Chem classes out for perusal/playing/testing

Still not using the Sci/Chem naming proposal. You can
look at the PHPDoc (with known array<->string doc bug)
generated documentation at:

www.castagnetto.org/Chem/index.html

and download the .tar.gz from:

www.castagnetto.org/Chem/Chem.tar.gz

There is not much yet on that site (execpt for some
PHP classes, and PalmPilot stuff). Still working on my
free time on it.

The Chem are base classes, but the PDBFile and
Macromolecule* ones can really stress PHP, I got some
emalloc errors when trying really big molecules, so I
made a simpler ad-hoc one for those cases (PDBParser),
which is self-contained, but useful in those cases.

Had used the classes 2 nights ago for a 13 hour run of
a PHP script parsing approx 14,800 structures, and
extracting about 122,000 histidine residues. So they
seem usable, although I cheated a little and got some
help from "grep" via exec to get the processing time
in the 1-15 seconds per protein range, instead of the
45-530 seconds per protein range. See chi_crawler.php
and other sample scripts in the Chem/test dir. Yes, I
did put some examples :)



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--- Jesus M. Castagnetto ([email protected])

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