/*************************************************************************
* *
* 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 act.installer.reachablesexplorer;
import chemaxon.struc.Molecule;
import com.act.analysis.chemicals.molecules.MoleculeImporter;
import com.act.biointerpretation.mechanisminspection.ReactionRenderer;
import com.act.jobs.FileChecker;
import org.apache.commons.codec.digest.DigestUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.io.File;
import java.io.IOException;
import java.nio.file.Paths;
import java.util.Optional;
public class MoleculeRenderer {
private static final Logger LOGGER = LogManager.getFormatterLogger(MoleculeRenderer.class);
private static final String PNG_EXTENSION = ".png";
private static ReactionRenderer renderer = new ReactionRenderer();
private File assetLocation;
public MoleculeRenderer(File assetLocation) {
if (assetLocation.exists()) {
this.assetLocation = assetLocation;
} else {
String msg = String.format("Could not find or create directory at %s for storing assets.", assetLocation.getAbsolutePath());
LOGGER.error(msg);
throw new RuntimeException(msg);
}
}
public File getRenderingFile(String inchi) {
String md5 = DigestUtils.md5Hex(inchi);
String postfix = String.format("-%s%s", md5, PNG_EXTENSION);
String renderingFilename = String.join("", "molecule", postfix);
return Paths.get(this.assetLocation.getPath(), renderingFilename).toFile();
}
public Optional<File> generateRendering(String inchi) {
File rendering = getRenderingFile(inchi);
if (!rendering.exists()) {
try {
Molecule mol = MoleculeImporter.importMolecule(inchi);
renderer.drawMolecule(mol, rendering);
FileChecker.verifyInputFile(rendering);
} catch (IOException e) {
LOGGER.error("Unable to generate rendering for %s at location %s", inchi, rendering.toPath().toString());
return Optional.empty();
} catch (StackOverflowError e) {
// Very rarely, a very large molecule will trigger a StackOverFlowError. Catch it and move on!
LOGGER.error("Unable to generate rendering for %s at location %s", inchi, rendering.toPath().toString());
return Optional.empty();
}
}
return Optional.of(rendering);
}
}