Thanks Greg, can you explain what is GetConformer?
In [3]: m = Chem.MolFromSmiles('Cc1ccccc1')
In [4]: CoordsAreAllZero(m)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/home/mnowotka/Documents/ci/curation_interface/trunk/src/curation_interface/<ipython-input-4-2d89c7fee0d4>
in <module>()
----> 1 CoordsAreAllZero(m)
/home/mnowotka/Documents/ci/curation_interface/trunk/src/curation_interface/<ipython-input-2-6b9ec261d3ef>
in CoordsAreAllZero(m, confId)
1 def CoordsAreAllZero(m,confId=-1):
----> 2 conf = m.GetConformer(confId)
3 for i in range(m.GetNumAtoms()):
4 if list(conf.GetAtomPosition(i))!=[0.0,0.0,0.0]:
5 return False
ValueError: Bad Conformer Id
On Wed, Aug 28, 2013 at 1:20 PM, Greg Landrum <[email protected]>wrote:
> Hi Michal,
>
>
> On Wed, Aug 28, 2013 at 1:16 PM, Michał Nowotka <[email protected]> wrote:
>
>> Imagine this scenario:
>>
>> I read random molfile and I want to produce an image of it:
>>
>> 1. If the molfile already contains coordinates, use them
>> 2. If the molfile coordinates are all zeros, compute them
>>
>> I don't know how to check if Mol (python object) has coordinates without
>> parsing original molfile, which doesn't seem to be a good idea.
>> And Compute2DCoords doesn't respect coordinates but computes them from
>> scratch.
>>
>> So, do you know any way to check if Mol (python object) already contains
>> not trivial (all zeros) coordinates, so I can call Compute2DCorrds only on
>> those of them which doesn't have coords?
>>
>>
> There's no easy way I can think of that's built in, but you could do
> something like this:
>
> In [19]: def CoordsAreAllZero(m,confId=-1):
> ....: conf = m.GetConformer(confId)
> ....: for i in range(m.GetNumAtoms()):
> ....: if list(conf.GetAtomPosition(i))!=[0.0,0.0,0.0]:
> ....: return False
> ....: return True
> ....:
>
> In [20]: print mb
>
> RDKit
>
> 2 1 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> M END
>
> In [21]: m = Chem.MolFromMolBlock(mb)
>
> In [22]: CoordsAreAllZero(m)
> Out[22]: True
>
> In [25]: AllChem.Compute2DCoords(m)
> Out[25]: 0
>
> In [26]: CoordsAreAllZero(m)
> Out[26]: False
>
>
> That ought to work at least most of the time.
>
> -greg
>
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