[Joelib-devel] Re: [Joelib-help] MM and partial charges and CML2

[Peter Murray-R. <pm...@ca...>]

At 16:17 21/03/2004 +0100, Joerg Wegner wrote:
>Hi all,
>
>1. I've added Amber,Mopac import to JOELib.
>2. The partial charges entries in Mopac and Sybyl are now not any more
>overwritten by JOELib's Gasteiger-Marsili partial charges. So they can be
>forwarded to e.g. CML2.
>I've added two test files. Please try:
>sh convert.sh src/joelib/test/1bhf-ligand.mol2 sybyl.cml
>sh convert.sh src/joelib/test/Ethanol.mopout mopac.cml

Thanks very much. I reply before looking at the details...


>Please attend that at the actual implementation the partial charges are
>used to calculate the hashcode and the molecule ID for CML (hopefully
>nearly unique), if you do not use the canonical SMILES hashcode, you will
>get different results for different partial charges.
>To avoid this, we simply use the canonicalized SMILES hashcode in
>CMLIDCreator.
>
>So we get:
><cml:scalar units="units:electron" dataType="xsd:float"
>dictRef="MOPAC">-0.0192</cml:scalar>

This is valid CML but we are gently moving towards more structured 
dictRefs. I suggest:

<molecule xmlns:MOPAC="http://www.tuebingen.de/dict/MOPAC">...

><cml:scalar units="units:electron" dataType="xsd:float"
>dictRef="MOPAC:partialCharge73">-0.0192</cml:scalar>

the MOPAC:partialCharge is an XML QName. You are in control of it. it acts 
as a pointer to an ID in a dictionary - i.e. somewhere you have something like:

<dictionary id="mopacDict" dictRef="MOPAC" 
xmlns:MOPAC="http://www.tuebingen.de/dict/MOPAC">
<entry id="partialCharge73" term="partial charge from MOPAC">
   <appinfo>
     <scalar type="xsd:float"/>
   </appinfo>
   <description>The partial charge as defined on p. 333 of the 
manual...</description>
</entry>

I am writing this without looking at the details but to give the idea. The 
appinfo stuff is new and still being developed. Your input will be 
important. The main thing is that you have a dictionary defining the 
concept. The actual ID doesn't matter - it could be JW:id376 as long as 
this was linked to a jJW namespace and there was an entry id376.

><cml:scalar units="units:electron" dataType="xsd:float"
>dictRef="MMFF94_CHARGES">0.569</cml:scalar>

I would suggest either JW:MMFF94_CHARGES or if you have a large list of 
MMFF94 terms MMFF94:charges


>If no charges are defined we get, as previously:
><cml:scalar units="units:electron" dataType="xsd:float"
>dictRef="joelib:partialCharge">-0.2686233439216685</cml:scalar>
>
>3. Peter: Can these dictRef entries be used ? If not what then, because
>Sybyl itself contains a  string  line where the 'partial charge vendor' is
>already given. I've simply replaced ' ' by '_'.

If manufacturers have IDs that conform to XML we can use them. If not there 
has to be a mapping.

In haste

P.


>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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Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069