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

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

I've written some working code for assigning atom types for the various 
forcefields by Perl API. It's pretty simple, but there are differences 
from the v2.02 API.

I get the following error with each atom, even though it performs the 
appropriate transformation. I am uncertain what it is trying to do that 
fails. Error:
==============================
*** Open Babel Warning  in Translate
   Cannot perform atom type translation: table cannot find requested types.

I have a feeling I may be trying to get it to do the translation twice.

Line 23 of my code $newtype = $atom_typer->Translate($type); does not 
match the API documentation which claims to return Boolean from the 
Translate call, rather than the new atom type.

Here's the code:
---------------
#!/usr/bin/perl

use strict;
use Chemistry::OpenBabel;

my $obMol = new Chemistry::OpenBabel::OBMol;
my $obConverter = new Chemistry::OpenBabel::OBConversion;

$obConverter->SetInAndOutFormats("xyz","mol2");
$obConverter->ReadFile($obMol,"file.xyz");

my $atom_typer = new Chemistry::OpenBabel::OBTypeTable;

$atom_typer->SetFromType("INT");
$atom_typer->SetToType("DRE");
# DRE = Dreiding, INT = internal, others found in
# OpenBabel/data/types.txt

for (1..$obMol->NumAtoms() )
{
	my $atom = $obMol->GetAtom($_);
	my $type = $atom->GetType();
	my $newtype = $atom_typer->Translate($type);
	$atom->SetType($newtype);
}
$obConverter->WriteFile($obMol, "typed_molecule.mol2") ;

----end-of-Perl---------

Any ideas what I'm missing here?

Thanks,

Kieron