Dear All,
Here's my log report on RDKitjs ... that finally works:
For all I used the 2015_03_1 code not the head.
https://github.com/cheminfo/RDKitjs
> [email protected] test /Users/mbp/Github/RDKitjs
> npm run build-test && mocha test/unit --require should --reporter
> mocha-better-spec-reporter --recursive
> [email protected] build-test /Users/mbp/Github/RDKitjs
> cat javascript/pre.js build/src/rdkit.js javascript/post.js > test/rdkit.js
RDKit loading
✓ JS functions Hello
Molecule Creations
✓ Murko
- Mol2BlockToMol
✓ MolBlockToMol
✓ fromSmarts
✓ fromSmiles
✓ molFromPickle
✓ MolToBinary
Compute all descriptors
✓ calc_all_desc
✓ getCrippenAtomContribs
✓ getTPSAAtomContribs
✓ getASAContribs
FingerPrints
✓ getRDKFP
✓ getMorganFP
✓ getMorganFP_GetOnBits
✓ getLayeredFP
✓ getMACCSFP
✓ getPatternFP
3D Force Field minimization
✓ MMFFoptimizeMolecule
✓ MMFFoptimizeMolecule with paramaters
✓ MMFFOptimizeMoleculeConfs
✓ UFFOptimizeMolecule
✓ EmbedMolecule
Strings - 2D - Drawing
✓ smilewrite
✓ sdwriteConfs
✓ 2D generation
✓ 2D Drawing
molecule manipulation & cleaning
✓ addHs
✓ removeHs
✓ sanitizeMol
✓ cleanUp
✓ Kekulize
SubStructures search
✓ getSubstructMatches
✓ HasSubstructMatchStr
Executed 34 tests in 8 suites in 2s 721ms
33 passes
1 pending
Do you have a Mol2 file that I can use in my unit test ?
Important, there is an issue if we request multiple times this
MMFFOptimizeMoleculeConfs :
it('MMFFOptimizeMoleculeConfs', function () {
var smi = 'CCCCCOC(CO)';
for (i=0;i<100;i++){
var mol = RDKit.Molecule.fromSmiles(smi);
mol.addHs();
mol.EmbedMultipleConfsarg(2,200,2015); // 2 number of
conformers, 200 iterations, 2015 seed
mol.MMFFOptimizeMoleculeConfs(8,200,'MMFF94'); // 8 numCores, 200
iterations, 'MMFF94' model
process.stdout.write('.');
mol.delete();
}
}
it's always failed after 89 iterations everytime!
There are no increase of memory.
Removing the "mol.MMFFOptimizeMoleculeConfs(8,200,'MMFF94');" line remove this
issue (tested with 100000 iterations without issues).
Thank you,
Best regards,
Guillaume
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