[Joelib-help] MM and partial charges and CML2

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

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

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>

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

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 '_'.

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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