chiral centers are not respected during generation

[missuse]

Hi iwatobipen,

and thanks for a cool tool.

I started experimenting with it to generate some glycoside conformations and noticed that chirality is not respected during this.

See attached images:

this one is as it should be:

this one is off:

File to reproduce the problem is the 3D sdf file from:

PUBCHEM_COMPOUND_CID: 88708

code I used is

confgen -i Gentiopicroside.sdf -o Gentiopicroside_chiral.sdf -t 0.1 --numconf 50 -r true

I am not an rdkit user to make suggestions.

Thanks,

Milan

[missuse]

It seems to me that after this line:

mol = Chem.AddHs(Chem.MolFromMolFile(input), addCoords=True)

information about chirality should be added:

Chem.rdmolops.AssignStereochemistryFrom3D(mol)
Chem.rdmolops.AssignAtomChiralTagsFromStructure(mol)

It looks like this fixed it.