[chemfp] chemfp-1.0b1 available

[Andrew Dalke]

AFter many months (of which only a few weeks was for this project), I've turned "chemfp-1.0a1" into "chemfp-1.0b1"!

Much of my time was spent reworking the search API. I've greatly reduced the amount of time spent in Python code, and I made the low-level code more flexible. I've included the new part of the CHANGELOG after my signature.

You can get the new version from

http://code.google.com/p/chem-fingerprints/downloads/detail?name=chemfp-1.0b1.tar.gz

During the next week I'll be working on test cases and documentation.

Let me know what you think, and tell me if there are problems. Also let me know if you have experience making precompiled Python extensions for Windows or Linux, and can help make them for me for the 1.0 release.

Cheers!

				Andrew
				dalke at dalkescientific.com


The chemfp format is now a tab-delimited format. I talked with two
people who have spaces in their ids: one in their corporate ids and
the other wants to use IUPAC names. In discussion with others, having
a pure tab-delimited format would not be a problem with the primary
audience.

The simsearch output format is also tab delimited.

Completely redeveloped the in-memory search interface. The core data
structure is a "FingerprintArena", which can optionally hold
population count information.

The similarity searches use a compressed row representation,
which is a more efficient use of memory and reduces the number
Python-to-C calls I need to make.

The FPS knearest search is push oriented, and keeps track of the
identifiers at the C level.

Major restructuring of the API so that public functions are at the top
of the "chemfp" package. Made high-level functions for the expected
common tasks of searching an FPSReader and a FingerprintArena.

The oe2fps, ob2fps, and rdkit2fps readers now support multiple
structure filenames. Each filename is listed on its own "source" line.

New --id-tag to use one of the SD tag fields rather than the title
line. This is needed for ChEBI where you should use --id-tag "ChEBI ID"
to get ids like "CHEBI:776".

New --aromaticity option for oe2fps, and a corresponding "aromaticity"
field in the FPS header.

Improved docstring comments.

Improved error reporting.