[Cdk-devel] AromaticityFixer - questions

[Rajarshi G. <rg...@in...>]

Hi, I've been looking at the AromaticityFixer code from Todd Martin
(called DeduceBondSystemTool in the CDK).

Firstly, what is its usage? Should it be:

molecule = read in smiles
molecule = AromaticityFixer(molecule)

Or is it meant to be used in some other manner?

Currently I put in a test case using the SMILES:
c2ccc3n([H])c1ccccc1c3(c2) which the CDK parses incorrectly at the
moment.

When I run the test case, it breaks with an OutOfMemory error. In the
code itself, it looks like the loop() method is eating up the cycles.

As far as I can see the loop() function is not changed from what Todd
originally supplied.

How is it trying to fix the bond orders?

Also what is the status of the other patches? I noted that Egon has put
in the a number of items. Is it correct to say that the remaining stuff
are the actual descriptors (except AlogP)?

Also it seems that AtomicProperties is only used in the descriptors from
Todd. Is that correct? 

In the case of Todd's WHIM descriptor where do the atomic property
values come from? They seem to be different from what I have for the
current WHIM implementation (which are taken from 

  <bibtex:entry id="TOD98">
    <bibtex:article>
      <bibtex:author>Todeschini, R. and Gramatica, P.</bibtex:author>
      <bibtex:title>New 3D Molecular Descriptors: The WHIM theory and
QAR Applications</bibtex:title>
      <bibtex:journal>Persepectives in Drug Discovery and
Design</bibtex:journal>
      <bibtex:year>1998</bibtex:year>
      <bibtex:pages>355-380</bibtex:pages>
    </bibtex:article>
  </bibtex:entry>

)

For the molecular distance edge descriptor why do we need the e-state
indices? I have an implementation (that is validated with ADAPT) but
does not need the e-state indices. (I follow the description by Liu
JCICS, 1998, 38, 387-394)

-------------------------------------------------------------------
Rajarshi Guha <rg...@in...>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
-------------------------------------------------------------------
Artificial intelligence has the same relation to intelligence as
artificial flowers have to flowers.
-- David Parnas