Maybe if you can give an example of the problem with aromaticity, we
can help? The only information that is used by that function is the
structure, so it was probably wrong at that point.
On 23 May 2017 at 13:16, Marcos Villarreal <mvillarr...@unc.edu.ar> wrote:
>
> 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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