Dear Jongyoung,
2010/8/10 정종영 <[email protected]>:
>>
>> That code looks fine to me.
>>
>> To help debug this, can you please provide the CTAB from the SDfile
>> and the RDKit output for a molecule where you see a difference?
>>
>> Thanks,
>> -greg
>>
>>
>
> I attached a sd file that has coordinate problem.
> It is from 1A30 pdb file and saved as sdf file.
>
> Would you check and compare coordinates of Conformer class and sdf file?
The look the same to me:
[36]>>> suppl = Chem.SDMolSupplier('test.sdf',True,False)
[37]>>> m = suppl.next()
[38]>>> conf = m.GetConformer()
[39]>>> for i in range(m.GetNumAtoms()): print list(conf.GetAtomPosition(i))
....:
[4.8410000000000002, 27.576000000000001, 5.3099999999999996]
[5.7329999999999997, 26.393999999999998, 5.165]
[7.1740000000000004, 26.771999999999998, 5.5039999999999996]
[7.6239999999999997, 27.887, 5.218]
[5.6379999999999999, 25.818000000000001, 3.75]
[5.827, 26.846, 2.6520000000000001]
[5.625, 26.274999999999999, 1.262]
[4.6630000000000003, 25.497, 1.0649999999999999]
[6.4249999999999998, 26.620000000000001, 0.36299999999999999]
....
When you use this file, what do you see?
-greg
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