Hi All,
I was about to write a function to reassemble a molecule from a core +
R-groups, but I thought I'd check and see if such a function already
exists. This is work with the output of rdRGroupDecomposition
Gvien a core:
CN(C)CC(Br)c1cc([*:2])c([*:1])cn1
Plus a set of R-groups
Hi Pat,
I wrote something like this for mmpdb, which is the MMPA code I helped
develop, at https://github.com/rdkit/mmpdb .
It has one restriction, which I'll get to in a moment.
The general idea is to convert the attachment points to closures, join them
with a ".", and canonicalize:
>>>
Thanks Andrew, the SMILES approach seemed to have quite a few edge cases so
I wrote something to work directly on a molecule.
#!/usr/bin/env python
import sys
from rdkit import Chem
from collections import defaultdict
from rdkit.Chem.rdchem import EditableMol
# Thanks to steeveslab-blog for
Ah, I'm replying too late... sorry about that.
There's a command line utility in rdkit.Chem.ChemUtils.TemplateExpand that
could also be used for this purpose. The big difference is that it uses
isotope labels on the dummy atoms to do the matching.
A style point: you can now create an RWMol
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