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

[Jose Duarte]

In the move towards version 5.0 (still in development), bonds were unified
by using the Bond class to represent them. The Bond objects are a better
representation and provide easier access since they are referenced directly
from Atom objects.

It seems that CONECT records in current HEAD are indeed not used at all
(they are parsed but nothing is done with them). In any case Bonds are
created for these cases: SSBOND records, peptide bonds (inferred from chain
geometry) and intra-residue bonds (by getting information from chemical
component dictionary). The question here would be: are the CONECT records
adding anything on top of that? What kind of other bonds do we miss that
CONECT records have?

If the CONECT records are providing extra info that we don't have elsewhere
then this would be an issue in 5.0-SNAPSHOT that would need to be solved.
If they don't provide extra info, then we'd better get rid of all code
dealing with CONECT records to be sure we don't have unnecessary parsing
problems.

Jose



On Wed, Nov 30, 2016 at 1:44 PM, Matt Larson <larsonmattr at gmail.com> wrote:

> 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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>
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