Dear Noel Thank you for your answer. Please see my comments bellow.
2017-05-22 16:00 GMT-03:00 Noel O'Boyle <baoille...@gmail.com>:
> In other words, you want to assign atom types based on the structure.
>
Yes, that's right.
> The source of the structure is immaterial except in so far as it
> introduces noise. For example, to read a PDB file you need to guess
> various things. To read a MOL file, you don't need to guess anything.
>
That noise is what we are trying to avoid by always calculating (guessing)
things with the same algorithm.
> Regarding your code, you should never throw away information and then
> try to guess it.
Well, that depend on your faith on the quality of the information putted in
the input format.
One can always set a flag to keep the input information if its considered
accurate enough, but if you want consistency regarding the input file
format I don't see other way but to strip off all the information in the
input and recalculate it.
Also, I note in passing that DeleteHydrogens()
> doesn't delete anything, it just suppresses any explicit hydrogens.
>
I'm a bit unclear why you are using the internal Open Babel atom
> types. Personally, I would avoid this as the atom types may not be
> suitable.
Instead, just implement your own atom type function to suit
> your needs. Any atom typing can be implemented as a function that
> takes an OBAtom* and returns the type, perhaps as an enum.
>
Are you referring to functions like "IsAmideNitrogen" or so?. We used
these functions, and they worked just fine for our needs.
The problem we faced was with "IsAromatic" that we couldn't make it
input-format agnostic. Our guess is that some information of the input
format is always remaining when calling it, regardless
UnsetAromaticPerceived and the like were called before.
This lead us to try the route of put all the atom types in internal Open
Babel types and build upon it.
> - Noel
>
> On 22 May 2017 at 18:56, Marcos Villarreal <mvillarr...@unc.edu.ar> wrote:
> > Hello,
> >
> > For an application we are developing, we would like to get an atom typing
> > independent of the input format.
> > For example a mol2 with all Hydrogen atoms and a pdb without Hydrogens of
> > the same molecule (i.e. identical heavy atom coordinates) should get the
> > same atom types.
> > The attached program is our try in that direction, but unfortunately
> without
> > success. How could one get ride off all the input information and let
> babel
> > do all the new calculations of atom types?
> >
> > Thank you in advance.
> >
> >
> > int main(int argc,char **argv)
> > {
> >
> > OpenBabel::OBConversion conv;
> > OpenBabel::OBMol mol;
> > std::string filename;
> > filename = argv[1];
> >
> > conv.ReadFile(&mol,filename);
> >
> > mol.DeleteHydrogens();
> > mol.ConnectTheDots();
> > mol.PerceiveBondOrders();
> >
> > int i=0;
> > FOR_ATOMS_OF_MOL(atom, mol) {
> > i++;
> > std::cout << i << ": " << atom->GetType() << std::endl ;
> > }
> >
> > }
> >
> >
> >
> > --
> > Marcos Villarreal
> > Dpto de Química Teórica y Computacional
> > Facultad de Ciencias Químicas
> > Universidad Nacional de Córdoba
> > Argentina.
> >
> > ------------------------------------------------------------
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> >
>
--
Marcos Villarreal
Dpto de Química Teórica y Computacional
Facultad de Ciencias Químicas
Universidad Nacional de Cordoba
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