[Cdk-devel] Common molecule interface

[Joerg K. W. <we...@in...>]

Hi,

I've had a short look and i'm missing some things functionalities in octet:
- i would prefer Node and Edge objects as Atom and Bond base
- i would prefer a general NodeKey, EdgeKey, MoleculeKey, RingKey object 
as labelling the attributed molecular graph
both things are required for general graph algorithms, for the keys a 
factory pattern could/should be used, especially for assigning default 
labels.
This avoids calculating e.g. a ring search twice by using:
if(!mol.hasKey(myRingSearchKey))mol.calculateRingSearch()
- The AtomPair is ambigous, there exists a descriptor with an additional 
  distance parameter, here you are using always one. Hashing is 
important here.
- Force Copy/Clone/Hash-methods.
- The reader should provide, readAsString, readToMoleculeObject, so we 
can catch corrupted file entries. Don't ask me why there are such a lot 
of corrupted entries, but they exists
- Add MoleculeIOException to read/write, to catch these corrupted 
entries, this will us enable to write skip files
- A general SubstructureSearch object would be fine, also a 
UniqueSubstructureSearch object or a transformer object.
- General descriptor objects are missing completely, but they can be 
handled by the hashed MoleculeKey objects, but eventually we distinguish 
between keys which can handle only one object (hashed) and keys which 
can handle multiple objects, so we need a GeneralPropertyHandler which 
accepts single and multiple entries by key.
- For descriptors IO helper classes are required, which have 
read(IOType) and write(IOType)

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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