Format code with Blackdeepsource-transform-b65b5545

1 files changed, 555 insertions, 51 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",
+]