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structure-constants.ts
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structure-constants.ts
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/**
* @file Structure Constants
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @private
*/
// entity types
export const UnknownEntity = 0
export const PolymerEntity = 1
export const NonPolymerEntity = 2
export const MacrolideEntity = 3
export const WaterEntity = 4
// molecule types
export const UnknownType = 0
export const WaterType = 1
export const IonType = 2
export const ProteinType = 3
export const RnaType = 4
export const DnaType = 5
export const SaccharideType = 6
// backbone types
export const UnknownBackboneType = 0
export const ProteinBackboneType = 1
export const RnaBackboneType = 2
export const DnaBackboneType = 3
export const CgProteinBackboneType = 4
export const CgRnaBackboneType = 5
export const CgDnaBackboneType = 6
// chemical component types
export 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'
]
export const ChemCompRna = [
'RNA OH 3 PRIME TERMINUS', 'RNA OH 5 PRIME TERMINUS', 'RNA LINKING'
]
export const ChemCompDna = [
'DNA OH 3 PRIME TERMINUS', 'DNA OH 5 PRIME TERMINUS', 'DNA LINKING',
'L-DNA LINKING', 'L-RNA LINKING'
]
export 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'
]
export const ChemCompOther = [
'OTHER'
]
export const ChemCompNonPolymer = [
'NON-POLYMER'
]
export const ChemCompHetero = ChemCompNonPolymer.concat(ChemCompOther, ChemCompSaccharide)
// secondary structure
export const SecStrucHelix = [ 'h', 'g', 'i' ]
export const SecStrucSheet = [ 'e', 'b' ]
export const SecStrucTurn = [ 's', 't', 'l', '' ]
export const AtomicNumbers: { [e: string]: number | undefined } = {
'H': 1, 'D': 1, 'T': 1, 'HE': 2, 'LI': 3, 'BE': 4, 'B': 5, 'C': 6, 'N': 7, 'O': 8, 'F': 9, 'NE': 10, 'NA': 11, 'MG': 12, 'AL': 13, 'SI': 14, 'P': 15, 'S': 16, 'CL': 17, 'AR': 18, 'K': 19, 'CA': 20, 'SC': 21, 'TI': 22, 'V': 23, 'CR': 24, 'MN': 25, 'FE': 26, 'CO': 27, 'NI': 28, 'CU': 29, 'ZN': 30, 'GA': 31, 'GE': 32, 'AS': 33, 'SE': 34, 'BR': 35, 'KR': 36, 'RB': 37, 'SR': 38, 'Y': 39, 'ZR': 40, 'NB': 41, 'MO': 42, 'TC': 43, 'RU': 44, 'RH': 45, 'PD': 46, 'AG': 47, 'CD': 48, 'IN': 49, 'SN': 50, 'SB': 51, 'TE': 52, 'I': 53, 'XE': 54, 'CS': 55, 'BA': 56, 'LA': 57, 'CE': 58, 'PR': 59, 'ND': 60, 'PM': 61, 'SM': 62, 'EU': 63, 'GD': 64, 'TB': 65, 'DY': 66, 'HO': 67, 'ER': 68, 'TM': 69, 'YB': 70, 'LU': 71, 'HF': 72, 'TA': 73, 'W': 74, 'RE': 75, 'OS': 76, 'IR': 77, 'PT': 78, 'AU': 79, 'HG': 80, 'TL': 81, 'PB': 82, 'BI': 83, 'PO': 84, 'AT': 85, 'RN': 86, 'FR': 87, 'RA': 88, 'AC': 89, 'TH': 90, 'PA': 91, 'U': 92, 'NP': 93, 'PU': 94, 'AM': 95, 'CM': 96, 'BK': 97, 'CF': 98, 'ES': 99, 'FM': 100, 'MD': 101, 'NO': 102, 'LR': 103, 'RF': 104, 'DB': 105, 'SG': 106, 'BH': 107, 'HS': 108, 'MT': 109, 'DS': 110, 'RG': 111, 'CN': 112, 'NH': 113, 'FL': 114, 'MC': 115, 'LV': 116, 'TS': 117, 'OG': 118
}
export const DefaultAtomicNumber = 0
/**
* Enum mapping element to atomic number
*/
export const enum Elements {
H = 1, D = 1, T = 1, HE = 2, LI = 3, BE = 4, B = 5, C = 6, N = 7, O = 8, F = 9, NE = 10, NA = 11, MG = 12, AL = 13, SI = 14, P = 15, S = 16, CL = 17, AR = 18, K = 19, CA = 20, SC = 21, TI = 22, V = 23, CR = 24, MN = 25, FE = 26, CO = 27, NI = 28, CU = 29, ZN = 30, GA = 31, GE = 32, AS = 33, SE = 34, BR = 35, KR = 36, RB = 37, SR = 38, Y = 39, ZR = 40, NB = 41, MO = 42, TC = 43, RU = 44, RH = 45, PD = 46, AG = 47, CD = 48, IN = 49, SN = 50, SB = 51, TE = 52, I = 53, XE = 54, CS = 55, BA = 56, LA = 57, CE = 58, PR = 59, ND = 60, PM = 61, SM = 62, EU = 63, GD = 64, TB = 65, DY = 66, HO = 67, ER = 68, TM = 69, YB = 70, LU = 71, HF = 72, TA = 73, W = 74, RE = 75, OS = 76, IR = 77, PT = 78, AU = 79, HG = 80, TL = 81, PB = 82, BI = 83, PO = 84, AT = 85, RN = 86, FR = 87, RA = 88, AC = 89, TH = 90, PA = 91, U = 92, NP = 93, PU = 94, AM = 95, CM = 96, BK = 97, CF = 98, ES = 99, FM = 100, MD = 101, NO = 102, LR = 103, RF = 104, DB = 105, SG = 106, BH = 107, HS = 108, MT = 109, DS = 110, RG = 111, CN = 112, NH = 113, FL = 114, MC = 115, LV = 116, TS = 117, OG = 118
}
// https://doi.org/10.1515/pac-2015-0305 (table 2, 3, and 4)
export const AtomWeights: { [e: number]: number | undefined } = {
1: 1.008, 2: 4.0026, 3: 6.94, 4: 9.0122, 5: 10.81, 6: 10.81, 7: 14.007, 8: 15.999, 9: 18.998, 10: 20.180, 11: 22.990, 12: 24.305, 13: 26.982, 14: 28.085, 15: 30.974, 16: 32.06, 17: 35.45, 18: 39.948, 19: 39.098, 20: 40.078, 21: 44.956, 22: 47.867, 23: 50.942, 24: 51.996, 25: 54.938, 26: 55.845, 27: 58.933, 28: 58.693, 29: 63.546, 30: 65.38, 31: 69.723, 32: 72.630, 33: 74.922, 34: 78.971, 35: 79.904, 36: 83.798, 37: 85.468, 38: 87.62, 39: 88.906, 40: 91.224, 41: 92.906, 42: 95.95, 43: 96.906, 44: 101.07, 45: 102.91, 46: 106.42, 47: 107.87, 48: 112.41, 49: 114.82, 50: 118.71, 51: 121.76, 52: 127.60, 53: 127.60, 54: 131.29, 55: 132.91, 56: 137.33, 57: 138.91, 58: 140.12, 59: 140.91, 60: 144.24, 61: 144.912, 62: 150.36, 63: 151.96, 64: 157.25, 65: 158.93, 66: 162.50, 67: 164.93, 68: 167.26, 69: 168.93, 70: 173.05, 71: 174.97, 72: 178.49, 73: 180.95, 74: 183.84, 75: 186.21, 76: 190.23, 77: 192.22, 78: 195.08, 79: 196.97, 80: 200.59, 81: 204.38, 82: 207.2, 83: 208.98, 84: 1.97, 85: 2.02, 86: 2.2, 87: 3.48, 88: 2.83, 89: 2.0, 90: 232.04, 91: 231.04, 92: 238.03, 93: 237.048, 94: 244.064, 95: 243.061, 96: 247.070, 97: 247.070, 98: 251.079, 99: 252.083, 100: 257.095, 101: 258.098, 102: 259.101, 103: 262.110, 104: 267.122, 105: 270.131, 106: 271.134, 107: 270.133, 108: 270.134, 109: 278.156, 110: 281.165, 111: 281.166, 112: 285.177, 113: 286.182, 114: 289.190, 115: 289.194, 116: 293.204, 117: 293.208, 118: 294.214
}
export const DefaultAtomWeight = 10.81 // C
// http://dx.doi.org/10.1021/jp8111556 (or 2.0)
export const VdwRadii: { [e: number]: number | undefined } = {
1: 1.1, 2: 1.4, 3: 1.81, 4: 1.53, 5: 1.92, 6: 1.7, 7: 1.55, 8: 1.52, 9: 1.47, 10: 1.54, 11: 2.27, 12: 1.73, 13: 1.84, 14: 2.1, 15: 1.8, 16: 1.8, 17: 1.75, 18: 1.88, 19: 2.75, 20: 2.31, 21: 2.3, 22: 2.15, 23: 2.05, 24: 2.05, 25: 2.05, 26: 2.05, 27: 2.0, 28: 2.0, 29: 2.0, 30: 2.1, 31: 1.87, 32: 2.11, 33: 1.85, 34: 1.9, 35: 1.83, 36: 2.02, 37: 3.03, 38: 2.49, 39: 2.4, 40: 2.3, 41: 2.15, 42: 2.1, 43: 2.05, 44: 2.05, 45: 2.0, 46: 2.05, 47: 2.1, 48: 2.2, 49: 2.2, 50: 1.93, 51: 2.17, 52: 2.06, 53: 1.98, 54: 2.16, 55: 3.43, 56: 2.68, 57: 2.5, 58: 2.48, 59: 2.47, 60: 2.45, 61: 2.43, 62: 2.42, 63: 2.4, 64: 2.38, 65: 2.37, 66: 2.35, 67: 2.33, 68: 2.32, 69: 2.3, 70: 2.28, 71: 2.27, 72: 2.25, 73: 2.2, 74: 2.1, 75: 2.05, 76: 2.0, 77: 2.0, 78: 2.05, 79: 2.1, 80: 2.05, 81: 1.96, 82: 2.02, 83: 2.07, 84: 1.97, 85: 2.02, 86: 2.2, 87: 3.48, 88: 2.83, 89: 2.0, 90: 2.4, 91: 2.0, 92: 2.3, 93: 2.0, 94: 2.0, 95: 2.0, 96: 2.0, 97: 2.0, 98: 2.0, 99: 2.0, 100: 2.0, 101: 2.0, 102: 2.0, 103: 2.0, 104: 2.0, 105: 2.0, 106: 2.0, 107: 2.0, 108: 2.0, 109: 2.0, 110: 2.0, 111: 2.0, 112: 2.0, 113: 2.0, 114: 2.0, 115: 2.0, 116: 2.0, 117: 2.0, 118: 2.0
}
export const DefaultVdwRadius = 2.0 // C
// Peter Rose (peter.rose@rcsb.org), private communication, average accross PDB
export const ResidueRadii: { [k: string]: number } = {
'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
}
export const DefaultResidueRadius = 5.0
// http://dx.doi.org/10.1039/b801115j (or 1.6)
export const CovalentRadii: { [e: number]: number | undefined } = {
1: 0.31, 2: 0.28, 3: 1.28, 4: 0.96, 5: 0.84, 6: 0.76, 7: 0.71, 8: 0.66, 9: 0.57, 10: 0.58, 11: 1.66, 12: 1.41, 13: 1.21, 14: 1.11, 15: 1.07, 16: 1.05, 17: 1.02, 18: 1.06, 19: 2.03, 20: 1.76, 21: 1.7, 22: 1.6, 23: 1.53, 24: 1.39, 25: 1.39, 26: 1.32, 27: 1.26, 28: 1.24, 29: 1.32, 30: 1.22, 31: 1.22, 32: 1.2, 33: 1.19, 34: 1.2, 35: 1.2, 36: 1.16, 37: 2.2, 38: 1.95, 39: 1.9, 40: 1.75, 41: 1.64, 42: 1.54, 43: 1.47, 44: 1.46, 45: 1.42, 46: 1.39, 47: 1.45, 48: 1.44, 49: 1.42, 50: 1.39, 51: 1.39, 52: 1.38, 53: 1.39, 54: 1.4, 55: 2.44, 56: 2.15, 57: 2.07, 58: 2.04, 59: 2.03, 60: 2.01, 61: 1.99, 62: 1.98, 63: 1.98, 64: 1.96, 65: 1.94, 66: 1.92, 67: 1.92, 68: 1.89, 69: 1.9, 70: 1.87, 71: 1.87, 72: 1.75, 73: 1.7, 74: 1.62, 75: 1.51, 76: 1.44, 77: 1.41, 78: 1.36, 79: 1.36, 80: 1.32, 81: 1.45, 82: 1.46, 83: 1.48, 84: 1.4, 85: 1.5, 86: 1.5, 87: 2.6, 88: 2.21, 89: 2.15, 90: 2.06, 91: 2.0, 92: 1.96, 93: 1.9, 94: 1.87, 95: 1.8, 96: 1.69, 97: 1.6, 98: 1.6, 99: 1.6, 100: 1.6, 101: 1.6, 102: 1.6, 103: 1.6, 104: 1.6, 105: 1.6, 106: 1.6, 107: 1.6, 108: 1.6, 109: 1.6, 110: 1.6, 111: 1.6, 112: 1.6, 113: 1.6, 114: 1.6, 115: 1.6, 116: 1.6, 117: 1.6, 118: 1.6
}
export const DefaultCovalentRadius = 1.6
export const Valences: { [e: number]: number[] | undefined } = {
1: [ 1 ],
2: [ 0 ],
3: [ 1 ],
4: [ 2 ],
5: [ 3 ],
6: [ 4 ],
7: [ 3 ],
8: [ 2 ],
9: [ 1 ],
10: [ 0 ],
11: [ 1 ],
12: [ 2 ],
13: [ 6 ],
14: [ 6 ],
15: [ 3, 5, 7 ],
16: [ 2, 4, 6 ],
17: [ 1 ],
18: [ 0 ],
19: [ 1 ],
20: [ 2 ],
31: [ 3 ],
32: [ 4 ],
33: [ 3, 5 ],
34: [ 2, 4, 6 ],
35: [ 1 ],
36: [ 0 ],
37: [ 1 ],
38: [ 2 ],
49: [ 3 ],
50: [ 4 ],
51: [ 3, 5 ],
52: [ 2 ],
53: [ 1, 2, 5 ],
54: [ 0, 2 ],
55: [ 1 ],
56: [ 2 ],
81: [ 3 ],
82: [ 4 ],
83: [ 3 ],
84: [ 2 ],
85: [ 1 ],
86: [ 0 ],
87: [ 1 ],
88: [ 2 ]
}
export const DefaultValence = -1
export const OuterShellElectronCounts: { [e: number]: number | undefined } = {
1: 1, 2: 2, 3: 1, 4: 2, 5: 3, 6: 4, 7: 5, 8: 6, 9: 7, 10: 8, 11: 1, 12: 2, 13: 3, 14: 4, 15: 5, 16: 6, 17: 7, 18: 8, 19: 1, 20: 2, 21: 3, 22: 4, 23: 5, 24: 6, 25: 7, 26: 8, 27: 9, 28: 10, 29: 11, 30: 2, 31: 3, 32: 4, 33: 5, 34: 6, 35: 7, 36: 8, 37: 1, 38: 2, 39: 3, 40: 4, 41: 5, 42: 6, 43: 7, 44: 8, 45: 9, 46: 10, 47: 11, 48: 2, 49: 3, 50: 4, 51: 5, 52: 6, 53: 7, 54: 8, 55: 1, 56: 2, 57: 3, 58: 4, 59: 3, 60: 4, 61: 5, 62: 6, 63: 7, 64: 8, 65: 9, 66: 10, 67: 11, 68: 12, 69: 13, 70: 14, 71: 15, 72: 4, 73: 5, 74: 6, 75: 7, 76: 8, 77: 9, 78: 10, 79: 11, 80: 2, 81: 3, 82: 4, 83: 5, 84: 6, 85: 7, 86: 8, 87: 1, 88: 2, 89: 3, 90: 4, 91: 3, 92: 4, 93: 5, 94: 6, 95: 7, 96: 8, 97: 9, 98: 10, 99: 11, 100: 12, 101: 13, 102: 14, 103: 15, 104: 2, 105: 2, 106: 2, 107: 2, 108: 2, 109: 2, 110: 2, 111: 2, 112: 2, 113: 3, 114: 4, 115: 5, 116: 6, 117: 7, 118: 8
}
export const DefaultOuterShellElectronCount = 2
// http://blanco.biomol.uci.edu/Whole_residue_HFscales.txt
// https://www.nature.com/articles/nsb1096-842
export const ResidueHydrophobicity: { [k: string]: [number, number, number] } = {
// 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 ]
}
export const DefaultResidueHydrophobicity = [ 0.00, 0.00, 0.00 ]
export const AA1: { [k: string]: string } = {
'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',
'SEC': 'U', // as per IUPAC definition
'PYL': 'O', // as per IUPAC definition
}
export const AA3 = Object.keys(AA1)
export const RnaBases = [ 'A', 'C', 'T', 'G', 'U' ]
export const DnaBases = [ 'DA', 'DC', 'DT', 'DG', 'DU' ]
export const PurinBases = [ 'A', 'G', 'DA', 'DG' ]
export const Bases = RnaBases.concat(DnaBases)
export 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;
export 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;
export 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',