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authordeepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>2020-07-07 14:55:17 +0000
committerGitHub <noreply@github.com>2020-07-07 14:55:17 +0000
commit0d135d611506e81d322596c7827b08bbfd3b7c08 (patch)
treea281b8e1f140ad3de77d818747fce03bcfa5b77b /plip/basic/config.py
parent7059ee2a4ced23e467741cc846eb185886ffca38 (diff)
Format code with Blackdeepsource-transform-b65b5545
Diffstat (limited to 'plip/basic/config.py')
-rw-r--r--plip/basic/config.py606
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",
+]