[Bioperl-l] Parsing PDB entries in BioPerl

[Ewan Birney]

On Wed, 14 Nov 2001, Kris Boulez wrote:

> Quoting Ewan Birney (birney@ebi.ac.uk):
> > 
> > 
> The following basic object layout was proposed by Ewan. It looks
> reasonable to me (see small remarks).
> > 
> >   Bio::Structure::Chain.pm (a particular PDB chain)
> 
> you also need 
> 		  ::Model.pm (one Entry can consists of multiple models,
> 		  NMR data is like this)
> 
> >                 ::Entry.pm (a structure entry, containing one or more
> > chains and an annotation object)
> 
> - An Entry then consists of one or more models. Default would be the first/only
> model.
> - I think the Entry also should contain a Bio::PrimarySeq which would give
> people access to the protein sequence (to do similarity searches, ...)

I would make Bio::Structure::Chain comply to teh Bio::PrimarySeqI
interface. That seems the most natural...


> - All the non-coordinate stuff from PDB can be hidden in this annotation
> object.
> 
> >                 ::Residue.pm (perhaps - chain made of residues?)
> 
> - Most definitely a Residue object is needed. People in this field tend to
> think in terms of residues.
> - Do we store the 'non-standard' residues (e.g. haem group) ('HET'
>   records in PDB) in here as well. Or is the name 'residue' in peoples
>   heads linked to "amino acid residue". I could envision a ::HeteroGroup
>   object.
> 
> >                 ::Atom.pm (Residue made from Atoms)
> 
> - one small question here: what do people expect to happen with atoms
>   that have alternate locations (i.e. position of the atom could not be
>   uniquely be defined and n possibilities are given) ? Should the first
>   alternate be choosen, or the one with the highest occupancy, or ?
> 
> 
> We need a place to store the (non standard) links between
> residues/hetero groups. Also things like disulfide bridges, cis peptide
> bonds (CONECT, SSBOND, LINK, ... from PDB).
> 		
> 		::Connect.pm (two (or more) Atoms are connected)
> 
> > 
> >                 ::IO.pm   (Bio::Structure::IO top level file, ala SeqIO)
> >                 ::IO::pdb (pdb IO module)
> >                 ::IO::cif (cif IO module)
> >                 ::IO::mmdb (mmdb IO module)
> > 
> 
> Kris,
> -- 
> Kris Boulez 				Tel: +32-9-241.11.00
> AlgoNomics NV 				Fax: +32-9-241.11.02
> Technologiepark 4 			email: kris.boulez@algonomics.com
> B 9052 Zwijnaarde 			http://www.algonomics.com/
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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