Dearest RDKitters,
I am trying to help a friend of mine, with an RDKit issue (using the latest
RDKit) and I am surprised by some output we are getting. Perhaps someone
here has an explanation.
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
core = Chem.MolFromSmiles('c1cncs1') # first molecule
print AllChem.EmbedMolecule(core)
AllChem.UFFOptimizeMolecule(core)
Chem.MolToMolBlock(core) # we have some coordinates
print "****************"
mol = Chem.MolFromSmiles('C(=O)(O)c1cncs1')
AllChem.ConstrainedEmbed(mol, core, randomseed=123)
Chem.MolToMolBlock(mol)
We get the following error:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/home/jp/<ipython-input-30-f4834f0dae19> in <module>()
11 mol = Chem.MolFromSmiles('C(=O)(O)c1cncs1')
12
---> 13 AllChem.ConstrainedEmbed(mol, core, randomseed=123)
14 Chem.MolToMolBlock(mol)
/opt/RDKit_2012_12_1/rdkit/Chem/AllChem.pyc in ConstrainedEmbed(mol, core,
useTethers, coreConfId, randomseed)
295 ci = EmbedMolecule(mol,coordMap=coordMap,randomSeed=randomseed)
296 if ci<0:
--> 297 raise ValueError,'Could not embed molecule.'
298
299 algMap=[(j,i) for i,j in enumerate(match)]
ValueError: Could not embed molecule.
0
****************
*(0) Why does this happen?* We have coordinates in core and the match
between core and mol is obvious.
(1) If we change the aromatic s to o, the code works and we get coorindates
for mol - but these coordinates do not match exactly core. Why is this?
>>> Chem.MolToMolBlock(mol)
RDKit 3D
8 8 0 0 0 0 0 0 0 0999 V2000
-2.4927 0.7025 0.1023 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8250 1.8875 0.5227 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.5158 -0.2123 -0.3041 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.0822 0.3130 0.0474 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6171 -0.9082 -0.3781 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7280 -0.8842 -0.2830 N 0 0 0 0 0 0 0 0 0 0 0 0
1.0322 0.3482 0.1959 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0608 1.1312 0.4178 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
1 3 1 0
1 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
7 8 1 0
8 4 1 0
M END
>>> Chem.MolToMolBlock(core) # we have some coordinates
RDKit 3D
5 5 0 0 0 0 0 0 0 0999 V2000
-1.0880 0.3145 0.0476 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6149 -0.9044 -0.3765 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7299 -0.8840 -0.2828 N 0 0 0 0 0 0 0 0 0 0 0 0
1.0336 0.3470 0.1955 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0606 1.1269 0.4162 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 1 1 0
M END
>>>
Can you help explain the mystery please?
Many Thanks
JP
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