Hi all,
I am assigning the stereochemistry of a carbon stereocenter with RDKit from
molecule's 3D coordinates.
Although the stereocenter is been correctly labeled, I guess the applied
Cahn-Ingold-Prehlog rules aren't correct.
The first CIP rule says that the greater atomic number atom should recieve the
higher priority. In this context, higher priority means the lowest possible
number.
But atom.GetProp('_CIPRank') result is in reverse order.
Did i miss something?
Here's my R-1-carbon.mol file
R
OpenBabel07231810353D
[ callto:5%204%200%200%200%200%200%200 | 5 4 0 0 0 0 0 0 ] 0 0999 V2000
[ callto:0.0000%200.0000%200 | 0.0000 0.0000 0 ] .0000 C [
callto:0%200%200%200%200 | 0 0 0 0 0 ]
[ callto:0.0000%201.6326%20-1 | 0.0000 1.6326 -1 ] .1544 N [
callto:0%200%200%200%200 | 0 0 0 0 0 ]
[ callto:0.0000%20-1.6326%20-1 | 0.0000 -1.6326 -1 ] .1544 O [
callto:0%200%200%200%200 | 0 0 0 0 0 ]
[ callto:1.6326%200.0000%201 | 1.6326 0.0000 1 ] .1544 P [
callto:0%200%200%200%200 | 0 0 0 0 0 ]
- [ callto:1.6326%200.0000%201 | 1.6326 0.0000 1 ] .1544 I [
callto:0%200%200%200%200 | 0 0 0 0 0 ]
[ callto:3%201%201%206%200%200 | 3 1 1 6 0 0 ]
[ callto:1%205%201%206%200%200 | 1 5 1 6 0 0 ]
[ callto:1%202%201%206%200%200 | 1 2 1 6 0 0 ]
[ callto:1%204%201%206%200%200 | 1 4 1 6 0 0 ]
M END
Here's my code to find priorites of each atom:
from rdkit import Chem
mol = Chem.MolFromMolFile('R-1-carbon.mol' , removeHs = True)
Chem.AssignStereochemistry(mol, force=True, flagPossibleStereoCenters=True)
for atom in mol.GetAtoms():
print('Atom: ',atom.GetSymbol(), ' priority: ', atom.GetProp('_CIPRank'))
print('Stereocenter is: ',mol.GetAtomWithId(0).GetProp('_CIPCode'))
Here's the result:
Atom: C priority: 0
Atom: N priority: 1
Atom: O priority: 2
Atom: P priority: 3
Atom: I priority: 4
Stereocenter is: R
Thanks in advance,
Sincerely,
Frederico Teixeira Silva
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