Dear Greg,
My own source code has some problems, not because of Conformer class.
I fixed it
Thank you
- Jongyoung
> 2010/8/10 정종영 <lis...@yonsei.ac.kr>:
>> Dear Greg,
>>
>>>>
>>>> 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
>>>
>>>
>>
>> I executed below source code..
>>
>> ...
>>
>> SDMolSupplier ligandMolSup(fname, true, false);
>> ROMol *ligand = ligandMolSup.next();
>>
>> ///////////////////////////////////////////////
>> /// This is extended modules to calculate in-house molecular
>> properties
>> ///////////////////////////////////////////////
>> assignCSBAtomTypes(ligand);
>> MolecularPropertiesCalculator molPropCalcator(ligand);
>> molPropCalcator.calculateMPEOE();
>> molPropCalcator.calculateCDEAP();
>> ////////////////////////////////////////////////////
>>
>> int numOfAtom = ligand->getNumAtoms();
>> Conformer conf = ligand->getConformer();
>> Point3D atomPos;
>> for (int i=0; i<numOfAtom; i++){
>> atomPos = conf.getAtomPos(i);
>> std::cout << atomPos << std::endl;
>> }
>>
>>
>> <output>
>> 1.2333 0.554 0.7792
>> -0.6952 -2.7148 -0.7502
>> 0.7958 -2.1843 0.8685
>> 1.7813 0.8105 -1.4821
>> -0.0857 0.6088 0.4403
>> -0.7927 -0.5515 0.1244
>> -0.7288 1.8464 0.4133
>> -2.1426 -0.4741 -0.2184
>> -2.0787 1.9238 0.0706
>> ...
>>
>>
>> I guess that center of coordinate is translated to origin "(0.0, 0.0,
>> 0.0)"
>> in Conformer class.
>
> There is code in the RDKit to do this (specifically in
> GraphMol/MolTransforms/MolTransforms.h), but that code is not used by
> the SDMolSupplier.
>
> Could it be that your MolecularPropertiesCalculator modifies the
> conformation?
>
> Best,
> -greg
>
>
>
>
>
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