Re: [Open Babel] pdb to xml

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

Meaghan Pilcher wrote:
> I have a list of pdb files that I need to convert to xml format.  This 
> cannot be done by simply using -ipdb -oxml.  How would I go about making 
> this format change?

The principal xml format for molecules is Chemical Markup Language, 
cml. Assuming this is the required format,
    babel *.pdb out.cml
will read all the pdb files in the current directory and put all the 
molecules into a single cml file. If you want them in separate cml 
files use
    babel  *.pdb out.cml -m
or alternatively in Windows
    babel *.pdb *.cml

OpenBabel's XMLFormat for input only and uses the xml namespace to 
choose the appropriate format, currently cml and PubChem, with the 
former used if there is no namespace.

Chris