[Biojava-dev] Should SEQRES/_pdbx_poly_seq_scheme records be part of headerOnly?

[Jose Duarte]

I've replied to some of this in issue 353 (
https://github.com/biojava/biojava/issues/353). I think it'd be better to
discuss things over there.

Jose

On Mon, Nov 23, 2015 at 4:08 PM, Steve Darnell <darnells at dnastar.com> wrote:

> Greetings,
>
> My company is preparing to submit a PR for Issue 353, "mmCIF parsing
> support for missing SEQRES information." The PR passes existing integration
> tests where an empty SEQRES component list is expected when
> FileParsingParameters.headerOnly = True.
>
> I suggest that SEQRES (PDB format) and _pdbx_poly_seq_scheme (mmCIF
> format) should be considered part of the header, which would allow a user
> to extract the chain sequences from a file without requiring the full,
> heavy weight parsing of the atom coordinate records. This is a valuable
> computational saving for people who are data mining information from header
> records across the PDB. Examples include creating custom sequence
> collections for compiling PDB-based BLAST databases, quickly converting
> local PDB/mmCIF structure files to sequences for calculating multiple
> sequence alignment, among others.
>
> I am asking the BioJava community for their thoughts to these questions:
>
> 1. Is it acceptable to elevate this sequence information to "the header?"
> 2. If so, is it acceptable to include this feature as part of Issue 353?
> 3. If not, is it acceptable to create a new FileParsingParameter (e.g.
> "setParseSeqRes") to allow extracting the sequence information without the
> atomic coordinates?
>
> Best regards,
> Steve
>
> --
> Steve Darnell
> DNASTAR, Inc.
> Madison, WI USA
>
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>
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