/*************************************************************************
* *
* 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.twentyn;
import chemaxon.formats.MolFormatException;
import chemaxon.formats.MolImporter;
import chemaxon.struc.Molecule;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
public class TargetMolecule {
public static final CSVFormat TSV_FORMAT = CSVFormat.newFormat('\t').
withRecordSeparator('\n').withQuote('"').withIgnoreEmptyLines(true).withHeader();
Molecule molecule;
String inchi;
String displayName;
String inchiKey;
String imageName;
public TargetMolecule(Molecule molecule, String inchi, String displayName, String inchiKey, String imageName) {
this.molecule = molecule;
this.inchi = inchi;
this.displayName = displayName;
this.inchiKey = inchiKey;
this.imageName = imageName;
}
public Molecule getMolecule() {
return molecule;
}
public String getInchi() {
return inchi;
}
public String getDisplayName() {
return displayName;
}
public String getInchiKey() {
return inchiKey;
}
public String getImageName() {
return imageName;
}
public static TargetMolecule fromCSVRecord(CSVRecord record) throws MolFormatException {
String inchi = record.get("inchi");
String displayName = record.get("display_name");
String inchiKey = record.get("inchi_key");
String imageName = record.get("image_name");
Molecule mol = MolImporter.importMol(inchi);
return new TargetMolecule(mol, inchi, displayName, inchiKey, imageName);
}
public static List<TargetMolecule> loadTargets(File inputFile) throws IOException {
List<TargetMolecule> results = new ArrayList<>();
try (CSVParser parser = new CSVParser(new FileReader(inputFile), TSV_FORMAT)) {
for (CSVRecord record : parser) {
results.add(TargetMolecule.fromCSVRecord(record));
}
}
return results;
}
}