Hi Milinda,
As an aside, most of the isotopes you listed are stable. The only nuclides
in the list that are actually unstable are 14C, 3H, 24P and 46P.
If your goal is to exclude isotopically enriched structures rather than
radioactive ones, it might be better to just look for ANY isotopic
specification, rather than for a specific list.
Kind Regards,
Bob
--
Bob Funchess, Ph.D. Kelaroo,
Inc
Director of Software Support & Development
www.kelaroo.com
bfunch...@kelaroo.com (858)
259-7561 x3
*From:* Milinda Samaraweera [mailto:milindaatw...@gmail.com]
*Sent:* Wednesday, January 18, 2017 11:48 AM
*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
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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
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