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
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