Hi,
> Looks interesting, I particularly appreciate the quick reference card! I
> had a quick glance at the documentation to see if it could be useful for
> my purposes. It seems there is no support for reading external files
> yet, correct?
No. However, when built with OpenBabel 2 support, the obhelium tool will be
built which can covert any of the formats supported by OB to a Helium
binary molecule file. In the future there will be native support for a few
formats (e.g. sdf, cml, smi)
> And is there an algorithm for atomtyping, like the one in OB?
>
Not yet but this is mostly SMARTS matching so it would not be difficult to
add.
> As a side note, you might consider to clarify some of the class and
> method names, I have no clue for instance what DFS and BFS stand for.
> Further a method named "bond" or "atom" is not descriptive - does it
> create a bond, fetch an existing bond or delete one? Just my 2€.
>
I think DFS (depth-first search) and BFS (breadth-first search) is only
used for the DFSVisitor and BFSVisitor classes. The functions using these
visitors do use full names though.
Regarding the bond() and atom() functions: These are getter functions
following the convention used in Qt and many other projects. It might be a
good idea to briefly clarify this on the quick reference card though.
Thanks for the feedback.
Tim
Cheers, David.
>
> > Kind regards,
> > Tim Vandermeersch
> >
> >
> >
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>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> sp...@xray.bmc.uu.se http://folding.bmc.uu.se
>
>
> ------------------------------------------------------------------------------
> Open source business process management suite built on Java and Eclipse
> Turn processes into business applications with Bonita BPM Community Edition
> Quickly connect people, data, and systems into organized workflows
> Winner of BOSSIE, CODIE, OW2 and Gartner awards
> http://p.sf.net/sfu/Bonitasoft
> _______________________________________________
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Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
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