/*************************************************************************
* *
* This file is part of the 20n/act project. *
* 20n/act enables DNA prediction for synthetic biology/bioengineering. *
* Copyright (C) 2017 20n Labs, Inc. *
* *
* Please direct all queries to act@20n.com. *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
*************************************************************************/
package com.act.lcms;
import com.ggasoftware.indigo.Indigo;
import com.ggasoftware.indigo.IndigoInchi;
import com.ggasoftware.indigo.IndigoObject;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.tuple.Pair;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* Adapted from Chris's org.twentyn.services.emerald.IonChooser#calculateMass in the Experimental project.
*
* For additional masses and confirmation of the values used below, see
* http://www.sisweb.com/referenc/tools/exactmass.js (the js that drives
* http://www.sisweb.com/referenc/tools/exactmass.htm).
*/
public class MassCalculator {
private static final Indigo indigo = new Indigo();
private static final IndigoInchi iinchi = new IndigoInchi(indigo);;
public static Pair<Double, Integer> calculateMassAndCharge(String inchi) {
IndigoObject mol = iinchi.loadMolecule(inchi);
Double mass = calculateMass(mol);
Integer charge = calculateCharge(mol);
return Pair.of(mass, charge);
}
public static Integer calculateCharge(String inchi) {
return calculateCharge(iinchi.loadMolecule(inchi));
}
public static Integer calculateCharge(IndigoObject mol) {
int out = 0;
for (int i = 0; i < mol.countAtoms(); i++) {
IndigoObject atom = mol.getAtom(i);
int charge = atom.charge();
out += charge;
}
return out;
}
public static final Map<String, Double> ATOMIC_WEIGHTS = Collections.unmodifiableMap(new HashMap<String, Double>() {{
put("Ag", 106.905095d);
put("Al", 26.981541d);
put("Ar", 39.962383d);
put("As", 74.921596d);
put("Au", 196.966560d);
put("B", 11.009305d);
put("Ba", 137.905236d);
put("Be", 9.012183d);
put("Bi", 208.980388d);
put("Br", 78.918336d);
put("C", 12.000000d);
put("Ca", 39.962591d);
put("Cd", 113.903361d);
put("Ce", 139.905442d);
put("Cl", 34.968853d);
put("Co", 58.933198d);
put("Cr", 51.940510d);
put("Cs", 132.905433d);
put("Cu", 62.929599d);
put("Dy", 163.929183d);
put("Er", 165.930305d);
put("Eu", 152.921243d);
put("F", 18.998403d);
put("Fe", 55.934939d);
put("Ga", 68.925581d);
put("Gd", 157.924111d);
put("Ge", 73.921179d);
put("H", 1.007825d);
put("He", 4.002603d);
put("Hf", 179.946561d);
put("Hg", 201.970632d);
put("Ho", 164.930332d);
put("I", 126.904477d);
put("In", 114.903875d);
put("Ir", 192.962942d);
put("K", 38.963708d);
put("Kr", 83.911506d);
put("La", 138.906355d);
put("Li", 7.016005d);
put("Lu", 174.940785d);
put("Mg", 23.985045d);
put("Mn", 54.938046d);
put("Mo", 97.905405d);
put("N", 14.003074d);
put("Na", 22.989770d);
put("Nb", 92.906378d);
put("Nd", 141.907731d);
put("Ne", 19.992439d);
put("Ni", 57.935347d);
put("O", 15.994915d);
put("Os", 191.961487d);
put("P", 30.973763d);
put("Pb", 207.976641d);
put("Pd", 105.903475d);
put("Pr", 140.907657d);
put("Pt", 194.964785d);
put("Rb", 84.911800d);
put("Re", 186.955765d);
put("Rh", 102.905503d);
put("Ru", 101.90434d);
put("S", 31.972072d);
put("Sb", 120.903824d);
put("Sc", 44.955914d);
put("Se", 79.916521d);
put("Si", 27.976928d);
put("Sm", 151.919741d);
put("Sn", 119.902199d);
put("Sr", 87.905625d);
put("Ta", 180.948014d);
put("Tb", 158.925350d);
put("Te", 129.906229d);
put("Th", 232.038054d);
put("Ti", 47.947947d);
put("Tl", 204.974410d);
put("Tm", 168.934225d);
put("U", 238.050786d);
put("V", 50.943963d);
put("W", 183.950953d);
put("Xe", 131.904148d);
put("Y", 88.905856d);
put("Yb", 173.938873d);
put("Zn", 63.929145d);
put("Zr", 89.904708d);
}});
public static Double calculateMass(String inchi) {
return calculateMass(iinchi.loadMolecule(inchi));
}
private static final Pattern MOL_COUNT_PATTERN = Pattern.compile("^([A-Za-z]+)(\\d+)?$");
public static Double calculateMass(IndigoObject mol) {
String formula = mol.grossFormula();
double out = 0.0;
String[] molCounts = StringUtils.split(formula, " ");
for (String atomEntry : molCounts) {
//Extract the atom count
Matcher matcher = MOL_COUNT_PATTERN.matcher(atomEntry);
if (!matcher.matches()) {
throw new RuntimeException("Found unexpected malformed atomEntry: " + atomEntry);
}
String element = matcher.group(1);
String countStr = matcher.group(2);
Integer count = 1;
if (countStr != null && !countStr.isEmpty()) {
count = Integer.parseInt(countStr);
}
if (!ATOMIC_WEIGHTS.containsKey(element)) {
throw new RuntimeException("Atomic weights table is missing an expected element: " + element);
}
out += ATOMIC_WEIGHTS.get(element) * count.doubleValue();
}
// TODO: log difference between mol.molecularWeight(), mol.monoisotopicMass(), and our value.
return out;
}
public static void main(String[] args) throws Exception {
if (args.length == 0) {
System.err.format("Usage: %s [InChI [...]]\n", MassCalculator.class.getCanonicalName());
return;
}
System.out.format("InChI\tMass\tCharge\n");
for (String arg : args) {
Pair<Double, Integer> massCharge = calculateMassAndCharge(arg);
System.out.format("%s\t%.6f\t%d\n", arg, massCharge.getLeft(), massCharge.getRight());
}
}
}