Re: [Rdkit-discuss] Stereo information lost

2017-12-14 Thread Marina Garcia de Lomana 
Thanks! It works great!


> El 13 dic 2017, a las 12:15, Paolo Tosco  escribió:
> 
> Hi Marina,
> 
> If you wish to assign stereochemistry from the atom block parity flag rather 
> than from 3D coordinates you might try the following:
> 
> #include 
> #include 
> #include 
> #include 
> #include 
> 
> int main(int argc, char **argv) {
> std::string in_file_name = "zinc_3833800.sdf";
> 
> RDKit::SDMolSupplier mol_supplier( in_file_name , true );
> 
> for (unsigned int i = 0; i < mol_supplier.length(); ++i) {
> RDKit::ROMOL_SPTR mol(mol_supplier[i]);
> 
> if (!mol){
> std::cout << "Error, molecule not found!" << std::endl;
> continue;
> }
> 
> 
> for (unsigned int j = 0; j < mol->getNumAtoms(); j++){
> RDKit::Atom* atom = mol->getAtomWithIdx(j);
> if (atom->hasProp(RDKit::common_properties::molParity)) {
> int parity;
> atom->getProp(RDKit::common_properties::molParity, 
> parity);
> switch (parity) {
> case 1:
> atom->setChiralTag(RDKit::Atom::CHI_TETRAHEDRAL_CW);
> break;
> case 2:
> atom->setChiralTag(RDKit::Atom::CHI_TETRAHEDRAL_CCW);
> break;
> default:
> atom->setChiralTag(RDKit::Atom::CHI_UNSPECIFIED);
> break;
> }
> }
> std::cout << "Chirality atom " << j+1  << ": " << 
> atom->getChiralTag() << std::endl;
> }
> 
> std::string usmiles = RDKit::MolToSmiles (*mol, true);
> std::cout << "Mol: " << usmiles << std::endl;
> }
> }
> 
> Cheers,
> p.
> 

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Re: [Rdkit-discuss] SanitizeMol changing drawing

2017-12-14 Thread Jason Biggs 
Greg,
That really helps!  The CIP rank property is the key I was looking for.
Now I can put in a check for to see if the property is defined before
calling prepareMolForDrawing, and if it isn't then call assignAtomCIPRanks
first.

I was having issues where molecules created from a SMILES would not
round-trip through my internal molecule representation (in Mathematica) and
back perfectly, and this fixes most of those issues.

Thanks,

Jason

On Wed, Dec 13, 2017 at 11:26 PM, Greg Landrum 
wrote:

> Hi Jason,
>
> This is a nice one.
>
> Here's what's going on:
> The depiction code (the piece that generates 2D coordinates) attempts to
> generate "canonical" coordinates : it tries to generate the same
> coordinates for a molecule no matter what the input atom ordering is.
> In order to do that it needs a canonical numbering of the atoms (or at
> least something approximating one).
> The current code uses the calculated CIP ranks of the atoms as this
> canonical ordering. These ranks are generated as part of the standard
> stereochemistry assignment that is done on molecule construction and are
> stored as computed properties on the atoms. If the CIP ranks are not there
> it more or less gives up and just uses the atomic number.
> The call to SanitizeMol() clears the computed properties on atoms, thus
> blowing out the CIP rank information that the depiction code uses.
>
> If you want to resolve this, you can call 
> Chem.AssignStereochemistry(m2,cleanIt=True,
> force=True) after you sanitize the molecule. Note that this can be a
> computationally expensive call, so you may not want to make a habit out of
> it.
>
> I'll create an issue to explore updating the depiction code and replacing
> the use of CIP ranks with the atom ranking generated by Nadine's
> canonicalization code
>
> -greg
>
>
> On Wed, Dec 13, 2017 at 10:38 PM, Jason Biggs 
> wrote:
>
>> using the recent release,
>>
>>
>> m = Chem.MolFromSmiles("N[C@@H](C)C(=O)O")
>> m2 = Chem.MolFromSmiles("N[C@@H](C)C(=O)O")
>> Chem.rdmolops.SanitizeMol(m2)
>>
>>
>>
>> The two molecules above seem identical - MolFromSmiles already performs a
>> sanitization so why wouldn't they be?  They produce the same pickle,
>>
>> pickle.dumps(m) == pickle.dumps(m2)
>>
>> True
>>
>>
>> So why do they get treated differently by the drawing code? The only way
>> to return m2 to its original state is to run AssignStereoChemistry with
>> force = True.  What variable is being thrown off by SanitizeMol?
>>
>> [image: Inline image 1]
>>
>> Jason Biggs
>>
>>
>> 
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>
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