Re: [OpenBabel-scripting] How to use option when converting a file..

[Chris M. <c.m...@ga...>]

Jérôme Hert wrote:
> Dear Colleaugues,
> 
> I was trying to use an option when converting a file into a different 
> format.
> 
> I use Perl so I write something like
> use Chemistry::OpenBabel;
> my $obMol = new Chemistry::OpenBabel::OBMol;
> my $obConversion = new Chemistry::OpenBabel::OBConversion;
> $obConversion->SetInAndOutFormats( "mol2", "pdb" ); 
> $obConversion->ReadFile( $obMol, "infile.mol2");
> $obConversion->WriteFile( $obMol, "outfile.pdb" );
> 
> That works fine.
> 
> Now I am trying to add something like:
> $obConversion->AddOption("d");
> before reading thr file in, the program doesn't complain but nothing 
> happens (i.e., the hydrogens are still present in the output file).
> 
> Anybody has any idea how these options are named? Any has any clue about 
> all those GetOptions, SetOption, GetOptions etc of that class in Perl?
> 
In C++ it would be necessary to use:

obConversion->AddOption("d", OBConversion::GENOPTIONS);

where the second parameter is an enum. I don't know how this is 
translated with the scripting interfaces.

There are three types of option INOPTIONS, OUTOPTIONS and GENOPTIONS. 
On the babel command-line the INOPTIONS, OUTOPTIONS have a prefix, 
e.g. -as and -xn respectively.
The default for this function is OUTOPTIONS, but -d needs GENOPTIONS.
Multi-character options are all GENOPTIONS.

It's a bit confusing for the scripting interface user, and perhaps we 
need something like AddGenOption("d")

You could also use a direct function call of DeleteHydrogens().

Chris