Hard-coded values in 3 descriptors without support for new materials

enanomapper / nanojava

Java library for descriptor calculation for (nano)materials.

GNU Lesser General Public License v2.1

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Hard-coded values in 3 descriptors without support for new materials #5

Open ammar257ammar opened 4 years ago

ammar257ammar commented 4 years ago

Dear Egon,

I am trying to apply NanoJava descriptor calculation on Gold oxide and Silver oxide nano particles. I made a CML XML file containing both of them (please see the attachment)

There are 11 descriptors in NanoJava, 3 of them contains hard coded values for metal oxide descriptors which don't include Au/Ag so these descriptors can not be generated for our nanoparticles, and there descriptors are:

1- EnergyBandDescriptor: no support for Au and Ag 2- HeatOfFormation: no support for Au and Ag 3- HeatOfFormationMopac2012: no support for Au and Ag

oxides.zip

Thank you

egonw commented 4 years ago

The values for EnergyBandDescriptor come from the article, IIRC, while for the other two I have taken them from the article but also recalculated and added values for metal oxides not in the article. I guess we have to calculate them for your two.

ammar257ammar commented 4 years ago

Can you please send me the related article to see how the descriptor is calculated and do it for my compounds?

egonw commented 4 years ago

HeatOfFormation descriptors, see http://doi.org/10.1038/nnano.2011.10
EnergyBand descriptor, see https://doi.org/10.3109/17435390.2010.502980

Now, these things should actually be provided by the ontology annotation and Blue Obelisk descriptor ontology, see https://link.springer.com/article/10.1186/1758-2946-3-37 But then the JavaDoc should also actually give the ontology annotation, which it currently does not seem to.