On Dec 9, 2016, at 9:50 PM, Brian Kelley wrote:
> >>> from rdkit import Chem
> >>> m = Chem.MolFromSmiles("F/C=C/F")
> >>> for bond in m.GetBonds():
> ... print bond.GetStereo()
> ...
> STEREONONE
> STEREOE
> STEREONONE
>
> However, setting bond stereo doesn't appear to be exposed.
I thought I knew a way to change it, via GetBondDir()/SetBondDir() on the
directional bonds. It doesn't seem to work.
First, get the existing bond directions:
>>> from rdkit import Chem
>>> mol = Chem.MolFromSmiles("F/C=C/F")
>>> for bond in mol.GetBonds():
... print(bond.GetBondDir())
...
ENDUPRIGHT
NONE
ENDUPRIGHT
I'll change the first "/" to a "\" (That's "\\" when escaped for a normal
Python string.)
>>> mol.GetBondWithIdx(0)
<rdkit.Chem.rdchem.Bond object at 0x10fe26600>
>>> mol.GetBondWithIdx(0).GetBondDir()
rdkit.Chem.rdchem.BondDir.ENDUPRIGHT
>>> mol.GetBondWithIdx(0).SetBondDir(Chem.BondDir.ENDDOWNRIGHT)
If I generate the SMILES I see the old "F/C=C/F" instead of the new direction.
I need to clear internal computed properties when I make structure edits:
>>> Chem.MolToSmiles(mol, isomericSmiles=True)
'F/C=C/F'
>>> mol.ClearComputedProps()
>>> Chem.MolToSmiles(mol, isomericSmiles=True)
'F/C=C\\F'
I'll set the directions to "NONE" and clear computed properties. The SMILES is
correct:
>>> mol.GetBondWithIdx(0).SetBondDir(Chem.BondDir.NONE)
>>> mol.GetBondWithIdx(2).SetBondDir(Chem.BondDir.NONE)
>>> mol.ClearComputedProps()
>>> Chem.MolToSmiles(mol, isomericSmiles=True)
'FC=CF'
although the stereo setting is unchanged:
>>> for bond in mol.GetBonds():
... print(bond.GetStereo())
...
STEREONONE
STEREOE
STEREONONE
I expected it to give me all STEREONONEs, as if it were the same as the
following:
>>> mol2 = Chem.MolFromSmiles("FC=CF")
>>> for bond in mol2.GetBonds():
... print(bond.GetStereo())
...
STEREONONE
STEREONONE
STEREONONE
Andrew
[email protected]
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