Hi,
Am Donnerstag, den 03.02.2011, 20:35 +0100 schrieb Greg Landrum:
> Hi Hari,
>
> On Thu, Feb 3, 2011 at 4:47 PM, hari jayaram <[email protected]> wrote:
> > I have some rdkit code that calculates the Lipinski parameters for a given
> > rdkitmoleule.
> > I am working with someone who wants to port this code to java. I know very
> > little about swig or jython but wondering what the best way to accomplish
> > an equivalent functionality using rdkit within a java ecosystem would be.
> > Is there a jar file readily available for rdkit whereby one could write this
> > function in java . I did see some swig examples on the wiki that did this
> > from c code...but I dont know how to apply that to my case.
>
> There is not currently a convenient way to use the RDKit from java.
> We're currently working on something that should be ready in the next
> month or so that will make things easier than they are now. I will
> post an announcement when it's ready.
As a temporary workaround you can use jep
( http://jepp.sourceforge.net/ ) .
But you still have to install the complete (with python) rdkit on the
system which is running the python code. Not sure if this qualifies as a
solution. It's a workable solution if you have a relative narrow
interface between the rdkit and your java program.
Attached are a java and the corresponding python file.
regards,
Uwe
package jep;
import java.io.*;
import java.util.ArrayList;
import jep.python.*;
public class RDKTest implements Runnable {
private Jep jep = null;
public RDKTest() {}
public void run() {
try {
File pwd = new File(".");
this.jep = new Jep(false, pwd.getAbsolutePath());
jep.runScript("rdkit_test_descriptor.py");
int[] lipinskiResults = new int[10];
String[] lipinskiDescriptionResults = new String[10];
jep.invoke("lipinski",
"c1ccncc1CCCCCC(=O)OS",
lipinskiResults,
lipinskiDescriptionResults);
for(int i = 0; i < lipinskiResults.length; i++)
System.out.println(lipinskiDescriptionResults[i]+" : "+lipinskiResults[i]);
} catch(JepException e) {
System.out.println(e.getMessage());
}
}
public static void main(String argv[]) throws Throwable {
new Thread(new RDKTest()).start();
System.gc();
}
}
from jep import *
__builtins__.__import__ = jep.jimport
from java.lang import *
from java.util import HashMap
from java.io import FileInputStream
from rdkit import Chem
from rdkit.Chem import Lipinski
lipinski_methods = dict(
NOCount=Lipinski.NOCount,
NumHAcceptors=Lipinski.NumHAcceptors,
NumHDonors=Lipinski.NumHDonors,
NumHeteroatoms=Lipinski.NumHeteroatoms,
NumRotatableBonds=Lipinski.NumRotatableBonds,
RingCount=Lipinski.RingCount,
NHOHCount=Lipinski.NHOHCount)
def lipinski(smiles,resultArray,resultDescriptionArray):
mol = Chem.MolFromSmiles(smiles)
for ind,name in enumerate(lipinski_methods.keys()):
res=lipinski_methods[name](mol)
resultArray[ind] = res
resultDescriptionArray[ind] = name
resultArray.commit()
resultDescriptionArray.commit()
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