"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
config.py - Store thresholds used by PLIP.
"""

VERBOSE = False  # Set verbose mode
DEBUG = False  # Set debug 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

# 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 = 4.0  # Max. distance between water oxygen and polar atom (Jiang et al., 2005) +0.4
WATER_BRIDGE_OMEGA_MIN = 75  # Min. angle between acceptor, water oxygen and donor hydrogen (Jiang et al., 2005) - 5
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']
