Re: [Rdkit-discuss] non-smallest rings
On 22/01/13 05:40, Greg Landrum wrote: Hi Paul, On Mon, Jan 21, 2013 at 4:13 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: I am making heavy weather of the following problem - and am wondering if I am missing something (such as a useful RDKit function). I am working on this beasty (as an example): http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=0CP COc1ccc(cc1O[C@H]1C[C@@H]2CC[C@H]1C2)C1CNC(=O)NC1 which has a norbornane substituent. I am trying to prepare input for a downstream program that needs to know if the norbornane atoms are in a 6-membered ring [1]. RingInfo gives me the 2 5-membered rings. I am strugging to make use of that information to find 6-membered rings. I have been using makeRingNeighborMap() and pickFusedRings(). Am I missing an RDKit function that finds all rings? There's not currently any RDKit functionality which finds all rings. It wouldn't be terribly difficult to add, but it could return a huge number of rings (imagine the results for C60). Another option would be to add a function bool atomIsInAnyRingOfSize(const Atom *at,unsigned int size) that does the check on demand. Not terribly difficult, as you say, but easier for you than me, I imagine. I had a bash with the trace_path() and handle_bigger_rings_from_fused_rings() methods, for the record, here: http://code.google.com/p/coot/source/browse/trunk/lidia-core/cod-types.cc I'll try and get it released under the same licence as the RDKit, fwtw. The thing that was non-trivial (for me) was the shall we recur deeper? rule. Cheers, Paul. -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] non-smallest rings
If you're just looking for 6 membered rings, you can define a SMARTS that matches 6 membered rings like this *1~*~*~*~*~*1. You can also use this approach to identify all rings (at least those within reason). You can use an expression like this [*1+string.join([*~]*x,)+*1 for x in range(1,19)] to generate SMARTS for all rings with size 3 to 20. Now you can match these to your molecule and get all of the rings (example below). import string from rdkit import Chem class RingFinder: def __init__(self): self.ringSmartsList = [*1+string.join([*~]*x,)+*1 for x in range(1,19)] self.ringPatList = [(x.count(*),Chem.MolFromSmarts(x)) for x in self.ringSmartsList] def findAllRings(self,mol): ringList = [] for size,pat in self.ringPatList: for match in mol.GetSubstructMatches(pat): ringList.append([size,match]) return ringList ringFinder = RingFinder() smiles = COc1ccc(cc1O[C@H]1C[C@@H]2CC[C@H]1C2)C1CNC(=O)NC1 mol = Chem.MolFromSmiles(smiles) print ringFinder.findAllRings(mol) If you run this you'll get two 5 membered rings and 3 six membered rings for the molecule above. Pat On Mon, Jan 21, 2013 at 10:13 AM, Paul Emsley pems...@mrc-lmb.cam.ac.ukwrote: I am making heavy weather of the following problem - and am wondering if I am missing something (such as a useful RDKit function). I am working on this beasty (as an example): http://www.rcsb.org/pdb/**ligand/ligandsummary.do?hetId=**0CPhttp://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=0CP COc1ccc(cc1O[C@H]1C[C@@H]2CC[**C@H]1C2)C1CNC(=O)NC1 which has a norbornane substituent. I am trying to prepare input for a downstream program that needs to know if the norbornane atoms are in a 6-membered ring [1]. RingInfo gives me the 2 5-membered rings. I am strugging to make use of that information to find 6-membered rings. I have been using makeRingNeighborMap() and pickFusedRings(). Am I missing an RDKit function that finds all rings? Cheers, Paul. [1] actually, all atoms but it is the norbornane atoms with which I struggle. -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] non-smallest rings
On Wed, Jan 23, 2013 at 2:47 AM, Patrick Walters wpwalt...@gmail.com wrote: If you're just looking for 6 membered rings, you can define a SMARTS that matches 6 membered rings like this *1~*~*~*~*~*1. You can also use this approach to identify all rings (at least those within reason). You can use an expression like this [*1+string.join([*~]*x,)+*1 for x in range(1,19)] Or you can do it that easy way right away. (I'm smacking myself for not thinking of that...) Thanks Pat! -greg -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] non-smallest rings
do you just have to check if an atom is in a 6-membered ring? If so then
In [8]: m =
Chem.MolFromSmiles('COc1ccc(cc1O[C@H]1C[C@@H]2CC[C@H]1C2)C1CNC(=O)NC1')
In [9]: [a.IsInRingSize(6) for a in m.GetAtoms()]
Out[9]:
[False,
False,
True,
True,
True,
True,
True,
True,
False,
False,
False,
False,
False,
False,
False,
False,
True,
True,
True,
True,
False,
True,
True]
Should help.
Sorry - maybe I do not fully understand your question
Ciao
Nik
On 1/21/13 4:13 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote:
I am making heavy weather of the following problem - and am wondering if
I am missing something (such as a useful RDKit function).
I am working on this beasty (as an example):
http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=0CP
COc1ccc(cc1O[C@H]1C[C@@H]2CC[C@H]1C2)C1CNC(=O)NC1
which has a norbornane substituent. I am trying to prepare input for a
downstream program that needs to know if the norbornane atoms are in a
6-membered ring [1]. RingInfo gives me the 2 5-membered rings. I am
strugging to make use of that information to find 6-membered rings. I
have been using makeRingNeighborMap() and pickFusedRings(). Am I
missing an RDKit function that finds all rings?
Cheers,
Paul.
[1] actually, all atoms but it is the norbornane atoms with which I
struggle.
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