Thanks Greg,
that works great. I’ve reconverted the isotopic smarts to smiles with the
function suggested in
(http://rdkit.org/docs/Cookbook.html#using-custom-mcs-atom-types):
def getMCSSmiles(mol,labelledMol,mcs):
mcsp = Chem.MolFromSmarts(mcs.smartsString)
match = labelledMol.GetSubstructMatch(mcsp)
return Chem.MolFragmentToSmiles(ms[0],atomsToUse=match,
isomericSmiles=True,
canonical=False)
However, I think there may be a typo, and it should be:
def getMCSSmiles(mol,labelledMol,mcs):
mcsp = Chem.MolFromSmarts(mcs.smartsString)
match = labelledMol.GetSubstructMatch(mcsp)
return Chem.MolFragmentToSmiles(mol,atomsToUse=match,
isomericSmiles=True,
canonical=False)
I’ll see if I can use the custom atom types to get rid of more unwanted
matches, such as those you highlighted in my previous email.
Thanks again,
Luca Fenu – Computational Chemist
Computational Chemist, CADD Group, Chemistry
Eli Lilly and Company Limited
Erl Wood Manor, Sunninghill Road, Windlesham, Surrey, GU20 6PH
012.764.83354 (office) | 07858.701.646 (mobile)
fenu_l...@network.lilly.com<mailto:surname_n...@network.lilly.com> |
www.lilly.co.uk<http://www.lilly.co.uk>
[cid:image005.jpg@01D0842C.DF674960]
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 18 June 2016 05:16
To: Luca Fenu - Network
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] MCS on fused ring systems
Hi Luca,
On Fri, Jun 17, 2016 at 5:28 PM, Luca Fenu - Network
<fenu_l...@network.lilly.com<mailto:fenu_l...@network.lilly.com>> wrote:
I’m back again with what seems to me like puzzling behaviour from the
rdfMCS.findMCS function when dealing with fused ring systems:
> mol3RA = Chem.MolFromSmiles('c1ccc2cc3ccccc3cc2c1')
> mol3RB = Chem.MolFromSmiles('c1ccc2c(c1)ccc1ccccc21')
> rdFMCS.FindMCS([mol3RA, mol3RB], matchValences=True,
matchChiralTag=True,
ringMatchesRingOnly=True,
completeRingsOnly=True # False will return the same result
).smartsString
'[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1'
Or, in pictures:
[cid:image002.png@01D1CB10.0E013350]
The MCS shown above is the same whether or not I turn on the ‘completeRingsOnly
flag.
So, the atoms are all there, but the MCS ring can’t be closed because the
attachment point doesn’t match.
Since we’re requesting completeRingsOnly, wouldn’t make sense for the MCS be
reduced to just a naphthalene?
What’s the rationale behind the current implementation? Is there a way to force
it to drop the open circle?
That's a bug in the current implementation. I'll take a look at it and see if I
can track it down.
And another, related, question: is there a way to make the MCS computation even
more restrictive,
only returning a ring as part of the MCS if the whole fused system is matched,
not just a portion (albeit a complete ring by itself?). In the example
described above, there would be no MCS.
I’d be fine with some post-processing to the same aim. Another example:
[cid:image003.png@01D1CB10.0E013350]
That's an interesting question. I think you can get at least part of what
you're looking for using the "atom labeling" trick from here:
http://rdkit.org/docs/Cookbook.html#using-custom-mcs-atom-types
Here's a pass at the first step of that:
In [70]: def label(a):
return 100*a.GetOwningMol().GetRingInfo().NumAtomRings(a.GetIdx()) +
a.GetAtomicNum()
....:
In [71]: bz = Chem.MolFromSmiles('c1ccccc1')
In [72]: napth = Chem.MolFromSmiles('c1ccc2ccccc2c1')
In [73]: rdFMCS.FindMCS([bz,napth]).smartsString
Out[73]: '[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1'
In [74]: nms = [Chem.Mol(x) for x in (bz,napth)]
In [75]: for nm in nms:
....: for at in nm.GetAtoms():
....: at.SetIsotope(label(at))
....:
In [76]: mcs =
rdFMCS.FindMCS(nms,atomCompare=rdFMCS.AtomCompare.CompareIsotopes)
In [77]: mcs.smartsString
Out[77]: '[106*](:[106*]:[106*]):[106*]'
In [78]: mcs =
rdFMCS.FindMCS(nms,atomCompare=rdFMCS.AtomCompare.CompareIsotopes,completeRingsOnly=True)
In [79]: mcs.smartsString
Out[79]: ''
Does that help?
-greg
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