[Rdkit-discuss] Coordgen library questions

[Lukas P. <lp...@eb...>]

Hi all,

 

I’m playing with the Coordgen library inside rdkit and I have a couple of questions I could not figure out by myself. Hopefully someone more experienced will know.

 
[comment] The way one can pass a scaling factor to the bond size is very unintuitive. If I don’t provide any parameter a single bond length is 1.0. If I pass 1.5 as a scaling factor, I’d expect to get single bond of a length 1.5. But instead I get 33.3. (measured in pymol) 
 

Snippet:

from rdkit import Chem

from rdkit.Chem import rdCoordGen

 

mol = Chem.MolFromSmiles('Cc1ccccc1', sanitize=True)

mol1 = Chem.MolFromSmiles('Cc1ccccc1', sanitize=True)

 

p = rdCoordGen.CoordGenParams()

p.coordgenScaling = 1.5

 

rdCoordGen.AddCoords(mol)

rdCoordGen.AddCoords(mol1, p)

 

Chem.MolToMolFile(mol, 'default.sdf') # bond length 1

Chem.MolToMolFile(mol1, '1.5_scale.sdf') # bond length 33.3

 

 

                Is that intended?

 
Is there any way to modify templates, which can be passed as the ‘templateFileDir’ parameter to match general groups and bonds as described here: http://rdkit.blogspot.com/2016/07/tuning-substructure-queries-ii.html? 
By default, rdCoordGen module writes to stderr by putting ‘TEMPLATES: /path/to/templates’ line for each depiction generated. Is there any simple way of muting that piece of information without manually hijacking the stderr (rdkit.rdBase.DisableLog('rdApp.*') does not work)?
 

Thanks for possible suggestions.

 

 

Cheers, 

Lukas