Java tutorial
/************************************************************************* * * * 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()); } } }