Hello!
I have CSV files with several hundred chemicals that I need to populate with their molecular weights. Is there an online database or R-package that can batch-search in that direction (name to MW)?
Afterwards, I want to compare the retrieved data against another list of molecular weights obtained by non-fragmenting mass spectroscopy of an unknown sample.
Thanks for any hints!
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Would ChemmineR (http://www.bioconductor.org/packages/devel/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html) work?
I'm afraid not. The documentation mentioned molecular weight only in the context of computing it from a given set with structural data. I have only the chemicals' names.
Cambridgesoft provides a command-line tool to convert IUPAC names as a batch into structures:
http://www.cambridgesoft.com/support/DesktopSupport/Documentation/N2S/
From these structures, you should be able calculate the molecular weight...
Alternatively, you could use OPSIN (http://opsin.ch.cam.ac.uk/). I took the liberty of converting your csv files (attached). Note that I've not checked the generated SMILES codes. Also some names could not successfully be converted. But those limited number of substances, you could maybe do by hand...
@Pepijen: Thanks for the hints, I will try this CLI tool. ChemmineR can apparently use the SMILE data as input, it will be useful after all :-)
@Thomas: Yes, and only their API can do batch operations (also confirmed by customer support). I can't do enough programming yet for that.
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