src/structure/structure-constants.js
/**
* @file Structure Constants
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @private
*/
// entity types
const UnknownEntity = 0
const PolymerEntity = 1
const NonPolymerEntity = 2
const MacrolideEntity = 3
const WaterEntity = 4
// molecule types
const UnknownType = 0
const WaterType = 1
const IonType = 2
const ProteinType = 3
const RnaType = 4
const DnaType = 5
const SaccharideType = 6
// backbone types
const UnknownBackboneType = 0
const ProteinBackboneType = 1
const RnaBackboneType = 2
const DnaBackboneType = 3
const CgProteinBackboneType = 4
const CgRnaBackboneType = 5
const CgDnaBackboneType = 6
// chemical component types
const ChemCompProtein = [
'D-BETA-PEPTIDE, C-GAMMA LINKING', 'D-GAMMA-PEPTIDE, C-DELTA LINKING',
'D-PEPTIDE COOH CARBOXY TERMINUS', 'D-PEPTIDE NH3 AMINO TERMINUS', 'D-PEPTIDE LINKING',
'L-BETA-PEPTIDE, C-GAMMA LINKING', 'L-GAMMA-PEPTIDE, C-DELTA LINKING',
'L-PEPTIDE COOH CARBOXY TERMINUS', 'L-PEPTIDE NH3 AMINO TERMINUS', 'L-PEPTIDE LINKING',
'PEPTIDE LINKING', 'PEPTIDE-LIKE'
]
const ChemCompRna = [
'RNA OH 3 PRIME TERMINUS', 'RNA OH 5 PRIME TERMINUS', 'RNA LINKING'
]
const ChemCompDna = [
'DNA OH 3 PRIME TERMINUS', 'DNA OH 5 PRIME TERMINUS', 'DNA LINKING',
'L-DNA LINKING', 'L-RNA LINKING'
]
const ChemCompSaccharide = [
'D-SACCHARIDE', 'D-SACCHARIDE 1,4 AND 1,4 LINKING', 'D-SACCHARIDE 1,4 AND 1,6 LINKING',
'L-SACCHARIDE', 'L-SACCHARIDE 1,4 AND 1,4 LINKING', 'L-SACCHARIDE 1,4 AND 1,6 LINKING',
'SACCHARIDE'
]
const ChemCompOther = [
'OTHER'
]
const ChemCompNonPolymer = [
'NON-POLYMER'
]
const ChemCompHetero = ChemCompNonPolymer.concat(ChemCompOther, ChemCompSaccharide)
// secondary structure
const SecStrucHelix = [ 'h', 'g', 'i' ]
const SecStrucSheet = [ 'e', 'b' ]
const SecStrucTurn = [ 's', 't', 'l', '' ]
// http://dx.doi.org/10.1021/jp8111556 (or 2.0)
const VdwRadii = {
'H': 1.1,
'HE': 1.4,
'LI': 1.81,
'BE': 1.53,
'B': 1.92,
'C': 1.7,
'N': 1.55,
'O': 1.52,
'F': 1.47,
'NE': 1.54,
'NA': 2.27,
'MG': 1.73,
'AL': 1.84,
'SI': 2.1,
'P': 1.8,
'S': 1.8,
'CL': 1.75,
'AR': 1.88,
'K': 2.75,
'CA': 2.31,
'SC': 2.3,
'TI': 2.15,
'V': 2.05,
'CR': 2.05,
'MN': 2.05,
'FE': 2.05,
'CO': 2.0,
'NI': 2.0,
'CU': 2.0,
'ZN': 2.1,
'GA': 1.87,
'GE': 2.11,
'AS': 1.85,
'SE': 1.9,
'BR': 1.83,
'KR': 2.02,
'RB': 3.03,
'SR': 2.49,
'Y': 2.4,
'ZR': 2.3,
'NB': 2.15,
'MO': 2.1,
'TC': 2.05,
'RU': 2.05,
'RH': 2.0,
'PD': 2.05,
'AG': 2.1,
'CD': 2.2,
'IN': 2.2,
'SN': 1.93,
'SB': 2.17,
'TE': 2.06,
'I': 1.98,
'XE': 2.16,
'CS': 3.43,
'BA': 2.68,
'LA': 2.5,
'CE': 2.48,
'PR': 2.47,
'ND': 2.45,
'PM': 2.43,
'SM': 2.42,
'EU': 2.4,
'GD': 2.38,
'TB': 2.37,
'DY': 2.35,
'HO': 2.33,
'ER': 2.32,
'TM': 2.3,
'YB': 2.28,
'LU': 2.27,
'HF': 2.25,
'TA': 2.2,
'W': 2.1,
'RE': 2.05,
'OS': 2.0,
'IR': 2.0,
'PT': 2.05,
'AU': 2.1,
'HG': 2.05,
'TL': 1.96,
'PB': 2.02,
'BI': 2.07,
'PO': 1.97,
'AT': 2.02,
'RN': 2.2,
'FR': 3.48,
'RA': 2.83,
'AC': 2.0,
'TH': 2.4,
'PA': 2.0,
'U': 2.3,
'NP': 2.0,
'PU': 2.0,
'AM': 2.0,
'CM': 2.0,
'BK': 2.0,
'CF': 2.0,
'ES': 2.0,
'FM': 2.0,
'MD': 2.0,
'NO': 2.0,
'LR': 2.0,
'RF': 2.0,
'DB': 2.0,
'SG': 2.0,
'BH': 2.0,
'HS': 2.0,
'MT': 2.0,
'DS': 2.0,
'RG': 2.0,
'CN': 2.0,
'UUT': 2.0,
'FL': 2.0,
'UUP': 2.0,
'LV': 2.0,
'UUH': 2.0
}
const DefaultVdwRadius = 2.0
// Peter Rose (peter.rose@rcsb.org), private communication, average accross PDB
const ResidueRadii = {
'2QY': 6.58,
'CY0': 11.98,
'2QZ': 2.52,
'CY1': 6.59,
'HHK': 5.11,
'CXM': 4.69,
'HHI': 4.58,
'CY4': 4.57,
'S12': 18.57,
'CY3': 2.79,
'C5C': 5.35,
'PFX': 11.84,
'2R3': 6.94,
'2R1': 3.78,
'ILX': 4.99,
'32S': 5.68,
'BTK': 8.59,
'32T': 5.72,
'FAK': 9.8,
'B27': 2.78,
'ILM': 3.84,
'C4R': 5.63,
'32L': 6.75,
'SYS': 3.01,
'1MH': 5.04,
'ILE': 3.65,
'YNM': 6.39,
'2RX': 4.91,
'B3A': 2.48,
'GEE': 4.76,
'7MN': 7.34,
'B3E': 5.4,
'ARG': 6.33,
'200': 6.89,
'HIP': 5.47,
'HIA': 4.64,
'B3K': 5.89,
'HIC': 5.76,
'B3L': 4.96,
'B3M': 5.07,
'ARM': 6.86,
'ARO': 7.35,
'AR4': 8.42,
'PG1': 10.67,
'YOF': 6.44,
'IML': 3.74,
'SXE': 6.65,
'HIQ': 7.98,
'PFF': 6.31,
'HIS': 4.52,
'0TD': 3.62,
'C3Y': 5.24,
'1OP': 11.55,
'02Y': 4.77,
'02V': 4.83,
'ASB': 5.59,
'30V': 8.53,
'S2P': 4.81,
'ASP': 3.55,
'ASN': 3.54,
'2OR': 6.91,
'QMM': 6.13,
'2P0': 8.52,
'ASL': 5.36,
'HFA': 5.14,
'5PG': 5.69,
'B3X': 4.38,
'AS9': 4.1,
'ARV': 7.59,
'B3U': 6.06,
'S2C': 7.54,
'B3T': 3.34,
'175': 5.64,
'GFT': 8.18,
'HG7': 6.8,
'B3Q': 4.48,
'ASA': 3.64,
'02K': 2.94,
'B3Y': 7.45,
'PHD': 5.35,
'C6C': 6.42,
'BUC': 5.8,
'HGL': 8.07,
'PHE': 5.06,
'03Y': 2.6,
'PHA': 5.11,
'OCY': 5.0,
'4PH': 6.79,
'5OH': 4.7,
'31Q': 10.46,
'BTR': 7.98,
'3PX': 4.7,
'1PA': 8.07,
'ASX': 3.54,
'IOR': 7.23,
'03E': 3.38,
'PHL': 5.17,
'KWS': 5.09,
'PHI': 7.12,
'NAL': 7.22,
'S1H': 19.21,
'2ML': 3.86,
'2MR': 7.35,
'GHG': 4.83,
'TYY': 6.54,
'2MT': 3.67,
'56A': 13.01,
'SVA': 5.46,
'TYX': 8.31,
'TYS': 8.59,
'TYR': 6.38,
'TYQ': 6.43,
'HLU': 3.99,
'MYK': 19.47,
'TYO': 7.71,
'HLX': 4.98,
'TYN': 9.87,
'TYJ': 6.25,
'TYI': 6.49,
'LYH': 5.13,
'LYF': 12.19,
'SUN': 6.73,
'LYR': 18.28,
'TYB': 6.46,
'11W': 14.39,
'LYS': 5.54,
'LYN': 4.8,
'11Q': 4.85,
'LYO': 4.71,
'LYZ': 1.76,
'TXY': 6.44,
'MYN': 4.71,
'TY5': 10.6,
'HMR': 5.09,
'01W': 8.55,
'LYX': 13.36,
'TY8': 7.22,
'TY2': 6.49,
'KYN': 6.18,
'KYQ': 9.75,
'CZZ': 5.14,
'IIL': 3.81,
'HNC': 10.41,
'OIC': 4.62,
'LVN': 2.89,
'QIL': 3.84,
'JJL': 8.3,
'VAH': 3.88,
'JJJ': 7.5,
'JJK': 7.43,
'VAD': 2.56,
'CYW': 4.65,
'0QL': 5.72,
'143': 8.22,
'SVX': 7.04,
'CYJ': 11.64,
'SVY': 7.1,
'SVZ': 6.6,
'CYG': 8.03,
'CYF': 13.54,
'SVV': 5.09,
'GL3': 2.72,
'8SP': 14.26,
'CYS': 2.78,
'004': 4.33,
'CYR': 10.33,
'PLJ': 3.71,
'EXY': 7.37,
'HL2': 3.75,
'A5N': 5.21,
'CYQ': 5.67,
'CZ2': 5.16,
'LWY': 4.12,
'PM3': 8.78,
'OHS': 6.98,
'OHI': 5.35,
'3TY': 8.42,
'CYD': 8.55,
'DYS': 7.87,
'DAH': 6.47,
'4IK': 11.81,
'3EG': 3.66,
'AYA': 3.65,
'4IN': 6.31,
'DAB': 3.48,
'4HT': 6.03,
'RGL': 7.03,
'DAM': 2.49,
'NFA': 5.04,
'WFP': 6.07,
'2JC': 2.97,
'HAR': 7.55,
'2JG': 5.67,
'MH6': 1.72,
'2JF': 9.13,
'3FG': 4.96,
'MGN': 4.84,
'AZH': 5.36,
'AZK': 6.03,
'ZBZ': 7.79,
'TBG': 2.58,
'VAL': 2.51,
'MGG': 7.34,
'AZS': 5.61,
'FHL': 9.75,
'2JH': 4.56,
'IEL': 7.07,
'FHO': 6.75,
'DA2': 7.79,
'FH7': 6.99,
'ME0': 4.52,
'3GL': 4.84,
'MDO': 5.03,
'AZY': 7.37,
'A8E': 3.76,
'ZCL': 6.71,
'MDH': 2.58,
'LA2': 14.07,
'4FW': 6.1,
'YCM': 5.32,
'MDF': 4.95,
'YCP': 3.01,
'TEF': 8.63,
'FGP': 4.34,
'UF0': 19.72,
'XCN': 4.57,
'FGL': 2.56,
'MF3': 6.37,
'MEQ': 5.13,
'LAA': 3.23,
'IGL': 5.52,
'MET': 4.49,
'NIY': 6.81,
'QCS': 5.18,
'TCQ': 8.56,
'MEN': 4.33,
'4HL': 8.79,
'MEA': 4.95,
'EFC': 5.28,
'LAL': 2.41,
'2HF': 5.52,
'KBE': 5.64,
'OCS': 3.94,
'CAF': 5.46,
'NC1': 11.4,
'NBQ': 9.82,
'CAB': 4.19,
'MBQ': 9.55,
'193': 7.38,
'192': 2.44,
'0WZ': 7.61,
'CAS': 5.35,
'NB8': 11.98,
'OBS': 11.71,
'1AC': 2.42,
'PCA': 3.48,
'MCL': 9.73,
'LBY': 7.75,
'GAU': 4.67,
'PBF': 9.75,
'MCG': 6.46,
'DDE': 6.86,
'19W': 3.94,
'MD5': 9.33,
'MD6': 6.44,
'MD3': 8.41,
'MCS': 7.56,
'OBF': 3.64,
'UAL': 4.68,
'PAT': 6.05,
'IAM': 8.88,
'PAQ': 8.77,
'FDL': 9.49,
'NCB': 3.45,
'LCK': 9.81,
'DDZ': 2.52,
'2FM': 5.54,
'IAR': 6.77,
'OAS': 4.8,
'HBN': 8.8,
'TA4': 5.55,
'1C3': 7.43,
'ECX': 5.51,
'PF5': 6.28,
'RE3': 5.29,
'FCL': 6.25,
'ECC': 4.79,
'LDH': 7.06,
'NCY': 2.91,
'CCS': 4.58,
'PEC': 6.54,
'2CO': 4.45,
'LE1': 2.72,
'HCM': 5.53,
'07O': 8.05,
'HCL': 4.96,
'NEP': 6.94,
'PE1': 8.01,
'LEF': 4.37,
'FC0': 5.18,
'LED': 4.34,
'HCS': 4.09,
'DBU': 2.49,
'RE0': 5.53,
'LEN': 3.82,
'1E3': 8.71,
'BB9': 2.56,
'BB8': 5.14,
'PCS': 5.05,
'BB7': 4.56,
'BB6': 2.62,
'LEU': 3.83,
'DBZ': 7.08,
'LET': 11.29,
'DBY': 6.46,
'ICY': 7.76,
'MAA': 2.4,
'CGA': 7.91,
'5CS': 8.34,
'UGY': 3.7,
'LGY': 11.71,
'N10': 8.96,
'AAR': 6.39,
'FT6': 7.5,
'MOD': 12.62,
'5CW': 7.21,
'PVH': 4.58,
'BBC': 6.42,
'YYA': 7.3,
'O12': 14.08,
'NOT': 7.15,
'KGC': 9.88,
'MP4': 5.86,
'0CS': 4.07,
'MP8': 3.75,
'VLL': 2.54,
'VLM': 2.51,
'BCS': 8.03,
'MNL': 4.9,
'AA4': 4.47,
'SAC': 3.49,
'BCX': 2.99,
'3CF': 6.47,
'SAH': 11.7,
'NNH': 6.86,
'CGU': 4.71,
'SIB': 12.41,
'TLY': 8.78,
'SIC': 4.81,
'VMS': 8.82,
'TMD': 6.76,
'MMO': 6.53,
'PXU': 2.46,
'4AW': 6.22,
'OTH': 3.6,
'DLS': 6.84,
'MME': 4.99,
'DM0': 6.99,
'0FL': 2.76,
'SBL': 8.96,
'CDV': 3.72,
'OTY': 6.51,
'PYA': 7.75,
'2AS': 3.57,
'DMH': 4.92,
'ELY': 7.42,
'GVL': 9.6,
'FVA': 2.9,
'SAR': 2.48,
'4BF': 6.92,
'EME': 4.69,
'CDE': 2.51,
'3AR': 7.86,
'3AH': 9.11,
'AC5': 2.44,
'FTR': 6.08,
'MLL': 3.76,
'NPH': 11.66,
'NPI': 6.9,
'DMT': 6.67,
'PYX': 11.3,
'MLE': 3.87,
'PYL': 9.67,
'ZZU': 6.94,
'H5M': 3.61,
'SCH': 4.46,
'DMK': 3.52,
'FTY': 9.07,
'2AG': 3.7,
'ABA': 2.55,
'ZZJ': 2.44,
'MLZ': 6.8,
'MLY': 6.88,
'KCX': 7.28,
'ZZD': 8.16,
'3A5': 5.37,
'LHC': 7.75,
'9AT': 2.47,
'OZT': 3.4,
'THO': 2.62,
'THR': 2.5,
'DFI': 3.93,
'MKD': 6.42,
'4CY': 4.6,
'SDP': 6.07,
'DFO': 3.94,
'0A0': 3.45,
'4DB': 9.73,
'ML3': 6.26,
'BG1': 8.02,
'SD4': 4.57,
'THC': 3.8,
'SCS': 5.48,
'TH5': 4.65,
'BFD': 5.33,
'AEI': 6.34,
'TH6': 2.85,
'SCY': 4.53,
'TIS': 4.81,
'SEE': 4.53,
'BHD': 3.48,
'SEB': 8.18,
'SEC': 2.96,
'SEP': 4.8,
'CLH': 7.13,
'TIH': 5.02,
'CLG': 13.62,
'SEN': 6.43,
'XXA': 7.34,
'SEL': 2.46,
'SE7': 4.19,
'4CF': 7.72,
'G8M': 3.57,
'BH2': 3.51,
'UN2': 3.22,
'VR0': 10.51,
'MK8': 4.76,
'DHA': 2.32,
'LMQ': 4.69,
'SFE': 5.01,
'AHB': 3.47,
'OXX': 7.05,
'BIF': 9.63,
'IZO': 4.47,
'NMM': 8.25,
'0BN': 7.0,
'HZP': 3.12,
'NMC': 4.23,
'DHL': 2.69,
'9DS': 9.29,
'SER': 2.41,
'CHG': 4.2,
'MIR': 6.54,
'AGQ': 7.79,
'SET': 2.46,
'MIS': 6.32,
'4FB': 3.08,
'0AR': 8.46,
'LME': 3.99,
'FZN': 24.42,
'AGT': 9.04,
'IYR': 6.46,
'9DN': 9.31,
'CHP': 5.75,
'UNK': 1.64,
'XX1': 9.92,
'AGM': 6.57,
'0AH': 5.78,
'LLP': 10.22,
'0AF': 6.72,
'4DP': 9.28,
'HYP': 2.25,
'DIR': 5.8,
'LLY': 8.71,
'0AK': 6.11,
'NLE': 4.67,
'OYL': 6.42,
'WVL': 4.69,
'0A8': 8.1,
'NLY': 6.37,
'MHO': 4.89,
'VOL': 2.55,
'0A1': 7.1,
'MHL': 3.92,
'NLP': 4.81,
'NLQ': 4.65,
'MHW': 2.74,
'BIL': 4.7,
'NLO': 4.8,
'MHU': 7.51,
'XW1': 9.36,
'LLO': 10.13,
'SGB': 6.88,
'MHV': 3.6,
'MHS': 4.51,
'0A9': 5.17,
'0LF': 9.96,
'HT7': 6.82,
'X2W': 6.6,
'YPZ': 9.38,
'I58': 6.73,
'FLA': 2.4,
'M0H': 4.83,
'HSL': 2.46,
'FLE': 6.17,
'KOR': 10.1,
'1VR': 3.89,
'HSO': 4.56,
'TTS': 9.41,
'RVX': 7.01,
'TTQ': 7.71,
'H14': 5.27,
'HTI': 7.8,
'ONH': 6.14,
'LP6': 8.58,
'ONL': 4.83,
'AHH': 5.06,
'HS8': 7.4,
'HS9': 4.71,
'BL2': 5.82,
'AHP': 5.26,
'6HN': 7.34,
'HRP': 5.46,
'POM': 3.6,
'WPA': 5.11,
'2ZC': 4.29,
'CPC': 2.65,
'AIB': 2.4,
'XSN': 3.47,
'M2S': 5.28,
'GND': 6.67,
'GNC': 4.6,
'MVA': 2.56,
'OLZ': 5.32,
'M2L': 6.15,
'TRF': 6.69,
'NZH': 7.66,
'SRZ': 5.27,
'OLD': 10.47,
'CME': 5.86,
'CMH': 5.3,
'ALA': 2.38,
'TRQ': 7.36,
'PPN': 7.24,
'TRP': 6.07,
'TRO': 5.82,
'TRN': 5.95,
'NYS': 8.1,
'ALC': 5.26,
'U3X': 11.7,
'HVA': 2.58,
'TS9': 3.92,
'TRX': 7.27,
'TRW': 11.8,
'LPL': 7.51,
'GMA': 4.4,
'OMT': 5.07,
'CMT': 3.54,
'GME': 4.66,
'NYB': 6.07,
'PR3': 5.12,
'LPD': 2.48,
'GLU': 4.49,
'1X6': 6.84,
'LPG': 2.39,
'GLX': 4.52,
'PR4': 4.52,
'CML': 6.16,
'FME': 4.52,
'HTR': 6.48,
'PR7': 4.66,
'Z3E': 7.2,
'GLZ': 2.39,
'BMT': 6.37,
'WRP': 8.16,
'GLY': 2.37,
'OMY': 6.11,
'MTY': 5.46,
'OMX': 6.15,
'GLN': 4.46,
'2XA': 8.25,
'28X': 7.84,
'7JA': 9.46,
'FLT': 9.65,
'GLJ': 3.7,
'OMH': 5.26,
'TSY': 4.26,
'PRV': 4.28,
'CS4': 11.21,
'DOA': 12.33,
'23P': 5.42,
'CS3': 8.24,
'6CL': 6.47,
'PRR': 5.58,
'KST': 11.58,
'CS1': 7.23,
'PRS': 2.63,
'ZYJ': 11.4,
'IT1': 9.75,
'UU5': 4.98,
'ESB': 6.69,
'UU4': 2.49,
'ESC': 5.65,
'LSO': 10.58,
'ZYK': 11.45,
'9NV': 8.99,
'23F': 5.27,
'ORN': 4.25,
'HOX': 6.61,
'CSD': 3.95,
'FP9': 3.03,
'DO2': 4.44,
'SLL': 11.53,
'P3Q': 9.54,
'ORQ': 6.04,
'MSL': 5.21,
'DNP': 2.45,
'CSB': 3.51,
'WLU': 4.24,
'CSA': 5.7,
'MT2': 5.51,
'CSO': 3.53,
'TPO': 4.73,
'MSP': 13.11,
'23S': 6.09,
'MSO': 4.96,
'PRO': 2.41,
'TPL': 5.41,
'DNS': 8.79,
'CSK': 3.91,
'Z70': 7.4,
'CSJ': 7.51,
'DNW': 7.97,
'PRK': 9.15,
'GSU': 11.81,
'LTA': 6.57,
'HPE': 6.63,
'TPQ': 6.48,
'PRJ': 5.26,
'PSW': 4.65,
'L3O': 3.89,
'CSU': 4.89,
'ALY': 7.38,
'M3L': 7.12,
'CSW': 3.68,
'XPR': 7.68,
'D4P': 5.66,
'FOE': 8.17,
'SLZ': 5.69,
'CSP': 5.26,
'TQI': 7.68,
'ALT': 2.72,
'CSR': 5.42,
'CSS': 3.61,
'M3R': 7.18,
'ALO': 2.57,
'R4K': 4.67,
'SMF': 9.0,
'MSA': 2.73,
'SMC': 3.39,
'CSX': 3.47,
'SME': 4.8,
'ETA': 2.4,
'CSZ': 3.6,
'22G': 8.8,
'MSE': 4.62,
'ALN': 6.16,
'PSH': 7.26,
'CTE': 7.27,
'DON': 6.72,
'CTH': 3.45,
'U2X': 11.54,
'6CW': 7.56,
'TQZ': 6.97,
'3YM': 6.52,
'OSE': 4.49,
'2VA': 9.82,
'TQQ': 7.76,
'NRG': 8.35,
'BPE': 7.24,
'F2F': 6.25,
'1TQ': 8.58,
'I2M': 3.13,
'NVA': 3.76,
'R1A': 8.2,
'QPA': 6.95,
'C1X': 11.63,
'FRD': 5.05,
'HR7': 6.98,
'SNC': 3.93,
'QPH': 5.15,
'26B': 8.39,
'DPQ': 6.54,
'DPP': 2.51,
'2TY': 8.65,
'TNR': 6.88,
'PTH': 8.35,
'DPL': 3.58,
'APK': 8.79,
'1TY': 8.84,
'HRG': 7.36,
'PTM': 8.74,
'1U8': 3.62,
'PTR': 8.64,
'LVG': 3.01,
'6FL': 4.85,
'SOC': 4.05,
'KPI': 9.79,
'IPG': 2.91,
'P2Y': 2.51,
'N2C': 3.55,
'T0I': 7.34,
'MPH': 5.29,
'R2T': 4.71,
'TOX': 6.78,
'P2Q': 9.8,
'GPL': 10.77,
'MPJ': 5.07,
'F2Y': 6.2,
'T11': 8.58,
'9NR': 9.33,
'FPR': 8.85,
'9NF': 8.93,
'KPY': 10.17,
'9NE': 9.77,
'TOQ': 7.5,
'MPQ': 4.2,
'FPK': 3.08,
'HQA': 7.25,
'SOY': 10.94
}
const DefaultResidueRadius = 5.0
// http://dx.doi.org/10.1039/b801115j (or 1.6)
const CovalentRadii = {
'H': 0.31,
'HE': 0.28,
'LI': 1.28,
'BE': 0.96,
'B': 0.84,
'C': 0.76,
'N': 0.71,
'O': 0.66,
'F': 0.57,
'NE': 0.58,
'NA': 1.66,
'MG': 1.41,
'AL': 1.21,
'SI': 1.11,
'P': 1.07,
'S': 1.05,
'CL': 1.02,
'AR': 1.06,
'K': 2.03,
'CA': 1.76,
'SC': 1.7,
'TI': 1.6,
'V': 1.53,
'CR': 1.39,
'MN': 1.39,
'FE': 1.32,
'CO': 1.26,
'NI': 1.24,
'CU': 1.32,
'ZN': 1.22,
'GA': 1.22,
'GE': 1.2,
'AS': 1.19,
'SE': 1.2,
'BR': 1.2,
'KR': 1.16,
'RB': 2.2,
'SR': 1.95,
'Y': 1.9,
'ZR': 1.75,
'NB': 1.64,
'MO': 1.54,
'TC': 1.47,
'RU': 1.46,
'RH': 1.42,
'PD': 1.39,
'AG': 1.45,
'CD': 1.44,
'IN': 1.42,
'SN': 1.39,
'SB': 1.39,
'TE': 1.38,
'I': 1.39,
'XE': 1.4,
'CS': 2.44,
'BA': 2.15,
'LA': 2.07,
'CE': 2.04,
'PR': 2.03,
'ND': 2.01,
'PM': 1.99,
'SM': 1.98,
'EU': 1.98,
'GD': 1.96,
'TB': 1.94,
'DY': 1.92,
'HO': 1.92,
'ER': 1.89,
'TM': 1.9,
'YB': 1.87,
'LU': 1.87,
'HF': 1.75,
'TA': 1.7,
'W': 1.62,
'RE': 1.51,
'OS': 1.44,
'IR': 1.41,
'PT': 1.36,
'AU': 1.36,
'HG': 1.32,
'TL': 1.45,
'PB': 1.46,
'BI': 1.48,
'PO': 1.4,
'AT': 1.5,
'RN': 1.5,
'FR': 2.6,
'RA': 2.21,
'AC': 2.15,
'TH': 2.06,
'PA': 2.0,
'U': 1.96,
'NP': 1.9,
'PU': 1.87,
'AM': 1.8,
'CM': 1.69,
'BK': 1.6,
'CF': 1.6,
'ES': 1.6,
'FM': 1.6,
'MD': 1.6,
'NO': 1.6,
'LR': 1.6,
'RF': 1.6,
'DB': 1.6,
'SG': 1.6,
'BH': 1.6,
'HS': 1.6,
'MT': 1.6,
'DS': 1.6,
'RG': 1.6,
'CN': 1.6,
'UUT': 1.6,
'FL': 1.6,
'UUP': 1.6,
'LV': 1.6,
'UUH': 1.6
}
const DefaultCovalentRadius = 1.6
// http://blanco.biomol.uci.edu/Whole_residue_HFscales.txt
const ResidueHydrophobicity = {
// AA DGwif DGwoct Oct-IF
'ALA': [ 0.17, 0.50, 0.33 ],
'ARG': [ 0.81, 1.81, 1.00 ],
'ASN': [ 0.42, 0.85, 0.43 ],
'ASP': [ 1.23, 3.64, 2.41 ],
'ASH': [ -0.07, 0.43, 0.50 ],
'CYS': [ -0.24, -0.02, 0.22 ],
'GLN': [ 0.58, 0.77, 0.19 ],
'GLU': [ 2.02, 3.63, 1.61 ],
'GLH': [ -0.01, 0.11, 0.12 ],
'GLY': [ 0.01, 1.15, 1.14 ],
// "His+": [ 0.96, 2.33, 1.37 ],
'HIS': [ 0.17, 0.11, -0.06 ],
'ILE': [ -0.31, -1.12, -0.81 ],
'LEU': [ -0.56, -1.25, -0.69 ],
'LYS': [ 0.99, 2.80, 1.81 ],
'MET': [ -0.23, -0.67, -0.44 ],
'PHE': [ -1.13, -1.71, -0.58 ],
'PRO': [ 0.45, 0.14, -0.31 ],
'SER': [ 0.13, 0.46, 0.33 ],
'THR': [ 0.14, 0.25, 0.11 ],
'TRP': [ -1.85, -2.09, -0.24 ],
'TYR': [ -0.94, -0.71, 0.23 ],
'VAL': [ 0.07, -0.46, -0.53 ]
}
const DefaultResidueHydrophobicity = [ 0.00, 0.00, 0.00 ]
const AA1 = {
'HIS': 'H',
'ARG': 'R',
'LYS': 'K',
'ILE': 'I',
'PHE': 'F',
'LEU': 'L',
'TRP': 'W',
'ALA': 'A',
'MET': 'M',
'PRO': 'P',
'CYS': 'C',
'ASN': 'N',
'VAL': 'V',
'GLY': 'G',
'SER': 'S',
'GLN': 'Q',
'TYR': 'Y',
'ASP': 'D',
'GLU': 'E',
'THR': 'T',
'ASH': 'D',
'GLH': 'E',
'UNK': ''
}
const AA3 = Object.keys(AA1)
const RnaBases = [ 'A', 'C', 'T', 'G', 'U' ]
const DnaBases = [ 'DA', 'DC', 'DT', 'DG', 'DU', 'TCY', 'MCY', '5CM' ]
const PurinBases = [ 'A', 'G', 'DA', 'DG' ]
const WaterNames = [
'SOL', 'WAT', 'HOH', 'H2O', 'W', 'DOD', 'D3O', 'TIP3', 'TIP4', 'SPC'
]
// all chemical components with the word "ion" in their name, Sep 2016
//
// SET SESSION group_concat_max_len = 1000000;
// SELECT GROUP_CONCAT(id_ ORDER BY id_ ASC SEPARATOR '", "') from
// (
// SELECT count(obj_id) as c, id_
// FROM pdb.chem_comp WHERE name LIKE "% ION%"
// GROUP BY id_
// ) AS t1;
const IonNames = [
'118', '119', '1AL', '1CU', '2FK', '2HP', '2OF', '3CO',
'3MT', '3NI', '3OF', '3P8', '4MO', '4PU', '543', '6MO', 'ACT', 'AG', 'AL',
'ALF', 'AM', 'ATH', 'AU', 'AU3', 'AUC', 'AZI', 'BA', 'BCT', 'BEF', 'BF4', 'BO4',
'BR', 'BS3', 'BSY', 'CA', 'CAC', 'CD', 'CD1', 'CD3', 'CD5', 'CE', 'CHT', 'CL',
'CO', 'CO3', 'CO5', 'CON', 'CR', 'CS', 'CSB', 'CU', 'CU1', 'CU3', 'CUA', 'CUZ',
'CYN', 'DME', 'DMI', 'DSC', 'DTI', 'DY', 'E4N', 'EDR', 'EMC', 'ER3', 'EU',
'EU3', 'F', 'FE', 'FE2', 'FPO', 'GA', 'GD3', 'GEP', 'HAI', 'HG', 'HGC', 'IN',
'IOD', 'IR', 'IR3', 'IRI', 'IUM', 'K', 'KO4', 'LA', 'LCO', 'LCP', 'LI', 'LU',
'MAC', 'MG', 'MH2', 'MH3', 'MLI', 'MLT', 'MMC', 'MN', 'MN3', 'MN5', 'MN6',
'MO1', 'MO2', 'MO3', 'MO4', 'MO5', 'MO6', 'MOO', 'MOS', 'MOW', 'MW1', 'MW2',
'MW3', 'NA', 'NA2', 'NA5', 'NA6', 'NAO', 'NAW', 'NCO', 'NET', 'NH4', 'NI',
'NI1', 'NI2', 'NI3', 'NO2', 'NO3', 'NRU', 'O4M', 'OAA', 'OC1', 'OC2', 'OC3',
'OC4', 'OC5', 'OC6', 'OC7', 'OC8', 'OCL', 'OCM', 'OCN', 'OCO', 'OF1', 'OF2',
'OF3', 'OH', 'OS', 'OS4', 'OXL', 'PB', 'PBM', 'PD', 'PDV', 'PER', 'PI', 'PO3',
'PO4', 'PR', 'PT', 'PT4', 'PTN', 'RB', 'RH3', 'RHD', 'RU', 'SB', 'SCN', 'SE4',
'SEK', 'SM', 'SMO', 'SO3', 'SO4', 'SR', 'T1A', 'TB', 'TBA', 'TCN', 'TEA', 'TH',
'THE', 'TL', 'TMA', 'TRA', 'UNX', 'V', 'VN3', 'VO4', 'W', 'WO5', 'Y1', 'YB',
'YB2', 'YH', 'YT3', 'ZCM', 'ZN', 'ZN2', 'ZN3', 'ZNO', 'ZO3',
// additional ion names
'OHX'
]
// all chemical components with the word "%saccharide%" in their type, Sep 2016
//
// SET SESSION group_concat_max_len = 1000000;
// select GROUP_CONCAT(id_ ORDER BY id_ ASC SEPARATOR '", "') from
// (
// SELECT count(obj_id), id_
// FROM pdb.chem_comp WHERE type like "%SACCHARIDE%"
// GROUP BY id_
// ) AS t1;
const SaccharideNames = [
'045', '0AT', '0BD', '0MK', '0NZ', '0TS', '0V4', '0XY', '0YT', '10M',
'147', '149', '14T', '15L', '16G', '18T', '18Y', '1AR', '1BW', '1GL', '1GN',
'1JB', '1LL', '1NA', '1S3', '26M', '26Q', '26R', '26V', '26W', '26Y', '27C',
'289', '291', '293', '2DG', '2F8', '2FG', '2FL', '2FP', '2GL', '2M4', '2M5',
'32O', '34V', '3CM', '3DO', '3DY', '3FM', '3LR', '3MF', '3MG', '3SA', '3ZW',
'46D', '46M', '46Z', '48Z', '4CQ', '4GC', '4NN', '50A', '5DI', '5GF', '5MM',
'5RP', '5SA', '5SP', '64K', '6PG', '6SA', '7JZ', '7SA', 'A1Q', 'A2G', 'AAB',
'AAL', 'AAO', 'ABC', 'ABD', 'ABE', 'ABF', 'ABL', 'ACG', 'ACI', 'ACR', 'ACX',
'ADA', 'ADG', 'ADR', 'AF1', 'AFD', 'AFL', 'AFO', 'AFP', 'AFR', 'AGC', 'AGH',
'AGL', 'AHR', 'AIG', 'ALL', 'ALX', 'AMU', 'AOG', 'AOS', 'ARA', 'ARB', 'ARE',
'ARI', 'ASG', 'ASO', 'AXP', 'AXR', 'B0D', 'B16', 'B2G', 'B4G', 'B6D', 'B8D',
'B9D', 'BBK', 'BCD', 'BDG', 'BDP', 'BDR', 'BEM', 'BFP', 'BGC', 'BGL', 'BGP',
'BGS', 'BHG', 'BMA', 'BMX', 'BNG', 'BNX', 'BOG', 'BRI', 'BXF', 'BXP', 'BXX',
'BXY', 'C3X', 'C4X', 'C5X', 'CAP', 'CBI', 'CBK', 'CBS', 'CDR', 'CEG', 'CGF',
'CHO', 'CR1', 'CR6', 'CRA', 'CT3', 'CTO', 'CTR', 'CTT', 'D6G', 'DAF', 'DAG',
'DDA', 'DDB', 'DDL', 'DEL', 'DFR', 'DFX', 'DG0', 'DGC', 'DGD', 'DGM', 'DGS',
'DIG', 'DLF', 'DLG', 'DMU', 'DNO', 'DOM', 'DP5', 'DQQ', 'DQR', 'DR2', 'DR3',
'DR4', 'DRI', 'DSR', 'DT6', 'DVC', 'E4P', 'E5G', 'EAG', 'EBG', 'EBQ', 'EGA',
'EJT', 'EPG', 'ERE', 'ERI', 'F1P', 'F1X', 'F6P', 'FBP', 'FCA', 'FCB', 'FCT',
'FDP', 'FDQ', 'FFC', 'FIX', 'FMO', 'FRU', 'FSI', 'FU4', 'FUB', 'FUC', 'FUD',
'FUL', 'FXP', 'G16', 'G1P', 'G2F', 'G3I', 'G4D', 'G4S', 'G6D', 'G6P', 'G6S',
'GAC', 'GAD', 'GAL', 'GC1', 'GC4', 'GCD', 'GCN', 'GCO', 'GCS', 'GCT', 'GCU',
'GCV', 'GCW', 'GCX', 'GE1', 'GFG', 'GFP', 'GIV', 'GL0', 'GL2', 'GL5', 'GL6',
'GL7', 'GL9', 'GLA', 'GLB', 'GLC', 'GLD', 'GLF', 'GLG', 'GLO', 'GLP', 'GLS',
'GLT', 'GLW', 'GMH', 'GN1', 'GNX', 'GP1', 'GP4', 'GPH', 'GPM', 'GQ1', 'GQ2',
'GQ4', 'GS1', 'GS4', 'GSA', 'GSD', 'GTE', 'GTH', 'GTK', 'GTR', 'GTZ', 'GU0',
'GU1', 'GU2', 'GU3', 'GU4', 'GU5', 'GU6', 'GU8', 'GU9', 'GUF', 'GUP', 'GUZ',
'GYP', 'GYV', 'H2P', 'HDL', 'HMS', 'HS2', 'HSD', 'HSG', 'HSH', 'HSJ', 'HSQ',
'HSR', 'HSU', 'HSX', 'HSY', 'HSZ', 'IAB', 'IDG', 'IDR', 'IDS', 'IDT', 'IDU',
'IDX', 'IDY', 'IMK', 'IN1', 'IPT', 'ISL', 'KBG', 'KD2', 'KDA', 'KDM', 'KDO',
'KFN', 'KO1', 'KO2', 'KTU', 'L6S', 'LAG', 'LAI', 'LAK', 'LAO', 'LAT', 'LB2',
'LBT', 'LCN', 'LDY', 'LGC', 'LGU', 'LM2', 'LMT', 'LMU', 'LOG', 'LOX', 'LPK',
'LSM', 'LTM', 'LVZ', 'LXB', 'LXZ', 'M1F', 'M3M', 'M6P', 'M8C', 'MA1', 'MA2',
'MA3', 'MAB', 'MAG', 'MAL', 'MAN', 'MAT', 'MAV', 'MAW', 'MBG', 'MCU', 'MDA',
'MDM', 'MDP', 'MFA', 'MFB', 'MFU', 'MG5', 'MGA', 'MGL', 'MLB', 'MMA', 'MMN',
'MN0', 'MRP', 'MTT', 'MUG', 'MVP', 'MXY', 'N1L', 'N9S', 'NAA', 'NAG', 'NBG',
'NDG', 'NED', 'NG1', 'NG6', 'NGA', 'NGB', 'NGC', 'NGE', 'NGF', 'NGL', 'NGS',
'NGY', 'NHF', 'NM6', 'NM9', 'NTF', 'NTO', 'NTP', 'NXD', 'NYT', 'OPG', 'OPM',
'ORP', 'OX2', 'P3M', 'P53', 'P6P', 'PA5', 'PNA', 'PNG', 'PNW', 'PRP', 'PSJ',
'PSV', 'PTQ', 'QDK', 'QPS', 'QV4', 'R1P', 'R1X', 'R2B', 'R5P', 'RAA', 'RAE',
'RAF', 'RAM', 'RAO', 'RAT', 'RB5', 'RBL', 'RCD', 'RDP', 'REL', 'RER', 'RF5',
'RG1', 'RGG', 'RHA', 'RIB', 'RIP', 'RNS', 'RNT', 'ROB', 'ROR', 'RPA', 'RST',
'RUB', 'RUU', 'RZM', 'S6P', 'S7P', 'SA0', 'SCR', 'SDD', 'SF6', 'SF9', 'SG4',
'SG5', 'SG6', 'SG7', 'SGA', 'SGC', 'SGD', 'SGN', 'SGS', 'SHB', 'SHG', 'SI3',
'SIO', 'SOE', 'SOL', 'SSG', 'SUC', 'SUP', 'SUS', 'T6P', 'T6T', 'TAG', 'TCB',
'TDG', 'TGK', 'TGY', 'TH1', 'TIA', 'TM5', 'TM6', 'TM9', 'TMR', 'TMX', 'TOA',
'TOC', 'TRE', 'TYV', 'UCD', 'UDC', 'VG1', 'X0X', 'X1X', 'X2F', 'X4S', 'X5S',
'X6X', 'XBP', 'XDN', 'XDP', 'XIF', 'XIM', 'XLF', 'XLS', 'XMM', 'XUL', 'XXR',
'XYP', 'XYS', 'YO5', 'Z3Q', 'Z6J', 'Z9M', 'ZDC', 'ZDM'
]
const ProteinBackboneAtoms = [
'CA', 'C', 'N', 'O',
'O1', 'O2', 'OC1', 'OC2', 'OX1', 'OXT',
'H', 'H1', 'H2', 'H3', 'HA', 'HN',
'BB'
]
const NucleicBackboneAtoms = [
'P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2',
'O3*', 'O5*', 'C5*', 'C4*', 'C3*'
]
const ResidueTypeAtoms = {}
ResidueTypeAtoms[ ProteinBackboneType ] = {
trace: 'CA',
direction1: 'C',
direction2: [ 'O', 'OC1', 'O1', 'OX1', 'OXT' ],
backboneStart: 'N',
backboneEnd: 'C'
}
ResidueTypeAtoms[ RnaBackboneType ] = {
trace: [ "C4'", 'C4*' ],
direction1: [ "C1'", 'C1*' ],
direction2: [ "C3'", 'C3*' ],
backboneStart: 'P',
backboneEnd: [ "O3'", 'O3*' ]
}
ResidueTypeAtoms[ DnaBackboneType ] = {
trace: [ "C3'", 'C3*' ],
direction1: [ "C2'", 'C2*' ],
direction2: [ "O4'", 'O4*' ],
backboneStart: 'P',
backboneEnd: [ "O3'", 'O3*' ]
}
ResidueTypeAtoms[ CgProteinBackboneType ] = {
trace: [ 'CA', 'BB' ],
backboneStart: [ 'CA', 'BB' ],
backboneEnd: [ 'CA', 'BB' ]
}
ResidueTypeAtoms[ CgRnaBackboneType ] = {
trace: [ "C4'", 'C4*', 'P' ],
backboneStart: [ "C4'", 'C4*', 'P' ],
backboneEnd: [ "C4'", 'C4*', 'P' ]
}
ResidueTypeAtoms[ CgDnaBackboneType ] = {
trace: [ "C3'", 'C3*', "C2'", 'P' ], // C2' is used in martini ff
backboneStart: [ "C3'", 'C3*', "C2'", 'P' ],
backboneEnd: [ "C3'", 'C3*', "C2'", 'P' ]
}
ResidueTypeAtoms[ UnknownBackboneType ] = {}
export {
UnknownEntity,
PolymerEntity,
NonPolymerEntity,
MacrolideEntity,
WaterEntity,
UnknownType,
WaterType,
IonType,
ProteinType,
RnaType,
DnaType,
SaccharideType,
UnknownBackboneType,
ProteinBackboneType,
RnaBackboneType,
DnaBackboneType,
CgProteinBackboneType,
CgRnaBackboneType,
CgDnaBackboneType,
ChemCompProtein,
ChemCompRna,
ChemCompDna,
ChemCompSaccharide,
ChemCompOther,
ChemCompNonPolymer,
ChemCompHetero,
SecStrucHelix,
SecStrucSheet,
SecStrucTurn,
VdwRadii,
DefaultVdwRadius,
ResidueRadii,
DefaultResidueRadius,
CovalentRadii,
DefaultCovalentRadius,
ResidueHydrophobicity,
DefaultResidueHydrophobicity,
AA1,
AA3,
RnaBases,
DnaBases,
PurinBases,
WaterNames,
IonNames,
SaccharideNames,
ProteinBackboneAtoms,
NucleicBackboneAtoms,
ResidueTypeAtoms
}
