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chemfp is a set of command-lines tools for generating cheminformaticsfingerprints and searching those fingerprints by Tanimoto similarity,as well as a Python library which can be used to build new tools.These algorithms are designed for the dense, 100-10,000 bitfingerprints which occur in small-molecule/pharmaceuticalchemisty. The Tanimoto search algorithms are implemented in C forperformance and support both threshold and k-nearest searches.Fingerprint generation can be done either by extracting existingfingerprint data from an SD file or by using an existing chemistrytoolkit. chemfp supports the Python libraries from Open Babel,OpenEye, and RDKit toolkits.

Project description

chemfp 1.1p1

A Python library and set of tools for working with cheminformatics
fingerprint data. For more information, see http://chemfp.com/ .

Copyright under "the MIT license." See COPYING for details.

See THANKS for the people who have contributed in some fashion. (If
I've left your name out or didn't credit you correctly, let me know.)

Install in the normal Python way:

python setup.py install

You may need a 'sudo' or be root, depending on your system.

If you get a message like:
unrecognized command line option "-fopenmp"
then your compiler does not understand OpenMP. To compile without
OpenMP append "--without-openmp" to the setup.py line.

If you get a message like:

cc1: error: invalid option ssse3
-or-
cc1: error: unrecognized command line option "-mssse3"

then your compiler does not understand the SSSE3 intrinsics. To
compile without the SSSE3 intrinsics, append "--without-ssse3" to
the setup.py line.

For example, to compile in a Mac with gcc-4.0 using sudo:

sudo python setup.py install --without-openmp --without-ssse3


Note: chemfp requires a C compiler to build the _chemfp extension. If
you use Visual Studio for Microsoft Window then you will either need
the 2008 version or you will have to patch your version of Python to
handle 2010 or newer. See http://bugs.python.org/issue13210 .


Documentation? Certainly! Go to:

https://chemfp.readthedocs.org/en/latest/

or use '--help' on any of the command-line programs:

rdkit2fps --help
ob2fps --help
oe2fps --help
sdf2fps --help
simsearch --help

or (for parts of the public API), look at the doc strings

import chemfp
help(chemfp)

There are many tests. To run them:

cd tests
python unit2 discover

Project details


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