Here's a bit more info, perhaps useful...
For whatever reason
Inside of
OBRotorList::FindRotors
The call to HasFixedAtoms() returns false, even though I've previously
specified constraints to the setup of the force field.
So... it seem that _fix is empy (HasFixedAtoms() is declared in
include/openbabel/rotor.h)
Seems _fix is not in sync with _constraints._fixed
Anyway, it would seem that the rotor search codes should be calling
OBRotorList.SetFixAtoms(...) specifying the _fixed OBBitVec from
_constraints... but I can't find any where they are doing so.
At least that's my naive take on it. I must admit my C++ is very
rusty and I've just started looking at this code base last week, so
take this with the appropriate caution. :)
Cheers,
Chris.
On Mon, Jun 28, 2010 at 7:43 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> I've never used OBConstraints, but just as general advice: when
> setting up the forcefield, you should ensure that (a) the atoms have
> 3D coordinates, (b) hydrogens have already been added, and (c) that
> calling the Setup function is successful.
>
> // We pass the constraints as argument for Setup()
> if (!pFF->Setup(mol, constraints)) {
> cerr << "ERROR: could not setup force field." << endl;
> }
>
> - Noel
>
> On 25 June 2010 01:03, Christopher Wassman <cwass...@ics.uci.edu> wrote:
>> Tried to implement fixing atoms as part of a conformational search....
>> as a straightforward
>> modification of the 'obconformer' tool.... but perhaps I'm missing
>> something. I'm using the source from
>> openbabel-2.2.3
>>
>>
>> I simply added this (in the "while(ifs.peek() != EOF && ifs.good())" loop):
>>
>> OBFFConstraints constraints;
>> int i = 0;
>> for (i=1; i<=3; i++) {
>> cout << " Fixing atom index " << i << "...\n";
>> OBAtom *atom;
>> atom = mol.GetAtom(i);
>> if (!atom->IsHydrogen())
>> {
>> constraints.AddAtomConstraint(i);
>> }
>> else
>> {
>> cerr << "Error! heavy atoms first !" << endl;
>> }
>> }
>>
>> pFF->Setup(mol,constraints);
>> pFF->WeightedRotorSearch(weightSteps, geomSteps);
>> ...
>> etc as in "tools/obconfomer.cpp"
>>
>>
>> and removed the old "pFF->Setup(mol);" statement
>>
>> I tried this on a simple butane molecule (defined in a pdb), where the
>> first atoms listed are the carbon backbone, in linear order.
>>
>> I'd expect this to "freeze" the first 3 carbon atoms, however, in the
>> output only 2 of the 4 carbon atoms are held in fixed position. (The
>> first and the last carbons moved.)
>>
>> Trying this approach to freeze all 4 of the carbon atoms, results in a
>> conformer where only 1 of the carbon atoms have moved. (The first
>> carbon moved.)
>>
>> Anyone able to shed some light on this for me? What am I missing?
>>
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>
>
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