On Tue, Jan 25, 2011 at 10:10 AM, [email protected] <[email protected]> wrote:
> On Tue, Jan 25, 2011 at 5:51 AM, Greg Landrum <[email protected]> wrote:
>> The current release of the code doesn't really support this but it's
>> one of those easy-to-add features that make sense to me. I just
>> checked in some changes to the drawing code so that it supports the
>> ignoreHs argument:
>>
>> [5]>>> Draw.ShowMol(mh,ignoreHs=True)
>>
>> or:
>>
>> [6]>>> Draw.MolToFile(mh,'blah.png',ignoreHs=True)
>
> I downloaded the latest revision and tested it briefly.
>
> While this change is doing a good job at removing H atoms from the
> final image, they are still used to compute 2D coordinates so the
> resulting depiction is often distorted; do you think adding the same
> "IgnoreHs" parameter to AllChem.Compute2DCoords() would be much more
> involved?
Yeah, that's definitely more complicated.
This little bit of code should do what you want though:
#--------------------
from rdkit import Chem
from rdkit.Chem import AllChem
def Compute2DCoordsNoHs(mol):
mh = Chem.RemoveHs(mol)
AllChem.Compute2DCoords(mh)
match = mol.GetSubstructMatch(mh)
conf = Chem.Conformer(mol.GetNumAtoms())
refconf = mh.GetConformer()
for i,idx in enumerate(match):
conf.SetAtomPosition(idx,refconf.GetAtomPosition(i))
cid=mol.AddConformer(conf,assignId=True)
return cid
if __name__=='__main__':
testmol = Chem.AddHs(Chem.MolFromSmiles('c1ccccn1'))
AllChem.Compute2DCoords(testmol)
print Chem.MolToMolBlock(testmol)
cid=Compute2DCoordsNoHs(testmol)
print Chem.MolToMolBlock(testmol,confId=cid)
#--------------------
>
> I've implemented a workaround in my code (store a map of {indexH:
> indexNoH} pairs and use it to highlight the requested atom in the
> hydrogen-free depiction) but a more proper solution would be probably
> appreciated (not only by me :-) )
take a look at the above and see if it does what you want.
-greg
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