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

[Spencer Bliven]

I guess that if you have a novel ligand in a non-deposited file then it
wouldn't have a chemical component and so CONECT would be the only place to
find those bonds. Is that an important enough use case to warrant the
development effort?

Matt, your comments re #330 are well taken. +1 to a high-level try-catch to
handle IndexOutOfBounds, NullPointer, and other nonspecific parsing errors.

-Spencer

On Thu, Dec 1, 2016 at 12:24 AM, Jose Duarte <jose.duarte at rcsb.org> wrote:

> 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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