Hello folks,
In a way this is a continuation of a previous discussion.
My question is: so is there a simple way to obtain the original
indexing with all hydrogen atoms included? Do I have to write
my own function?
Thank you.
Ling
Re: [Rdkit-discuss] SMILES and atom indexing
greg landrum Tue, 19 Mar 2013 13:09:32 -0700
Hi Nick, On Mar 19, 2013, at 5:00 PM, Nicholas Firth <nicholas.fi...@icr.ac.uk>
wrote:
> Hi RDKitters,
>
> I'm sure this must of been covered somewhere else but I can't find it in the
> forum or the source.
>
> I am manipulating SMILES strings and wonder whether I can use RDKit as a
> shortcut, so my question is does the order of occurrence in a SMILES string
> of an atom match the atom index that is given by RDKit. It seems to me that
> it does but I'd like to know for all cases. For example
>
> >>> from rdkit import Chem
> >>> mol=Chem.MolFromSmiles('CSNOC')
> >>> for atom in mol.GetAtoms(): print atom.GetAtomicNum(),atom.GetIdx()
> ...
> 6 0
> 16 1
> 7 2
> 8 3
> 6 4
>
> This is what I would expect, but is there a case when this order might not be
> conserved? The atom and bond order will be preserved unless the smiles
> contains hydrogens
as explicit atoms, i.e. as [H]. In that case, the hydrogens are removed and the
remaining indices are what your would expect. > If the order isn't always
conserved, how does the indexing cope with RDKit
> canonical smiles? I don't understand the question but maybe that doesn't
> matter since the order
is preserved? -greg > Thanks in advance.
>
> Best,
> Nick
>
> Nicholas C. Firth | PhD Student | Cancer Therapeutics
> The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton |
> Surrey | SM2 5NG
> T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter
> @ICRnews
> Facebook www.facebook.com/theinstituteofcancerresearch
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