Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-19 Thread Stiefl, Nikolaus
<milindaatw...@gmail.com> Date: Wednesday 18 January 2017 at 23:01 To: Bob Funchess <bfunch...@kelaroo.com> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>, Greg Landrum <greg.land...@gmail.com> Subject: Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit Hi Bo

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Milinda Samaraweera
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

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Peter S. Shenkin
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;

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Milinda Samaraweera
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

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Bob Funchess
1 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 RdKi

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Stiefl, Nikolaus
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 the

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Milinda Samaraweera
> 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...@g

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Milinda Samaraweera
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

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Greg Landrum
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

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

2017-01-18 Thread Peter S. Shenkin
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