ch.unibas.fittingwizard.mocks.MockLRAScript.java Source code

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Here is the source code for ch.unibas.fittingwizard.mocks.MockLRAScript.java

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/*
 * Copyright (c) 2015, Florent Hedin, Markus Meuwly, and the University of Basel
 * All rights reserved.
 *
 * The 3-clause BSD license is applied to this software.
 * see LICENSE.txt
 *
 */
package ch.unibas.fittingwizard.mocks;

import ch.unibas.fittingwizard.application.scripts.lra.ILRAScript;
import ch.unibas.fittingwizard.application.scripts.lra.LRAScriptInput;
import ch.unibas.fittingwizard.application.scripts.lra.LRAScriptOutput;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.log4j.Logger;

/**
 * User: mhelmer Date: 05.12.13 Time: 17:25
 */
public class MockLRAScript implements ILRAScript {

    private final List<String> filesToCopy = Arrays.asList("_l.pun");
    private final String lpunExtension = "_l.pun";

    private final static Logger logger = Logger.getLogger(MockLRAScript.class);
    private File moleculesDir;
    private final File testMoleculesDir;

    public MockLRAScript(File moleculesDir, File testMoleculesDir) {
        this.moleculesDir = moleculesDir;
        this.testMoleculesDir = testMoleculesDir;
    }

    @Override
    public LRAScriptOutput execute(LRAScriptInput input) {
        // /esp-fit.pc-mtp/src/calc_LRA.py -in co2
        // This generates a *_l.pun file.

        String moleculeName = getMoleculeName(input.getSdfFile());

        File specificMoleculeDir = new File(moleculesDir, moleculeName);

        File lpunOutputFile = new File(specificMoleculeDir, moleculeName + lpunExtension);

        File precomputedDataDir = new File(testMoleculesDir, moleculeName);

        for (String fileExtension : filesToCopy) {

            File precomputedFile = new File(precomputedDataDir, moleculeName + fileExtension);

            try {
                FileUtils.copyFile(precomputedFile, new File(specificMoleculeDir, moleculeName + fileExtension));
            } catch (IOException e) {
                logger.error("Could not copy precomputed file " + precomputedFile);
                throw new RuntimeException("Could not copy precomputed file " + precomputedFile);
            }
        }

        return new LRAScriptOutput(lpunOutputFile);
    }

    private String getMoleculeName(File input) {
        return FilenameUtils.removeExtension(input.getName());
    }

}