[BioRuby] Re: BioRuby PDB Classes

[Toshiaki Katayama]

Hi Alex,

I have received a patch developed by you and N. Goto.

Changes are already commited to the CVS to the CVS repository :
* Added Patches from Alex Gutteridge
   - New classes: PDB::Atom, PDB::Residue, PDB::Chain, PDB::Model
   - New modules: Bio::PDBUtils, Bio::{Atom|Residue|Chain|Model}Finder
   - New methods: iterators, ...
   - Bug fix
* Bio::Coordinate class storing coordinate data (inherits Vector)
* Many imcompatible (but very useful) changes are made, please be 
careful.

Regards,
Toshiaki Katayama

On 2004/02/13, at 18:51, Alex Gutteridge wrote:

>>> My question(s) to the list are:
>>>
>>> 1. Am I treading on other peoples toes here? Is someone else actively
>>> developing the pdb.rb module? Naohisa Goto?
>>
>> I'm Naohisa Goto, but I'm not actively developing the pdb.rb now,
>> and no one (except you) are doing, as far as I know.
>> So, you can freely modify the pdb.rb.
>>
>> If you want to change existing class/method's name, or massively 
>> change
>> existing class/method's specification or definition, please tell us.
>
> I've left the main PDB class alone except for:
>
> - I've changed the seqres method to return Bio::Seq objects rather 
> than just strings
> - I've removed the old model parsing section and replaced it with mine
>
>>> 2. If not, should I post the code to the mailing list, or somewhere
>>> else? I'm sure it needs some tidying up and bioruby-fication. It 
>>> would
>>> be great if someone more experienced than I could give some
>>> comments/criticisms.
>>
>> If the code is short, please post to the mailing list.
>> For long codes, please send to staff at bioruby.org, or you can use
>> the BioRuby Project Wiki page (http://wiki.bioruby.org/English/).
>
> pdb.rb is now ~2000 lines, so I won't post it to the list! I'll post 
> it to staff at bioruby.org (the wiki seems to be broken at the moment). 
> pdb.rb probably needs splitting up into separate files, but like I 
> said, I'm not sure what the BioRuby conventions are for doing this 
> (would it need a new bio/db/pdb directory?). Currently it looks like 
> this:
>
> module bio
> 	#This module provides some generic mixin methods that all classes use
> 	module PDBUtils
> 		[snip!]
> 	end
> 	#There are several *Finder mixins which provide some of the searching 
> methods
> 	module AtomFinder
> 		[snip!]
> 	end
> 	#This is the main PDB class that was here originally - I've only 
> added methods
> 	#so all the old interface is still here (apart from .seqres and 
> .model)
> 	class PDB
> 		#There are a few modules and classes here used for the old style 
> parsing
> 		class FieldDef
> 			[snip!]
> 		end
> 		class Record < Hash
> 			[snip!]
> 		end
> 		[snip!]		
> 		#My new classes for atoms, residues, chains and modules go here
> 		class Atom
> 			[snip!]
> 		end
> 		class Residue
> 			[snip!]
> 		end
> 		class Chain
> 			[snip!]
> 		end
> 		class Model
> 			[snip!]
> 		end
> 	end #class PDB
> end #module Bio
>
> Perhaps the PDBUtils and Finder modules should go inside the PDB 
> class? Or a separate file for each class and the mixins?
>
> Alex Gutteridge
> European Bioinformatics Institute
> Cambridge CB10 1SD
> UK
>
> Tel: 01223 492550
> Email: alexg at ebi.ac.uk
>
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