Did you call OBForceField::GetCoordinates after minimizing? The
forcefield works on a copy of the molecule so you have to get the
updated coordinates explicitly.
On Sun, Aug 1, 2010 at 12:44 AM, N David Brown <hubd...@googlemail.com> wrote:
> ..whoops, that's FOR_ATOMS_OF_MOL of course, just a typo (!).
>
>
> On 31 July 2010 23:43, N David Brown <hubd...@googlemail.com> wrote:
>> Hi all,
>>
>> I'm having issues with OBForceField.
>>
>> I perform a crude layout of a SMILES string using a simulated
>> annealing method. I then pass the resulting structure to an
>> OBForceField instance to generate more accurate geometry. However, the
>> coordinates in the OBMol operated on remain the same after performing
>> the force field simulation. I'm using the UFF force field.
>>
>> I've used the demo code listed in the OBForceField API documentation,
>> and then view the resulting coordinates by
>>
>> FOR_ATOMS_IN_MOL(atom, mol)
>> {
>> // ...
>> cout << atom->GetX() << ","
>> << atom->GetY() << ", "
>> << atom->GetZ() << endl;
>> }
>>
>> It is clear from the output that the positions remain identical. Yet
>> the OBFF logs a successful convergence:
>>
>> C O N J U G A T E G R A D I E N T S
>>
>> STEPS = 1000
>>
>> STEP n E(n) E(n-1)
>> --------------------------------
>> 1 141098.938 468447.427
>> 6 43405.513 43405.513
>> CONJUGATE GRADIENTS HAS CONVERGED
>>
>>
>> Has anyone a suggestion as to why this is happening? Any advice would
>> be welcome.
>>
>> With thanks and kind regards,
>>
>> David
>>
>
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