Re: NWChem2CML stand alone jar

[Peter Murray-Rust]

I have copied this to the list

On Thu, Nov 10, 2011 at 7:55 PM, Jorge Estrada <jorge....@unizar.es> wrote:

Sam, Peter,

While in my adventures in Compchem&ChempoundLand I have created a small project to create a NWChem2CML executable jar.

You can check it at https://bitbucket.org/jestrada/nwchem2cml/overview (it includes a README explaining how it works).

 

Many thanks - that is a great idea 

I still have the question on the differences between the CML created with DepositNWChem and the CML created with NWChemLog2CompchemConverter. For the code I've read, I think it is a question of format and of InChi fields. Is that right?

Maybe Sam can help.

 

There is no fundamental reason why they should not be the same. Assuming Chempound uses jumbo-converters it should go through the same path. There are no configuration fiels, so maybe it is a post conversion filter.

 

Jorge

--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069

[Sam Adams]

On 10 November 2011 22:43, Peter Murray-Rust <pm...@cam.ac.uk> wrote:

I still have the question on the differences between the CML created with DepositNWChem and the CML created with NWChemLog2CompchemConverter. For the code I've read, I think it is a question of format and of InChi fields. Is that right?

Maybe Sam can help.

 

There is no fundamental reason why they should not be the same. Assuming Chempound uses jumbo-converters it should go through the same path. There are no configuration fiels, so maybe it is a post conversion filter.

The jumbo-converters simply convert the information in the NWChem log file into CML.  The NWChem log file doesn't contain any InChIs, so they're not included in the CML.  After converting the log file into CML, the Chempound's NWChemLogImporter attaches InChIs - take a look at the NWChemLogImporter.generateCml() method.

Sam