/*************************************************************************
* *
* 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.act.utils.TSVParser;
import org.apache.commons.lang3.tuple.Pair;
import org.junit.Test;
import java.io.InputStream;
import java.util.List;
import java.util.Map;
import static org.junit.Assert.assertEquals;
public class MassCalculator2Test {
public static final String TEST_CASE_RESOURCE = "mass_calculator_test_cases.txt";
public static final Double ACCEPTABLE_MASS_DELTA_THRESHOLD = 0.00054858; // one electron's mass in Daltons.
@Test
public void testMC2MatchesMC1WithinMeaningfulTolerance() throws Exception {
List<Map<String, String>> rows;
try (InputStream is = MassCalculator2Test.class.getResourceAsStream(TEST_CASE_RESOURCE)) {
TSVParser parser = new TSVParser();
parser.parse(is);
rows = parser.getResults();
}
int testCase = 1;
for (Map<String, String> row : rows) {
String inchi = row.get("InChI");
Double expectedMass = Double.valueOf(row.get("Mass"));
Integer expectedCharge = Integer.valueOf(row.get("Charge"));
Pair<Double, Integer> actualMassAndCharge = MassCalculator2.calculateMassAndCharge(inchi);
Double threshold = ACCEPTABLE_MASS_DELTA_THRESHOLD;
if (actualMassAndCharge.getRight() < 0) {
// Widen the window for added electrons' masses included in Chemaxon's calculations for negative ions.
threshold += ACCEPTABLE_MASS_DELTA_THRESHOLD * -1.0 * actualMassAndCharge.getRight().doubleValue();
} else if (actualMassAndCharge.getRight() > 0) {
// Positively charged molecules have the missing electrons' masses subtracted
threshold += ACCEPTABLE_MASS_DELTA_THRESHOLD * actualMassAndCharge.getRight().doubleValue();
}
assertEquals(String.format("Case %d: mass for %s is within delta threshold: %.6f vs. %.6f",
testCase, inchi, expectedMass, actualMassAndCharge.getLeft()),
expectedMass, actualMassAndCharge.getLeft(), threshold);
assertEquals(String.format("Case %d: charge %s matches expected", testCase, inchi),
expectedCharge, actualMassAndCharge.getRight());
testCase++;
}
}
}