gov.nih.ncats.molwitch.cdk.writer.SdfWriterFactory Maven / Gradle / Ivy
/*
* NCATS-MOLWITCH-CDK
*
* Copyright (c) 2019.
*
* This work is free software; you can redistribute it and/or modify it under the terms of the
* GNU Lesser General Public License as published by the Free Software Foundation;
* either version 2.1 of the License, or (at your option) any later version.
*
* This work 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License along with this library;
* if not, write to:
*
* the Free Software Foundation, Inc.
* 59 Temple Place, Suite 330
* Boston, MA 02111-1307 USA
*/
package gov.nih.ncats.molwitch.cdk.writer;
import java.io.IOException;
import java.io.OutputStream;
import java.util.Properties;
import org.openscience.cdk.io.SDFWriter;
import org.openscience.cdk.io.listener.PropertiesListener;
import gov.nih.ncats.molwitch.io.ChemFormat.ChemFormatWriterSpecification;
import gov.nih.ncats.molwitch.io.ChemFormat.KekulizationEncoding;
import gov.nih.ncats.molwitch.io.ChemFormat.MolFormatSpecification.Version;
import gov.nih.ncats.molwitch.io.ChemFormat.SdfFormatSpecification;
import gov.nih.ncats.molwitch.spi.ChemicalWriterImpl;
import gov.nih.ncats.molwitch.spi.ChemicalWriterImplFactory;
public class SdfWriterFactory implements ChemicalWriterImplFactory{
@Override
public ChemicalWriterImpl newInstance(OutputStream out, ChemFormatWriterSpecification spec) throws IOException {
SdfFormatSpecification sdfSpec = (SdfFormatSpecification) spec;
SDFWriter writer = new SDFWriter(out);
if(sdfSpec.getMolSpec().getVersion() == Version.V3000) {
writer.setAlwaysV3000(true);
}
if(sdfSpec.getMolSpec().getKekulization() == KekulizationEncoding.FORCE_AROMATIC) {
Properties customSettings = new Properties();
customSettings.setProperty("WriteAromaticBondTypes", Boolean.TRUE.toString());
writer.addChemObjectIOListener( new PropertiesListener(customSettings));
}
return new CdkChemicalWriter(writer);
}
@Override
public boolean supports(ChemFormatWriterSpecification spec) {
return SdfFormatSpecification.NAME.equals(spec.getFormatName()) && spec instanceof SdfFormatSpecification;
}
}