Hi Jean-Marc and others,
There is also CanonicalRankAtoms [
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolfiles-module.html#CanonicalRankAtoms]
which seams to be forgotten.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-12-18 23:14 GMT+01:00 Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr>:
> Thank you Andrew, Brian and David for your answers.
>
> mol.GetProp("_smilesAtomOutputOrder") does the job.
> I also expected a.GetProp("molAtomMapNumber") could do it for each atom a.
>
> All the best,
>
> Jean-Marc
>
> Le 18/12/2016 à 19:04, Andrew Dalke a écrit :
> > On Dec 18, 2016, at 6:32 PM, Brian Kelley wrote:
> >>>>> m.GetProp("_smilesAtomOutputOrder")
> >> '[3,2,1,0,]'
> >>
> >> Note that this returns the list as a string which is sub-optimal.
> GetPropsAsDict will convert these to proper python objects, however, this
> is considered a private member so you need to return these as well:
> >>
> >>>>> list(m.GetPropsAsDict(True,True)["_smilesAtomOutputOrder"])
> >> [3, 2, 1, 0]
> > For fun, here are a few timing numbers:
> >
> > # Common setup
> > from rdkit import Chem
> > mol = Chem.MolFromSmiles("c1ccccc1Oc1ccccc1")
> > Chem.MolToSmiles(mol)'
> > import json
> > import ujson # third-party JSON decoder
> > import re
> > integer_pat = re.compile("[0-9]+")
> >
> >
> > # Get the string (give a lower bound)
> > mol.GetProp("_smilesAtomOutputOrder")'
> > 10000 loops, best of 3: 31.3 usec per loop
> >
> >
> > Here are variations for how to get that information as a list of
> integers:
> >
> > # Using Python's "eval()" to decode the list (this is generally UNSAFE!)
> > eval(mol.GetProp("_smilesAtomOutputOrder"))'
> > 10000 loops, best of 3: 157 usec per loop
> >
> > # Use the built-in json module (need to remove the terminal ",")
> > json.loads(mol.GetProp("_smilesAtomOutputOrder")[:-2]+"]")'
> > 10000 loops, best of 3: 66.5 usec per loop
> >
> > # Use the third-party "ujson" package, which is faster than json.
> > ujson.loads(mol.GetProp("_smilesAtomOutputOrder")[:-2]+"]")
> > 10000 loops, best of 3: 41.2 usec per loop
> >
> > ("cjson" takes 49.7 usec per loop)
> >
> > # Use the properties dictionary
> > mol.GetPropsAsDict(True,True)["_smilesAtomOutputOrder"]
> > 1000 loops, best of 3: 462 usec per loop
> >
> > # Parse it more directly
> > map(int, integer_pat.findall(mol.GetProp("_smilesAtomOutputOrder")))
> > 10000 loops, best of 3: 89 usec per loop
> >
> >
> > Andrew
> > da...@dalkescientific.com
> >
> >
> >
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>
>
> --
> Jean-Marc Nuzillard
> Institut de Chimie Moléculaire de Reims
> CNRS UMR 7312
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> CPCBAI, Bâtiment 18
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> 51687 REIMS Cedex 2
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>
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>
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>
>
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