GAMESS-US parser

[Peter Murray-Rust]

I have completed a first pass of a parser for GAMESS-US punch/dat files. This is based on a single example and I'll try some more of Mark's examples.
The parse to XML gives:
https://bitbucket.org/wwmm/jumbo-converters/src/tip/jumbo-converters-compchem/src/test/resources/compchem/gamessus/punch/ref/test1.xml
and the parse of that to CML gives:
https://bitbucket.org/wwmm/jumbo-converters/src/tip/jumbo-converters-compchem/src/test/resources/compchem/gamessus/punch/ref/test1.cml

Note that this is a "push" approach - all the input has been captured except for whitespace.

In the CML file I have made a best guess as to how to structure the file into CompCML. It has an init module, a final module and an intermediate one which contains the iteration steps. CML is capable of holding arbitrarily complex structures. However it requires some art to be able to write a generic parse which recreates the structure. I'll be trying all of Mark's outputs and intend this will act as a good Lensfield exercise for us.

We should also move this to the Wiki



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