Re: [Rdkit-discuss] InChI roundtrip

2014-01-28 Thread Gianluca Sforna
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

[Rdkit-discuss] AssignStereochemistry flagPossibleStereoCenters flag and how it works?

2014-01-28 Thread Michał Nowotka
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

[Rdkit-discuss] What does Cleanup function do?

2014-01-28 Thread Michał Nowotka
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

[Rdkit-discuss] Building RDKit on Windows

2014-01-28 Thread James Davidson
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.

Re: [Rdkit-discuss] What does Cleanup function do?

2014-01-28 Thread Mikolaj Kowalik
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

Re: [Rdkit-discuss] What does Cleanup function do?

2014-01-28 Thread Greg Landrum
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

Re: [Rdkit-discuss] Building RDKit on Windows

2014-01-28 Thread Greg Landrum
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

Re: [Rdkit-discuss] AssignStereochemistry flagPossibleStereoCenters flag and how it works?

2014-01-28 Thread Greg Landrum
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)