[Biojava-dev] mmCIF parser development

[Andreas Prlic]

Hi Steve,

I'd say these are excellent feature requests for the current mmCIF parsing
framework.

We definitely want to enable all of the categories mentioned by you. The
data categories need to be added in either the SimpleMmCifParser/Consumer,
and the ChemCompConsumer.

If you want to provide a patch for parsing ligand information, sites, and
ssbonds, that would be welcome. I'd say these should go all into
the SimpleMMCIFConsumer.

Having said that, we need to double check that some of your requests are
not already implemented. E.g. there is already the BondMaker class that
assigns bonds based on mmCif definitions. (check the shouldCreateAtomBonds
flag in FileParsingParameters)

Do you want to open up (multiple) tickets on GitHub for the requested data
categories, then we can discuss them in detail there?

Thanks,

Andreas



On Tue, Oct 27, 2015 at 1:11 PM, Steve Darnell <darnells at dnastar.com> wrote:

> Greetings,
>
> Our group uses the BioJava mmCIF parser to handle reading mmCIF files to
> provide structural information.  The parsing and writing of mmCIF provide
> some of the important data entries but we would like to extend these to
> provide more details.  We are looking in particular to add the ability to
> parse ligand bond information, the _struct_site records for sites, and
> _struct_conn for disulfide bonds.  We are hoping to contribute any
> implementations for parsing back to the BioJava code base.
>
> For the ligand bond information, we could parse connectivity via the
> Chemical Component library since the bond information is not present within
> mmCIF as CONECT was for PDB.
>
> Is there planned development to get the equivalent bond information for
> ligands in the SimpleMMCIFParser as is present for CONECT records for PDB
> parsing?  If we were to implement parsing of ligand information, sites, and
> ssbonds, would it be best to add this SimpleMMCIFConsumer or as another
> consumer?
>
> Is this discussion best suited for the github issue tracker? If so, we
> will start a discussion there.
>

-- 
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Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
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