From 9dadfdb3332b073aaff508d126e90200ad09868d Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Fri, 11 Sep 2020 16:18:38 +0530 Subject: removed downloaded plip --- plip/basic/config.py | 625 --------------------------------------------------- 1 file changed, 625 deletions(-) delete mode 100644 plip/basic/config.py (limited to 'plip/basic/config.py') diff --git a/plip/basic/config.py b/plip/basic/config.py deleted file mode 100644 index 91103fa..0000000 --- a/plip/basic/config.py +++ /dev/null @@ -1,625 +0,0 @@ -__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", -] -- cgit v1.2.3