Re: [Rdkit-discuss] Standardizer code from Java

[Greg Landrum]

Not yet, sorry.
Still on my list, but I'm not sure when it'll actually get done.

On Sun, Feb 23, 2020 at 8:56 PM Tim Dudgeon  wrote:

> 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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>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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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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Re: [Rdkit-discuss] Standardizer code from Java

[Greg Landrum]

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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> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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[Rdkit-discuss] Standardizer code from Java

[Tim Dudgeon]

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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