Dear Greg/RDKitters,
This may be user error, or misunderstanding of rSMARTS, so can anyone throw
some light on the following behaviour?
First example works as expected - there are 2× Ph in m4, so we end up with
2×2×2 copies of the expected product:
rSMARTS4='([*:1]-&!@c1:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:1.[*:2]-&!@c1:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:1)>>([*:1]-!@c:1:c:c(-F):c:c:c1.[*:2]-!@c:1:c:c(-F):c:c:c1)<mailto:-&!@c1:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:1.[*:2]-&!@c1:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:[c&!H0]:1)%3e%3e([*:1]-!@c:1:c:c(-F):c:c:c1.[*:2]-!@c:1:c:c(-F):c:c:c1)>'
#Replace 2× Ph-* with 2× 3-Fl-C6H4-*
rxn4=AllChem.ReactionFromSmarts(rSMARTS4)
rxn4
[cid:image001.png@01D2A957.14773010]
m4=Chem.MolFromSmiles('c1ccccc1CCOCc1ccccc1')
m4
[cid:image002.png@01D2A957.14773010]
prodsbi=rxn4.RunReactants((m4,))
for prod in prodsbi:
Chem.SanitizeMol(prod[0])
Draw.MolsToGridImage([prod[0] for prod in prodsbi],molsPerRow=4,
subImgSize=(200,200))
[cid:image003.png@01D2A957.14773010]
Now consider the following - the only difference I can think of is that the
[*:1] and [*:2] atoms map to adjacent, directly bonded atoms - I cant see why
that should matter...
m3=Chem.MolFromSmiles('c1ccccc1COc1ccccc1')
m3
[cid:image004.png@01D2A957.14773010]
prodsbi=rxn4.RunReactants((m3,))
for prod in prodsbi:
Chem.SanitizeMol(prod[0])
Draw.MolsToGridImage([prod[0] for prod in prodsbi],molsPerRow=8,
subImgSize=(200,200))
[cid:image005.png@01D2A957.7D27E0A0]
Just to be sure this is as I think it looks..
prodsbi[0][0]
[cid:image006.png@01D2A957.7D27E0A0]
Any suggestions as to why this happens, and whether it is the expected
behaviour? (And how to avoid it?!)
Thanks,
Steve
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