Thanks Noel, it works. I though that GetCoordinates would write the
coordinates in a new object, whereas it seems to be made to update the
used object.
2014-04-18 15:01 GMT-04:00 Noel O'Boyle <baoille...@gmail.com>:
> Does GetCoordinates(obMol) work?
>
>
> On 18 April 2014 03:36, Nicolas Cheron <nche...@fas.harvard.edu> wrote:
>>
>> Hello,
>>
>> I am trying to use the optimize options of OpenBabel. I have written
>> the following code using some of the online examples (I am simplifying
>> the code), but it doesn't work as expected:
>>
>> // Open the file
>> OpenBabel::OBConversion obConversion;
>> OpenBabel::OBMol obMol;
>> obConversion.SetInFormat("xyz");
>> obConversion.ReadFile(&obMol,"Ligand.xyz");
>>
>> // Define the forcefield
>> OpenBabel::OBForceField *ff =
>> OpenBabel::OBForceField::FindForceField("MMFF94");
>> // Setup the forcefield.
>> ff->Setup(obMol);
>> // Print the energy and unit before optimization
>> cout << ff->Energy() << " " << ff->GetUnit() << endl;
>>
>> // Perform the minimization
>> ff->SteepestDescent(1000);
>> cout << ff->Energy() << " " << ff->GetUnit() << endl;
>> ff->ConjugateGradients(1000);
>> cout << ff->Energy() << " " << ff->GetUnit() << endl;
>>
>> // Write the output
>> OpenBabel::OBMol mol;
>> OpenBabel::OBConversion conv;
>> ff->GetCoordinates(mol);
>> conv.SetOutFormat("xyz");
>> conv.WriteFile(&mol,"Ligand_Opt.xyz");
>> cout << mol.NumAtoms() << endl;
>>
>> The output is for example:
>> 285.045 kcal/mol
>> 57.897 kcal/mol
>> 57.8942 kcal/mol
>> 0
>>
>> So the two optimization are working. However, the molecule is not
>> written in the Ligand_Opt.xyz file since the mol object is empty as
>> seen by the "0" in the output. I must be doing something wrong with
>> "ff->GetCoordinates(mol);" but I have not find what.
>>
>> Can you please help me or point me toward the good direction.
>>
>> Thank you
>>
>> Nicolas
>>
>>
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>
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
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