| Toggle-off absolute configuration while determining Murcko scaffold [message #608] |
Wed, 21 August 2019 14:00  |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Dear Thomas,
using both DW as well as third-party python module rdkit to
determine the Murcko scaffolds of molecules including those with
a stereogenic center, I noticed DataWarrior (DW) retains the
stereochemical information in the trimmed fragment. Reading the
same SMILES string as DW (5.0.0), rdkit (version 2019.1 with
Python2) however trims this information off.
Question: Is there an option to instruct DW equally to 'forget'
about this piece of information when writing the SMILES string?
Pristine SMILES string in question used in both programs:
C(=O)(C)O[C@H]1[C@H]([C@H](n2c3c(c(ncn3)N)nc2)O[C@@H]1CO)O
DW's output SMILES string about the Murcko scaffold:
C(C1)CO[C@H]1n1c2ncncc2nc1
MWE for processing with rdkit:
from rdkit.Chem.Scaffolds import MurckoScaffold
from rdkit.Chem import AllChem
source = 'C(=O)(C)O[C@H]1[C@H]([C@H](n2c3c(c(ncn3)N)nc2)O[C@@H]1CO)O'
mol = Chem.MolFromSmiles(source)
core = MurckoScaffold.GetScaffoldForMol(mol)
print(Chem.MolToSmiles(core))
>>> c1ncc2ncn(C3CCCO3)c2n1
which constitutionally is about the same molecular structure.
This may be more than a cosmetic issue, because the search for
the Murcko scaffold of
Brc1ccc([C@@]2(CC(=O)CCC2)CN(=O)=O)cc1
actually leads DW to invert the absolute configuration from
initial R to now S (expressed by the lost of one @ in
string O=C(CCC1)C[C@H]1c1ccccc1).
[Updated on: Wed, 21 August 2019 14:34] Report message to a moderator |
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