AtomMap maps atoms in chemical reactions.
AtomMap requires OCaml compiler (version 4.11.1 or newer) together with xml-light library
(package libxml-light-ocaml-dev for Ubuntu) and xlib library.
In order to install xlib library clone:
git clone https://github.com/w-jaworski/xlib
and install it according to README provided.
Compile AtomMap:
make
The following executable files will be created:
map_reaction maps single reaction
map_reaction_server establishes a server
map_reaction takes a single command line argument which is a reaction in SMILES format
and generate matching results are provded in XML format on standart output. For example:
./map_reaction "ClC(C1=CC=CC=C1)=O.C1=CC=CC=C1>>O=C(C1=CC=CC=C1)C2=CC=CC=C2.[H]Cl"
map_reaction_server is a socket server that awaits for queries on port 2727.
A new process is created for each connection.
Queries are reactions in SMILES format to be mapped.
Matching results are provded in XML format. For example:
./map_reaction_server &
echo "ClC(C1=CC=CC=C1)=O.C1=CC=CC=C1>>O=C(C1=CC=CC=C1)C2=CC=CC=C2.[H]Cl" | netcat localhost 2727
Copyright (C) 2015-2017 Wojciech Jaworski Copyright (C) 2015-2017 Institute of Informatics, University of Warsaw
Copyright (C) 2015-2017 Sara Szymkuc Copyright (C) 2015-2017 Barbara Mikulak Copyright (C) 2015-2017 Institute of Organic Chemistry, Polish Academy of Sciences
The economic rights to the work belongs in 50% to University of Warsaw and in 50% to Institute of Organic Chemistry, Polish Academy of Sciences