Hi RDKitters,
I would like to renumber atoms of molecules according to a canonized order.
I used the code below and noticed that the 3D flag "RDKIT 2D" turns into
"RDKIT 3D". Is it expected?
How could I switch it back to "RDKIT 2D"?
I remember seeing some function to toggle this flag, but just cannot put
my fingers on it anymore...
Thank you!
Jose Manuel
RDKIT 2015.03.1
#/usr/bin/env python
from rdkit import Chem, rdBase
# define test molecule
molblock="""TEST_INPUT
RDKit 2D
5 5 0 0 0 0 0 0 0 0999 V2000
-0.1105 -0.5357 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.7779 -1.0207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5230 -1.8052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3020 -1.8052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5569 -1.0207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
4 5 1 0
1 5 1 0
M END
$$$$
"""
print rdBase.rdkitVersion
print molblock # RDKIT 2D
# renumber test molecule by canonical atom rank
mol = Chem.MolFromMolBlock(molblock)
order_c = list(Chem.CanonicalRankAtoms(mol, breakTies=True,
includeChirality=True))
mol_c = Chem.RenumberAtoms(mol,order_c)
mol_c.SetProp("_Name", "TEST_OUTPUT")
# check result
print Chem.MolToMolBlock(mol_c) # RDKIT 3D!
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