MolImporter: Problems Creating Molecule From InChi String

I'm getting various errors trying to use the MolImporter to import an InChi string to obtain a Molecule. Note that I've been successful importing SMILES strings to get the Molecule, so the basic mechanism is working.

Sample Code

final String inchi = "InChI=1S/C2H8NO3P/c3-1-2-7(4,5)6/h1-3H2,(H2,4,5,6)";			
MolImporter importer = null;
try {
	// NOTE: I've tried calling without "inchi" option and get the same results:
	importer = new MolImporter(new ByteArrayInputStream(inchi.getBytes()), "inchi");
	Molecule molecule = importer.read();
	// Assert.fail("Expected MolFormatException for inchiKey!");
} catch (IOException e) {
	e.printStackTrace();
} finally {
	IOUtils.INSTANCE.closeCloseable(importer, "We couldn't close the InChi importer!");
}

Specific Problem (Junit Test Output)

Running com.agilent.amp.unittests.ChemAxonTest
Mar 31, 2016 11:22:45 AM chemaxon.marvin.io.formats.inchi.Inchi installFromResource
WARNING: could not open from resource: inchi64.dll
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.283 sec <<< FAILURE! - in com.agilent.amp.unittests.ChemAxonTest
MoleculeImporterTest(com.agilent.amp.unittests.ChemAxonTest)  Time elapsed: 0.27 sec  <<< ERROR!
java.lang.IllegalAccessError: tried to access method net.sf.jniinchi.JniInchiStructure.getAtomIndex(Lnet/sf/jniinchi/JniInchiAtom;)I from class chemaxon.marvin.io.formats.inchi.InchiImport
	at com.agilent.amp.unittests.ChemAxonTest.MoleculeImporterTest(ChemAxonTest.java:67)

Maven pom.xml

Note that I've had to add other dependencies for jchem  that I would have thought are self contained. I've also tried directly using the jchem.jar library (without maven) and get the same problem:

  	<repository>

        	<id>jni-inchi</id>

        	<name>JNI-InChI Maven Repository</name>

        	<url>http://jni-inchi.sourceforge.net/m2repo</url>;

        </repository>

        <repository>

           <id>ChemAxon Public Repository</id>

           <url>https://repository.chemaxon.com/artifactory/libs-release</url>;

        </repository>

		<!--  Chemaxon molImporter uses PIG(?) which requires the following: -->
		<dependency>
      		<groupId>dk.brics.automaton</groupId>
      		<artifactId>automaton</artifactId>
      		<version>1.11-8</version>
   		 </dependency>
		<!--  Chemaxon molImporter uses jni-inchi: -->
    	<dependency>
	        <groupId>net.sf.jni-inchi</groupId>
	        <artifactId>jni-inchi</artifactId>
	        <version>0.7</version>
    	</dependency>
        <dependency>
           <groupId>com.chemaxon</groupId>
           <artifactId>jchem</artifactId>
           <version>16.1.18.0</version>
        </dependency>

System

Java 1.8.0_71, Windows 7, JChem Java library 16.1.18.0 (both via Maven repository and direct use from jchem.jar)

Hi,

The code works well in my computer, so you are right about that. Can you check the inchi64.dll file in your home\chemaxon\lib\inchi-(version) folder and the CHEMAXON_HOME environment variable?

Janos

I don't have any ChemAxon stuff directly installed on my machine except for whatever Maven downloads to my local maven repository. I'm trying to use the jchem library from a Java application (via Maven) to run calculators and do substructure searching (which mostly works).

So, does the MolImporter, for inchi, require some ChemAxon .dll -based software to be installed on the machine where the application is running?

 

Hi,

Can you check your local maven repo for the inchi64.dll file?

I think you doesn't need any installed ChemAxon software to make the inchi import work, but you can try installing MarvinBeans.