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diff --git a/plip/basic/config.py b/plip/basic/config.py
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-__version__ = "2.1.3"
-__maintainer__ = "PharmAI GmbH (2020) - www.pharm.ai - hello@pharm.ai"
-
-import logging
-
-DEFAULT_LOG_LEVEL = logging.INFO
-VERBOSE = False # Set verbose mode
-QUIET = False # Set verbose mode
-SILENT = False # Set verbose mode
-MAXTHREADS = 1 # Maximum number of main threads for binding site visualization
-XML = False
-TXT = False
-PICS = False
-PYMOL = False
-STDOUT = False
-RAWSTRING = False # use raw strings for input / output
-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)
-NOFIX = False # Turn off fixing of errors in PDB files
-NOFIXFILE = False # Turn off writing to files for fixed PDB structures
-PEPTIDES = [] # Definition which chains should be considered as peptide ligands
-INTRA = None
-KEEPMOD = False
-DNARECEPTOR = False
-OUTPUTFILENAME = "report" # Naming for the TXT and XML report files
-NOPDBCANMAP = False # Skip calculation of mapping canonical atom order: PDB atom order
-NOHYDRO = False # Do not add hydrogen bonds (in case already present in the structure)
-
-# Configuration file for Protein-Ligand Interaction Profiler (PLIP)
-# Set thresholds for detection of interactions
-
-# 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
-)
-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)
-)
-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_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_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)
-)
-
-# Other thresholds
-MAX_COMPOSITE_LENGTH = 200 # Filter out ligands with more than 200 fragments
-
-#########
-# Names #
-#########
-
-# Names of RNA and DNA residues to be considered (detection by name)
-RNA = ["U", "A", "C", "G"]
-DNA = ["DT", "DA", "DC", "DG"]
-
-#############
-# Whitelist #
-#############
-
-# 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",
-]
-
-##############
-# Blacklists #
-##############
-
-# Other Ions/Atoms (not yet supported)
-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",
-]
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-09 17:37:55 +0000