Thank you all!
One more point:
How do I get the bond indexes for which the E/Z configuration has been set?
I seems there are no "magic" properties for bonds and no HasProp()
function for bonds.
All the best,
Jean-Marc
Le 19/12/2016 à 04:40, Greg Landrum a écrit :
One more piece that might help: the allHsExplicit to MolToSmiles() is
there to make sure that implicit Hs (Hs not actually in the graph)
show up in the output SMILES inside square brackets:
In [12]: m = Chem.MolFromSmiles('CC(O)(Cl)')
In [13]: Chem.MolToSmiles(m,allHsExplicit=True)
Out[13]: '[CH3][CH]([OH])[Cl]'
If you actually have Hs in the molecular graph they will always be in
the output SMILES, you don't need to use the allHsExplicit argument::
In [17]: m = Chem.MolFromSmiles('CC(O)(Cl)')
In [18]: mh = Chem.AddHs(m)
In [19]: Chem.MolToSmiles(mh)
Out[19]: '[H]OC([H])(Cl)C([H])([H])[H]'
-greg
On Mon, Dec 19, 2016 at 1:00 AM, Paolo Tosco <paolo.to...@unito.it
<mailto:paolo.to...@unito.it>> wrote:
Dear Jean-Marc,
as lactic2.sdf is a 3D structure which does not carry any
stereochemistry information in the SDF file, you will need to
perceive stereochemistry from the 3D structure with
Chem.AssignAtomChiralTagsFromStructure(mol)
before calling Chem.AssignStereochemistry().
It looks like allHsExplicit=True prevents SMILES chirality
specifications from being output:
In [1]: from rdkit import Chem
In [2]: molfilename = "lactic2.sdf"
In [3]: mol = Chem.SDMolSupplier(molfilename, removeHs = False)[0]
In [4]: Chem.AssignAtomChiralTagsFromStructure(mol)
In [5]: Chem.AssignStereochemistry(mol, cleanIt=False,
force=False, flagPossibleStereoCenters=True)
In [6]: chiralAtoms = [a for a in mol.GetAtoms() if
a.HasProp("_ChiralityPossible")]
In [7]: chiralAtomNums = [a.GetIdx()+1 for a in chiralAtoms]
In [8]: chiralAtomNums
Out[8]: [4]
In [9]: configs = [a.GetProp("_CIPCode") for a in chiralAtoms]
In [10]: configs
Out[10]: ['S']
In [11]: smi = Chem.MolToSmiles(mol, isomericSmiles=True)
In [12]: smi
Out[12]: '[H]OC(=O)[C@@]([H])(O[H])C([H])([H])[H]'
In [13]: smi = Chem.MolToSmiles(mol, isomericSmiles=True,
allHsExplicit=True)
In [14]: smi
Out[14]: '[H][O][C](=[O])[C]([H])([O][H])[C]([H])([H])[H]'
Cheers,
p.
On 12/18/2016 11:29 PM, Jean-Marc Nuzillard wrote:
Hi again,
When I run:
#------------
from rdkit import Chem
molfilename = "lactic2.sdf"
mol = Chem.SDMolSupplier(molfilename, removeHs = False)[0]
Chem.AssignStereochemistry(mol, cleanIt=False, force=False,
flagPossibleStereoCenters=True)
chiralAtoms = [a for a in mol.GetAtoms() if
a.HasProp("_ChiralityPossible")]
chiralAtomNums = [a.GetIdx()+1 for a in chiralAtoms]
print "chiral centers: ",
print chiralAtomNums
configs = [a.GetProp("_CIPCode") for a in chiralAtoms]
print configs
smi = Chem.MolToSmiles(mol, isomericSmiles=True, allHsExplicit=True)
print smi
#------------
Two (related?) problems arise.
First, _CIPCode rises a KeyError, even for atoms for which
_ChiralityPossible is defined.
When I comment the lines that define and print the configs
variable, the second problem arises.
The string smi does not contain any '@' or '@@', something I
expected from a chiral molecule
for an isomeric smiles string.
The attached lactic2.sdf file comes from PubChem. I removed (set
to 0) the parity flag for atom 4 (index 3)
because there are no parity flags in the files I will have to
deal with later.
Keeping the parity flag does not change anything.
What did I miss?
All the best,
Jean-Marc
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Jean-Marc Nuzillard
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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