On Tue, Jan 28, 2014 at 2:49 AM, Igor Filippov
igor.v.filip...@gmail.com wrote:
I noticed that if I convert mol to inchi and then back to mol in quite a few
cases
the stereochemistry information gets lost. Is it something that is handled
completely by InChI library
or is RDKit not reading the
Look at this code:
from rdkit import Chem
mol =
Chem.MolFromSmiles('O=C(O)C2N3C(=O)C(NC(=O)C(c1ccc(O)cc1)NC(=O)C(N)CC(=O)NC)C3SC2(C)C')
Chem.AssignStereochemistry(mol, flagPossibleStereoCenters=True)
[atom.HasProp('_ChiralityPossible') for atom in mol.GetAtoms()]
[0,0,0, ... only zeros ...]
I
According to the documentation
(http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#Cleanup):
cleans up certain common bad functionalities in the molecule
What are those 'certain common bad functionalities' that are being cleaned up?
Regards,
Michał Nowotka
Dear All,
As part of a New Year's resolution, I decided I should try to enjoy the
benefits of a cutting-edge version of RDKit built from source(!) So far this
has proven to be much more realistic than eg 'not drinking for January' - as I
now have a working build to show for my efforts.
On Tue, 28 Jan 2014 12:22:34 +
Michał Nowotka mmm...@gmail.com wrote:
According to the documentation
(http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#Cleanup):
cleans up certain common bad functionalities in the molecule
What are those 'certain common bad
Looks like you guys have this one answered, but just for the sake of
completeness here's a bit of explanation.
the cleanUp() function currently makes the following modifications:
1) neutral 5 coordinate N with a double bond to O is converted to
the charge-separated form. This cleans up nitro
Dear James,
On Tue, Jan 28, 2014 at 4:09 PM, James Davidson j.david...@vernalis.comwrote:
As part of a New Year's resolution, I decided I should try to enjoy the
benefits of a cutting-edge version of RDKit built from source(!) So far
this has proven to be much more realistic than eg 'not
On Tue, Jan 28, 2014 at 1:20 PM, Michał Nowotka mmm...@gmail.com wrote:
Look at this code:
from rdkit import Chem
mol =
Chem.MolFromSmiles('O=C(O)C2N3C(=O)C(NC(=O)C(c1ccc(O)cc1)NC(=O)C(N)CC(=O)NC)C3SC2(C)C')
Chem.AssignStereochemistry(mol, flagPossibleStereoCenters=True)
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