octet-devel Mailing List for Octet (Page 3)

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Hi Rich,

> * Molecule implements AtomGraph. In the near future, BondingSystem should also implement AtomGraph to enable traversal/query with the same tools used for Molecules (any objections to this?)
Good.

> * Traversers traverse the graph structure of any AtomGraph. Traversers are low-level components that are helpful for building higher-level functionality. Currently two types of Traverser are available: DepthFirstTraverser and CycleTraverser. Both use a system of Handlers and Controllers - Handlers for handling events generated at various stages of a traversal algorithm and Controllers for exercising limited control over the algorithm itself. This system borrows from SAX's ContentHandler idea. HanserCycleTraverser is an implementation of CycleTraverser that uses Hanser's algorithm for finding the set of all cycles of an AtomGraph using collapsing Path-Graphs.
CycleTraverser should use an interface, so that we can switch the traverser.
If nothing is said a default traverser should be used.
The traverser should also have an ID and version number analogue to 
descriptors.

> * MoleculeComparator compares two AtomGraphs for isomorphism, but without comparing atom/bonding properties. UllmanComparator implements MoleculeComparator by using Ullman's subgraph isomorphism algorithm. Like Traverser, MoleculeComparator uses a system of Handlers and Controllers for fine-grained control. It should be possible to use this sytem to create additional isomorphism algorithms implementing MoleculeComparator.
Isn't this only a formulation problem ?
Can't we use a boolean method compareNode(LabelSet) which uses a set of 
labels to check isomorphism ?

> * QueryBuilder enables clients to build a molecular query using the same process that is used for building a Molecule with MoleculeBuilder. In fact, QueryBuilder extends MoleculeBuilder and can be used in many contexts calling for a MoleculeBuilder. QueryBuilder is designed for building queries that are based on a template molecule with constraints placed on individual Atoms with AtomQuery.
Can 'pharmacophores' treated also with this approach. So are combined 
features, e.g. carbon acid group combined to a single feature and a 
distance to all other features allowed ?

> * SmartsQueryFactory is in the early stages, but is intended to simplify the process of using QueryBuilder by enabling clients to use SMARTS Atomic Primitive strings as keys to obtain a fully functional AtomQuery. Although this isn't exactly a SMARTS parser, it isn't that far from being one given Octet's SmilesReader. Currenly only the wildcard Atomic Primitive ("*") is supported, but other should be appearing soon. The approach here has some elements in common with that of CDK's growing SMARTS support, but there are also some interesting differences.
Same as above, so atom based (not feature based) compareNode(LabelSet) 
method, where the LabelSet is what i would call the chemical kernel atom 
labelling set.

> Looking a little further down the road for QSAR, what are people's thoughts on a framework for molecular descriptors? Of course, there hundreds of descriptors, and of course we all have our ideas on what a particular descriptor means or doesn't mean. What  I'm actually wondering about is what a descriptor facility in QSAR would look and feel like. I've been looking at JOELib's descriptor framework, which has some reasonable concepts. From what I can tell, there are two basic kinds of descriptor: a "holistic" descriptor that is a single value (i.e. TPSA) and which is primitive-like, and everything else, which tends to be higher-resolution in nature (i.e. Topological Torsion) and more object-like. Are there any other ideas? 
With respect to query i would prefer the object approach, so we can use:
result=molecule.calculate("XYZ")
or as in JOELib
result1=calculator.calculate(mol1,"XYZ", Properties)
result2=calculator.calculate(mol2,"XYZ", Properties)

for matching or similarity we can then use
// inherited from Comparator in Java API
// applicable for euclidian, tanimoto, atom-pairs
similarity=metricThatILike(result1,result2, Properties);

For simple single value descriptors it would be also interesting to have:
similarity=metricThatILike(ResultSet1,ResultSet2, Properties);
Also with pharmacophore outlook or multiple graph isomorphism and not 
only pair-wise matching.

So a query is from my standpoint a kind of similarity-metric which can 
only return 0 and 1. Sometimes, as in SMARTS matching we are only 
interested in subgraph isomorphism.
result1=calculator.calculate(mol1,"XYZ", LabelSet)
result2=calculator.calculate(mol2,"XYZ", LabelSet)
// only applicable for this specific calculator
// can be used for maximum common substructure search (MCS)
matchings=matchingsThatILike(result1,result2, Properties);

So, for SMARTS matching we need also:
matchings=matchingsThatILike(query1,result2, Properties);

For pharmacophores 2D/3D/Shape we can also use this appraoch, because 
the representation for the similarity/matching is the relevant point.
matchings=matchingsThatILike(query1,result2, Properties);
or
similarity=metricThatILike(result1,result2, Properties);

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
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

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octet-devel Mailing List for Octet (Page 3)

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