ing on docking (autodock vina) whose score depends on
atom typing. As you know the ligands come in different formats, usually
pdb, mol2 or sdf. We would expect to obtain the same docking result
regardless the input format.
-Marcos.
> -Geoff
--
Marcos Villarreal
Dpto de
the same as
> Open Babel but that's no excuse.
>
> The PDB file of course does not contain any bond orders and so we
> guess them. We do an okay job - this is an example where we miss the
> bond. If you removed these bond orders from the MOL2 file you would
> get the same wrong st
if needed)
> then compute the atom types from that file and see what happens...
>
> On 22 May 2017 19:24, "Marcos Villarreal" wrote:
>
>> Hello,
>>
>> For an application we are developing, we would like to get an atom typing
>> independent of the inpu
rmat 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 wrote:
> > He
::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() << st
