diff options
Diffstat (limited to 'plip/basic/config.py')
| -rw-r--r-- | plip/basic/config.py | 121 |
1 files changed, 121 insertions, 0 deletions
diff --git a/plip/basic/config.py b/plip/basic/config.py new file mode 100644 index 0000000..a7468cf --- /dev/null +++ b/plip/basic/config.py @@ -0,0 +1,121 @@ +__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'] |