[Biojava-dev] mmCIF parser development

[Steve Darnell]

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.

Best regards,
Steve

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Steve Darnell
DNASTAR, Inc.
Madison, WI USA