Nik,

That works too...

Thanks
Milinda

On Wed, Jan 18, 2017 at 3:08 PM, Stiefl, Nikolaus <
nikolaus.sti...@novartis.com> wrote:

> Hi
>
> Maybe this is much less efficient but I guess if you need it for specific
> isotopes then you could try using a smarts pattern and check for that?
>
>
>
> In [*20*]: q = Chem.MolFromSmarts("[13C,14C,2H,3H,15N,24P,46P,33S,34S,36S]
> ")
>
>
>
> In [*21*]: m = Chem.MolFromSmiles('CC[15NH2]')
>
>
>
> In [*22*]: m.HasSubstructMatch(q)
>
> Out[*22*]: True
>
>
>
>
>
> So you could loop over your molecules and then remove the ones that match
> the smarts.
>
> Ciao
>
> Nik
>
>
>
>
>
> *From: *Milinda Samaraweera <milindaatw...@gmail.com>
> *Date: *Wednesday 18 January 2017 at 20:47
> *To: *Greg Landrum <greg.land...@gmail.com>
> *Cc: *RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
> *Subject: *Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit
>
>
>
> Greg,
>
> I am looking to remove entries that contain un-stable isotopes of elements
> CHNOPS (e.g. heavy_isotopes =['13C', '14C', '2H', '3H', '15N', '24P',
> '46P', '33S', '34S', '36S'] ). Is there a way to modify the above code to
> achieve that?
>
> Thanks,
>
> Milinda
>
>
>
>
>
> On Wed, Jan 18, 2017 at 11:16 AM, Greg Landrum <greg.land...@gmail.com>
> wrote:
>
> Hi Milinda,
>
>
>
> Here's an approach that finds all the atoms that have an isotope specified:
>
>
>
> In [1]: from rdkit import Chem
>
>
>
> In [2]: from rdkit.Chem import rdqueries
>
>
>
> In [3]: q = rdqueries.IsotopeGreaterQueryAtom(1)
>
>
>
> In [7]: list(x.GetIdx() for x in Chem.MolFromSmiles('CC[13CH3]'
> ).GetAtomsMatchingQuery(q))
>
> Out[7]: [2]
>
>
>
> In [8]: list(x.GetIdx() for x in Chem.MolFromSmiles('[12CH3]CC[13CH3]').
> GetAtomsMatchingQuery(q))
>
> Out[8]: [0, 3]
>
>
>
> Does that do what you want it to do?
>
>
>
> -greg
>
>
>
>
>
>
>
> On Wed, Jan 18, 2017 at 3:56 PM, Milinda Samaraweera <
> milindaatw...@gmail.com> wrote:
>
> Dear Experts,
>
> I am trying to figure out a way to exclude entries which contain heavy
> atoms (13C, 2H, 3H, etc), from a SD file (which has close to two thousand
> entries) and write an updated file with the remaining entries.
>
> I do understand how to read/write SD files using rdkit.
>
> What I do understand is how to detect entries with heavy isotopes: Is
> there an efficient and correct way of achieving this using rdkit?
>
>
>
> thanks,
>
> --
>
> Milinda Samaraweera
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
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> _______________________________________________
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> Rdkit-discuss@lists.sourceforge.net
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>
>
>
>
>
>
> --
>
> Milinda Samaraweera, Ph.D.
>
> Postdoctoral Fellow, Department of Pharmacy
>
> University of Connecticut
>
> 69 North Eagleville road
>
> Storrs, CT, 06269
>
> milindaatw...@gmail.com
> 860-617-8046 <(860)%20617-8046>
>



-- 
Milinda Samaraweera, Ph.D.
Postdoctoral Fellow, Department of Pharmacy
University of Connecticut
69 North Eagleville road
Storrs, CT, 06269
milindaatw...@gmail.com
860-617-8046
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