Program to create a tautomer-independent compound representation, for use when registering compounds to a database.
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README

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

This project builds 3 programs that are intended to generate 'compound
keys' for use in structural databases.  The purpose is that whatever
tautomer of a compound the user puts in, the same compound key is
generated at the end.  The key won't be a proper molecule, it will
have unsatisfied valences.  In this implementation, the key is a
canonical SMILES string.

The approach taken is to do a tautomer enumeration, which identifies
tautomer systems or skeletons (hereinafter 't_skels'). The mobile
hydrogens in the t_skels are removed, all unsaturated bonds are set to
1 and relevant chirality removed.  Thus the two tautomers
`C1=CC2=NC3=C(C2=CC1=O)C=NNC3NN` and `c1cc2c(cc1O)C3=CN=NC(C3=N2)NN`
give the t_skel
`[CH]1[CH][C]2[C]([CH][C]1[O])[C]3[CH][N][N][C]([C]3[N]2)[N][NH]`.

The Algorithm
-------------

The identification of t_skels is based heavily on 'A Branch-and-Bound
Approach for Tautomer Enumeration', T. Thalheim, B. Wagner, R. Kuhne,
M. Middendorf and G. Shuurmann, Molecular Informatics, _34_,
263-275 (2015). The basis of the algorithm is to use a set of rules to
identify atoms that are hydrogen donors, and those that are hydrogen
acceptors.  It's an unfortunate choice of terms (but they are German,
we should make linguistic allowances) as it lends itself to confusion
with hydrogen bond donors and acceptors which are clearly different.
The hydrogen acceptors and donors (HADs) come in pairs and have an
unsaturated path between them such that it's possible to take a
hydrogen off the donor, add it to the acceptor, and re-arrange the
single and double bonds between them such that all valences are
satisfied again.  The t_skel is thus the intermediate step in this
process, with the hydrogens removed from the donors and the bonds in
the paths set to 1. 

You might think (and indeed, I did) that if all you're interested in
is the compound key, you could dispense with the time-consuming
enumeration of tautomers and just output the t_skel.  However, you
need to make allowances for the especially awkward user who puts in a
tautomer that doesn't generate a full tautomer system.  To deal with
this, the code enumerates all tautomers and passes them back into the
t_skel generating code before amalgamating all possibilities at the
end.  An example would be the delightful CHEMBL19253,
`C[C@H](C(C)(C)C)/N=c\1/c(=N/c2ccc(cc2O)C#N)/c(c1O)O`,
which after 1 pass gives the compound key
C[C](C(C)(C)C)[N][C]1[C]([C]([C]1[O])[O])[N][C]2[CH][CH][C]([CH][C]2[O])[C]=[N]`
Another tautomer,
CC(C)(C)C(=C)Nc1c(c(=O)c1=O)NC2C=CC(C=C2O)C#N`
gives the compound key
`CC(C)(C)[C]([CH2])[N][C]1[C]([C]([C]1[O])[O])[N]C2C=C[C]([CH][C]2[O])[C]=[N]`. With
the iterative approach, they both agree on
`CC(C)(C)[C]([CH2])[N][C]1[C]([C]([C]1[O])[O])[N][C]2[CH][CH][C]([CH][C]2[O])[C]=[N]`,
albeit after several seconds' thought.  For especially prolific
tautomer systems, there's a timeout that gives up and returns the best
it has found so far.

The Code
--------

There are 3 programs, tt_tauts, tt\_tauts\_batch and gen\_t\_skel.  The
first is a graphical program that I knocked together for development
purposes. It reads a structure file, generates all tautomers of the
first structure, and draws the input structure, the t_skel and the
tautomers it found.  It needs Qt V5 to do this, of which more later.
The second, tt\_tauts\_batch is another test program. This one takes an
input structure, generates its t_skel and all tautomers, passes the
tautomers back through the t_skel generator and whinges loudly if the
generated tautomers produce a different t_skel from the input
structure.  It was an invaluable tool and the bane of my life when
developing the code.  Finally, gen\_t\_skel is the program that reads
structures and spits out the compound keys.  It's the thing to use in
production. 

Building the programs
---------------------

You will need a recent OEChem installation, Qt version >5.2, Boost of
version > 1.55 and cmake at least version 2.8.9.  None of latter are
the default versions on Centos 6, the system versions of those are
really out of date.

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

OE_DIR - the top level of an OEChem distribution.

For the Qt program tt_tauts, the qmake from an appropriate Qt must be
in your path. At least, I think that's how cmake finds it.

A successful build should be produced by: 
       cd src
       mkdir dev-build
       cd dev-build
       cmake -DCMAKE\_BUILD\_TYPE=DEBUG ..
       make

The executables should be in src/exe_DEBUG.  When you're happy
with everything, you can repeat the above replacing DEBUG with RELEASE
and you'll get fully optimised code in exe_RELEASE.  The Qt libraries
are only required for tt_tauts, so if you don't think you'll need
that, don't bother.  Just comment out the relevant bits in the
CMakeLists.txt file. Qt can be a bit of a faff to install on a Centos
6 system, in my experience.  You may be more competent.

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
(>1.55) 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 14.04
Linux systems.  I have no experience of using them on Windows or OSX,
and no means of doing so.

In directory test_dir are a whole load of SMILES files taken from
Chembl v20 that contain structures that provided interesting problems
during development, and are retained for test purposes.  There's a
script test_tt_tauts_batch.sh which runs tt_tauts_batch on them and
looks out for cases where 2 tautomers of the same input molecule don't
produce the same compound key.  The files 1082532.smi and 18048.smi
should produce such errors.  The script takes a while to run.

Some Notes on the Code
----------------------

All the exciting stuff happens in file make_taut_skeleton.cc. All the
other files are merely the supporting cast that allow it to strut its
stuff to full effect.  There are 2 entry points,
make_taut_skeleton_and_tauts and make_taut_skeleton.  The program
gen_t_skel uses the latter. Both call generate_t_skel to do the hard
work. 

An important aspect of the way the algorithm works is that there has
to be a unique label for each atom and bond that is preserved on copy
and editing.  The code uses DACLIB::atom_index and DACLIB::bond_index
for this.  These are functions that put a unique number on each atom
or bond as an attribute.  OpenEye's atom and bond indices
(atom->GetIdx(), for example) are not guaranteed to maintained if a
molecule is edited and then copied.  For example, if a molecule has 3
atoms, GetIdx() for them will probably return 0,1,2.  If atom 1 is
deleted and a new atom added, the indices will be 0,2,3.  If the
molecule is then copied, the new molecule will have atom indices 0,1,2
again, but what was atom 2 in the original molecule is now atom 1 in
the copy.  With DACLIB::atom_index, the atom indices in the new
molecule will be 0,2,3 as you'd expect.  Having been burnt by this
early on in my life as a happy OpenEye user, I never use GetIdx()
except on rare occasions when it is really convenient and I can be
absolutely sure it won't be a problem. 

Throughout the code, there are references to CHEMBL compounds, such as
CHEMBL34961.  These are compounds that showed up particular issues,
and should be available as separate SMILES files in the test_dir
directory which will have been checked out from the repo along
with everything else. 

I think the code is pretty well annotated.  If you start in function
generate_t_skel and follow the function calls, it should all be pretty
clear, I hope.  If it isn't clear, then I would hope there are
sufficient clarifying comments. 

David Cosgrove
AstraZeneca
12th February 2016

davidacosgroveaz@gmail.com