Program to display 2D structures of molecules, and create, edit and match SMARTS patterns. Think picto, with a slider.
C++ CMake SMT
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README

README

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

This project contains the means to build the program smiv.

Smiv (SMIles Viewer) is a simple program that allows the user to
display the contents of a structure file in 2D and match SMARTS
patterns to them.  The intended use is to assist in the development of
SMARTS patterns. To that end, SMARTS can be input from file or by
picking atoms from a molecule in a dialog.  When matched against the
molecules, the set is divided into 2 display panels, with molecules
that matched the selected SMARTS (1 or more at a time) in the left
panel, with the matches highlighted by colour, and those that didn't
match on the right.

Smiv can also show a table of data, read from a CSV or tab-separated
file, linked to the panel displays so that you can keep track of
properties of molecules as you look at them.  It's very primitive, but
possibly of use.

Usage
=====

Hopefully it'll be fairly self-explanatory.  There are a few
command-line options that can be revealed either by running with the
--help option, or from the Help->About box.

SMARTS are matched using the SMARTS->Match menu option, or Ctrl-M.
All definitions currently available are presented in a dialog. You can
select those of interest with normal extended selection rules.  When
matched, two independent panels are made for the hits and non-hits.
Atoms that matched a SMARTS are coloured, with the colour giving the
number of times an atom was matched, in the order Red, Orange, Yellow,
Green, Blue, Purple for once, twice...many.  Further matching can be
carried out, and subsequent queries will only be done on the contents
of the left panel (if there's only 1 panel, it's the left one, the
right one comes and goes).  So if you want to find the molecules that
match SMARTS1 and SMARTS2 and SMARTS3, you would do the match with
SMARTS1, then SMARTS2 and then SMARTS3 in sequence.  At any point, you
can save a list with Molecules->Lists->New and the contents of the
currently selected panel (shown by the checkbox on the top left of the
panel) will be remembered. These lists can be recalled using the same
menu.

When using the SMARTS->'Interactive Pick' option, the currently
displayed molecule will shown in a dialog.  Pick the atoms you're
interested in, and they'll be turned into a SMARTS pattern. This is
done by extracting the atoms from a copy of the original molecule, and
is generally mostly successful.  Something resembling it will be
drawn in the right panel of the dialog.  You have to be quite precise
with the atom picking, and it's a good idea to have the control key
down as you pick, so as to avoid unnecessary swearing.  You can pick
multiple atoms without the control key down, but if you miss an atom
it clears the selection, which is all too easy to do.

SMARTS File Format
==================

The SMARTS file format is a bit weird, as you might expect of
something invented by Pete Kenny.  There's an example, hbond.smt, in
the test_dir.  As well as demonstrating the format, it's potentially
of use in itself being his best guess of what h-bond donors and
acceptors look like.  Each line that isn't a comment has 4 fields,
space- or tab-separated.  The first field is a label, the second is
the SMARTS pattern, the third is always a 1 (and its purpose is
shrouded in mystery) and the fourth is either a 1 or 0, and defines
whether the SMARTS is a final definition (1) or what Daylight used to
call a vector binding, and we might these days wall a macro (0).  Only
final definitions (with a 1 in the fourth field) will be offered for
matching by smiv.  Final definitions can also be used as macros.

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

Requires: a recent version of OEChem, a relatively recent version of
Boost (1.55 and 1.60 are known to work).  You will also need Qt
(version >5.2) and Cairo. The qmake from an appropriate Qt must be
in your path.

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.

If you're not wanting to use the system-supplied Boost distribution in
/usr/include then set BOOST_ROOT to point to the location of a recent
(>1.48) build of the Boost libraries.  On my Centos 6.5 machine, the
system boost is 1.41 which isn't good enough. You will also probably
need to use '-DBoost\_NO\_BOOST\_CMAKE=TRUE' when running cmake:

cmake -DCMAKE\_BUILD\_TYPE=RELEASE -DBoost\_NO\_BOOST\_CMAKE=TRUE ..

These instructions have only been tested in Centos 6 and Ubuntu 14.0
Linux systems.  I have no experience of using them on Windows of OSX,
and no means of doing so.

David Cosgrove
AstraZeneca
12th February 2016

davidacosgroveaz@gmail.com