org.xmlcml.cml.inchi.InChIGeneratorFactory Maven / Gradle / Ivy

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A container for JUMBO's InChI functionality
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/**
 *    Copyright 2011 Peter Murray-Rust et. al.
 *
 *    Licensed under the Apache License, Version 2.0 (the "License");
 *    you may not use this file except in compliance with the License.
 *    You may obtain a copy of the License at
 *
 *        http://www.apache.org/licenses/LICENSE-2.0
 *
 *    Unless required by applicable law or agreed to in writing, software
 *    distributed under the License is distributed on an "AS IS" BASIS,
 *    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *    See the License for the specific language governing permissions and
 *    limitations under the License.
 */

package org.xmlcml.cml.inchi;

import java.util.List;

import net.sf.jniinchi.INCHI_OPTION;
import net.sf.jniinchi.JniInchiWrapper;
import net.sf.jniinchi.LoadNativeLibraryException;

import org.xmlcml.cml.element.CMLMolecule;

/**
 * Factory providing access to InChIGenerator and InChIToStructure. See those
 * classes for examples of use. These methods make use of the JNI-InChI library.
 * 
 * 
InChI/Structure interconversion is implemented in this way so that we can
 * check whether or not the native code required is available. If the native
 * code cannot be loaded a CDKException will be thrown when the constructor
 * is called. The most common problem is that the native code is not in the
 * the correct location. Java searches the locations in the PATH environmental
 * variable, under Windows, and LD_LIBRARY_PATH under Linux, so the JNI-InChI
 * native libraries must be in one of these locations. If the JNI-InChI jar file
 * is being used and either the current working directory, or '.' are contained
 * in PATH of LD_LIBRARY_PATH then the native code should be placed
 * automatically. If the native files are in the correct location but fail to
 * load, then they may need to be recompiled for your system. See:
 * 

 * http://sourceforge.net/projects/jni-inchi
 * 
http://www.iupac.org/inchi/
 * 
 * 
 * @author Sam Adams
 */
public class InChIGeneratorFactory implements InChIGeneratorFactoryInterface {
    
    /**
     * Constructor for InChIGeneratorFactory. Ensures that native code
     * required for InChI/Structure interconversion is available, otherwise
     *.
     * 
     * @throws RuntimeException
     */
    public InChIGeneratorFactory() {
        try {
            JniInchiWrapper.loadLibrary();
        } catch (LoadNativeLibraryException lnle) {
            throw new RuntimeException("Unable to load native code; " + lnle.getMessage(), lnle);
        }
    }
    
    /**
     * 
Gets InChI generator for CMLMolecule.
     * 
     * @param molecule     CMLMolecule to generate InChI for.
     * @throws RuntimeException
      * @return InChIGenrator
      * 
     */
    public InChIGenerator getInChIGenerator(CMLMolecule molecule) {
        return(new InChIGenerator(molecule));
    }
    
    /**
     * 
Gets InChI generator for CMLMolecule.
     * 
     * @param molecule     CMLMolecule to generate InChI for.
     * @param options       String of options for InChI generation.
     * @return inchi generator
     * @throws RuntimeException
     */
    public InChIGenerator getInChIGenerator(CMLMolecule molecule, String options) {
        return(new InChIGenerator(molecule, options));
    }
    
    /**
     * 
Gets InChI generator for CMLMolecule.
     * 
     * @param molecule     CMLMolecule to generate InChI for.
     * @param options      List of options (net.sf.jniinchi.INCHI_OPTION) for InChI generation.
     * @return Inchi generator
     * @throws RuntimeException
     */
    public InChIGenerator getInChIGenerator(CMLMolecule molecule, List options) {
        return(new InChIGenerator(molecule, options));
    }
    
    /**
     * 
Gets structure generator for an InChI string.
     * 
     * @param inchi         InChI to generate structure from.
     * @return InChIToStructure
     * @throws RuntimeException
     */
    public InChIToStructure getInChIToStructure(String inchi) {
        return(new InChIToStructure(inchi));
    }
    
    /**
     * 
Gets structure generator for an InChI string.
     * 
     * @param inchi         InChI to generate structure from.
     * @param options       String of options for structure generation.
     * @return InChIToStructure
     * @throws RuntimeException
     */
    public InChIToStructure getInChIToStructure(String inchi, String options) {
        return(new InChIToStructure(inchi, options));
    }
    
    /**
     * Gets structure generator for an InChI string.
     * 
     * @param inchi         InChI to generate structure from.
     * @param options       List of options (net.sf.jniinchi.INCHI_OPTION) for structure generation.
     * @return InChIToStructure
     * @throws RuntimeException
     */
    public InChIToStructure getInChIToStructure(String inchi, List options) {
        return(new InChIToStructure(inchi, options));
    }
}