Hello:
I am puzzled by the output from ReplaceSubstructs as it can produce two
fragments.
So I went and tried the examples in the manual and I observed this:
The example in the intro manual with the recursive smarts pattern works as
expected.
repl = Chem.MolFromSmiles('OC')
patt = Chem.MolFromSmarts('[$(NC(=O))]')
m = Chem.MolFromSmiles('CC(=O)N')
rms = AllChem.ReplaceSubstructs(m,patt,repl)
One expected product is formed.
The example form the ReplaceSubstructs manual produces two solutions.
I have used the following commands:
from rdkit import Chem
from rdkit.Chem import AllChem
#ReplaceSubstructs(‘CCOC’,’OC’,’NC’) -> (‘CCNC’,)
repl = Chem.MolFromSmiles('NC')
patt = Chem.MolFromSmarts('OC')
m = Chem.MolFromSmiles('CCOC')
rms = AllChem.ReplaceSubstructs(m,patt,repl)
for rm in rms:
print(CHem.MolToSmiles(rm))
output is: C.CNC and CCNC
Why is the first result produced?
I checked the mailing list and could find this older threat
https://sourceforge.net/p/rdkit/mailman/message/28777648/.
But the answer to the related question is missing.
rdkit version is 2020.03.1dev1
Best wishes,
Markus
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