[Biojava-dev] CONECT records, issue 330, and the refactoring of bonds.

[Matt Larson]

Hi,

I was looking back at issue 330 (short lines when parsing PDB) but there
have been some large API changes ~ 4.2.x to move BioJava to more resemble
mmCIF structure formats.  These API changes dropped LINK (and possibly
CONECT records?).

The question I have is whether CONECT records should now be used to create
Bond(s), like what happens for SSBonds?  Is BioJava only going to use Bond
instances to describe bond-like interactions?  CONECT records are still
being parsed but they may no longer be stored or accessible from a
Structure, since they are not creating Bond instances and getConnections()
was deprecated.

It would be helpful to still provide CONECT information from PDB files to
describe bonding between atoms especially for ligands.  If not, then CONECT
records should not be parsed.

For issue 330:
Parsing CONECT can cause string out-of-bounds exceptions when they have
only 2 atoms are present.  Besides implementing line length checks when
parsing CONECTs, adding a try/catch block for string out of bound
exceptions around the parsePDBFile(..) handler blocks that skip invalid
lines and log warnings rather than breaking parsing would make the parser
more robust.

-- 
Matt Larson, PhD
Madison, WI  53705 U.S.A.
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