Description
===========

This project builds the program smg (SMARTS Multiplet Generator).  It
generates what might loosely be called 2D pharmacophore fingerprints.
In this case, it's a file of 1s and 0s for each input molecule,
denoting the presence or absence of a particular pharmacophore
grouping.  Smg can output sites, pairs or triplets.  Sites are the
individual pharmacophore features, pairs are combinations of 2
features and a through-bond distance (i.e. the counts of the number of
bonds between the two features via the shortest path) and triplets are
three features with through-bond distances.

An example pair would be acceptor:3:posch i.e. an h-bond acceptor 3
bonds from a positive charge.

An example triplet would be
acceptor:10:acceptor-acceptor:11:rings-acceptor:12:rings which
describes 2 h-bond acceptors and a ring 10, 11 and 12 bonds apart.
When calculating the distance of a ring to another feature, it is
always taken as the nearest ring atom to the feature, so the distance
is always the shortest possible.

The pharmacophore features are described using a set of SMARTS
definitions and a description of how the SMARTS patterns should be
combined to form the feature.  An example of each input file is in the
test_dir directory, as test.smt and test.points respectively.

In the output file, the columns are headed by a short, unintelligble
label.  This a hashed version of the full name for the feature.  A
subsidiary file with suffix name_decode is made which provides a
translation.  This was done to keep the file of a manageable size, and
dates from the days when people at AZ were analysing stuff using SAS
which had a relatively short upper limit on the length of a column
name.

Building the program
====================

Requires: a recent version of OEChem.

To build it, use the CMakeLists.txt file in the src directory. It
requires the following environment variable to point to a relevant
place:

OE_DIR - the top level of an OEChem distribution

Then cd to src and do something like:
     mkdir dev-build
     cd dev-build
     cmake -DCMAKE\_BUILD\_TYPE=DEBUG ..
     make

If all goes to plan, this will make a directory src/../exe_DEBUG with the
executables in it. These will have debugging information in them.

For a release version:
    mkdir prod-build
    cd prod-build
    cmake -DCMAKE\_BUILD\_TYPE=RELEASE ..
    make

and you'll get stuff in src/../exe_RELEASE which should have full
compiler optimisation applied.

These instructions have only been tested in Centos 6 and Ubuntu 14.04
Linux systems.  I have no experience of using them on Windows or OSX,
and no means of doing so.

David Cosgrove
AstraZeneca
12th February 2016

davidacosgroveaz@gmail.com