Re: [Cdk-user] get the number of valence electrons in an atom

[Egon W. <ewi...@un...>]

Ok, here's that forward

E.

----------  Forwarded Message  ----------

Subject: [Cdk-devel] QSAR descriptors: where to put the algorithm 
implementation...
Date: Thursday 26 October 2006 16:11
From: Egon Willighagen <ewi...@un...>
To: cdk...@li...

Hi all,

a short discussion today urged to send around a small email on QSAR
descriptors and algorithms that those descriptors use.

First, let's define a few concepts.

1. a descriptor is a numerical representation of some chemical property
2. a chemical property is a property inherent to a molecule, bond or atom
3. a chemical property does not have to consist of a numerical vector as
   a descriptor does

The difference between a property and a descriptor is important. Algorithm
implementations to calculate a descriptor should be part of the source code
of qsar/*/*.java, but the implementations to calculate properties *must* not.
The rationale here is that properties *are* interesting outside a QSAR
modeling framework too: you want to be able to calculate them without the
intention to use the outcome in model building. The latter is what the
cdk-qsar module is about.

For example, the atomic descriptor 'gasteiger partial charge' should *not*
contain the algorithm to calculate this charge. Instead, the QSAR descriptor
class source code should call the class which calculates this, and just wrap
the outcome. The partial charge is a property.

However, another descriptor is might be the first two values of a SVD on the
adjacency matrix of the molecule. This algorithm will very like be part of
the QSAR descriptor class source code, as the matrix is the property and the
svd values are just a numerical representation of it, as QSAR modeling
methods generally cannot work with matrices. These SVD values are really
descriptors.

Now, properties can be, and often are, used as descriptor, which is likely
causing the confusion.

Hope this clarifies things, and do file bug reports if QSAR descriptor
 classes have source code internally that calculate properties.

Egon

--
CUBIC
blog: http://chem-bla-ics.blogspot.com/

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CUBIC
blog: http://chem-bla-ics.blogspot.com/