action="store_true", + ) + parser.add_argument( + "--maxthreads", + dest="maxthreads", + default=multiprocessing.cpu_count(), + help="Set maximum number of main threads (number of binding sites processed simultaneously)." + "If not set, PLIP uses all available CPUs if possible.", + type=int, + ) + parser.add_argument( + "--breakcomposite", + dest="breakcomposite", + default=False, + help="Don't combine ligand fragments with covalent bonds but treat them as single ligands for the analysis.", + action="store_true", + ) + parser.add_argument( + "--altlocation", + dest="altlocation", + default=False, + help="Also consider alternate locations for atoms (e.g. alternate conformations).", + action="store_true", + ) + parser.add_argument( + "--nofix", + dest="nofix", + default=False, + help="Turns off fixing of PDB files.", + action="store_true", + ) + parser.add_argument( + "--nofixfile", + dest="nofixfile", + default=False, + help="Turns off writing files for fixed PDB files.", + action="store_true", + ) + parser.add_argument( + "--nopdbcanmap", + dest="nopdbcanmap", + default=False, + help="Turns off calculation of mapping between canonical and PDB atom order for ligands.", + action="store_true", + ) + parser.add_argument( + "--dnareceptor", + dest="dnareceptor", + default=False, + help="Uses the DNA instead of the protein as a receptor for interactions.", + action="store_true", + ) + parser.add_argument( + "--name", + dest="outputfilename", + default="report", + help="Set a filename for the report TXT and XML files. Will only work when processing single structures.", + ) + ligandtype = ( + parser.add_mutually_exclusive_group() + ) # Either peptide/inter or intra mode + ligandtype.add_argument( + "--peptides", + "--inter", + dest="peptides", + default=[], + help="Allows to define one or multiple chains as peptide ligands or to detect inter-chain contacts", + nargs="+", + ) + ligandtype.add_argument( + "--intra", + dest="intra", + help="Allows to define one chain to analyze intra-chain contacts.", + ) + parser.add_argument( + "--keepmod", + dest="keepmod", + default=False, + help="Keep modified residues as ligands", + action="store_true", + ) + parser.add_argument( + "--nohydro", + dest="nohydro", + default=False, + help="Do not add polar hydrogens in case your structure already contains hydrogens.", + action="store_true", + ) # Optional threshold arguments, not shown in help - thr = namedtuple('threshold', 'name type') - thresholds = [thr(name='aromatic_planarity', type='angle'), - thr(name='hydroph_dist_max', type='distance'), thr(name='hbond_dist_max', type='distance'), - thr(name='hbond_don_angle_min', type='angle'), thr(name='pistack_dist_max', type='distance'), - thr(name='pistack_ang_dev', type='other'), thr(name='pistack_offset_max', type='distance'), - thr(name='pication_dist_max', type='distance'), thr(name='saltbridge_dist_max', type='distance'), - thr(name='halogen_dist_max', type='distance'), thr(name='halogen_acc_angle', type='angle'), - thr(name='halogen_don_angle', type='angle'), thr(name='halogen_angle_dev', type='other'), - thr(name='water_bridge_mindist', type='distance'), thr(name='water_bridge_maxdist', type='distance'), - thr(name='water_bridge_omega_min', type='angle'), thr(name='water_bridge_omega_max', type='angle'), - thr(name='water_bridge_theta_min', type='angle')] + thr = namedtuple("threshold", "name type") + thresholds = [ + thr(name="aromatic_planarity", type="angle"), + thr(name="hydroph_dist_max", type="distance"), + thr(name="hbond_dist_max", type="distance"), + thr(name="hbond_don_angle_min", type="angle"), + thr(name="pistack_dist_max", type="distance"), + thr(name="pistack_ang_dev", type="other"), + thr(name="pistack_offset_max", type="distance"), + thr(name="pication_dist_max", type="distance"), + thr(name="saltbridge_dist_max", type="distance"), + thr(name="halogen_dist_max", type="distance"), + thr(name="halogen_acc_angle", type="angle"), + thr(name="halogen_don_angle", type="angle"), + thr(name="halogen_angle_dev", type="other"), + thr(name="water_bridge_mindist", type="distance"), + thr(name="water_bridge_maxdist", type="distance"), + thr(name="water_bridge_omega_min", type="angle"), + thr(name="water_bridge_omega_max", type="angle"), + thr(name="water_bridge_theta_min", type="angle"), + ] for t in thresholds: - parser.add_argument('--%s' % t.name, dest=t.name, type=lambda val: threshold_limiter(parser, val), - help=argparse.SUPPRESS) + parser.add_argument( + "--%s" % t.name, + dest=t.name, + type=lambda val: threshold_limiter(parser, val), + help=argparse.SUPPRESS, + ) arguments = parser.parse_args() # configure log levels config.VERBOSE = True if arguments.verbose else False @@ -261,8 +416,11 @@ def main(): config.STDOUT = arguments.stdout config.RAWSTRING = arguments.use_raw_string config.OUTPATH = arguments.outpath - config.OUTPATH = tilde_expansion("".join([config.OUTPATH, '/']) - if not config.OUTPATH.endswith('/') else config.OUTPATH) + config.OUTPATH = tilde_expansion( + "".join([config.OUTPATH, "/"]) + if not config.OUTPATH.endswith("/") + else config.OUTPATH + ) config.BASEPATH = config.OUTPATH # Used for batch processing config.BREAKCOMPOSITE = arguments.breakcomposite config.ALTLOC = arguments.altlocation @@ -280,32 +438,50 @@ def main(): try: import pymol except ImportError: - logger.error('PyMOL is required for the --pics and --pymol option') + logger.error("PyMOL is required for the --pics and --pymol option") sys.exit(1) # Assign values to global thresholds for t in thresholds: tvalue = getattr(arguments, t.name) if tvalue is not None: - if t.type == 'angle' and not 0 < tvalue < 180: # Check value for angle thresholds - parser.error("Threshold for angles need to have values within 0 and 180.") - if t.type == 'distance': + if ( + t.type == "angle" and not 0 < tvalue < 180 + ): # Check value for angle thresholds + parser.error( + "Threshold for angles need to have values within 0 and 180." + ) + if t.type == "distance": if tvalue > 10: # Check value for angle thresholds - parser.error("Threshold for distances must not be larger than 10 Angstrom.") - elif tvalue > config.BS_DIST + 1: # Dynamically adapt the search space for binding site residues + parser.error( + "Threshold for distances must not be larger than 10 Angstrom." + ) + elif ( + tvalue > config.BS_DIST + 1 + ): # Dynamically adapt the search space for binding site residues config.BS_DIST = tvalue + 1 setattr(config, t.name.upper(), tvalue) # Check additional conditions for interdependent thresholds if not config.HALOGEN_ACC_ANGLE > config.HALOGEN_ANGLE_DEV: - parser.error("The halogen acceptor angle has to be larger than the halogen angle deviation.") + parser.error( + "The halogen acceptor angle has to be larger than the halogen angle deviation." + ) if not config.HALOGEN_DON_ANGLE > config.HALOGEN_ANGLE_DEV: - parser.error("The halogen donor angle has to be larger than the halogen angle deviation.") + parser.error( + "The halogen donor angle has to be larger than the halogen angle deviation." + ) if not config.WATER_BRIDGE_MINDIST < config.WATER_BRIDGE_MAXDIST: - parser.error("The water bridge minimum distance has to be smaller than the water bridge maximum distance.") + parser.error( + "The water bridge minimum distance has to be smaller than the water bridge maximum distance." + ) if not config.WATER_BRIDGE_OMEGA_MIN < config.WATER_BRIDGE_OMEGA_MAX: - parser.error("The water bridge omega minimum angle has to be smaller than the water bridge omega maximum angle") - expanded_path = tilde_expansion(arguments.input) if arguments.input is not None else None + parser.error( + "The water bridge omega minimum angle has to be smaller than the water bridge omega maximum angle" + ) + expanded_path = ( + tilde_expansion(arguments.input) if arguments.input is not None else None + ) run_analysis(expanded_path, arguments.pdbid) # Start main script -if __name__ == '__main__': +if __name__ == "__main__": main() diff --git a/plip/structure/preparation.py b/plip/structure/preparation.py index c2631d3..32083c7 100644 --- a/plip/structure/preparation.py +++ b/plip/structure/preparation.py @@ -10,12 +10,39 @@ from openbabel import pybel from plip.basic import config, logger from plip.basic.supplemental import centroid, tilde_expansion, tmpfile, classify_by_name -from plip.basic.supplemental import cluster_doubles, is_lig, normalize_vector, vector, ring_is_planar -from plip.basic.supplemental import extract_pdbid, read_pdb, create_folder_if_not_exists, canonicalize +from plip.basic.supplemental import ( + cluster_doubles, + is_lig, + normalize_vector, + vector, + ring_is_planar, +) +from plip.basic.supplemental import ( + extract_pdbid, + read_pdb, + create_folder_if_not_exists, + canonicalize, +) from plip.basic.supplemental import read, nucleotide_linkage, sort_members_by_importance -from plip.basic.supplemental import whichchain, whichrestype, whichresnumber, euclidean3d, int32_to_negative -from plip.structure.detection import halogen, pication, water_bridges, metal_complexation -from plip.structure.detection import hydrophobic_interactions, pistacking, hbonds, saltbridge +from plip.basic.supplemental import ( + whichchain, + whichrestype, + whichresnumber, + euclidean3d, + int32_to_negative, +) +from plip.structure.detection import ( + halogen, + pication, + water_bridges, + metal_complexation, +) +from plip.structure.detection import ( + hydrophobic_interactions, + pistacking, + hbonds, + saltbridge, +) logger = logger.get_logger() @@ -25,8 +52,16 @@ class PDBParser: self.as_string = as_string self.pdbpath = pdbpath self.num_fixed_lines = 0 - self.covlinkage = namedtuple("covlinkage", "id1 chain1 pos1 conf1 id2 chain2 pos2 conf2") - self.proteinmap, self.modres, self.covalent, self.altconformations, self.corrected_pdb = self.parse_pdb() + self.covlinkage = namedtuple( + "covlinkage", "id1 chain1 pos1 conf1 id2 chain2 pos2 conf2" + ) + ( + self.proteinmap, + self.modres, + self.covalent, + self.altconformations, + self.corrected_pdb, + ) = self.parse_pdb() def parse_pdb(self): """Extracts additional information from PDB files. @@ -38,7 +73,9 @@ class PDBParser: IV. Alternative conformations """ if self.as_string: - fil = self.pdbpath.rstrip('\n').split('\n') # Removing trailing newline character + fil = self.pdbpath.rstrip("\n").split( + "\n" + ) # Removing trailing newline character else: f = read(self.pdbpath) fil = f.readlines() @@ -57,19 +94,23 @@ class PDBParser: lastnum = 0 # Atom numbering (has to be consecutive) other_models = False for line in fil: - if not other_models: # Only consider the first model in an NRM structure + if ( + not other_models + ): # Only consider the first model in an NRM structure corrected_line, newnum = self.fix_pdbline(line, lastnum) if corrected_line is not None: - if corrected_line.startswith('MODEL'): + if corrected_line.startswith("MODEL"): try: # Get number of MODEL (1,2,3) model_num = int(corrected_line[10:14]) if model_num > 1: # MODEL 2,3,4 etc. other_models = True except ValueError: - logger.debug(f'ignoring invalid MODEL entry: {corrected_line}') + logger.debug( + f"ignoring invalid MODEL entry: {corrected_line}" + ) corrected_lines.append(corrected_line) lastnum = newnum - corrected_pdb = ''.join(corrected_lines) + corrected_pdb = "".join(corrected_lines) else: corrected_pdb = self.pdbpath corrected_lines = fil @@ -81,8 +122,8 @@ class PDBParser: if line.startswith(("ATOM", "HETATM")): # Retrieve alternate conformations atomid, location = int(line[6:11]), line[16] - location = 'A' if location == ' ' else location - if location != 'A': + location = "A" if location == " " else location + if location != "A": alt.append(atomid) if not previous_ter: @@ -107,12 +148,18 @@ class PDBParser: def fix_pdbline(self, pdbline, lastnum): """Fix a PDB line if information is missing.""" pdbqt_conversion = { - "HD": "H", "HS": "H", "NA": "N", - "NS": "N", "OA": "O", "OS": "O", "SA": "S"} + "HD": "H", + "HS": "H", + "NA": "N", + "NS": "N", + "OA": "O", + "OS": "O", + "SA": "S", + } fixed = False new_num = 0 forbidden_characters = "[^a-zA-Z0-9_]" - pdbline = pdbline.strip('\n') + pdbline = pdbline.strip("\n") # Some MD / Docking tools produce empty lines, leading to segfaults if len(pdbline.strip()) == 0: self.num_fixed_lines += 1 @@ -121,9 +168,9 @@ class PDBParser: self.num_fixed_lines += 1 return None, lastnum # TER Entries also have continuing numbering, consider them as well - if pdbline.startswith('TER'): + if pdbline.startswith("TER"): new_num = lastnum + 1 - if pdbline.startswith('ATOM'): + if pdbline.startswith("ATOM"): new_num = lastnum + 1 current_num = int(pdbline[6:11]) resnum = pdbline[22:27].strip() @@ -132,73 +179,107 @@ class PDBParser: try: int(resnum) except ValueError: - pdbline = pdbline[:22] + ' 0 ' + pdbline[27:] + pdbline = pdbline[:22] + " 0 " + pdbline[27:] fixed = True # Invalid characters in residue name if re.match(forbidden_characters, resname.strip()): - pdbline = pdbline[:17] + 'UNK ' + pdbline[21:] + pdbline = pdbline[:17] + "UNK " + pdbline[21:] fixed = True if lastnum + 1 != current_num: - pdbline = pdbline[:6] + (5 - len(str(new_num))) * ' ' + str(new_num) + ' ' + pdbline[12:] + pdbline = ( + pdbline[:6] + + (5 - len(str(new_num))) * " " + + str(new_num) + + " " + + pdbline[12:] + ) fixed = True # No chain assigned - if pdbline[21] == ' ': - pdbline = pdbline[:21] + 'A' + pdbline[22:] + if pdbline[21] == " ": + pdbline = pdbline[:21] + "A" + pdbline[22:] fixed = True - if pdbline.endswith('H'): + if pdbline.endswith("H"): self.num_fixed_lines += 1 return None, lastnum # Sometimes, converted PDB structures contain PDBQT atom types. Fix that. for pdbqttype in pdbqt_conversion: if pdbline.strip().endswith(pdbqttype): - pdbline = pdbline.strip()[:-2] + ' ' + pdbqt_conversion[pdbqttype] + '\n' + pdbline = ( + pdbline.strip()[:-2] + " " + pdbqt_conversion[pdbqttype] + "\n" + ) self.num_fixed_lines += 1 - if pdbline.startswith('HETATM'): + if pdbline.startswith("HETATM"): new_num = lastnum + 1 try: current_num = int(pdbline[6:11]) except ValueError: current_num = None - logger.debug(f'invalid HETATM entry: {pdbline}') + logger.debug(f"invalid HETATM entry: {pdbline}") if lastnum + 1 != current_num: - pdbline = pdbline[:6] + (5 - len(str(new_num))) * ' ' + str(new_num) + ' ' + pdbline[12:] + pdbline = ( + pdbline[:6] + + (5 - len(str(new_num))) * " " + + str(new_num) + + " " + + pdbline[12:] + ) fixed = True # No chain assigned or number assigned as chain - if pdbline[21] == ' ': - pdbline = pdbline[:21] + 'Z' + pdbline[22:] + if pdbline[21] == " ": + pdbline = pdbline[:21] + "Z" + pdbline[22:] fixed = True # No residue number assigned - if pdbline[23:26] == ' ': - pdbline = pdbline[:23] + '999' + pdbline[26:] + if pdbline[23:26] == " ": + pdbline = pdbline[:23] + "999" + pdbline[26:] fixed = True # Non-standard Ligand Names ligname = pdbline[17:21].strip() if len(ligname) > 3: - pdbline = pdbline[:17] + ligname[:3] + ' ' + pdbline[21:] + pdbline = pdbline[:17] + ligname[:3] + " " + pdbline[21:] fixed = True if re.match(forbidden_characters, ligname.strip()): - pdbline = pdbline[:17] + 'LIG ' + pdbline[21:] + pdbline = pdbline[:17] + "LIG " + pdbline[21:] fixed = True if len(ligname.strip()) == 0: - pdbline = pdbline[:17] + 'LIG ' + pdbline[21:] + pdbline = pdbline[:17] + "LIG " + pdbline[21:] fixed = True - if pdbline.endswith('H'): + if pdbline.endswith("H"): self.num_fixed_lines += 1 return None, lastnum # Sometimes, converted PDB structures contain PDBQT atom types. Fix that. for pdbqttype in pdbqt_conversion: if pdbline.strip().endswith(pdbqttype): - pdbline = pdbline.strip()[:-2] + ' ' + pdbqt_conversion[pdbqttype] + ' ' + pdbline = ( + pdbline.strip()[:-2] + " " + pdbqt_conversion[pdbqttype] + " " + ) self.num_fixed_lines += 1 self.num_fixed_lines += 1 if fixed else 0 - return pdbline + '\n', max(new_num, lastnum) + return pdbline + "\n", max(new_num, lastnum) def get_linkage(self, line): """Get the linkage information from a LINK entry PDB line.""" - conf1, id1, chain1, pos1 = line[16].strip(), line[17:20].strip(), line[21].strip(), int(line[22:26]) - conf2, id2, chain2, pos2 = line[46].strip(), line[47:50].strip(), line[51].strip(), int(line[52:56]) - return self.covlinkage(id1=id1, chain1=chain1, pos1=pos1, conf1=conf1, - id2=id2, chain2=chain2, pos2=pos2, conf2=conf2) + conf1, id1, chain1, pos1 = ( + line[16].strip(), + line[17:20].strip(), + line[21].strip(), + int(line[22:26]), + ) + conf2, id2, chain2, pos2 = ( + line[46].strip(), + line[47:50].strip(), + line[51].strip(), + int(line[52:56]), + ) + return self.covlinkage( + id1=id1, + chain1=chain1, + pos1=pos1, + conf1=conf1, + id2=id2, + chain2=chain2, + pos2=pos2, + conf2=conf2, + ) class LigandFinder: @@ -212,15 +293,20 @@ class LigandFinder: self.covalent = covalent self.mapper = mapper self.ligands = self.getligs() - self.excluded = sorted(list(self.lignames_all.difference(set(self.lignames_kept)))) + self.excluded = sorted( + list(self.lignames_all.difference(set(self.lignames_kept))) + ) def getpeptides(self, chain): """If peptide ligand chains are defined via the command line options, try to extract the underlying ligand formed by all residues in the given chain without water """ - all_from_chain = [o for o in pybel.ob.OBResidueIter( - self.proteincomplex.OBMol) if o.GetChain() == chain] # All residues from chain + all_from_chain = [ + o + for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) + if o.GetChain() == chain + ] # All residues from chain if len(all_from_chain) == 0: return None else: @@ -240,7 +326,9 @@ class LigandFinder: # Filter for ligands using lists ligand_residues, self.lignames_all, self.water = self.filter_for_ligands() - all_res_dict = {(a.GetName(), a.GetChain(), a.GetNum()): a for a in ligand_residues} + all_res_dict = { + (a.GetName(), a.GetChain(), a.GetNum()): a for a in ligand_residues + } self.lignames_kept = list(set([a.GetName() for a in ligand_residues])) if not config.BREAKCOMPOSITE: @@ -249,22 +337,35 @@ class LigandFinder: # Find fragment linked by covalent bonds res_kmers = self.identify_kmers(all_res_dict) else: - res_kmers = [[a, ] for a in ligand_residues] - logger.debug(f'{len(res_kmers)} ligand kmer(s) detected for closer inspection') - for kmer in res_kmers: # iterate over all ligands and extract molecules + information + res_kmers = [[a,] for a in ligand_residues] + logger.debug( + f"{len(res_kmers)} ligand kmer(s) detected for closer inspection" + ) + for ( + kmer + ) in ( + res_kmers + ): # iterate over all ligands and extract molecules + information if len(kmer) > config.MAX_COMPOSITE_LENGTH: logger.debug( - f'ligand kmer(s) filtered out with a length of {len(kmer)} fragments ({config.MAX_COMPOSITE_LENGTH} allowed)') + f"ligand kmer(s) filtered out with a length of {len(kmer)} fragments ({config.MAX_COMPOSITE_LENGTH} allowed)" + ) else: ligands.append(self.extract_ligand(kmer)) else: # Extract peptides from given chains - self.water = [o for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) if o.GetResidueProperty(9)] + self.water = [ + o + for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) + if o.GetResidueProperty(9) + ] if config.PEPTIDES: peptide_ligands = [self.getpeptides(chain) for chain in config.PEPTIDES] elif config.INTRA is not None: - peptide_ligands = [self.getpeptides(config.INTRA), ] + peptide_ligands = [ + self.getpeptides(config.INTRA), + ] ligands = [p for p in peptide_ligands if p is not None] self.covalent, self.lignames_kept, self.lignames_all = [], [], set() @@ -273,35 +374,50 @@ class LigandFinder: def extract_ligand(self, kmer): """Extract the ligand by copying atoms and bonds and assign all information necessary for later steps.""" - data = namedtuple('ligand', 'mol hetid chain position water members longname type atomorder can_to_pdb') - members = [(res.GetName(), res.GetChain(), int32_to_negative(res.GetNum())) for res in kmer] + data = namedtuple( + "ligand", + "mol hetid chain position water members longname type atomorder can_to_pdb", + ) + members = [ + (res.GetName(), res.GetChain(), int32_to_negative(res.GetNum())) + for res in kmer + ] members = sort_members_by_importance(members) rname, rchain, rnum = members[0] - logger.debug(f'finalizing extraction for ligand {rname}:{rchain}:{rnum} with {len(kmer)} elements') + logger.debug( + f"finalizing extraction for ligand {rname}:{rchain}:{rnum} with {len(kmer)} elements" + ) names = [x[0] for x in members] - longname = '-'.join([x[0] for x in members]) + longname = "-".join([x[0] for x in members]) if config.PEPTIDES: - ligtype = 'PEPTIDE' + ligtype = "PEPTIDE" elif config.INTRA is not None: - ligtype = 'INTRA' + ligtype = "INTRA" else: # Classify a ligand by its HETID(s) ligtype = classify_by_name(names) - logger.debug(f'ligand classified as {ligtype}') + logger.debug(f"ligand classified as {ligtype}") hetatoms = dict() for obresidue in kmer: - cur_hetatoms = {obatom.GetIdx(): obatom for obatom in pybel.ob.OBResidueAtomIter(obresidue) if - obatom.GetAtomicNum() != 1} + cur_hetatoms = { + obatom.GetIdx(): obatom + for obatom in pybel.ob.OBResidueAtomIter(obresidue) + if obatom.GetAtomicNum() != 1 + } if not config.ALTLOC: # Remove alternative conformations (standard -> True) - ids_to_remove = [atom_id for atom_id in hetatoms.keys() if - self.mapper.mapid(atom_id, mtype='protein', to='internal') in self.altconformations] + ids_to_remove = [ + atom_id + for atom_id in hetatoms.keys() + if self.mapper.mapid(atom_id, mtype="protein", to="internal") + in self.altconformations + ] for atom_id in ids_to_remove: del cur_hetatoms[atom_id] hetatoms.update(cur_hetatoms) - logger.debug(f'hetero atoms determined (n={len(hetatoms)})') + logger.debug(f"hetero atoms determined (n={len(hetatoms)})") lig = pybel.ob.OBMol() # new ligand mol neighbours = dict() @@ -309,15 +425,24 @@ class LigandFinder: idx = obatom.GetIdx() lig.AddAtom(obatom) # ids of all neighbours of obatom - neighbours[idx] = set([neighbour_atom.GetIdx() for neighbour_atom - in pybel.ob.OBAtomAtomIter(obatom)]) & set(hetatoms.keys()) - logger.debug(f'atom neighbours mapped') + neighbours[idx] = set( + [ + neighbour_atom.GetIdx() + for neighbour_atom in pybel.ob.OBAtomAtomIter(obatom) + ] + ) & set(hetatoms.keys()) + logger.debug(f"atom neighbours mapped") ############################################################## # map the old atom idx of OBMol to the new idx of the ligand # ############################################################## - newidx = dict(zip(hetatoms.keys(), [obatom.GetIdx() for obatom in pybel.ob.OBMolAtomIter(lig)])) + newidx = dict( + zip( + hetatoms.keys(), + [obatom.GetIdx() for obatom in pybel.ob.OBMolAtomIter(lig)], + ) + ) mapold = dict(zip(newidx.values(), newidx)) # copy the bonds for obatom in hetatoms: @@ -327,16 +452,16 @@ class LigandFinder: lig = pybel.Molecule(lig) # For kmers, the representative ids are chosen (first residue of kmer) - lig.data.update({'Name': rname, 'Chain': rchain, 'ResNr': rnum}) + lig.data.update({"Name": rname, "Chain": rchain, "ResNr": rnum}) # Check if a negative residue number is represented as a 32 bit integer if rnum > 10 ** 5: rnum = int32_to_negative(rnum) - lig.title = ':'.join((rname, rchain, str(rnum))) + lig.title = ":".join((rname, rchain, str(rnum))) self.mapper.ligandmaps[lig.title] = mapold - logger.debug('renumerated molecule generated') + logger.debug("renumerated molecule generated") if not config.NOPDBCANMAP: atomorder = canonicalize(lig) @@ -347,9 +472,18 @@ class LigandFinder: if atomorder is not None: can_to_pdb = {atomorder[key - 1]: mapold[key] for key in mapold} - ligand = data(mol=lig, hetid=rname, chain=rchain, position=rnum, water=self.water, - members=members, longname=longname, type=ligtype, atomorder=atomorder, - can_to_pdb=can_to_pdb) + ligand = data( + mol=lig, + hetid=rname, + chain=rchain, + position=rnum, + water=self.water, + members=members, + longname=longname, + type=ligtype, + atomorder=atomorder, + can_to_pdb=can_to_pdb, + ) return ligand def is_het_residue(self, obres): @@ -374,20 +508,35 @@ class LigandFinder: def filter_for_ligands(self): """Given an OpenBabel Molecule, get all ligands, their names, and water""" - candidates1 = [o for o in pybel.ob.OBResidueIter( - self.proteincomplex.OBMol) if not o.GetResidueProperty(9) and self.is_het_residue(o)] + candidates1 = [ + o + for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) + if not o.GetResidueProperty(9) and self.is_het_residue(o) + ] if config.DNARECEPTOR: # If DNA is the receptor, don't consider DNA as a ligand - candidates1 = [res for res in candidates1 if res.GetName() not in config.DNA + config.RNA] + candidates1 = [ + res + for res in candidates1 + if res.GetName() not in config.DNA + config.RNA + ] all_lignames = set([a.GetName() for a in candidates1]) - water = [o for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) if o.GetResidueProperty(9)] + water = [ + o + for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) + if o.GetResidueProperty(9) + ] # Filter out non-ligands if not config.KEEPMOD: # Keep modified residues as ligands - candidates2 = [a for a in candidates1 if is_lig(a.GetName()) and a.GetName() not in self.modresidues] + candidates2 = [ + a + for a in candidates1 + if is_lig(a.GetName()) and a.GetName() not in self.modresidues + ] else: candidates2 = [a for a in candidates1 if is_lig(a.GetName())] - logger.debug(f'{len(candidates2)} ligand(s) after first filtering step') + logger.debug(f"{len(candidates2)} ligand(s) after first filtering step") ############################################ # Filtering by counting and artifacts list # @@ -396,7 +545,10 @@ class LigandFinder: unique_ligs = set(a.GetName() for a in candidates2) for ulig in unique_ligs: # Discard if appearing 15 times or more and is possible artifact - if ulig in config.biolip_list and [a.GetName() for a in candidates2].count(ulig) >= 15: + if ( + ulig in config.biolip_list + and [a.GetName() for a in candidates2].count(ulig) >= 15 + ): artifacts.append(ulig) selected_ligands = [a for a in candidates2 if a.GetName() not in artifacts] @@ -407,12 +559,19 @@ class LigandFinder: """Using the covalent linkage information, find out which fragments/subunits form a ligand.""" # Remove all those not considered by ligands and pairings including alternate conformations - ligdoubles = [[(link.id1, link.chain1, link.pos1), - (link.id2, link.chain2, link.pos2)] for link in - [c for c in self.covalent if c.id1 in self.lignames_kept and c.id2 in self.lignames_kept - and c.conf1 in ['A', ''] and c.conf2 in ['A', ''] - and (c.id1, c.chain1, c.pos1) in residues - and (c.id2, c.chain2, c.pos2) in residues]] + ligdoubles = [ + [(link.id1, link.chain1, link.pos1), (link.id2, link.chain2, link.pos2)] + for link in [ + c + for c in self.covalent + if c.id1 in self.lignames_kept + and c.id2 in self.lignames_kept + and c.conf1 in ["A", ""] + and c.conf2 in ["A", ""] + and (c.id1, c.chain1, c.pos1) in residues + and (c.id2, c.chain2, c.pos2) in residues + ] + ] kmers = cluster_doubles(ligdoubles) if not kmers: # No ligand kmers, just normal independent ligands return [[residues[res]] for res in residues] @@ -428,7 +587,9 @@ class LigandFinder: in_kmer.append((res.GetName(), res.GetChain(), res.GetNum())) for res in residues: if res not in in_kmer: - newres = [residues[res], ] + newres = [ + residues[res], + ] res_kmers.append(newres) return res_kmers @@ -437,26 +598,32 @@ class Mapper: """Provides functions for mapping atom IDs in the correct way""" def __init__(self): - self.proteinmap = None # Map internal atom IDs of protein residues to original PDB Atom IDs - self.ligandmaps = {} # Map IDs of new ligand molecules to internal IDs (or PDB IDs?) + self.proteinmap = ( + None # Map internal atom IDs of protein residues to original PDB Atom IDs + ) + self.ligandmaps = ( + {} + ) # Map IDs of new ligand molecules to internal IDs (or PDB IDs?) self.original_structure = None - def mapid(self, idx, mtype, bsid=None, to='original'): # Mapping to original IDs is standard for ligands - if mtype == 'reversed': # Needed to map internal ID back to original protein ID + def mapid( + self, idx, mtype, bsid=None, to="original" + ): # Mapping to original IDs is standard for ligands + if mtype == "reversed": # Needed to map internal ID back to original protein ID return self.reversed_proteinmap[idx] - if mtype == 'protein': + if mtype == "protein": return self.proteinmap[idx] - elif mtype == 'ligand': - if to == 'internal': + elif mtype == "ligand": + if to == "internal": return self.ligandmaps[bsid][idx] - elif to == 'original': + elif to == "original": return self.proteinmap[self.ligandmaps[bsid][idx]] def id_to_atom(self, idx): """Returns the atom for a given original ligand ID. To do this, the ID is mapped to the protein first and then the atom returned. """ - mapped_idx = self.mapid(idx, 'reversed') + mapped_idx = self.mapid(idx, "reversed") return pybel.Atom(self.original_structure.GetAtom(mapped_idx)) @@ -475,10 +642,15 @@ class Mol: def hydrophobic_atoms(self, all_atoms): """Select all carbon atoms which have only carbons and/or hydrogens as direct neighbors.""" atom_set = [] - data = namedtuple('hydrophobic', 'atom orig_atom orig_idx') - atm = [a for a in all_atoms if a.atomicnum == 6 and set([natom.GetAtomicNum() for natom - in pybel.ob.OBAtomAtomIter(a.OBAtom)]).issubset( - {1, 6})] + data = namedtuple("hydrophobic", "atom orig_atom orig_idx") + atm = [ + a + for a in all_atoms + if a.atomicnum == 6 + and set( + [natom.GetAtomicNum() for natom in pybel.ob.OBAtomAtomIter(a.OBAtom)] + ).issubset({1, 6}) + ] for atom in atm: orig_idx = self.Mapper.mapid(atom.idx, mtype=self.mtype, bsid=self.bsid) orig_atom = self.Mapper.id_to_atom(orig_idx) @@ -488,45 +660,88 @@ class Mol: def find_hba(self, all_atoms): """Find all possible hydrogen bond acceptors""" - data = namedtuple('hbondacceptor', 'a a_orig_atom a_orig_idx type') + data = namedtuple("hbondacceptor", "a a_orig_atom a_orig_idx type") a_set = [] for atom in filter(lambda at: at.OBAtom.IsHbondAcceptor(), all_atoms): - if atom.atomicnum not in [9, 17, 35, 53] and atom.idx not in self.altconf: # Exclude halogen atoms - a_orig_idx = self.Mapper.mapid(atom.idx, mtype=self.mtype, bsid=self.bsid) + if ( + atom.atomicnum not in [9, 17, 35, 53] and atom.idx not in self.altconf + ): # Exclude halogen atoms + a_orig_idx = self.Mapper.mapid( + atom.idx, mtype=self.mtype, bsid=self.bsid + ) a_orig_atom = self.Mapper.id_to_atom(a_orig_idx) - a_set.append(data(a=atom, a_orig_atom=a_orig_atom, a_orig_idx=a_orig_idx, type='regular')) + a_set.append( + data( + a=atom, + a_orig_atom=a_orig_atom, + a_orig_idx=a_orig_idx, + type="regular", + ) + ) a_set = sorted(a_set, key=lambda x: x.a_orig_idx) return a_set def find_hbd(self, all_atoms, hydroph_atoms): """Find all possible strong and weak hydrogen bonds donors (all hydrophobic C-H pairings)""" donor_pairs = [] - data = namedtuple('hbonddonor', 'd d_orig_atom d_orig_idx h type') - for donor in [a for a in all_atoms if a.OBAtom.IsHbondDonor() and a.idx not in self.altconf]: + data = namedtuple("hbonddonor", "d d_orig_atom d_orig_idx h type") + for donor in [ + a + for a in all_atoms + if a.OBAtom.IsHbondDonor() and a.idx not in self.altconf + ]: in_ring = False if not in_ring: - for adj_atom in [a for a in pybel.ob.OBAtomAtomIter(donor.OBAtom) if a.IsHbondDonorH()]: - d_orig_idx = self.Mapper.mapid(donor.idx, mtype=self.mtype, bsid=self.bsid) + for adj_atom in [ + a + for a in pybel.ob.OBAtomAtomIter(donor.OBAtom) + if a.IsHbondDonorH() + ]: + d_orig_idx = self.Mapper.mapid( + donor.idx, mtype=self.mtype, bsid=self.bsid + ) d_orig_atom = self.Mapper.id_to_atom(d_orig_idx) - donor_pairs.append(data(d=donor, d_orig_atom=d_orig_atom, d_orig_idx=d_orig_idx, - h=pybel.Atom(adj_atom), type='regular')) + donor_pairs.append( + data( + d=donor, + d_orig_atom=d_orig_atom, + d_orig_idx=d_orig_idx, + h=pybel.Atom(adj_atom), + type="regular", + ) + ) for carbon in hydroph_atoms: - for adj_atom in [a for a in pybel.ob.OBAtomAtomIter(carbon.atom.OBAtom) if a.GetAtomicNum() == 1]: - d_orig_idx = self.Mapper.mapid(carbon.atom.idx, mtype=self.mtype, bsid=self.bsid) + for adj_atom in [ + a + for a in pybel.ob.OBAtomAtomIter(carbon.atom.OBAtom) + if a.GetAtomicNum() == 1 + ]: + d_orig_idx = self.Mapper.mapid( + carbon.atom.idx, mtype=self.mtype, bsid=self.bsid + ) d_orig_atom = self.Mapper.id_to_atom(d_orig_idx) - donor_pairs.append(data(d=carbon, d_orig_atom=d_orig_atom, - d_orig_idx=d_orig_idx, h=pybel.Atom(adj_atom), type='weak')) + donor_pairs.append( + data( + d=carbon, + d_orig_atom=d_orig_atom, + d_orig_idx=d_orig_idx, + h=pybel.Atom(adj_atom), + type="weak", + ) + ) donor_pairs = sorted(donor_pairs, key=lambda x: (x.d_orig_idx, x.h.idx)) return donor_pairs def find_rings(self, mol, all_atoms): """Find rings and return only aromatic. Rings have to be sufficiently planar OR be detected by OpenBabel as aromatic.""" - data = namedtuple('aromatic_ring', 'atoms orig_atoms atoms_orig_idx normal obj center type') + data = namedtuple( + "aromatic_ring", "atoms orig_atoms atoms_orig_idx normal obj center type" + ) rings = [] - aromatic_amino = ['TYR', 'TRP', 'HIS', 'PHE'] + aromatic_amino = ["TYR", "TRP", "HIS", "PHE"] ring_candidates = mol.OBMol.GetSSSR() - logger.debug(f'number of aromatic ring candidates: {len(ring_candidates)}') + logger.debug(f"number of aromatic ring candidates: {len(ring_candidates)}") # Check here first for ligand rings not being detected as aromatic by Babel and check for planarity for ring in ring_candidates: r_atoms = [a for a in all_atoms if ring.IsMember(a.OBAtom)] @@ -534,28 +749,42 @@ class Mol: if 4 < len(r_atoms) <= 6: res = list(set([whichrestype(a) for a in r_atoms])) # re-sort ring atoms for only ligands, because HETATM numbering is not canonical in OpenBabel - if res[0] == 'UNL': - ligand_orig_idx = [self.Mapper.ligandmaps[self.bsid][a.idx] for a in r_atoms] + if res[0] == "UNL": + ligand_orig_idx = [ + self.Mapper.ligandmaps[self.bsid][a.idx] for a in r_atoms + ] sort_order = np.argsort(np.array(ligand_orig_idx)) r_atoms = [r_atoms[i] for i in sort_order] - if ring.IsAromatic() or res[0] in aromatic_amino or ring_is_planar(ring, r_atoms): + if ( + ring.IsAromatic() + or res[0] in aromatic_amino + or ring_is_planar(ring, r_atoms) + ): # Causes segfault with OpenBabel 2.3.2, so deactivated # typ = ring.GetType() if not ring.GetType() == '' else 'unknown' # Alternative typing - ring_type = '%s-membered' % len(r_atoms) - ring_atms = [r_atoms[a].coords for a in [0, 2, 4]] # Probe atoms for normals, assuming planarity + ring_type = "%s-membered" % len(r_atoms) + ring_atms = [ + r_atoms[a].coords for a in [0, 2, 4] + ] # Probe atoms for normals, assuming planarity ringv1 = vector(ring_atms[0], ring_atms[1]) ringv2 = vector(ring_atms[2], ring_atms[0]) - atoms_orig_idx = [self.Mapper.mapid(r_atom.idx, mtype=self.mtype, - bsid=self.bsid) for r_atom in r_atoms] + atoms_orig_idx = [ + self.Mapper.mapid(r_atom.idx, mtype=self.mtype, bsid=self.bsid) + for r_atom in r_atoms + ] orig_atoms = [self.Mapper.id_to_atom(idx) for idx in atoms_orig_idx] - rings.append(data(atoms=r_atoms, - orig_atoms=orig_atoms, - atoms_orig_idx=atoms_orig_idx, - normal=normalize_vector(np.cross(ringv1, ringv2)), - obj=ring, - center=centroid([ra.coords for ra in r_atoms]), - type=ring_type)) + rings.append( + data( + atoms=r_atoms, + orig_atoms=orig_atoms, + atoms_orig_idx=atoms_orig_idx, + normal=normalize_vector(np.cross(ringv1, ringv2)), + obj=ring, + center=centroid([ra.coords for ra in r_atoms]), + type=ring_type, + ) + ) return rings def get_hydrophobic_atoms(self): @@ -565,16 +794,24 @@ class Mol: return self.hbond_acc_atoms def get_hbd(self): - return [don_pair for don_pair in self.hbond_don_atom_pairs if don_pair.type == 'regular'] + return [ + don_pair + for don_pair in self.hbond_don_atom_pairs + if don_pair.type == "regular" + ] def get_weak_hbd(self): - return [don_pair for don_pair in self.hbond_don_atom_pairs if don_pair.type == 'weak'] + return [ + don_pair + for don_pair in self.hbond_don_atom_pairs + if don_pair.type == "weak" + ] def get_pos_charged(self): - return [charge for charge in self.charged if charge.type == 'positive'] + return [charge for charge in self.charged if charge.type == "positive"] def get_neg_charged(self): - return [charge for charge in self.charged if charge.type == 'negative'] + return [charge for charge in self.charged if charge.type == "negative"] class PLInteraction: @@ -591,65 +828,135 @@ class PLInteraction: self.altconf = protcomplex.altconf # #@todo Refactor code to combine different directionality - self.saltbridge_lneg = saltbridge(self.bindingsite.get_pos_charged(), self.ligand.get_neg_charged(), True) - self.saltbridge_pneg = saltbridge(self.ligand.get_pos_charged(), self.bindingsite.get_neg_charged(), False) - - self.all_hbonds_ldon = hbonds(self.bindingsite.get_hba(), - self.ligand.get_hbd(), False, 'strong') - self.all_hbonds_pdon = hbonds(self.ligand.get_hba(), - self.bindingsite.get_hbd(), True, 'strong') - - self.hbonds_ldon = self.refine_hbonds_ldon(self.all_hbonds_ldon, self.saltbridge_lneg, - self.saltbridge_pneg) - self.hbonds_pdon = self.refine_hbonds_pdon(self.all_hbonds_pdon, self.saltbridge_lneg, - self.saltbridge_pneg) + self.saltbridge_lneg = saltbridge( + self.bindingsite.get_pos_charged(), self.ligand.get_neg_charged(), True + ) + self.saltbridge_pneg = saltbridge( + self.ligand.get_pos_charged(), self.bindingsite.get_neg_charged(), False + ) + + self.all_hbonds_ldon = hbonds( + self.bindingsite.get_hba(), self.ligand.get_hbd(), False, "strong" + ) + self.all_hbonds_pdon = hbonds( + self.ligand.get_hba(), self.bindingsite.get_hbd(), True, "strong" + ) + + self.hbonds_ldon = self.refine_hbonds_ldon( + self.all_hbonds_ldon, self.saltbridge_lneg, self.saltbridge_pneg + ) + self.hbonds_pdon = self.refine_hbonds_pdon( + self.all_hbonds_pdon, self.saltbridge_lneg, self.saltbridge_pneg + ) self.pistacking = pistacking(self.bindingsite.rings, self.ligand.rings) - self.all_pi_cation_laro = pication(self.ligand.rings, self.bindingsite.get_pos_charged(), True) - self.pication_paro = pication(self.bindingsite.rings, self.ligand.get_pos_charged(), False) - - self.pication_laro = self.refine_pi_cation_laro(self.all_pi_cation_laro, self.pistacking) - - self.all_hydrophobic_contacts = hydrophobic_interactions(self.bindingsite.get_hydrophobic_atoms(), - self.ligand.get_hydrophobic_atoms()) - self.hydrophobic_contacts = self.refine_hydrophobic(self.all_hydrophobic_contacts, self.pistacking) - self.halogen_bonds = halogen(self.bindingsite.halogenbond_acc, self.ligand.halogenbond_don) - self.water_bridges = water_bridges(self.bindingsite.get_hba(), self.ligand.get_hba(), - self.bindingsite.get_hbd(), self.ligand.get_hbd(), - self.ligand.water) - - self.water_bridges = self.refine_water_bridges(self.water_bridges, self.hbonds_ldon, self.hbonds_pdon) - - self.metal_complexes = metal_complexation(self.ligand.metals, self.ligand.metal_binding, - self.bindingsite.metal_binding) + self.all_pi_cation_laro = pication( + self.ligand.rings, self.bindingsite.get_pos_charged(), True + ) + self.pication_paro = pication( + self.bindingsite.rings, self.ligand.get_pos_charged(), False + ) + + self.pication_laro = self.refine_pi_cation_laro( + self.all_pi_cation_laro, self.pistacking + ) + + self.all_hydrophobic_contacts = hydrophobic_interactions( + self.bindingsite.get_hydrophobic_atoms(), + self.ligand.get_hydrophobic_atoms(), + ) + self.hydrophobic_contacts = self.refine_hydrophobic( + self.all_hydrophobic_contacts, self.pistacking + ) + self.halogen_bonds = halogen( + self.bindingsite.halogenbond_acc, self.ligand.halogenbond_don + ) + self.water_bridges = water_bridges( + self.bindingsite.get_hba(), + self.ligand.get_hba(), + self.bindingsite.get_hbd(), + self.ligand.get_hbd(), + self.ligand.water, + ) + + self.water_bridges = self.refine_water_bridges( + self.water_bridges, self.hbonds_ldon, self.hbonds_pdon + ) + + self.metal_complexes = metal_complexation( + self.ligand.metals, + self.ligand.metal_binding, + self.bindingsite.metal_binding, + ) self.all_itypes = self.saltbridge_lneg + self.saltbridge_pneg + self.hbonds_pdon - self.all_itypes = self.all_itypes + self.hbonds_ldon + self.pistacking + self.pication_laro + self.pication_paro - self.all_itypes = self.all_itypes + self.hydrophobic_contacts + self.halogen_bonds + self.water_bridges + self.all_itypes = ( + self.all_itypes + + self.hbonds_ldon + + self.pistacking + + self.pication_laro + + self.pication_paro + ) + self.all_itypes = ( + self.all_itypes + + self.hydrophobic_contacts + + self.halogen_bonds + + self.water_bridges + ) self.all_itypes = self.all_itypes + self.metal_complexes self.no_interactions = all(len(i) == 0 for i in self.all_itypes) - self.unpaired_hba, self.unpaired_hbd, self.unpaired_hal = self.find_unpaired_ligand() - self.unpaired_hba_orig_idx = [self.Mapper.mapid(atom.idx, mtype='ligand', bsid=self.ligand.bsid) - for atom in self.unpaired_hba] - self.unpaired_hbd_orig_idx = [self.Mapper.mapid(atom.idx, mtype='ligand', bsid=self.ligand.bsid) - for atom in self.unpaired_hbd] - self.unpaired_hal_orig_idx = [self.Mapper.mapid(atom.idx, mtype='ligand', bsid=self.ligand.bsid) - for atom in self.unpaired_hal] - self.num_unpaired_hba, self.num_unpaired_hbd = len(self.unpaired_hba), len(self.unpaired_hbd) + ( + self.unpaired_hba, + self.unpaired_hbd, + self.unpaired_hal, + ) = self.find_unpaired_ligand() + self.unpaired_hba_orig_idx = [ + self.Mapper.mapid(atom.idx, mtype="ligand", bsid=self.ligand.bsid) + for atom in self.unpaired_hba + ] + self.unpaired_hbd_orig_idx = [ + self.Mapper.mapid(atom.idx, mtype="ligand", bsid=self.ligand.bsid) + for atom in self.unpaired_hbd + ] + self.unpaired_hal_orig_idx = [ + self.Mapper.mapid(atom.idx, mtype="ligand", bsid=self.ligand.bsid) + for atom in self.unpaired_hal + ] + self.num_unpaired_hba, self.num_unpaired_hbd = ( + len(self.unpaired_hba), + len(self.unpaired_hbd), + ) self.num_unpaired_hal = len(self.unpaired_hal) # Exclude empty chains (coming from ligand as a target, from metal complexes) - self.interacting_chains = sorted(list(set([i.reschain for i in self.all_itypes - if i.reschain not in [' ', None]]))) + self.interacting_chains = sorted( + list( + set( + [ + i.reschain + for i in self.all_itypes + if i.reschain not in [" ", None] + ] + ) + ) + ) # Get all interacting residues, excluding ligand and water molecules - self.interacting_res = list(set([''.join([str(i.resnr), str(i.reschain)]) for i in self.all_itypes - if i.restype not in ['LIG', 'HOH']])) + self.interacting_res = list( + set( + [ + "".join([str(i.resnr), str(i.reschain)]) + for i in self.all_itypes + if i.restype not in ["LIG", "HOH"] + ] + ) + ) if len(self.interacting_res) != 0: logger.info( - f'ligand interacts with {len(self.interacting_res)} binding site residue(s) in chain(s) {self.interacting_chains}') + f"ligand interacts with {len(self.interacting_res)} binding site residue(s) in chain(s) {self.interacting_chains}" + ) interactions_list = [] num_saltbridges = len(self.saltbridge_lneg + self.saltbridge_pneg) num_hbonds = len(self.hbonds_ldon + self.hbonds_pdon) @@ -658,34 +965,49 @@ class PLInteraction: num_halogen = len(self.halogen_bonds) num_waterbridges = len(self.water_bridges) if num_saltbridges != 0: - interactions_list.append('%i salt bridge(s)' % num_saltbridges) + interactions_list.append("%i salt bridge(s)" % num_saltbridges) if num_hbonds != 0: - interactions_list.append('%i hydrogen bond(s)' % num_hbonds) + interactions_list.append("%i hydrogen bond(s)" % num_hbonds) if num_pication != 0: - interactions_list.append('%i pi-cation interaction(s)' % num_pication) + interactions_list.append("%i pi-cation interaction(s)" % num_pication) if num_pistack != 0: - interactions_list.append('%i pi-stacking(s)' % num_pistack) + interactions_list.append("%i pi-stacking(s)" % num_pistack) if num_halogen != 0: - interactions_list.append('%i halogen bond(s)' % num_halogen) + interactions_list.append("%i halogen bond(s)" % num_halogen) if num_waterbridges != 0: - interactions_list.append('%i water bridge(s)' % num_waterbridges) + interactions_list.append("%i water bridge(s)" % num_waterbridges) if not len(interactions_list) == 0: - logger.info(f'complex uses {interactions_list}') + logger.info(f"complex uses {interactions_list}") else: - logger.info('no interactions for this ligand') + logger.info("no interactions for this ligand") def find_unpaired_ligand(self): """Identify unpaired functional in groups in ligands, involving H-Bond donors, acceptors, halogen bond donors. """ unpaired_hba, unpaired_hbd, unpaired_hal = [], [], [] # Unpaired hydrogen bond acceptors/donors in ligand (not used for hydrogen bonds/water, salt bridges/mcomplex) - involved_atoms = [hbond.a.idx for hbond in self.hbonds_pdon] + [hbond.d.idx for hbond in self.hbonds_ldon] - [[involved_atoms.append(atom.idx) for atom in sb.negative.atoms] for sb in self.saltbridge_lneg] - [[involved_atoms.append(atom.idx) for atom in sb.positive.atoms] for sb in self.saltbridge_pneg] + involved_atoms = [hbond.a.idx for hbond in self.hbonds_pdon] + [ + hbond.d.idx for hbond in self.hbonds_ldon + ] + [ + [involved_atoms.append(atom.idx) for atom in sb.negative.atoms] + for sb in self.saltbridge_lneg + ] + [ + [involved_atoms.append(atom.idx) for atom in sb.positive.atoms] + for sb in self.saltbridge_pneg + ] [involved_atoms.append(wb.a.idx) for wb in self.water_bridges if wb.protisdon] - [involved_atoms.append(wb.d.idx) for wb in self.water_bridges if not wb.protisdon] - [involved_atoms.append(mcomplex.target.atom.idx) for mcomplex in self.metal_complexes - if mcomplex.location == 'ligand'] + [ + involved_atoms.append(wb.d.idx) + for wb in self.water_bridges + if not wb.protisdon + ] + [ + involved_atoms.append(mcomplex.target.atom.idx) + for mcomplex in self.metal_complexes + if mcomplex.location == "ligand" + ] for atom in [hba.a for hba in self.ligand.get_hba()]: if atom.idx not in involved_atoms: unpaired_hba.append(atom) @@ -707,7 +1029,10 @@ class PLInteraction: # 1. Rings interacting via stacking can't have additional hydrophobic contacts between each other. for pistack, h in itertools.product(pistacks, all_h): h1, h2 = h.bsatom.idx, h.ligatom.idx - brs, lrs = [p1.idx for p1 in pistack.proteinring.atoms], [p2.idx for p2 in pistack.ligandring.atoms] + brs, lrs = ( + [p1.idx for p1 in pistack.proteinring.atoms], + [p2.idx for p2 in pistack.ligandring.atoms], + ) if h1 in brs and h2 in lrs: sel[(h1, h2)] = "EXCLUDE" hydroph = [h for h in all_h if not (h.bsatom.idx, h.ligatom.idx) in sel] @@ -726,7 +1051,9 @@ class PLInteraction: # 3. If a protein atom interacts with several neighboring ligand atoms, just keep the one with the closest dist for h in hydroph: if h.bsatom.idx not in bsclust: - bsclust[h.bsatom.idx] = [h, ] + bsclust[h.bsatom.idx] = [ + h, + ] else: bsclust[h.bsatom.idx].append(h) @@ -752,10 +1079,12 @@ class PLInteraction: tuples = list(set(tuples)) tuples = sorted(tuples, key=itemgetter(1)) - clusters = cluster_doubles(tuples) # Cluster connected atoms (i.e. find hydrophobic patches) + clusters = cluster_doubles( + tuples + ) # Cluster connected atoms (i.e. find hydrophobic patches) for cluster in clusters: - min_dist = float('inf') + min_dist = float("inf") min_h = None for atm_idx in cluster: h = idx_to_h[atm_idx] @@ -765,7 +1094,9 @@ class PLInteraction: hydroph_final.append(min_h) before, reduced = len(all_h), len(hydroph_final) if not before == 0 and not before == reduced: - logger.info(f'reduced number of hydrophobic contacts from {before} to {reduced}') + logger.info( + f"reduced number of hydrophobic contacts from {before} to {reduced}" + ) return hydroph_final def refine_hbonds_ldon(self, all_hbonds, salt_lneg, salt_pneg): @@ -774,11 +1105,17 @@ class PLInteraction: for hbond in all_hbonds: i_set[hbond] = False for salt in salt_pneg: - protidx, ligidx = [at.idx for at in salt.negative.atoms], [at.idx for at in salt.positive.atoms] + protidx, ligidx = ( + [at.idx for at in salt.negative.atoms], + [at.idx for at in salt.positive.atoms], + ) if hbond.d.idx in ligidx and hbond.a.idx in protidx: i_set[hbond] = True for salt in salt_lneg: - protidx, ligidx = [at.idx for at in salt.positive.atoms], [at.idx for at in salt.negative.atoms] + protidx, ligidx = ( + [at.idx for at in salt.positive.atoms], + [at.idx for at in salt.negative.atoms], + ) if hbond.d.idx in ligidx and hbond.a.idx in protidx: i_set[hbond] = True @@ -801,11 +1138,17 @@ class PLInteraction: for hbond in all_hbonds: i_set[hbond] = False for salt in salt_lneg: - protidx, ligidx = [at.idx for at in salt.positive.atoms], [at.idx for at in salt.negative.atoms] + protidx, ligidx = ( + [at.idx for at in salt.positive.atoms], + [at.idx for at in salt.negative.atoms], + ) if hbond.a.idx in ligidx and hbond.d.idx in protidx: i_set[hbond] = True for salt in salt_pneg: - protidx, ligidx = [at.idx for at in salt.negative.atoms], [at.idx for at in salt.positive.atoms] + protidx, ligidx = ( + [at.idx for at in salt.negative.atoms], + [at.idx for at in salt.positive.atoms], + ) if hbond.a.idx in ligidx and hbond.d.idx in protidx: i_set[hbond] = True @@ -829,7 +1172,10 @@ class PLInteraction: for picat in all_picat: exclude = False for stack in stacks: - if whichrestype(stack.proteinring.atoms[0]) == 'HIS' and picat.ring.obj == stack.ligandring.obj: + if ( + whichrestype(stack.proteinring.atoms[0]) == "HIS" + and picat.ring.obj == stack.ligandring.obj + ): exclude = True if not exclude: i_set.append(picat) @@ -848,18 +1194,27 @@ class PLInteraction: if (wbridge.water.idx, wbridge.a.idx) not in wb_dict: wb_dict[(wbridge.water.idx, wbridge.a.idx)] = wbridge else: - if abs(omega - wb_dict[(wbridge.water.idx, wbridge.a.idx)].w_angle) < abs(omega - wbridge.w_angle): + if abs( + omega - wb_dict[(wbridge.water.idx, wbridge.a.idx)].w_angle + ) < abs(omega - wbridge.w_angle): wb_dict[(wbridge.water.idx, wbridge.a.idx)] = wbridge for wb_tuple in wb_dict: water, acceptor = wb_tuple if water not in wb_dict2: - wb_dict2[water] = [(abs(omega - wb_dict[wb_tuple].w_angle), wb_dict[wb_tuple]), ] + wb_dict2[water] = [ + (abs(omega - wb_dict[wb_tuple].w_angle), wb_dict[wb_tuple]), + ] elif len(wb_dict2[water]) == 1: - wb_dict2[water].append((abs(omega - wb_dict[wb_tuple].w_angle), wb_dict[wb_tuple])) + wb_dict2[water].append( + (abs(omega - wb_dict[wb_tuple].w_angle), wb_dict[wb_tuple]) + ) wb_dict2[water] = sorted(wb_dict2[water], key=lambda x: x[0]) else: if wb_dict2[water][1][0] < abs(omega - wb_dict[wb_tuple].w_angle): - wb_dict2[water] = [wb_dict2[water][0], (wb_dict[wb_tuple].w_angle, wb_dict[wb_tuple])] + wb_dict2[water] = [ + wb_dict2[water][0], + (wb_dict[wb_tuple].w_angle, wb_dict[wb_tuple]), + ] filtered_wb = [] for fwbridges in wb_dict2.values(): @@ -870,12 +1225,19 @@ class PLInteraction: class BindingSite(Mol): def __init__(self, atoms, protcomplex, cclass, altconf, min_dist, mapper): """Find all relevant parts which could take part in interactions""" - Mol.__init__(self, altconf, mapper, mtype='protein', bsid=None) + Mol.__init__(self, altconf, mapper, mtype="protein", bsid=None) self.complex = cclass self.full_mol = protcomplex self.all_atoms = atoms self.min_dist = min_dist # Minimum distance of bs res to ligand - self.bs_res = list(set([''.join([str(whichresnumber(a)), whichchain(a)]) for a in self.all_atoms])) # e.g. 47A + self.bs_res = list( + set( + [ + "".join([str(whichresnumber(a)), whichchain(a)]) + for a in self.all_atoms + ] + ) + ) # e.g. 47A self.rings = self.find_rings(self.full_mol, self.all_atoms) self.hydroph_atoms = self.hydrophobic_atoms(self.all_atoms) self.hbond_acc_atoms = self.find_hba(self.all_atoms) @@ -886,118 +1248,228 @@ class BindingSite(Mol): def find_hal(self, atoms): """Look for halogen bond acceptors (Y-{O|P|N|S}, with Y=C,P,S)""" - data = namedtuple('hal_acceptor', 'o o_orig_idx y y_orig_idx') + data = namedtuple("hal_acceptor", "o o_orig_idx y y_orig_idx") a_set = [] # All oxygens, nitrogen, sulfurs with neighboring carbon, phosphor, nitrogen or sulfur for a in [at for at in atoms if at.atomicnum in [8, 7, 16]]: - n_atoms = [na for na in pybel.ob.OBAtomAtomIter(a.OBAtom) if na.GetAtomicNum() in [6, 7, 15, 16]] + n_atoms = [ + na + for na in pybel.ob.OBAtomAtomIter(a.OBAtom) + if na.GetAtomicNum() in [6, 7, 15, 16] + ] if len(n_atoms) == 1: # Proximal atom o_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid) - y_orig_idx = self.Mapper.mapid(n_atoms[0].GetIdx(), mtype=self.mtype, bsid=self.bsid) - a_set.append(data(o=a, o_orig_idx=o_orig_idx, y=pybel.Atom(n_atoms[0]), y_orig_idx=y_orig_idx)) + y_orig_idx = self.Mapper.mapid( + n_atoms[0].GetIdx(), mtype=self.mtype, bsid=self.bsid + ) + a_set.append( + data( + o=a, + o_orig_idx=o_orig_idx, + y=pybel.Atom(n_atoms[0]), + y_orig_idx=y_orig_idx, + ) + ) return a_set def find_charged(self, mol): """Looks for positive charges in arginine, histidine or lysine, for negative in aspartic and glutamic acid.""" - data = namedtuple('pcharge', 'atoms atoms_orig_idx type center restype resnr reschain') + data = namedtuple( + "pcharge", "atoms atoms_orig_idx type center restype resnr reschain" + ) a_set = [] # Iterate through all residue, exclude those in chains defined as peptides - for res in [r for r in pybel.ob.OBResidueIter(mol.OBMol) if not r.GetChain() in config.PEPTIDES]: + for res in [ + r + for r in pybel.ob.OBResidueIter(mol.OBMol) + if not r.GetChain() in config.PEPTIDES + ]: if config.INTRA is not None: if res.GetChain() != config.INTRA: continue a_contributing = [] a_contributing_orig_idx = [] - if res.GetName() in ('ARG', 'HIS', 'LYS'): # Arginine, Histidine or Lysine have charged sidechains + if res.GetName() in ( + "ARG", + "HIS", + "LYS", + ): # Arginine, Histidine or Lysine have charged sidechains for a in pybel.ob.OBResidueAtomIter(res): - if a.GetType().startswith('N') and res.GetAtomProperty(a, 8) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf: + if ( + a.GetType().startswith("N") + and res.GetAtomProperty(a, 8) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + ): a_contributing.append(pybel.Atom(a)) - a_contributing_orig_idx.append(self.Mapper.mapid(a.GetIdx(), mtype='protein')) + a_contributing_orig_idx.append( + self.Mapper.mapid(a.GetIdx(), mtype="protein") + ) if not len(a_contributing) == 0: - a_set.append(data(atoms=a_contributing, - atoms_orig_idx=a_contributing_orig_idx, - type='positive', - center=centroid([ac.coords for ac in a_contributing]), - restype=res.GetName(), - resnr=res.GetNum(), - reschain=res.GetChain())) - if res.GetName() in ('GLU', 'ASP'): # Aspartic or Glutamic Acid + a_set.append( + data( + atoms=a_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="positive", + center=centroid([ac.coords for ac in a_contributing]), + restype=res.GetName(), + resnr=res.GetNum(), + reschain=res.GetChain(), + ) + ) + if res.GetName() in ("GLU", "ASP"): # Aspartic or Glutamic Acid for a in pybel.ob.OBResidueAtomIter(res): - if a.GetType().startswith('O') and res.GetAtomProperty(a, 8) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf: + if ( + a.GetType().startswith("O") + and res.GetAtomProperty(a, 8) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + ): a_contributing.append(pybel.Atom(a)) - a_contributing_orig_idx.append(self.Mapper.mapid(a.GetIdx(), mtype='protein')) + a_contributing_orig_idx.append( + self.Mapper.mapid(a.GetIdx(), mtype="protein") + ) if not len(a_contributing) == 0: - a_set.append(data(atoms=a_contributing, - atoms_orig_idx=a_contributing_orig_idx, - type='negative', - center=centroid([ac.coords for ac in a_contributing]), - restype=res.GetName(), - resnr=res.GetNum(), - reschain=res.GetChain())) + a_set.append( + data( + atoms=a_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="negative", + center=centroid([ac.coords for ac in a_contributing]), + restype=res.GetName(), + resnr=res.GetNum(), + reschain=res.GetChain(), + ) + ) return a_set def find_metal_binding(self, mol): """Looks for atoms that could possibly be involved in chelating a metal ion. This can be any main chain oxygen atom or oxygen, nitrogen and sulfur from specific amino acids""" - data = namedtuple('metal_binding', 'atom atom_orig_idx type restype resnr reschain location') + data = namedtuple( + "metal_binding", "atom atom_orig_idx type restype resnr reschain location" + ) a_set = [] for res in pybel.ob.OBResidueIter(mol.OBMol): - restype, reschain, resnr = res.GetName().upper(), res.GetChain(), res.GetNum() - if restype in ['ASP', 'GLU', 'SER', 'THR', 'TYR']: # Look for oxygens here + restype, reschain, resnr = ( + res.GetName().upper(), + res.GetChain(), + res.GetNum(), + ) + if restype in ["ASP", "GLU", "SER", "THR", "TYR"]: # Look for oxygens here for a in pybel.ob.OBResidueAtomIter(res): - if a.GetType().startswith('O') and res.GetAtomProperty(a, 8) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf: - atom_orig_idx = self.Mapper.mapid(a.GetIdx(), mtype=self.mtype, bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(a), atom_orig_idx=atom_orig_idx, type='O', restype=restype, - resnr=resnr, reschain=reschain, - location='protein.sidechain')) - if restype == 'HIS': # Look for nitrogen here + if ( + a.GetType().startswith("O") + and res.GetAtomProperty(a, 8) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + ): + atom_orig_idx = self.Mapper.mapid( + a.GetIdx(), mtype=self.mtype, bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(a), + atom_orig_idx=atom_orig_idx, + type="O", + restype=restype, + resnr=resnr, + reschain=reschain, + location="protein.sidechain", + ) + ) + if restype == "HIS": # Look for nitrogen here for a in pybel.ob.OBResidueAtomIter(res): - if a.GetType().startswith('N') and res.GetAtomProperty(a, 8) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf: - atom_orig_idx = self.Mapper.mapid(a.GetIdx(), mtype=self.mtype, bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(a), atom_orig_idx=atom_orig_idx, type='N', restype=restype, - resnr=resnr, reschain=reschain, - location='protein.sidechain')) - if restype == 'CYS': # Look for sulfur here + if ( + a.GetType().startswith("N") + and res.GetAtomProperty(a, 8) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + ): + atom_orig_idx = self.Mapper.mapid( + a.GetIdx(), mtype=self.mtype, bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(a), + atom_orig_idx=atom_orig_idx, + type="N", + restype=restype, + resnr=resnr, + reschain=reschain, + location="protein.sidechain", + ) + ) + if restype == "CYS": # Look for sulfur here for a in pybel.ob.OBResidueAtomIter(res): - if a.GetType().startswith('S') and res.GetAtomProperty(a, 8) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf: - atom_orig_idx = self.Mapper.mapid(a.GetIdx(), mtype=self.mtype, bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(a), atom_orig_idx=atom_orig_idx, type='S', restype=restype, - resnr=resnr, reschain=reschain, - location='protein.sidechain')) + if ( + a.GetType().startswith("S") + and res.GetAtomProperty(a, 8) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + ): + atom_orig_idx = self.Mapper.mapid( + a.GetIdx(), mtype=self.mtype, bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(a), + atom_orig_idx=atom_orig_idx, + type="S", + restype=restype, + resnr=resnr, + reschain=reschain, + location="protein.sidechain", + ) + ) for a in pybel.ob.OBResidueAtomIter(res): # All main chain oxygens - if a.GetType().startswith('O') and res.GetAtomProperty(a, 2) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf and restype != 'HOH': - atom_orig_idx = self.Mapper.mapid(a.GetIdx(), mtype=self.mtype, bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(a), atom_orig_idx=atom_orig_idx, type='O', restype=res.GetName(), - resnr=res.GetNum(), reschain=res.GetChain(), - location='protein.mainchain')) + if ( + a.GetType().startswith("O") + and res.GetAtomProperty(a, 2) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + and restype != "HOH" + ): + atom_orig_idx = self.Mapper.mapid( + a.GetIdx(), mtype=self.mtype, bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(a), + atom_orig_idx=atom_orig_idx, + type="O", + restype=res.GetName(), + resnr=res.GetNum(), + reschain=res.GetChain(), + location="protein.mainchain", + ) + ) return a_set class Ligand(Mol): def __init__(self, cclass, ligand): altconf = cclass.altconf - self.hetid, self.chain, self.position = ligand.hetid, ligand.chain, ligand.position - self.bsid = ':'.join([self.hetid, self.chain, str(self.position)]) - Mol.__init__(self, altconf, cclass.Mapper, mtype='ligand', bsid=self.bsid) + self.hetid, self.chain, self.position = ( + ligand.hetid, + ligand.chain, + ligand.position, + ) + self.bsid = ":".join([self.hetid, self.chain, str(self.position)]) + Mol.__init__(self, altconf, cclass.Mapper, mtype="ligand", bsid=self.bsid) self.members = ligand.members self.longname = ligand.longname self.type = ligand.type self.complex = cclass self.molecule = ligand.mol # Pybel Molecule - self.smiles = self.molecule.write(format='can') # SMILES String - self.inchikey = self.molecule.write(format='inchikey') + self.smiles = self.molecule.write(format="can") # SMILES String + self.inchikey = self.molecule.write(format="inchikey") self.can_to_pdb = ligand.can_to_pdb if not len(self.smiles) == 0: self.smiles = self.smiles.split()[0] else: - logger.warning(f'could not write SMILES for ligand {ligand}') - self.smiles = '' + logger.warning(f"could not write SMILES for ligand {ligand}") + self.smiles = "" self.heavy_atoms = self.molecule.OBMol.NumHvyAtoms() # Heavy atoms count self.all_atoms = self.molecule.atoms self.atmdict = {l.idx: l for l in self.all_atoms} @@ -1006,9 +1478,9 @@ class Ligand(Mol): self.hbond_acc_atoms = self.find_hba(self.all_atoms) self.num_rings = len(self.rings) if self.num_rings != 0: - logger.info(f'contains {self.num_rings} aromatic ring(s)') + logger.info(f"contains {self.num_rings} aromatic ring(s)") descvalues = self.molecule.calcdesc() - self.molweight, self.logp = float(descvalues['MW']), float(descvalues['logP']) + self.molweight, self.logp = float(descvalues["MW"]), float(descvalues["logP"]) self.num_rot_bonds = int(self.molecule.OBMol.NumRotors()) self.atomorder = ligand.atomorder @@ -1016,48 +1488,73 @@ class Ligand(Mol): # Special Case for hydrogen bond acceptor identification # ########################################################## - self.inverse_mapping = {v: k for k, v in self.Mapper.ligandmaps[self.bsid].items()} + self.inverse_mapping = { + v: k for k, v in self.Mapper.ligandmaps[self.bsid].items() + } self.pdb_to_idx_mapping = {v: k for k, v in self.Mapper.proteinmap.items()} self.hbond_don_atom_pairs = self.find_hbd(self.all_atoms, self.hydroph_atoms) ###### donor_pairs = [] - data = namedtuple('hbonddonor', 'd d_orig_atom d_orig_idx h type') + data = namedtuple("hbonddonor", "d d_orig_atom d_orig_idx h type") for donor in self.all_atoms: - pdbidx = self.Mapper.mapid(donor.idx, mtype='ligand', bsid=self.bsid, to='original') + pdbidx = self.Mapper.mapid( + donor.idx, mtype="ligand", bsid=self.bsid, to="original" + ) d = cclass.atoms[self.pdb_to_idx_mapping[pdbidx]] if d.OBAtom.IsHbondDonor(): - for adj_atom in [a for a in pybel.ob.OBAtomAtomIter(d.OBAtom) if a.IsHbondDonorH()]: + for adj_atom in [ + a for a in pybel.ob.OBAtomAtomIter(d.OBAtom) if a.IsHbondDonorH() + ]: d_orig_atom = self.Mapper.id_to_atom(pdbidx) - donor_pairs.append(data(d=donor, d_orig_atom=d_orig_atom, d_orig_idx=pdbidx, - h=pybel.Atom(adj_atom), type='regular')) + donor_pairs.append( + data( + d=donor, + d_orig_atom=d_orig_atom, + d_orig_idx=pdbidx, + h=pybel.Atom(adj_atom), + type="regular", + ) + ) self.hbond_don_atom_pairs = donor_pairs ####### self.charged = self.find_charged(self.all_atoms) self.centroid = centroid([a.coords for a in self.all_atoms]) - self.max_dist_to_center = max((euclidean3d(self.centroid, a.coords) for a in self.all_atoms)) + self.max_dist_to_center = max( + (euclidean3d(self.centroid, a.coords) for a in self.all_atoms) + ) self.water = [] - data = namedtuple('water', 'oxy oxy_orig_idx') + data = namedtuple("water", "oxy oxy_orig_idx") for hoh in ligand.water: oxy = None for at in pybel.ob.OBResidueAtomIter(hoh): if at.GetAtomicNum() == 8 and at.GetIdx() not in self.altconf: oxy = pybel.Atom(at) # There are some cases where there is no oxygen in a water residue, ignore those - if not set([at.GetAtomicNum() for at in pybel.ob.OBResidueAtomIter(hoh)]) == {1} and oxy is not None: - if euclidean3d(self.centroid, oxy.coords) < self.max_dist_to_center + config.BS_DIST: - oxy_orig_idx = self.Mapper.mapid(oxy.idx, mtype='protein') + if ( + not set([at.GetAtomicNum() for at in pybel.ob.OBResidueAtomIter(hoh)]) + == {1} + and oxy is not None + ): + if ( + euclidean3d(self.centroid, oxy.coords) + < self.max_dist_to_center + config.BS_DIST + ): + oxy_orig_idx = self.Mapper.mapid(oxy.idx, mtype="protein") self.water.append(data(oxy=oxy, oxy_orig_idx=oxy_orig_idx)) self.halogenbond_don = self.find_hal(self.all_atoms) self.metal_binding = self.find_metal_binding(self.all_atoms, self.water) self.metals = [] - data = namedtuple('metal', 'm orig_m m_orig_idx') + data = namedtuple("metal", "m orig_m m_orig_idx") for a in [a for a in self.all_atoms if a.type.upper() in config.METAL_IONS]: m_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid) orig_m = self.Mapper.id_to_atom(m_orig_idx) self.metals.append(data(m=a, m_orig_idx=m_orig_idx, orig_m=orig_m)) - self.num_hba, self.num_hbd = len(self.hbond_acc_atoms), len(self.hbond_don_atom_pairs) + self.num_hba, self.num_hbd = ( + len(self.hbond_acc_atoms), + len(self.hbond_don_atom_pairs), + ) self.num_hal = len(self.halogenbond_don) def get_canonical_num(self, atomnum): @@ -1066,41 +1563,69 @@ class Ligand(Mol): def is_functional_group(self, atom, group): """Given a pybel atom, look up if it belongs to a function group""" - n_atoms = [a_neighbor.GetAtomicNum() for a_neighbor in pybel.ob.OBAtomAtomIter(atom.OBAtom)] + n_atoms = [ + a_neighbor.GetAtomicNum() + for a_neighbor in pybel.ob.OBAtomAtomIter(atom.OBAtom) + ] - if group in ['quartamine', 'tertamine'] and atom.atomicnum == 7: # Nitrogen + if group in ["quartamine", "tertamine"] and atom.atomicnum == 7: # Nitrogen # It's a nitrogen, so could be a protonated amine or quaternary ammonium - if '1' not in n_atoms and len(n_atoms) == 4: - return True if group == 'quartamine' else False # It's a quat. ammonium (N with 4 residues != H) + if "1" not in n_atoms and len(n_atoms) == 4: + return ( + True if group == "quartamine" else False + ) # It's a quat. ammonium (N with 4 residues != H) elif atom.OBAtom.GetHyb() == 3 and len(n_atoms) >= 3: - return True if group == 'tertamine' else False # It's sp3-hybridized, so could pick up an hydrogen + return ( + True if group == "tertamine" else False + ) # It's sp3-hybridized, so could pick up an hydrogen else: return False - if group in ['sulfonium', 'sulfonicacid', 'sulfate'] and atom.atomicnum == 16: # Sulfur - if '1' not in n_atoms and len(n_atoms) == 3: # It's a sulfonium (S with 3 residues != H) - return True if group == 'sulfonium' else False + if ( + group in ["sulfonium", "sulfonicacid", "sulfate"] and atom.atomicnum == 16 + ): # Sulfur + if ( + "1" not in n_atoms and len(n_atoms) == 3 + ): # It's a sulfonium (S with 3 residues != H) + return True if group == "sulfonium" else False elif n_atoms.count(8) == 3: # It's a sulfonate or sulfonic acid - return True if group == 'sulfonicacid' else False + return True if group == "sulfonicacid" else False elif n_atoms.count(8) == 4: # It's a sulfate - return True if group == 'sulfate' else False + return True if group == "sulfate" else False - if group == 'phosphate' and atom.atomicnum == 15: # Phosphor + if group == "phosphate" and atom.atomicnum == 15: # Phosphor if set(n_atoms) == {8}: # It's a phosphate return True - if group in ['carboxylate', 'guanidine'] and atom.atomicnum == 6: # It's a carbon atom - if n_atoms.count(8) == 2 and n_atoms.count(6) == 1: # It's a carboxylate group - return True if group == 'carboxylate' else False + if ( + group in ["carboxylate", "guanidine"] and atom.atomicnum == 6 + ): # It's a carbon atom + if ( + n_atoms.count(8) == 2 and n_atoms.count(6) == 1 + ): # It's a carboxylate group + return True if group == "carboxylate" else False elif n_atoms.count(7) == 3 and len(n_atoms) == 3: # It's a guanidine group nitro_partners = [] for nitro in pybel.ob.OBAtomAtomIter(atom.OBAtom): - nitro_partners.append(len([b_neighbor for b_neighbor in pybel.ob.OBAtomAtomIter(nitro)])) - if min(nitro_partners) == 1: # One nitrogen is only connected to the carbon, can pick up a H - return True if group == 'guanidine' else False - - if group == 'halocarbon' and atom.atomicnum in [9, 17, 35, 53]: # Halogen atoms - n_atoms = [na for na in pybel.ob.OBAtomAtomIter(atom.OBAtom) if na.GetAtomicNum() == 6] + nitro_partners.append( + len( + [ + b_neighbor + for b_neighbor in pybel.ob.OBAtomAtomIter(nitro) + ] + ) + ) + if ( + min(nitro_partners) == 1 + ): # One nitrogen is only connected to the carbon, can pick up a H + return True if group == "guanidine" else False + + if group == "halocarbon" and atom.atomicnum in [9, 17, 35, 53]: # Halogen atoms + n_atoms = [ + na + for na in pybel.ob.OBAtomAtomIter(atom.OBAtom) + if na.GetAtomicNum() == 6 + ] if len(n_atoms) == 1: # Halocarbon return True else: @@ -1108,18 +1633,32 @@ class Ligand(Mol): def find_hal(self, atoms): """Look for halogen bond donors (X-C, with X=F, Cl, Br, I)""" - data = namedtuple('hal_donor', 'x orig_x x_orig_idx c c_orig_idx') + data = namedtuple("hal_donor", "x orig_x x_orig_idx c c_orig_idx") a_set = [] for a in atoms: - if self.is_functional_group(a, 'halocarbon'): - n_atoms = [na for na in pybel.ob.OBAtomAtomIter(a.OBAtom) if na.GetAtomicNum() == 6] + if self.is_functional_group(a, "halocarbon"): + n_atoms = [ + na + for na in pybel.ob.OBAtomAtomIter(a.OBAtom) + if na.GetAtomicNum() == 6 + ] x_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid) orig_x = self.Mapper.id_to_atom(x_orig_idx) - c_orig_idx = [self.Mapper.mapid(na.GetIdx(), mtype=self.mtype, bsid=self.bsid) for na in n_atoms] - a_set.append(data(x=a, orig_x=orig_x, x_orig_idx=x_orig_idx, - c=pybel.Atom(n_atoms[0]), c_orig_idx=c_orig_idx)) + c_orig_idx = [ + self.Mapper.mapid(na.GetIdx(), mtype=self.mtype, bsid=self.bsid) + for na in n_atoms + ] + a_set.append( + data( + x=a, + orig_x=orig_x, + x_orig_idx=x_orig_idx, + c=pybel.Atom(n_atoms[0]), + c_orig_idx=c_orig_idx, + ) + ) if len(a_set) != 0: - logger.info(f'ligand contains {len(a_set)} halogen atom(s)') + logger.info(f"ligand contains {len(a_set)} halogen atom(s)") return a_set def find_charged(self, all_atoms): @@ -1128,76 +1667,189 @@ class Ligand(Mol): as mentioned in 'Cation-pi interactions in ligand recognition and catalysis' (Zacharias et al., 2002)). Identify negatively charged groups in the ligand. """ - data = namedtuple('lcharge', 'atoms orig_atoms atoms_orig_idx type center fgroup') + data = namedtuple( + "lcharge", "atoms orig_atoms atoms_orig_idx type center fgroup" + ) a_set = [] for a in all_atoms: a_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid) a_orig = self.Mapper.id_to_atom(a_orig_idx) - if self.is_functional_group(a, 'quartamine'): - a_set.append(data(atoms=[a, ], orig_atoms=[a_orig, ], atoms_orig_idx=[a_orig_idx, ], type='positive', - center=list(a.coords), fgroup='quartamine')) - elif self.is_functional_group(a, 'tertamine'): - a_set.append(data(atoms=[a, ], orig_atoms=[a_orig, ], atoms_orig_idx=[a_orig_idx, ], type='positive', - center=list(a.coords), - fgroup='tertamine')) - if self.is_functional_group(a, 'sulfonium'): - a_set.append(data(atoms=[a, ], orig_atoms=[a_orig, ], atoms_orig_idx=[a_orig_idx, ], type='positive', - center=list(a.coords), - fgroup='sulfonium')) - if self.is_functional_group(a, 'phosphate'): - a_contributing = [a, ] - a_contributing_orig_idx = [a_orig_idx, ] - [a_contributing.append(pybel.Atom(neighbor)) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom)] - [a_contributing_orig_idx.append(self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid)) - for neighbor in a_contributing] - orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx] + if self.is_functional_group(a, "quartamine"): + a_set.append( + data( + atoms=[a,], + orig_atoms=[a_orig,], + atoms_orig_idx=[a_orig_idx,], + type="positive", + center=list(a.coords), + fgroup="quartamine", + ) + ) + elif self.is_functional_group(a, "tertamine"): a_set.append( - data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, - type='negative', - center=a.coords, fgroup='phosphate')) - if self.is_functional_group(a, 'sulfonicacid'): - a_contributing = [a, ] - a_contributing_orig_idx = [a_orig_idx, ] - [a_contributing.append(pybel.Atom(neighbor)) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) if - neighbor.GetAtomicNum() == 8] - [a_contributing_orig_idx.append(self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid)) - for neighbor in a_contributing] - orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx] + data( + atoms=[a,], + orig_atoms=[a_orig,], + atoms_orig_idx=[a_orig_idx,], + type="positive", + center=list(a.coords), + fgroup="tertamine", + ) + ) + if self.is_functional_group(a, "sulfonium"): a_set.append( - data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, - type='negative', - center=a.coords, fgroup='sulfonicacid')) - elif self.is_functional_group(a, 'sulfate'): - a_contributing = [a, ] - a_contributing_orig_idx = [a_orig_idx, ] - [a_contributing_orig_idx.append(self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid)) - for neighbor in a_contributing] - [a_contributing.append(pybel.Atom(neighbor)) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom)] - orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx] + data( + atoms=[a,], + orig_atoms=[a_orig,], + atoms_orig_idx=[a_orig_idx,], + type="positive", + center=list(a.coords), + fgroup="sulfonium", + ) + ) + if self.is_functional_group(a, "phosphate"): + a_contributing = [ + a, + ] + a_contributing_orig_idx = [ + a_orig_idx, + ] + [ + a_contributing.append(pybel.Atom(neighbor)) + for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) + ] + [ + a_contributing_orig_idx.append( + self.Mapper.mapid( + neighbor.idx, mtype=self.mtype, bsid=self.bsid + ) + ) + for neighbor in a_contributing + ] + orig_contributing = [ + self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx + ] a_set.append( - data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, - type='negative', - center=a.coords, fgroup='sulfate')) - if self.is_functional_group(a, 'carboxylate'): - a_contributing = [pybel.Atom(neighbor) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) - if neighbor.GetAtomicNum() == 8] - a_contributing_orig_idx = [self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid) - for neighbor in a_contributing] - orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx] + data( + atoms=a_contributing, + orig_atoms=orig_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="negative", + center=a.coords, + fgroup="phosphate", + ) + ) + if self.is_functional_group(a, "sulfonicacid"): + a_contributing = [ + a, + ] + a_contributing_orig_idx = [ + a_orig_idx, + ] + [ + a_contributing.append(pybel.Atom(neighbor)) + for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) + if neighbor.GetAtomicNum() == 8 + ] + [ + a_contributing_orig_idx.append( + self.Mapper.mapid( + neighbor.idx, mtype=self.mtype, bsid=self.bsid + ) + ) + for neighbor in a_contributing + ] + orig_contributing = [ + self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx + ] a_set.append( - data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, - type='negative', - center=centroid([a.coords for a in a_contributing]), fgroup='carboxylate')) - elif self.is_functional_group(a, 'guanidine'): - a_contributing = [pybel.Atom(neighbor) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) - if neighbor.GetAtomicNum() == 7] - a_contributing_orig_idx = [self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid) - for neighbor in a_contributing] - orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx] + data( + atoms=a_contributing, + orig_atoms=orig_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="negative", + center=a.coords, + fgroup="sulfonicacid", + ) + ) + elif self.is_functional_group(a, "sulfate"): + a_contributing = [ + a, + ] + a_contributing_orig_idx = [ + a_orig_idx, + ] + [ + a_contributing_orig_idx.append( + self.Mapper.mapid( + neighbor.idx, mtype=self.mtype, bsid=self.bsid + ) + ) + for neighbor in a_contributing + ] + [ + a_contributing.append(pybel.Atom(neighbor)) + for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) + ] + orig_contributing = [ + self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx + ] a_set.append( - data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, - type='positive', - center=a.coords, fgroup='guanidine')) + data( + atoms=a_contributing, + orig_atoms=orig_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="negative", + center=a.coords, + fgroup="sulfate", + ) + ) + if self.is_functional_group(a, "carboxylate"): + a_contributing = [ + pybel.Atom(neighbor) + for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) + if neighbor.GetAtomicNum() == 8 + ] + a_contributing_orig_idx = [ + self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid) + for neighbor in a_contributing + ] + orig_contributing = [ + self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx + ] + a_set.append( + data( + atoms=a_contributing, + orig_atoms=orig_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="negative", + center=centroid([a.coords for a in a_contributing]), + fgroup="carboxylate", + ) + ) + elif self.is_functional_group(a, "guanidine"): + a_contributing = [ + pybel.Atom(neighbor) + for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) + if neighbor.GetAtomicNum() == 7 + ] + a_contributing_orig_idx = [ + self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid) + for neighbor in a_contributing + ] + orig_contributing = [ + self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx + ] + a_set.append( + data( + atoms=a_contributing, + orig_atoms=orig_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="positive", + center=a.coords, + fgroup="guanidine", + ) + ) return a_set def find_metal_binding(self, lig_atoms, water_oxygens): @@ -1206,67 +1858,173 @@ class Ligand(Mol): nitrogen from imidazole; sulfur from thiolate. """ a_set = [] - data = namedtuple('metal_binding', 'atom orig_atom atom_orig_idx type fgroup restype resnr reschain location') + data = namedtuple( + "metal_binding", + "atom orig_atom atom_orig_idx type fgroup restype resnr reschain location", + ) for oxygen in water_oxygens: - a_set.append(data(atom=oxygen.oxy, atom_orig_idx=oxygen.oxy_orig_idx, type='O', fgroup='water', - restype=whichrestype(oxygen.oxy), resnr=whichresnumber(oxygen.oxy), - reschain=whichchain(oxygen.oxy), location='water', - orig_atom=self.Mapper.id_to_atom(oxygen.oxy_orig_idx))) + a_set.append( + data( + atom=oxygen.oxy, + atom_orig_idx=oxygen.oxy_orig_idx, + type="O", + fgroup="water", + restype=whichrestype(oxygen.oxy), + resnr=whichresnumber(oxygen.oxy), + reschain=whichchain(oxygen.oxy), + location="water", + orig_atom=self.Mapper.id_to_atom(oxygen.oxy_orig_idx), + ) + ) # #@todo Refactor code for a in lig_atoms: - a_orig_idx = self.Mapper.mapid(a.idx, mtype='ligand', bsid=self.bsid) + a_orig_idx = self.Mapper.mapid(a.idx, mtype="ligand", bsid=self.bsid) n_atoms = pybel.ob.OBAtomAtomIter(a.OBAtom) # Neighboring atoms # All atomic numbers of neighboring atoms - n_atoms_atomicnum = [n.GetAtomicNum() for n in pybel.ob.OBAtomAtomIter(a.OBAtom)] + n_atoms_atomicnum = [ + n.GetAtomicNum() for n in pybel.ob.OBAtomAtomIter(a.OBAtom) + ] if a.atomicnum == 8: # Oxygen - if n_atoms_atomicnum.count('1') == 1 and len(n_atoms_atomicnum) == 2: # Oxygen in alcohol (R-[O]-H) - a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='O', fgroup='alcohol', - restype=self.hetid, resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) - if True in [n.IsAromatic() for n in n_atoms] and not a.OBAtom.IsAromatic(): # Phenolate oxygen - a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='O', fgroup='phenolate', - restype=self.hetid, resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + if ( + n_atoms_atomicnum.count("1") == 1 and len(n_atoms_atomicnum) == 2 + ): # Oxygen in alcohol (R-[O]-H) + a_set.append( + data( + atom=a, + atom_orig_idx=a_orig_idx, + type="O", + fgroup="alcohol", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) + if ( + True in [n.IsAromatic() for n in n_atoms] + and not a.OBAtom.IsAromatic() + ): # Phenolate oxygen + a_set.append( + data( + atom=a, + atom_orig_idx=a_orig_idx, + type="O", + fgroup="phenolate", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) if a.atomicnum == 6: # It's a carbon atom - if n_atoms_atomicnum.count(8) == 2 and n_atoms_atomicnum.count(6) == 1: # It's a carboxylate group + if ( + n_atoms_atomicnum.count(8) == 2 and n_atoms_atomicnum.count(6) == 1 + ): # It's a carboxylate group for neighbor in [n for n in n_atoms if n.GetAtomicNum() == 8]: - neighbor_orig_idx = self.Mapper.mapid(neighbor.GetIdx(), mtype='ligand', bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(neighbor), atom_orig_idx=neighbor_orig_idx, type='O', - fgroup='carboxylate', - restype=self.hetid, - resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + neighbor_orig_idx = self.Mapper.mapid( + neighbor.GetIdx(), mtype="ligand", bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(neighbor), + atom_orig_idx=neighbor_orig_idx, + type="O", + fgroup="carboxylate", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) if a.atomicnum == 15: # It's a phosphor atom if n_atoms_atomicnum.count(8) >= 3: # It's a phosphoryl for neighbor in [n for n in n_atoms if n.GetAtomicNum() == 8]: - neighbor_orig_idx = self.Mapper.mapid(neighbor.GetIdx(), mtype='ligand', bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(neighbor), atom_orig_idx=neighbor_orig_idx, type='O', - fgroup='phosphoryl', - restype=self.hetid, - resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) - if n_atoms_atomicnum.count(8) == 2: # It's another phosphor-containing group #@todo (correct name?) + neighbor_orig_idx = self.Mapper.mapid( + neighbor.GetIdx(), mtype="ligand", bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(neighbor), + atom_orig_idx=neighbor_orig_idx, + type="O", + fgroup="phosphoryl", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) + if ( + n_atoms_atomicnum.count(8) == 2 + ): # It's another phosphor-containing group #@todo (correct name?) for neighbor in [n for n in n_atoms if n.GetAtomicNum() == 8]: - neighbor_orig_idx = self.Mapper.mapid(neighbor.GetIdx(), mtype='ligand', bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(neighbor), atom_orig_idx=neighbor_orig_idx, type='O', - fgroup='phosphor.other', restype=self.hetid, - resnr=self.position, - reschain=self.chain, location='ligand', - orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + neighbor_orig_idx = self.Mapper.mapid( + neighbor.GetIdx(), mtype="ligand", bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(neighbor), + atom_orig_idx=neighbor_orig_idx, + type="O", + fgroup="phosphor.other", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) if a.atomicnum == 7: # It's a nitrogen atom if n_atoms_atomicnum.count(6) == 2: # It's imidazole/pyrrole or similar - a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='N', fgroup='imidazole/pyrrole', - restype=self.hetid, resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + a_set.append( + data( + atom=a, + atom_orig_idx=a_orig_idx, + type="N", + fgroup="imidazole/pyrrole", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) if a.atomicnum == 16: # It's a sulfur atom - if True in [n.IsAromatic() for n in n_atoms] and not a.OBAtom.IsAromatic(): # Thiolate - a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='S', fgroup='thiolate', - restype=self.hetid, resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + if ( + True in [n.IsAromatic() for n in n_atoms] + and not a.OBAtom.IsAromatic() + ): # Thiolate + a_set.append( + data( + atom=a, + atom_orig_idx=a_orig_idx, + type="S", + fgroup="thiolate", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) if set(n_atoms_atomicnum) == {26}: # Sulfur in Iron sulfur cluster - a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='S', fgroup='iron-sulfur.cluster', - restype=self.hetid, resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + a_set.append( + data( + atom=a, + atom_orig_idx=a_orig_idx, + type="S", + fgroup="iron-sulfur.cluster", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) return a_set @@ -1278,43 +2036,54 @@ class PDBComplex: """ def __init__(self): - self.interaction_sets = {} # Dictionary with site identifiers as keys and object as value + self.interaction_sets = ( + {} + ) # Dictionary with site identifiers as keys and object as value self.protcomplex = None self.filetype = None self.atoms = {} # Dictionary of Pybel atoms, accessible by their idx self.sourcefiles = {} self.information = {} - self.corrected_pdb = '' + self.corrected_pdb = "" self._output_path = tempfile.gettempdir() self.pymol_name = None self.modres = set() self.resis = [] self.altconf = [] # Atom idx of atoms with alternate conformations - self.covalent = [] # Covalent linkages between ligands and protein residues/other ligands + self.covalent = ( + [] + ) # Covalent linkages between ligands and protein residues/other ligands self.excluded = [] # Excluded ligands self.Mapper = Mapper() self.ligands = [] def __str__(self): - formatted_lig_names = [":".join([x.hetid, x.chain, str(x.position)]) for x in self.ligands] + formatted_lig_names = [ + ":".join([x.hetid, x.chain, str(x.position)]) for x in self.ligands + ] return "Protein structure %s with ligands:\n" % (self.pymol_name) + "\n".join( - [lig for lig in formatted_lig_names]) + [lig for lig in formatted_lig_names] + ) def load_pdb(self, pdbpath, as_string=False): """Loads a pdb file with protein AND ligand(s), separates and prepares them. If specified 'as_string', the input is a PDB string instead of a path.""" if as_string: - self.sourcefiles['pdbcomplex.original'] = None - self.sourcefiles['pdbcomplex'] = None - self.sourcefiles['pdbstring'] = pdbpath + self.sourcefiles["pdbcomplex.original"] = None + self.sourcefiles["pdbcomplex"] = None + self.sourcefiles["pdbstring"] = pdbpath else: - self.sourcefiles['pdbcomplex.original'] = pdbpath - self.sourcefiles['pdbcomplex'] = pdbpath - self.information['pdbfixes'] = False - pdbparser = PDBParser(pdbpath, as_string=as_string) # Parse PDB file to find errors and get additional data + self.sourcefiles["pdbcomplex.original"] = pdbpath + self.sourcefiles["pdbcomplex"] = pdbpath + self.information["pdbfixes"] = False + pdbparser = PDBParser( + pdbpath, as_string=as_string + ) # Parse PDB file to find errors and get additional data # #@todo Refactor and rename here self.Mapper.proteinmap = pdbparser.proteinmap - self.Mapper.reversed_proteinmap = {v: k for k, v in self.Mapper.proteinmap.items()} + self.Mapper.reversed_proteinmap = { + v: k for k, v in self.Mapper.proteinmap.items() + } self.modres = pdbparser.modres self.covalent = pdbparser.covalent self.altconf = pdbparser.altconformations @@ -1322,78 +2091,103 @@ class PDBComplex: if not config.PLUGIN_MODE: if pdbparser.num_fixed_lines > 0: - logger.info(f'{pdbparser.num_fixed_lines} lines automatically fixed in PDB input file') + logger.info( + f"{pdbparser.num_fixed_lines} lines automatically fixed in PDB input file" + ) # Save modified PDB file if not as_string: - basename = os.path.basename(pdbpath).split('.')[0] + basename = os.path.basename(pdbpath).split(".")[0] else: basename = "from_stdin" - pdbpath_fixed = tmpfile(prefix='plipfixed.' + basename + '_', direc=self.output_path) + pdbpath_fixed = tmpfile( + prefix="plipfixed." + basename + "_", direc=self.output_path + ) create_folder_if_not_exists(self.output_path) - self.sourcefiles['pdbcomplex'] = pdbpath_fixed - self.corrected_pdb = re.sub(r'[^\x00-\x7F]+', ' ', self.corrected_pdb) # Strip non-unicode chars - if not config.NOFIXFILE: # Only write to file if this option is not activated - with open(pdbpath_fixed, 'w') as f: + self.sourcefiles["pdbcomplex"] = pdbpath_fixed + self.corrected_pdb = re.sub( + r"[^\x00-\x7F]+", " ", self.corrected_pdb + ) # Strip non-unicode chars + if ( + not config.NOFIXFILE + ): # Only write to file if this option is not activated + with open(pdbpath_fixed, "w") as f: f.write(self.corrected_pdb) - self.information['pdbfixes'] = True + self.information["pdbfixes"] = True if not as_string: - self.sourcefiles['filename'] = os.path.basename(self.sourcefiles['pdbcomplex']) + self.sourcefiles["filename"] = os.path.basename( + self.sourcefiles["pdbcomplex"] + ) self.protcomplex, self.filetype = read_pdb(self.corrected_pdb, as_string=True) # Update the model in the Mapper class instance self.Mapper.original_structure = self.protcomplex.OBMol - logger.info('PDB structure successfully read') + logger.info("PDB structure successfully read") # Determine (temporary) PyMOL Name from Filename - self.pymol_name = pdbpath.split('/')[-1].split('.')[0] + '-Protein' + self.pymol_name = pdbpath.split("/")[-1].split(".")[0] + "-Protein" # Replace characters causing problems in PyMOL - self.pymol_name = self.pymol_name.replace(' ', '').replace('(', '').replace(')', '').replace('-', '_') + self.pymol_name = ( + self.pymol_name.replace(" ", "") + .replace("(", "") + .replace(")", "") + .replace("-", "_") + ) # But if possible, name it after PDBID in Header - if 'HEADER' in self.protcomplex.data: # If the PDB file has a proper header - potential_name = self.protcomplex.data['HEADER'][56:60].lower() - if extract_pdbid(potential_name) != 'UnknownProtein': + if "HEADER" in self.protcomplex.data: # If the PDB file has a proper header + potential_name = self.protcomplex.data["HEADER"][56:60].lower() + if extract_pdbid(potential_name) != "UnknownProtein": self.pymol_name = potential_name - logger.debug(f'PyMOL name set as: {self.pymol_name}') + logger.debug(f"PyMOL name set as: {self.pymol_name}") # Extract and prepare ligands - ligandfinder = LigandFinder(self.protcomplex, self.altconf, self.modres, self.covalent, self.Mapper) + ligandfinder = LigandFinder( + self.protcomplex, self.altconf, self.modres, self.covalent, self.Mapper + ) self.ligands = ligandfinder.ligands self.excluded = ligandfinder.excluded # decide whether to add polar hydrogens if not config.NOHYDRO: if not as_string: - basename = os.path.basename(pdbpath).split('.')[0] + basename = os.path.basename(pdbpath).split(".")[0] else: basename = "from_stdin" self.protcomplex.OBMol.AddPolarHydrogens() - output_path = os.path.join(self._output_path, f'{basename}_protonated.pdb') - self.protcomplex.write('pdb', output_path, overwrite=True) - logger.info(f'protonated structure written to {output_path}') + output_path = os.path.join(self._output_path, f"{basename}_protonated.pdb") + self.protcomplex.write("pdb", output_path, overwrite=True) + logger.info(f"protonated structure written to {output_path}") else: - logger.warning('no polar hydrogens will be assigned (make sure your structure contains hydrogens)') + logger.warning( + "no polar hydrogens will be assigned (make sure your structure contains hydrogens)" + ) for atm in self.protcomplex: self.atoms[atm.idx] = atm if len(self.excluded) != 0: - logger.info(f'excluded molecules as ligands: {self.excluded}') + logger.info(f"excluded molecules as ligands: {self.excluded}") if config.DNARECEPTOR: - self.resis = [obres for obres in pybel.ob.OBResidueIter( - self.protcomplex.OBMol) if obres.GetName() in config.DNA + config.RNA] + self.resis = [ + obres + for obres in pybel.ob.OBResidueIter(self.protcomplex.OBMol) + if obres.GetName() in config.DNA + config.RNA + ] else: - self.resis = [obres for obres in pybel.ob.OBResidueIter( - self.protcomplex.OBMol) if obres.GetResidueProperty(0)] + self.resis = [ + obres + for obres in pybel.ob.OBResidueIter(self.protcomplex.OBMol) + if obres.GetResidueProperty(0) + ] num_ligs = len(self.ligands) if num_ligs == 1: - logger.info('analyzing one ligand') + logger.info("analyzing one ligand") elif num_ligs > 1: - logger.info(f'analyzing {num_ligs} ligands') + logger.info(f"analyzing {num_ligs} ligands") else: - logger.info(f'structure contains no ligands') + logger.info(f"structure contains no ligands") def analyze(self): """Triggers analysis of all complexes in structure""" @@ -1405,42 +2199,66 @@ class PDBComplex: single_sites = [] for member in ligand.members: - single_sites.append(':'.join([str(x) for x in member])) - site = ' + '.join(single_sites) - site = site if not len(site) > 20 else site[:20] + '...' - longname = ligand.longname if not len(ligand.longname) > 20 else ligand.longname[:20] + '...' - ligtype = 'unspecified type' if ligand.type == 'UNSPECIFIED' else ligand.type - ligtext = f'{longname} [{ligtype}] -- {site}' - logger.info(f'processing ligand {ligtext}') - if ligtype == 'PEPTIDE': - logger.info(f'chain {ligand.chain} will be processed in [PEPTIDE / INTER-CHAIN] mode') - if ligtype == 'INTRA': - logger.info(f'chain {ligand.chain} will be processed in [INTRA-CHAIN] mode') - any_in_biolip = len(set([x[0] for x in ligand.members]).intersection(config.biolip_list)) != 0 - - if ligtype not in ['POLYMER', 'DNA', 'ION', 'DNA+ION', 'RNA+ION', 'SMALLMOLECULE+ION'] and any_in_biolip: - logger.info('may be biologically irrelevant') + single_sites.append(":".join([str(x) for x in member])) + site = " + ".join(single_sites) + site = site if not len(site) > 20 else site[:20] + "..." + longname = ( + ligand.longname + if not len(ligand.longname) > 20 + else ligand.longname[:20] + "..." + ) + ligtype = "unspecified type" if ligand.type == "UNSPECIFIED" else ligand.type + ligtext = f"{longname} [{ligtype}] -- {site}" + logger.info(f"processing ligand {ligtext}") + if ligtype == "PEPTIDE": + logger.info( + f"chain {ligand.chain} will be processed in [PEPTIDE / INTER-CHAIN] mode" + ) + if ligtype == "INTRA": + logger.info(f"chain {ligand.chain} will be processed in [INTRA-CHAIN] mode") + any_in_biolip = ( + len(set([x[0] for x in ligand.members]).intersection(config.biolip_list)) + != 0 + ) + + if ( + ligtype + not in ["POLYMER", "DNA", "ION", "DNA+ION", "RNA+ION", "SMALLMOLECULE+ION"] + and any_in_biolip + ): + logger.info("may be biologically irrelevant") lig_obj = Ligand(self, ligand) cutoff = lig_obj.max_dist_to_center + config.BS_DIST bs_res = self.extract_bs(cutoff, lig_obj.centroid, self.resis) # Get a list of all atoms belonging to the binding site, search by idx - bs_atoms = [self.atoms[idx] for idx in [i for i in self.atoms.keys() - if self.atoms[i].OBAtom.GetResidue().GetIdx() in bs_res] - if idx in self.Mapper.proteinmap and self.Mapper.mapid(idx, mtype='protein') not in self.altconf] - if ligand.type == 'PEPTIDE': + bs_atoms = [ + self.atoms[idx] + for idx in [ + i + for i in self.atoms.keys() + if self.atoms[i].OBAtom.GetResidue().GetIdx() in bs_res + ] + if idx in self.Mapper.proteinmap + and self.Mapper.mapid(idx, mtype="protein") not in self.altconf + ] + if ligand.type == "PEPTIDE": # If peptide, don't consider the peptide chain as part of the protein binding site - bs_atoms = [a for a in bs_atoms if a.OBAtom.GetResidue().GetChain() != lig_obj.chain] - if ligand.type == 'INTRA': + bs_atoms = [ + a for a in bs_atoms if a.OBAtom.GetResidue().GetChain() != lig_obj.chain + ] + if ligand.type == "INTRA": # Interactions within the chain - bs_atoms = [a for a in bs_atoms if a.OBAtom.GetResidue().GetChain() == lig_obj.chain] + bs_atoms = [ + a for a in bs_atoms if a.OBAtom.GetResidue().GetChain() == lig_obj.chain + ] bs_atoms_refined = [] # Create hash with BSRES -> (MINDIST_TO_LIG, AA_TYPE) # and refine binding site atom selection with exact threshold min_dist = {} for r in bs_atoms: - bs_res_id = ''.join([str(whichresnumber(r)), whichchain(r)]) + bs_res_id = "".join([str(whichresnumber(r)), whichchain(r)]) for l in ligand.mol.atoms: distance = euclidean3d(r.coords, l.coords) if bs_res_id not in min_dist: @@ -1450,25 +2268,40 @@ class PDBComplex: if distance <= config.BS_DIST and r not in bs_atoms_refined: bs_atoms_refined.append(r) num_bs_atoms = len(bs_atoms_refined) - logger.info(f'binding site atoms in vicinity ({config.BS_DIST} A max. dist: {num_bs_atoms})') - - bs_obj = BindingSite(bs_atoms_refined, self.protcomplex, self, self.altconf, min_dist, self.Mapper) + logger.info( + f"binding site atoms in vicinity ({config.BS_DIST} A max. dist: {num_bs_atoms})" + ) + + bs_obj = BindingSite( + bs_atoms_refined, + self.protcomplex, + self, + self.altconf, + min_dist, + self.Mapper, + ) pli_obj = PLInteraction(lig_obj, bs_obj, self) self.interaction_sets[ligand.mol.title] = pli_obj def extract_bs(self, cutoff, ligcentroid, resis): """Return list of ids from residues belonging to the binding site""" - return [obres.GetIdx() for obres in resis if self.res_belongs_to_bs(obres, cutoff, ligcentroid)] + return [ + obres.GetIdx() + for obres in resis + if self.res_belongs_to_bs(obres, cutoff, ligcentroid) + ] def res_belongs_to_bs(self, res, cutoff, ligcentroid): """Check for each residue if its centroid is within a certain distance to the ligand centroid. Additionally checks if a residue belongs to a chain restricted by the user (e.g. by defining a peptide chain)""" - rescentroid = centroid([(atm.x(), atm.y(), atm.z()) for atm in pybel.ob.OBResidueAtomIter(res)]) + rescentroid = centroid( + [(atm.x(), atm.y(), atm.z()) for atm in pybel.ob.OBResidueAtomIter(res)] + ) # Check geometry near_enough = True if euclidean3d(rescentroid, ligcentroid) < cutoff else False # Check chain membership restricted_chain = True if res.GetChain() in config.PEPTIDES else False - return (near_enough and not restricted_chain) + return near_enough and not restricted_chain def get_atom(self, idx): return self.atoms[idx] diff --git a/plip/test/test_command_line.py b/plip/test/test_command_line.py index d3ab332..b561997 100644 --- a/plip/test/test_command_line.py +++ b/plip/test/test_command_line.py @@ -20,35 +20,46 @@ class CommandLineTest(unittest.TestCase): def test_empty_input_file(self): """Input file is empty.""" - exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -f ./special/empty.pdb -o {self.tmp_dir.name}', - shell=True) + exitcode = subprocess.call( + f"{sys.executable} ../plipcmd.py -f ./special/empty.pdb -o {self.tmp_dir.name}", + shell=True, + ) self.assertEqual(exitcode, 1) def test_invalid_pdb_id(self): """A PDB ID with no valid PDB record is provided.""" - exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -i xx1x -o {self.tmp_dir.name}', shell=True) + exitcode = subprocess.call( + f"{sys.executable} ../plipcmd.py -i xx1x -o {self.tmp_dir.name}", shell=True + ) self.assertEqual(exitcode, 1) def test_invalid_input_file(self): """A file is provided which is not a PDB file.""" - exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -f ./special/non-pdb.pdb -o {self.tmp_dir.name}', - shell=True) + exitcode = subprocess.call( + f"{sys.executable} ../plipcmd.py -f ./special/non-pdb.pdb -o {self.tmp_dir.name}", + shell=True, + ) self.assertEqual(exitcode, 1) def test_pdb_format_not_available(self): """A valid PDB ID is provided, but there is no entry in PDB format from wwPDB""" - exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -i 4v59 -o {self.tmp_dir.name}', shell=True) + exitcode = subprocess.call( + f"{sys.executable} ../plipcmd.py -i 4v59 -o {self.tmp_dir.name}", shell=True + ) self.assertEqual(exitcode, 1) def test_valid_pdb(self): """A PDB ID with no valid PDB record is provided.""" - exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -x -f ./pdb/1eve.pdb -o {self.tmp_dir.name}', - shell=True) + exitcode = subprocess.call( + f"{sys.executable} ../plipcmd.py -x -f ./pdb/1eve.pdb -o {self.tmp_dir.name}", + shell=True, + ) self.assertEqual(len(os.listdir(self.tmp_dir.name)), 2) self.assertEqual(exitcode, 0) def test_stdout(self): """A PDB ID with no valid PDB record is provided.""" - exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -t -f ./pdb/1eve.pdb -O', shell=True) + exitcode = subprocess.call( + f"{sys.executable} ../plipcmd.py -t -f ./pdb/1eve.pdb -O", shell=True + ) self.assertEqual(exitcode, 0) - diff --git a/plip/test/test_hydrogen_bonds.py b/plip/test/test_hydrogen_bonds.py index 75cae6c..f673c6e 100644 --- a/plip/test/test_hydrogen_bonds.py +++ b/plip/test/test_hydrogen_bonds.py @@ -8,31 +8,35 @@ def characterize_complex(pdb_file: str, binding_site_id: str) -> PLInteraction: pdb_complex = PDBComplex() pdb_complex.load_pdb(pdb_file) for ligand in pdb_complex.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == binding_site_id: + if ( + ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) + == binding_site_id + ): pdb_complex.characterize_complex(ligand) return pdb_complex.interaction_sets[binding_site_id] class HydrogenBondTestCase(unittest.TestCase): - def test_4dst_nondeterministic_protonation(self): config.NOHYDRO = False for i in range(0, 10): - interactions = characterize_complex('./pdb/4dst.pdb', 'GCP:A:202') + interactions = characterize_complex("./pdb/4dst.pdb", "GCP:A:202") all_hbonds = interactions.hbonds_ldon + interactions.hbonds_pdon self.assertTrue(len(all_hbonds) == 16 or len(all_hbonds) == 17) def test_4dst_deterministic_protonation(self): config.NOHYDRO = True for i in range(0, 10): - interactions = characterize_complex('./pdb/4dst_protonated.pdb', 'GCP:A:202') + interactions = characterize_complex( + "./pdb/4dst_protonated.pdb", "GCP:A:202" + ) all_hbonds = interactions.hbonds_ldon + interactions.hbonds_pdon self.assertTrue(len(all_hbonds) == 16) def test_no_protonation(self): config.NOHYDRO = True - interactions1 = characterize_complex('./pdb/1x0n_state_1.pdb', 'DTF:A:174') + interactions1 = characterize_complex("./pdb/1x0n_state_1.pdb", "DTF:A:174") self.assertEqual(len(interactions1.hbonds_ldon), 0) config.NOHYDRO = False - interactions2 = characterize_complex('./pdb/1x0n_state_1.pdb', 'DTF:A:174') - self.assertEqual(len(interactions2.hbonds_ldon), 1)
\ No newline at end of file + interactions2 = characterize_complex("./pdb/1x0n_state_1.pdb", "DTF:A:174") + self.assertEqual(len(interactions2.hbonds_ldon), 1) |