Hi Lukas,
according to the source
code:https://github.com/rdkit/rdkit/blob/master/External/CoordGen/CoordGen.h
double coordgenScaling = 50.0;
the default scaling factor, actually more like a "shrinking factor" seems to be
50, producing bond lengths of 1A.
For 1.5A bond lengths, you would need to enter a scaling factor of 50.0/1.5,
maybe this should be changed internally to make it more intuitive ?
The code snippet below may save you the trouble going into pymol for
measurements. When getting the 50A bond lengths, depiction showed all single
bonds and did not take bond orders into account, wonder whether that is
intended.
Best wishes,Maria
from rdkit import Chemfrom rdkit.Chem import rdCoordGenfrom rdkit.Chem import
rdmolopsmol = Chem.MolFromSmiles('Cc1ccccc1', sanitize=True)mol1 =
Chem.MolFromSmiles('Cc1ccccc1', sanitize=True)
p = rdCoordGen.CoordGenParams()p.coordgenScaling =
50.0/1.5rdCoordGen.AddCoords(mol1,p)
print(Chem.MolToMolBlock(mol))print(Chem.MolToMolBlock(mol1))print(rdmolops.Get3DDistanceMatrix(mol1))
Chem.MolToMolFile(mol, 'default.sdf') # bond length 1Chem.MolToMolFile(mol1,
'scale.mol') # bond length 33.3from rdkit.Chem import rdDepictorfrom
rdkit.Chem.Draw import IPythonConsole
On Tuesday, 9 October 2018, 14:08:05 BST, Lukas Pravda <lpra...@ebi.ac.uk>
wrote:
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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