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 <tdudgeon...@gmail.com> 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 <tdudgeon...@gmail.com> 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 >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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