Thank you Malitha,
If I'm understanding the Draw code (not a given, my python ist nicht gut),
then MolToMPL (or MolToImage) is just using the 3D conformation generated
by EmbedMolecule. Is it just chopping off the z-coordinate? For
acetylene, this works out because it gets embedded mostly in the XY plane
by default, but it would fail if the 3D conformer were aligned along the
z-axis.
I would think GenerateDepictionMatching3DStructure is the safe way to do
this, but it also seems to have trouble with acetylene
m = Chem.MolFromSmiles('C#C')
m2=Chem.rdmolops.AddHs(m)
AllChem.EmbedMolecule(m2, AllChem.ETKDG())
m3=Chem.rdmolops.AddHs(m)
Chem.rdDepictor.GenerateDepictionMatching3DStructure(m3,m2)
m3.GetConformer(0).GetPositions()
array([[ 1.60734892e-16, 7.50000000e-01, 0.00000000e+00],
[ -1.14810637e-16, -7.50000000e-01, 0.00000000e+00],
[ -4.82204677e-16, -7.50000000e-01, 0.00000000e+00],
[ 4.36280422e-16, 7.50000000e-01, 0.00000000e+00]])
The above seems to happen with any terminal alkyne hydrogen. I will file
an issue for this
Jason
Jason Biggs
On Fri, Dec 1, 2017 at 4:59 AM, Malitha Kabir <malitha12...@gmail.com>
wrote:
> Hi Jason,
>
> I hope the following codes will help you a little.
>
> from rdkit import Chem
> from rdkit.Chem import Draw
> from rdkit.Chem import AllChem
> size = (120, 120)
> m = Chem.MolFromSmiles('C#C')
> m2=Chem.rdmolops.AddHs(m)
> AllChem.EmbedMolecule(m2, AllChem.ETKDG())
> Draw.MolToMPL(m2, size=size)
>
> *** source code link (non specific to your question though)
> https://github.com/rdkit/rdkit
>
> Thanks. - malitha
>
>
> On Fri, Dec 1, 2017 at 6:42 AM, Jason Biggs <jasondbi...@gmail.com> wrote:
>
>>
>> m = Chem.MolFromSmiles('C#C')
>>
>>
>> renders fine
>>
>> [image: Inline image 1]
>>
>> but adding in the hydrogens, they don't snap to a linear arrangement
>>
>> m2=Chem.rdmolops.AddHs(m)
>>
>>
>> [image: Inline image 3]
>>
>>
>> This doesn't just affect acetylene, but any terminal alkyne, like
>> 'c1ccc(CCC#C)cc1'.
>>
>> I can write a hack on my end to look for this special case, but where in
>> the drawing code does it decide where to place hydrogens?
>>
>> Jason Biggs
>>
>>
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>
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