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Nwchem mol2

Open nkkchem opened this issue 5 years ago • 4 comments

I added the NWChem optimized structures (mol2) of Yeast with partial charges computed with Mulliken population.

nkkchem avatar Jan 06 '20 09:01 nkkchem

What do you mean by "Yeast"? Do these structures map to any particular set of compound aliases in a published model for yeast? We can map the InChI-Keys to whatever we have, but we'd like to know where these came from.

samseaver avatar Jan 06 '20 15:01 samseaver

This is the compound list of Yarrowia lipolytica CL1B122  model curated on the pathway genome database.  https://cyc.pnnl.gov/organism-summary?object=YARROWIA

nkkchem avatar Jan 06 '20 18:01 nkkchem

Can you commit a flat file showing a direct mapping between the names of the mol files you committed and the Cyc identifiers in that database? We've a number of them in our aliases, but because of how different databases are curated with different policies, we get structural conflicts between Cyc identifiers that are supposed to be the same compound. Having the source will be a great help.

samseaver avatar Jan 06 '20 22:01 samseaver

Can you also add a simple README that explains the source of the data with links etc. Thanks

samseaver avatar Jan 07 '20 14:01 samseaver