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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
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* modification, are permitted provided that the following conditions are met:
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* derived from this software without specific prior written permission.
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package com.actelion.research.chem;
public class MolecularFormula {
private static final double[] sRelativeMass = { 0.0,
1.00794, 4.0026, 6.9410, 9.0122, 10.811, 12.011, // H , He, Li, Be, B , C ,
14.007, 15.999, 18.998, 20.180, 22.990, 24.305, // N , O , F , Ne, Na, Mg,
26.982, 28.086, 30.974, 32.066, 35.453, 39.948, // Al, Si, P , S , Cl, Ar,
39.098, 40.078, 44.956, 47.867, 50.942, 51.996, // K , Ca, Sc, Ti, V , Cr,
54.938, 55.845, 58.933, 58.693, 63.546, 65.390, // Mn, Fe, Co, Ni, Cu, Zn,
69.723, 72.610, 74.922, 78.960, 79.904, 83.800, // Ga, Ge, As, Se, Br, Kr,
85.468, 87.620, 88.906, 91.224, 92.906, 95.940, // Rb, Sr, Y , Zr, Nb, Mo,
98.906, 101.07, 102.91, 106.42, 107.87, 112.41, // Tc, Ru, Rh, Pd, Ag, Cd,
114.82, 118.71, 121.76, 127.60, 126.90, 131.29, // In, Sn, Sb, Te, I , Xe,
132.91, 137.33, 138.91, 140.12, 140.91, 144.24, // Cs, Ba, La, Ce, Pr, Nd,
146.92, 150.36, 151.96, 157.25, 158.93, 162.50, // Pm, Sm, Eu, Gd, Tb, Dy,
164.93, 167.26, 168.93, 173.04, 174.97, 178.49, // Ho, Er, Tm, Yb, Lu, Hf,
180.95, 183.84, 186.21, 190.23, 192.22, 195.08, // Ta, W, Re, Os, Ir, Pt,
196.97, 200.59, 204.38, 207.20, 208.98, 209.98, // Au, Hg, Tl, Pb, Bi, Po,
209.99, 222.02, 223.02, 226.03, 227.03, 232.04, // At, Rn, Fr, Ra, Ac, Th,
231.04, 238.03, 237.05, 239.05, 241.06, 244.06, // Pa, U, Np, Pu, Am, Cm,
249.08, 252.08, 252.08, 257.10, 258.10, 259.10, // Bk, C, Es, Fm, Md, No,
262.11, 267.12, 268.13, 271.13, 270.13, 277.15, // Lr, Rf, Db, Sg, Bh, Hs,
276.15, 281.17, 281.17, 283.17, 285.18, 289.19, // Mt ,Ds ,Rg ,Cn ,Nh ,Fl,
289.19, 293.20, 294.21, 294.21, 0.0, 0.0, // Mc ,Lv ,Ts ,Og ,?? ,??,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, // ??, ??, ??, ??, ??, ??,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, // ??, ??, R4, R5, R6, R7,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, // R8, R9, R10,R11,R12,R13,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, // R14,R15,R16,R1, R2, R3,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, // A , A1, A2, A3, ??, ??,
2.0141, 3.0160, 0.0, 0.0, 0.0, 0.0, // D , T , X , R , H2, H+,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, // Nnn,HYD,Pol,??, ??, ??,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, // ??, ??, ??, ??, ??, ??,
0.0, 0.0, 71.0787, 156.18828, 114.10364, 115.0877, // ??, ??, Ala,Arg,Asn,Asp, relative masses of amino acids reduced by one H2O
103.1447, 128.13052, 129.11458, 57.05182, 137.14158, 113.15934, // Cys,Gln,Glu,Gly,His,Ile,
113.15934, 128.17428, 131.19846, 147.17646, 97.11658, 87.0777, // Leu,Lys,Met,Phe,Pro,Ser,
101.10458, 186.2134 , 163.17546, 99.13246 }; // Thr,Trp,Tyr,Val,
private static final double[] sAbsoluteMass = { 0.0,
1.007825, 4.00260 , 7.016003, 9.012182, // H, He,Li,Be
11.009305, 12.000000, 14.003074, 15.994915, // B ,C ,N, O
18.998403, 19.992435, 22.989767, 23.985042, // F ,Ne,Na,Mg
26.98153 , 27.976927, 30.973762, 31.972070, // Al,Si,P ,S
34.968852, 39.962384, 38.963707, 39.962591, // Cl,Ar,K ,Ca
44.955910, 47.947947, 50.943962, 51.940509, // Sc,Ti,V ,Cr
54.938047, 55.934939, 58.933198, 57.935346, // Mn,Fe,Co,Ni
62.939598, 63.929145, 68.925580, 73.921177, // Cu,Zn,Ga,Ge
74.921594, 79.916520, 78.918336, 83.911507, // As,Se,Br,Kr
84.911794, 87.905619, 88.905849, 89.904703, // Rb,Sr,Y ,Zr
92.906377, 97.905406, 89.923810, 101.904348, // Nb,Mo,Tc,Ru
102.905500, 105.903478, 106.905092, 113.903357, // Rh,Pd,Ag,Cd
114.903880, 119.902200, 120.903821, 129.906229, // In,Sn,Sb,Te
126.904473, 131.904144, 132.905429, 137.905232, // I ,Xe,Cs,Ba
138.906346, 139.905433, 140.907647, 141.907719, // La,Ce,Pr,Nd
135.923980, 151.919729, 152.921225, 157.924099, // Pm,Sm,Eu,Gd
158.925342, 163.929171, 164.930319, 165.930290, // Tb,Dy,Ho,Er
168.934212, 173.938859, 174.940770, 179.946545, // Tm,Yb,Lu,Hf
180.947992, 183.950928, 186.955744, 191.961467, // Ta,W, Re,Os
192.962917, 194.964766, 196.966543, 201.970617, // Ir,Pt,Au,Hg
204.974401, 207.976627, 208.980374, 193.988180, // Tl,Pb,Bi,Po
195.995730, 199.995700, 201.004110, 206.003800, // At,Rn,Fr,Ra
210.009230, 232.038054, 216.018960, 238.050784, // Ac,Th,Pa,U
229.036230, 232.041169, 237.050050, 238.053020, // Np,Pu,Am,Cm
242.061940, 240.062280, 243.069470, 243.074460, // Bk,C ,Es,Fm
248.082750, 251.088870, 253.095150, 257.102950, // Md,No,Lr,Rf
257.107770, 271.13, 270.13, 277.15, // Db,Sg,Bh,Hs
276.15, 281.17, 281.17, 283.17, // Mt,Ds,Rg,Cn
285.18, 289.19, 289.19, 291.20, // Nh,Fl,Mc,Lv
294.21, 294.21, 0.0f, 0.0f, // Ts,Og,??,??
0.0f, 0.0f, 0.0f, 0.0f, // ??,??,??,??
0.0f, 0.0f, 0.0f, 0.0f, // ??,??,??,??
0.0f, 0.0f, 0.0f, 0.0f, // R4,R5,R6,R7
0.0f, 0.0f, 0.0f, 0.0f, // R8,R9,R10,R11
0.0f, 0.0f, 0.0f, 0.0f, // R12,R13,R14,R15
0.0f, 0.0f, 0.0f, 0.0f, // R16,R1,R2,R3
0.0f, 0.0f, 0.0f, 0.0f, // A ,A1,A2,A3
0.0f, 0.0f, 2.0140, 3.01605, // ??,??,D ,T
0.0f, 0.0f, 0.0f, 0.0f, // X ,R ,H2,H+
// 12/18/2007 CxR Added the following
0.0f, 0.0f, 0.0f, 0.0f, // Nnn,HYD,Pol,??
0.0f, 0.0f, 0.0f, 0.0f, // ??,??,??,??
0.0f, 0.0f, 0.0f, 0.0f, // ??,??,??,??
0.0f, 0.0f, 0.0f, 0.0f, // ??, ??, Ala,Arg
0.0f, 0.0f, 0.0f, 0.0f, // Asn,Asp,,Cys,Gln
0.0f, 0.0f, 0.0f, 0.0f, // Glu,Gly,His,Ile,
0.0f, 0.0f, 0.0f, 0.0f, // Leu,Lys,Met,Phe
0.0f, 0.0f, 0.0f, 0.0f, // Pro,Ser,Thr,Trp,
0.0f, 0.0f, // Tyr,Val
};
private static final int[] sFirstFormulaAtomicNo = { 6, 1, 7, 8 };
private int[] mAtomCount,mAtomicNo;
private double mAbsoluteIsotopeWeightIncrement,mRelativeIsotopeWeightIncrement;
public MolecularFormula(ExtendedMolecule mol) {
mol.ensureHelperArrays(Molecule.cHelperNeighbours);
int[] atomCount = new int[Molecule.cMaxAtomicNo+1];
for (int atom=0; atom= 171 && mol.getAtomicNo(atom) <= 190) // amino acids
atomCount[1] += 2 - mol.getOccupiedValence(atom);
else {
atomCount[1] += mol.getImplicitHydrogens(atom);
}
// count number of present atomicNos and initialize arrays
int atomicNoCount = 0;
for (int i=1; i<=Molecule.cMaxAtomicNo; i++)
if (atomCount[i] != 0)
atomicNoCount++;
mAtomCount = new int[atomicNoCount];
mAtomicNo = new int[atomicNoCount];
// list elements in sFirstFormulaAtomicNo[] first
atomicNoCount = 0;
for (int i=0; i 0
&& lowestLabel.compareTo(Molecule.cAtomLabel[atomicNo]) > 0) {
lowestLabel = Molecule.cAtomLabel[atomicNo];
lowestAtomicNo = atomicNo;
}
if (lowestAtomicNo == -1)
break;
mAtomCount[atomicNoCount] = atomCount[lowestAtomicNo];
mAtomicNo[atomicNoCount] = lowestAtomicNo;
atomicNoCount++;
atomCount[lowestAtomicNo] = 0;
}
mAbsoluteIsotopeWeightIncrement = 0.0;
mRelativeIsotopeWeightIncrement = 0.0;
for (int atom=0; atom 1)
formula.append(mAtomCount[i]);
}
return formula.toString();
}
@Override
public boolean equals(Object f) {
if (f == this)
return true;
if (!(f instanceof MolecularFormula))
return false;
for (int i=0; i