                       chemfp 1.4
                       
A Python library and set of tools for working with cheminformatics
fingerprint data. For more information, see http://chemfp.com/ .

There are two development lines. This is the chemfp-1.x line, which is
available for no cost under the MIT license. See COPYING for
details. There is also the commercial chemfp-3.x line, which costs
money to access and is also distributed under the MIT license. The 3.x
line includes the FPB binary fingerprint format, Tversky search, API
improvements for web service development, and Python 3 support. If you
have the money, consider buying a copy.

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.)

Chemfp is developed by Andrew Dalke <dalke@dalkescientific.com>.

INSTALLATION
============

Install in the normal Python way, either over the network::

  pip install chemfp

or using a local copy of the distribution::
  
  pip install chemfp-1.4.tar.gz

or the more manual way::

  tar xf chemfp-1.4.tar.gz
  cd chemfp-1.4
  python setup.py build
  python setup.py install

The install step may need a 'sudo' or need you to be be root,
depending on your system.

COMPILE-TIME OPTIONS
--------------------

There are three compile-time options, which can be specified from the
setup.py command-line or through an environment variable.

 *  --with-openmp or setenv CHEMFP_OPENMP=1 (this is the default)
 *  --without-openmp or setenv CHEMFP_OPENMP=0

The default is to compile chemfp with OpenMP support. You may want to
disable this if your compiler doesn't support OpenMP or if you are
using chemfp in a multi-threaded web server where you only want one
OpenMP thread per request.

If you get a message like:

   unrecognized command line option "-fopenmp"
      -or-
   ld: library not found for -lgomp
   
then your compiler does not understand OpenMP. To compile without
OpenMP append "--without-openmp" to the setup.py line or set
CHEMFP_OPENMP=0.

  
For example, if you are on a Mac where the built-in clang compiler
does not have OpenMP, and you do not want OpenMP, then you can install
from the distribution using the following:

  env CHEMFP_OPENMP=0 pip install chemfp-1.4.tar.gz

or you can unpack the tar file and configure it on the command-line
with:

  python setup.py install --without-openmp
  

If you want OpenMP support on a Mac then you should install
"clang-omp" or a new version of gcc and specify the alternate compiler
using the "CC" environment variable, as in the following:

  env CC=clang-omp python setup.py install
     -or-
  env CC=gcc-7 python setup.py install


  *  --with-ssse3 or setenv CHEMFP_SSSE3=1 (this is the default)
  *  --without-ssse3 or setenv CHEMFP_SSSE3=0

The default is to compile with support for the SSSE3 instruction
set. This was introduced in 2006 and should be on all modern AMD/Intel
hardware. 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 and you
should use the "--without-ssse3" option.

IMPORTANT! Because of limitations in how Python's setup.py works, the
--with-ssse3 compiles all code with SSSE3 support, even though only
one file needs it, and the file isn't used if chemfp detects at
run-time that SSSE3 support isn't available.

This may cause a bus error when using the binary on a CPU which
doesn't implement the SSSE3 instructions. If you want to use a gcc
binary with support for both SSSE3 and non-SSSE3 CPUs then compile
with:

  sudo env CC=$PWD/filter_gcc python setup.py install

Read filter_gcc for details.


DOCUMENTATION
=============

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
  fpcat --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
