Milinda Samaraweera
Date: Wednesday 18 January 2017 at 23:01
To: Bob Funchess
Cc: RDKit Discuss , Greg Landrum
Subject: Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit
Hi Bob,
I am trying to filter out any compound that does not have the most stable
isotopic form; (anything other than:
Yes, most common should be the correct term.
Thanks,
Milinda
On Wed, Jan 18, 2017 at 5:49 PM, Peter S. Shenkin wrote:
> You say "most stable", but I think you mean "most common." 2H is as stable
> as 1H, but less common.
>
> -P.
>
> On Wed, Jan 18, 2017 at 5:01 PM, Milinda Samaraweera <
> milin
You say "most stable", but I think you mean "most common." 2H is as stable
as 1H, but less common.
-P.
On Wed, Jan 18, 2017 at 5:01 PM, Milinda Samaraweera <
milindaatw...@gmail.com> wrote:
> Hi Bob,
>
> I am trying to filter out any compound that does not have the most stable
> isotopic form;
Hi Bob,
I am trying to filter out any compound that does not have the most stable
isotopic form; (anything other than: 12C,1H,14N,16O, 31P, 32S) or to
contain only MonoIsotopic compounds.
Thanks,
Milinda
--
Check out t
1 x3
*From:* Milinda Samaraweera [mailto:milindaatw...@gmail.com]
*Sent:* Wednesday, January 18, 2017 11:48 AM
*To:* Greg Landrum
*Cc:* RDKit Discuss
*Subject:* Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit
Greg,
I am looking to remove entries that contain un-stable isotope
5NH2]')
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
Date: Wednesday 18 January 2017 at 20:47
To: Greg Landrum
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] Check for Heavy Isotopes
>
>
> So you could loop over your molecules and then remove the ones that match
> the smarts.
>
> Ciao
>
> Nik
>
>
>
>
>
> *From: *Milinda Samaraweera
> *Date: *Wednesday 18 January 2017 at 20:47
> *To: *Greg Landrum
> *Cc: *RDKit Discuss
> *Subj
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
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]').GetAtomsMatchingQuer
How about a regex filter on the all-atom SMILES?
-P.
On Wed, Jan 18, 2017 at 9:56 AM, 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 tw
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 understa
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