[Rdkit-discuss] The RDKit and GSoC 2020

[Greg Landrum]

Dear all,

I'm happy to share that the RDKit will once again be part of Google Summer
of Code in 2020. This is a program where Google funds students to work on
open-source projects for a couple of months over the summer. We've
participated in each of the last three years and had some cool stuff come
out of it.

We're looking for a few more project ideas (along with possible mentors!)
as well as students.
Applications start in the middle of March. There's more info about
timelines here:
https://developers.google.com/open-source/gsoc/timeline

The current set of project ideas is here and we could use a few more:
http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas
I'm going to try and come up with something, but if you have something to
add, please let me know.

Best,
-greg
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Re: [Rdkit-discuss] Standardizer code from Java

[Tim Dudgeon]

Hi Greg,

Did you get a chance to add any more tests or docs here?
I'm happy to help to improve the docs (see my recent message about RDKit 
from Java), but not sure where to start.


More specifically I'm wanting to run the equivalent to this Python code 
from Java. Any hints would be appreciated.


uncharger = rdMolStandardize.Uncharger()

def remove_isotopes(mol):
    for atom in mol.GetAtoms():
    atom.SetIsotope(0)

def standardize(mol):
    mol = rdMolStandardize.Cleanup(mol)
    mol = uncharger.uncharge(mol)
    remove_isotopes(mol)
    return mol

Thanks
Tim


On 27/12/2019 14:20, Greg Landrum wrote:

Hi Tim,

Unfortunately I don't have decent example code for using the 
standardizer from Java. Normally I reference the tests, but in this 
case they are extremely minimal:
https://github.com/rdkit/rdkit/blob/master/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/MolStandardizeTest.java 



I will try to make some time to improve the situation here with the 
goal of

a) have better tests
b) making it more obvious how to use the code from Java

-greg


On Thu, Dec 26, 2019 at 4:55 PM Tim Dudgeon > wrote:


I'm trying to get my head round using the new standardizer code
from Java.
Looks like this should be accessible from the RDKFuncs class, but
I'm failing at stage 1.

Simple example is:

package org.exmple;

import org.RDKit.RDKFuncs;
import org.RDKit.RWMol;

public class Simple {

 static {
 System.loadLibrary("GraphMolWrap");
 }

 public static void main(String[] args) {
 RWMol mol1 = RWMol.MolFromSmiles("CC");
 try {
 RWMol mol2 = RDKFuncs.cleanup(mol1);
 System.out.println(mol2.MolToSmiles());
 }catch (Exception ex) {
 System.out.println("Exception! " + ex.getMessage());
 ex.printStackTrace();
 }
 }
}

Result is:

Exception! null
org.RDKit.GenericRDKitException
at org.RDKit.RDKFuncsJNI.cleanup__SWIG_1(Native Method)
at org.RDKit.RDKFuncs.cleanup(RDKFuncs.java:5173)
at org.squonk.fragnet.Simple.main(Simple.java:15)

Exception doesn't give much to go on!

This is running against code on RDKit Release_2019_09 branch and using Java 
11.

Has anyone got this working?

Tim

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