__version__ = "2.1.0-beta" __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", ]