diff options
Diffstat (limited to 'plip/basic')
| -rw-r--r-- | plip/basic/config.py | 606 | ||||
| -rw-r--r-- | plip/basic/logger.py | 8 | ||||
| -rw-r--r-- | plip/basic/parallel.py | 6 | ||||
| -rw-r--r-- | plip/basic/remote.py | 132 | ||||
| -rw-r--r-- | plip/basic/supplemental.py | 156 |
5 files changed, 753 insertions, 155 deletions
diff --git a/plip/basic/config.py b/plip/basic/config.py index a7468cf..3770d44 100644 --- a/plip/basic/config.py +++ b/plip/basic/config.py @@ -1,5 +1,5 @@ -__version__ = '2.1.0-beta' -__maintainer__ = 'PharmAI GmbH (2020) - www.pharm.ai - hello@pharm.ai' +__version__ = "2.1.0-beta" +__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/basic/logger.py b/plip/basic/logger.py index ca65411..f15650e 100644 --- a/plip/basic/logger.py +++ b/plip/basic/logger.py @@ -8,14 +8,16 @@ def get_logger(): """ frame = inspect.stack()[1] module_name = inspect.getmodule(frame[0]).__name__ - if module_name != '__main__': + if module_name != "__main__": logger = logging.getLogger(module_name) if not logger.parent.handlers: ch = logging.StreamHandler() - formatter = logging.Formatter('%(asctime)s [%(levelname)s] [%(filename)s:%(lineno)d] %(name)s: %(message)s') + formatter = logging.Formatter( + "%(asctime)s [%(levelname)s] [%(filename)s:%(lineno)d] %(name)s: %(message)s" + ) ch.setFormatter(formatter) logger.parent.addHandler(ch) else: - logger = logging.getLogger('plip') + logger = logging.getLogger("plip") return logger diff --git a/plip/basic/parallel.py b/plip/basic/parallel.py index 1f71943..cd0b93b 100644 --- a/plip/basic/parallel.py +++ b/plip/basic/parallel.py @@ -34,9 +34,9 @@ def parallel_fn(f): def simple_parallel(func, sequence, **args): """ f takes an element of sequence as input and the keyword args in **args""" - if 'processes' in args: - processes = args.get('processes') - del args['processes'] + if "processes" in args: + processes = args.get("processes") + del args["processes"] else: processes = multiprocessing.cpu_count() diff --git a/plip/basic/remote.py b/plip/basic/remote.py index 0c67f6f..18de4b7 100644 --- a/plip/basic/remote.py +++ b/plip/basic/remote.py @@ -1,14 +1,23 @@ from collections import namedtuple -hbonds_info = namedtuple('hbonds_info', 'ldon_id lig_don_id prot_acc_id pdon_id prot_don_id lig_acc_id') -hydrophobic_info = namedtuple('hydrophobic_info', 'bs_ids lig_ids pairs_ids') -halogen_info = namedtuple('halogen_info', 'don_id acc_id') -pistack_info = namedtuple('pistack_info', 'proteinring_atoms, proteinring_center ligandring_atoms ' - 'ligandring_center type') -pication_info = namedtuple('pication_info', 'ring_center charge_center ring_atoms charge_atoms, protcharged') -sbridge_info = namedtuple('sbridge_info', 'positive_atoms negative_atoms positive_center negative_center protispos') -wbridge_info = namedtuple('wbridge_info', 'don_id acc_id water_id protisdon') -metal_info = namedtuple('metal_info', 'metal_id, target_id location') +hbonds_info = namedtuple( + "hbonds_info", "ldon_id lig_don_id prot_acc_id pdon_id prot_don_id lig_acc_id" +) +hydrophobic_info = namedtuple("hydrophobic_info", "bs_ids lig_ids pairs_ids") +halogen_info = namedtuple("halogen_info", "don_id acc_id") +pistack_info = namedtuple( + "pistack_info", + "proteinring_atoms, proteinring_center ligandring_atoms " "ligandring_center type", +) +pication_info = namedtuple( + "pication_info", "ring_center charge_center ring_atoms charge_atoms, protcharged" +) +sbridge_info = namedtuple( + "sbridge_info", + "positive_atoms negative_atoms positive_center negative_center protispos", +) +wbridge_info = namedtuple("wbridge_info", "don_id acc_id water_id protisdon") +metal_info = namedtuple("metal_info", "metal_id, target_id location") class VisualizerData: @@ -21,7 +30,7 @@ class VisualizerData: # General Information self.lig_members = sorted(pli.ligand.members) - self.sourcefile = pcomp.sourcefiles['pdbcomplex'] + self.sourcefile = pcomp.sourcefiles["pdbcomplex"] self.corrected_pdb = pcomp.corrected_pdb self.pdbid = mol.pymol_name self.hetid = ligand.hetid @@ -39,57 +48,88 @@ class VisualizerData: # Hydrophobic Contacts # Contains IDs of contributing binding site, ligand atoms and the pairings - hydroph_pairs_id = [(h.bsatom_orig_idx, h.ligatom_orig_idx) for h in pli.hydrophobic_contacts] - self.hydrophobic_contacts = hydrophobic_info(bs_ids=[hp[0] for hp in hydroph_pairs_id], - lig_ids=[hp[1] for hp in hydroph_pairs_id], - pairs_ids=hydroph_pairs_id) + hydroph_pairs_id = [ + (h.bsatom_orig_idx, h.ligatom_orig_idx) for h in pli.hydrophobic_contacts + ] + self.hydrophobic_contacts = hydrophobic_info( + bs_ids=[hp[0] for hp in hydroph_pairs_id], + lig_ids=[hp[1] for hp in hydroph_pairs_id], + pairs_ids=hydroph_pairs_id, + ) # Hydrogen Bonds # #@todo Don't use indices, simplify this code here hbonds_ldon, hbonds_pdon = pli.hbonds_ldon, pli.hbonds_pdon hbonds_ldon_id = [(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_ldon] hbonds_pdon_id = [(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_pdon] - self.hbonds = hbonds_info(ldon_id=[(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_ldon], - lig_don_id=[hb[1] for hb in hbonds_ldon_id], - prot_acc_id=[hb[0] for hb in hbonds_ldon_id], - pdon_id=[(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_pdon], - prot_don_id=[hb[1] for hb in hbonds_pdon_id], - lig_acc_id=[hb[0] for hb in hbonds_pdon_id]) + self.hbonds = hbonds_info( + ldon_id=[(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_ldon], + lig_don_id=[hb[1] for hb in hbonds_ldon_id], + prot_acc_id=[hb[0] for hb in hbonds_ldon_id], + pdon_id=[(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_pdon], + prot_don_id=[hb[1] for hb in hbonds_pdon_id], + lig_acc_id=[hb[0] for hb in hbonds_pdon_id], + ) # Halogen Bonds - self.halogen_bonds = [halogen_info(don_id=h.don_orig_idx, acc_id=h.acc_orig_idx) - for h in pli.halogen_bonds] + self.halogen_bonds = [ + halogen_info(don_id=h.don_orig_idx, acc_id=h.acc_orig_idx) + for h in pli.halogen_bonds + ] # Pistacking - self.pistacking = [pistack_info(proteinring_atoms=pistack.proteinring.atoms_orig_idx, - proteinring_center=pistack.proteinring.center, - ligandring_atoms=pistack.ligandring.atoms_orig_idx, - ligandring_center=pistack.ligandring.center, - type=pistack.type) for pistack in pli.pistacking] + self.pistacking = [ + pistack_info( + proteinring_atoms=pistack.proteinring.atoms_orig_idx, + proteinring_center=pistack.proteinring.center, + ligandring_atoms=pistack.ligandring.atoms_orig_idx, + ligandring_center=pistack.ligandring.center, + type=pistack.type, + ) + for pistack in pli.pistacking + ] # Pi-cation interactions - self.pication = [pication_info(ring_center=picat.ring.center, - charge_center=picat.charge.center, - ring_atoms=picat.ring.atoms_orig_idx, - charge_atoms=picat.charge.atoms_orig_idx, - protcharged=picat.protcharged) - for picat in pli.pication_paro + pli.pication_laro] + self.pication = [ + pication_info( + ring_center=picat.ring.center, + charge_center=picat.charge.center, + ring_atoms=picat.ring.atoms_orig_idx, + charge_atoms=picat.charge.atoms_orig_idx, + protcharged=picat.protcharged, + ) + for picat in pli.pication_paro + pli.pication_laro + ] # Salt Bridges - self.saltbridges = [sbridge_info(positive_atoms=sbridge.positive.atoms_orig_idx, - negative_atoms=sbridge.negative.atoms_orig_idx, - positive_center=sbridge.positive.center, - negative_center=sbridge.negative.center, - protispos=sbridge.protispos) - for sbridge in pli.saltbridge_lneg + pli.saltbridge_pneg] + self.saltbridges = [ + sbridge_info( + positive_atoms=sbridge.positive.atoms_orig_idx, + negative_atoms=sbridge.negative.atoms_orig_idx, + positive_center=sbridge.positive.center, + negative_center=sbridge.negative.center, + protispos=sbridge.protispos, + ) + for sbridge in pli.saltbridge_lneg + pli.saltbridge_pneg + ] # Water Bridgese('wbridge_info', 'don_id acc_id water_id protisdon') - self.waterbridges = [wbridge_info(don_id=wbridge.d_orig_idx, - acc_id=wbridge.a_orig_idx, - water_id=wbridge.water_orig_idx, - protisdon=wbridge.protisdon) for wbridge in pli.water_bridges] + self.waterbridges = [ + wbridge_info( + don_id=wbridge.d_orig_idx, + acc_id=wbridge.a_orig_idx, + water_id=wbridge.water_orig_idx, + protisdon=wbridge.protisdon, + ) + for wbridge in pli.water_bridges + ] # Metal Complexes - self.metal_complexes = [metal_info(metal_id=metalc.metal_orig_idx, - target_id=metalc.target_orig_idx, - location=metalc.location) for metalc in pli.metal_complexes] + self.metal_complexes = [ + metal_info( + metal_id=metalc.metal_orig_idx, + target_id=metalc.target_orig_idx, + location=metalc.location, + ) + for metalc in pli.metal_complexes + ] diff --git a/plip/basic/supplemental.py b/plip/basic/supplemental.py index 6b3ef7b..7164497 100644 --- a/plip/basic/supplemental.py +++ b/plip/basic/supplemental.py @@ -18,22 +18,24 @@ from plip.basic import config, logger logger = logger.get_logger() # Windows and MacOS -if os.name != 'nt' and platform.system() != 'Darwin': # Resource module not available for Windows +if ( + os.name != "nt" and platform.system() != "Darwin" +): # Resource module not available for Windows import resource # Settings -np.seterr(all='ignore') # No runtime warnings +np.seterr(all="ignore") # No runtime warnings def tmpfile(prefix, direc): """Returns the path to a newly created temporary file.""" - return tempfile.mktemp(prefix=prefix, suffix='.pdb', dir=direc) + return tempfile.mktemp(prefix=prefix, suffix=".pdb", dir=direc) def is_lig(hetid): """Checks if a PDB compound can be excluded as a small molecule ligand""" h = hetid.upper() - return not (h == 'HOH' or h in config.UNSUPPORTED) + return not (h == "HOH" or h in config.UNSUPPORTED) def extract_pdbid(string): @@ -48,19 +50,25 @@ def extract_pdbid(string): def whichrestype(atom): """Returns the residue name of an Pybel or OpenBabel atom.""" - atom = atom if not isinstance(atom, Atom) else atom.OBAtom # Convert to OpenBabel Atom + atom = ( + atom if not isinstance(atom, Atom) else atom.OBAtom + ) # Convert to OpenBabel Atom return atom.GetResidue().GetName() if atom.GetResidue() is not None else None def whichresnumber(atom): """Returns the residue number of an Pybel or OpenBabel atom (numbering as in original PDB file).""" - atom = atom if not isinstance(atom, Atom) else atom.OBAtom # Convert to OpenBabel Atom + atom = ( + atom if not isinstance(atom, Atom) else atom.OBAtom + ) # Convert to OpenBabel Atom return atom.GetResidue().GetNum() if atom.GetResidue() is not None else None def whichchain(atom): """Returns the residue number of an PyBel or OpenBabel atom.""" - atom = atom if not isinstance(atom, Atom) else atom.OBAtom # Convert to OpenBabel Atom + atom = ( + atom if not isinstance(atom, Atom) else atom.OBAtom + ) # Convert to OpenBabel Atom return atom.GetResidue().GetChain() if atom.GetResidue() is not None else None @@ -82,7 +90,11 @@ def vector(p1, p2): :param p2: coordinates of point p2 :returns : numpy array with vector coordinates """ - return None if len(p1) != len(p2) else np.array([p2[i] - p1[i] for i in range(len(p1))]) + return ( + None + if len(p1) != len(p2) + else np.array([p2[i] - p1[i] for i in range(len(p1))]) + ) def vecangle(v1, v2, deg=True): @@ -97,7 +109,7 @@ def vecangle(v1, v2, deg=True): dm = np.dot(v1, v2) cm = np.linalg.norm(v1) * np.linalg.norm(v2) angle = np.arccos(dm / cm) # Round here to prevent floating point errors - return np.degrees([angle, ])[0] if deg else angle + return np.degrees([angle,])[0] if deg else angle def normalize_vector(v): @@ -114,7 +126,12 @@ def centroid(coo): :param coo: Array of coordinate arrays :returns : centroid coordinates as list """ - return list(map(np.mean, (([c[0] for c in coo]), ([c[1] for c in coo]), ([c[2] for c in coo])))) + return list( + map( + np.mean, + (([c[0] for c in coo]), ([c[1] for c in coo]), ([c[2] for c in coo])), + ) + ) def projection(pnormal1, ppoint, tpoint): @@ -150,11 +167,15 @@ def cluster_doubles(double_list): if a in location and b in location: if location[a] != location[b]: if location[a] < location[b]: - clusters[location[a]] = clusters[location[a]].union(clusters[location[b]]) # Merge clusters - clusters = clusters[:location[b]] + clusters[location[b] + 1:] + clusters[location[a]] = clusters[location[a]].union( + clusters[location[b]] + ) # Merge clusters + clusters = clusters[: location[b]] + clusters[location[b] + 1 :] else: - clusters[location[b]] = clusters[location[b]].union(clusters[location[a]]) # Merge clusters - clusters = clusters[:location[a]] + clusters[location[a] + 1:] + clusters[location[b]] = clusters[location[b]].union( + clusters[location[a]] + ) # Merge clusters + clusters = clusters[: location[a]] + clusters[location[a] + 1 :] # Rebuild index of locations for each element as they have changed now location = {} for i, cluster in enumerate(clusters): @@ -181,9 +202,10 @@ def cluster_doubles(double_list): # File operations ################# + def tilde_expansion(folder_path): """Tilde expansion, i.e. converts '~' in paths into <value of $HOME>.""" - return os.path.expanduser(folder_path) if '~' in folder_path else folder_path + return os.path.expanduser(folder_path) if "~" in folder_path else folder_path def folder_exists(folder_path): @@ -194,14 +216,21 @@ def folder_exists(folder_path): def create_folder_if_not_exists(folder_path): """Creates a folder if it does not exists.""" folder_path = tilde_expansion(folder_path) - folder_path = "".join([folder_path, '/']) if not folder_path[-1] == '/' else folder_path + folder_path = ( + "".join([folder_path, "/"]) if not folder_path[-1] == "/" else folder_path + ) direc = os.path.dirname(folder_path) if not folder_exists(direc): os.makedirs(direc) def cmd_exists(c): - return subprocess.call("type " + c, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0 + return ( + subprocess.call( + "type " + c, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE + ) + == 0 + ) ################ @@ -212,20 +241,22 @@ def cmd_exists(c): def initialize_pymol(options): """Initializes PyMOL""" import pymol + # Pass standard arguments of function to prevent PyMOL from printing out PDB headers (workaround) - pymol.finish_launching(args=['pymol', options, '-K']) + pymol.finish_launching(args=["pymol", options, "-K"]) pymol.cmd.reinitialize() -def start_pymol(quiet=False, options='-p', run=False): +def start_pymol(quiet=False, options="-p", run=False): """Starts up PyMOL and sets general options. Quiet mode suppresses all PyMOL output. Command line options can be passed as the second argument.""" import pymol - pymol.pymol_argv = ['pymol', '%s' % options] + sys.argv[1:] + + pymol.pymol_argv = ["pymol", "%s" % options] + sys.argv[1:] if run: initialize_pymol(options) if quiet: - pymol.cmd.feedback('disable', 'all', 'everything') + pymol.cmd.feedback("disable", "all", "everything") def nucleotide_linkage(residues): @@ -235,7 +266,7 @@ def nucleotide_linkage(residues): ####################################### # Basic support for RNA/DNA as ligand # ####################################### - nucleotides = ['A', 'C', 'T', 'G', 'U', 'DA', 'DC', 'DT', 'DG', 'DU'] + nucleotides = ["A", "C", "T", "G", "U", "DA", "DC", "DT", "DG", "DU"] dna_rna = {} # Dictionary of DNA/RNA residues by chain covlinkage = namedtuple("covlinkage", "id1 chain1 pos1 conf1 id2 chain2 pos2 conf2") # Create missing covlinkage entries for DNA/RNA @@ -243,7 +274,9 @@ def nucleotide_linkage(residues): resname, chain, pos = ligand if resname in nucleotides: if chain not in dna_rna: - dna_rna[chain] = [(resname, pos), ] + dna_rna[chain] = [ + (resname, pos), + ] else: dna_rna[chain].append((resname, pos)) for chain in dna_rna: @@ -253,8 +286,16 @@ def nucleotide_linkage(residues): name, pos = nucleotide nextnucleotide = nuc_list[i + 1] nextname, nextpos = nextnucleotide - newlink = covlinkage(id1=name, chain1=chain, pos1=pos, conf1='', - id2=nextname, chain2=chain, pos2=nextpos, conf2='') + newlink = covlinkage( + id1=name, + chain1=chain, + pos1=pos, + conf1="", + id2=nextname, + chain2=chain, + pos2=nextpos, + conf2="", + ) nuc_covalent.append(newlink) return nuc_covalent @@ -273,7 +314,12 @@ def ring_is_planar(ring, r_atoms): # Given all normals of ring atoms and their neighbors, the angle between any has to be 5.0 deg or less for n1, n2 in itertools.product(normals, repeat=2): arom_angle = vecangle(n1, n2) - if all([arom_angle > config.AROMATIC_PLANARITY, arom_angle < 180.0 - config.AROMATIC_PLANARITY]): + if all( + [ + arom_angle > config.AROMATIC_PLANARITY, + arom_angle < 180.0 - config.AROMATIC_PLANARITY, + ] + ): return False return True @@ -282,21 +328,21 @@ def classify_by_name(names): """Classify a (composite) ligand by the HETID(s)""" if len(names) > 3: # Polymer if len(set(config.RNA).intersection(set(names))) != 0: - ligtype = 'RNA' + ligtype = "RNA" elif len(set(config.DNA).intersection(set(names))) != 0: - ligtype = 'DNA' + ligtype = "DNA" else: ligtype = "POLYMER" else: - ligtype = 'SMALLMOLECULE' + ligtype = "SMALLMOLECULE" for name in names: if name in config.METAL_IONS: if len(names) == 1: - ligtype = 'ION' + ligtype = "ION" else: if "ION" not in ligtype: - ligtype += '+ION' + ligtype += "+ION" return ligtype @@ -323,7 +369,7 @@ def get_isomorphisms(reference, lig): isomorphs = pybel.ob.vpairUIntUInt() mappr.MapFirst(lig.OBMol, isomorphs) isomorphs = [isomorphs] - logger.debug(f'number of isomorphisms: {len(isomorphs)}') + logger.debug(f"number of isomorphisms: {len(isomorphs)}") # @todo Check which isomorphism to take return isomorphs @@ -340,15 +386,17 @@ def canonicalize(lig, preserve_bond_order=False): bond.SetBondOrder(1) lig.DeleteData(pybel.ob.StereoData) lig = pybel.Molecule(lig) - testcan = lig.write(format='can') + testcan = lig.write(format="can") try: - pybel.readstring('can', testcan) - reference = pybel.readstring('can', testcan) + pybel.readstring("can", testcan) + reference = pybel.readstring("can", testcan) except IOError: - testcan, reference = '', '' - if testcan != '': + testcan, reference = "", "" + if testcan != "": reference.removeh() - isomorphs = get_isomorphisms(reference, lig) # isomorphs now holds all isomorphisms within the molecule + isomorphs = get_isomorphisms( + reference, lig + ) # isomorphs now holds all isomorphisms within the molecule if not len(isomorphs) == 0: smi_dict = {} smi_to_can = isomorphs[0] @@ -365,7 +413,9 @@ def int32_to_negative(int32): 32 bit integer and returns the actual number. """ dct = {} - if int32 == 4294967295: # Special case in some structures (note, this is just a workaround) + if ( + int32 == 4294967295 + ): # Special case in some structures (note, this is just a workaround) return -1 for i in range(-1000, -1): dct[np.uint32(i)] = i @@ -378,7 +428,7 @@ def int32_to_negative(int32): def read_pdb(pdbfname, as_string=False): """Reads a given PDB file and returns a Pybel Molecule.""" pybel.ob.obErrorLog.StopLogging() # Suppress all OpenBabel warnings - if os.name != 'nt': # Resource module not available for Windows + if os.name != "nt": # Resource module not available for Windows maxsize = resource.getrlimit(resource.RLIMIT_STACK)[-1] resource.setrlimit(resource.RLIMIT_STACK, (min(2 ** 28, maxsize), maxsize)) sys.setrecursionlimit(10 ** 5) # increase Python recursion limit @@ -387,48 +437,50 @@ def read_pdb(pdbfname, as_string=False): def read(fil): """Returns a file handler and detects gzipped files.""" - if os.path.splitext(fil)[-1] == '.gz': - return gzip.open(fil, 'rb') - elif os.path.splitext(fil)[-1] == '.zip': - zf = zipfile.ZipFile(fil, 'r') + if os.path.splitext(fil)[-1] == ".gz": + return gzip.open(fil, "rb") + elif os.path.splitext(fil)[-1] == ".zip": + zf = zipfile.ZipFile(fil, "r") return zf.open(zf.infolist()[0].filename) else: - return open(fil, 'r') + return open(fil, "r") def readmol(path, as_string=False): """Reads the given molecule file and returns the corresponding Pybel molecule as well as the input file type. In contrast to the standard Pybel implementation, the file is closed properly.""" - supported_formats = ['pdb'] + supported_formats = ["pdb"] # Fix for Windows-generated files: Remove carriage return characters if "\r" in path and as_string: - path = path.replace('\r', '') + path = path.replace("\r", "") for sformat in supported_formats: obc = pybel.ob.OBConversion() obc.SetInFormat(sformat) - logger.debug(f'detected {sformat} as format, trying to read file with OpenBabel') + logger.debug( + f"detected {sformat} as format, trying to read file with OpenBabel" + ) # Read molecules with single bond information if as_string: try: mymol = pybel.readstring(sformat, path) except IOError: - logger.error('no valid file format provided') + logger.error("no valid file format provided") sys.exit(1) else: read_file = pybel.readfile(format=sformat, filename=path, opt={"s": None}) try: mymol = next(read_file) except StopIteration: - logger.error('file contains no valid molecules') + logger.error("file contains no valid molecules") sys.exit(1) - logger.debug('molecule successfully read') + logger.debug("molecule successfully read") # Assign multiple bonds mymol.OBMol.PerceiveBondOrders() return mymol, sformat - logger.error('no valid file format provided') + logger.error("no valid file format provided") sys.exit(1) |