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
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