Re: [OpenBabel-scripting] Atom typing via Perl API

[Kieron T. <kr...@so...>]

Geoffrey Hutchison wrote:
> 
< snip >
> So if you'd like to see what atom types are getting ignored (and  
> generating the warning):
> 
>     my $atom = $obMol->GetAtom($_);
>     my $type = $atom->GetType();
>     my $newtype = $atom_typer->Translate($type);
>     print "Requested type: $type Translated type: $newtype\n";
>     $atom->SetType($newtype);

Strangely, in the original code that started all this, the error in 
question doesn't appear until I actively call OBConverter's serialising 
routine. ( OBconverter->write )

It then generates one error for each and every atom, none of which have 
particularly exotic atom types.

It seems to me that the conversion operation is somehow invoking an 
additional atom type translation but without passing the atom types 
around. I can only guess that it is detecting the fact that a target 
type has been set. If I have already manually set the new atom types in 
the manner of your code snippet above, the serialisation has those new 
types in spite of the chain of errors that follow.

I hope that helps to clarify things.


Kieron