I should add, the try/except statement was a hack to get round creating the
same bond twice. I'm sure there's a more intelligent way to do this… but I
haven't had lunch yet so I cheated.
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E [email protected]<mailto:[email protected]> |
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On 9 Dec 2014, at 14:54, Nicholas Firth
<[email protected]<mailto:[email protected]>> wrote:
Hi Josh,
I've done a fair bit of breaking bonds and putting things back together, and
I've tended to use the EditableMol class to do this. However I haven't been
breaking any ring bonds.
As I'm sure you can see by looking at the molecule the reason you're getting
this behaviour is because you're breaking the 'wrong' bond here. You might want
to have a look at doing a different way, having a quick look at the code you
might want to try PathToSubmol here.
m3 = Chem.MolFromSmiles('n1ccc2nc3cc4cc5ccncc5cc4nc3nc2c1')
r = m3.GetRingInfo()
aMap={}
nm = Chem.PathToSubmol(m3,r.AtomRings()[0], atomMap = aMap)
Will give you the first ring, however it will break some bonds, but this is
easily fixed as aMap now contains the mapping from the previous molecule to the
new molecule. So a quick fix would be to iterate over each of the bonds in the
old molecule and then create the corresponding bonds in the new one.
em = Chem.EditableMol(nm)
for bond in m3.GetBonds():
if(bond.GetBeginAtomIdx() in aMap and bond.GetEndAtomIdx() in aMap):
try:
em.AddBond(aMap[bond.GetBeginAtomIdx()],
aMap[bond.GetEndAtomIdx()], Chem.BondType.AROMATIC)
except:
pass
nnm = em.GetMol()
Which I thought would solve your problem, however the Chem.PathToSubmol command
seems to give me an extra atom… Maybe someone else can help with that one??
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E [email protected]<mailto:[email protected]> |
W www.icr.ac.uk<http://www.icr.ac.uk/> | Twitter
@ICRnews<https://twitter.com/ICRnews>
Facebook
www.facebook.com/theinstituteofcancerresearch<http://www.facebook.com/theinstituteofcancerresearch>
Making the discoveries that defeat cancer
<image001.gif>
On 9 Dec 2014, at 14:23, Campbell J.E.
<[email protected]<mailto:[email protected]>> wrote:
break_atoms = [list(x) for x in
m3.GetSubstructMatches(Chem.MolFromSmarts('[R2]'))]
break_bonds = ((3,20), (5,18), (7,16), (9,14))
em = Chem.EditableMol(m3)
em.RemoveBond(3,20)
nm = em.GetMol()
frags = Chem.GetMolFrags(nm,asMols=True)
[Chem.MolToSmiles(x,True) for x in frags]
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