Dear Guillaume,
would it be a lot of work to try to build against the current head? I
have recently modified MMFFOptimizeMoleculeConfs() in the C++ layer to
make it more efficient when running multithreaded:
https://github.com/rdkit/rdkit/pull/534
So it would be interesting to know if the problem is still there in your
JavaScript version also with the current C++ code.
Cheers,
p.
On 05/09/2015 09:40, Guillaume GODIN wrote:
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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