ReactionCode is a new versatile format for searching, analysis, classification, transform, and encoding/decoding of reactions. ReactionCode is a multi-layer machine readable code, which has been created in the line of ClassCode and BINCODE format. In contrast to these formats, it can fully encode and decode a reaction without any information loss. This open source format is canonical and designed to be flexible, upgradeable and versatile in order to be applied in a broad range of applications. ReactionCode is particularly useful for reaction similarity searching and classification, but is also intended for machine learning applications and as a new transform reaction language.

Further information can be found in the publication: ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding https://doi.org/10.1186/s13321-020-00476-x

• ReactionCode has been submitted.
• ReactionCode 1.1.0 has been released: the transformer class has been fully recoded and some bugs have been corrected.
• ReactionCode 1.2.1 has been released: new sublayer for radical; new kulization algorithm; implementation of an algorithm for product correction and a function encodeAndRebalance ; bugs fixed
• ReactionCode 1.2.1 has been released: Minor update: replace radicalize by sanitize which tries to deduce the missing atom mapping in the reactants and correct the valence by radicalizing atoms with incorrect valence if hydrogens are setup
• ReactionCode 1.2.2 has been released: Minor update: Deuterium bug correction. In the previous version, Deuterium was decoded as 2* in the SMIRKS. It has been corrected and now is written as 2H

ReactionCode can be used as an API or a Command Line Interface:

API:
Import ReactionCode 1.2.2.jar as a Dependency
import com.nih.main.API
API reactionCodeApi = new API();

Command-line options:
java -jar ReactionCode 1.2.2.jar -h
will give you a list of available options with short descriptions.

java -jar ReactionCode 1.2.2.jar -e
will give you a list of examples.

This program is free software; the part of the software that was written at the National Cancer Institute is in the public domain. This does not preclude, however, that components such as specific libraries used in the software may be covered by specific licenses, including but not limited to the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version; which may impose specific terms for redistribution or modification.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA. See also http://www.gnu.org/.

See the file COPYING for details.

If there are more questions regarding the GPL software and the legal limitations on its redistribution, modifications, and usage we recommend reading GPL FAQ. In particular, regarding the output of the program we do not and cannot impose any limitations on the use of the output generated by OSRA which the input data did not previously have:

"...copyright law does not give you any say in the use of the output people make from their data using your program. If the user uses your program to enter or convert his own data, the copyright on the output belongs to him, not you. More generally, when a program translates its input into some other form, the copyright status of the output inherits that of the input it was generated from."

ReactionCode is Free and Open Source Software. You are welcome to download and use it, provided that you understand the terms described above. Participation in the development is highly encouraged!

Note: The last version of ReactionCode developed at NCI is 1.2.2. For future developments, you may also look at https://github.com/victoriendelannee/reactioncode/.

• ReactionCode 1.2.2 - Contains encoder,decoder and transformer
  • ReactionCode-1.2.2.jar - JAR executable (Linux, MacOS and Windows compatible)

We also welcome your feedback - send us your comments, suggestions, criticism, or praise to the contact email address below.

Victorien Delannée and Marc C. Nicklaus. ReactionCode: a new versatile format for searching, analysis, classification, transform, and encoding/decoding of reactions https://doi.org/10.1186/s13321-020-00476-x

ClassCode
Kraut H, Eiblmaier J, Grethe G, Löw P, Matuszczyk H, Saller H (2013) Algorithm for reaction classification. J Chem Inf Model 53(11):2884–2895

BINCODE
Elsevier: BinCoder. https://www.elsevier.com/solutions/reaxys. Accessed 6 Apr 2020.

Adobe Acrobat Reader for viewing PDF files can be downloaded here.

Victorien Delannée - 2020, Frederick National Laboratory for Cancer Research, NIH, DHHS, Frederick, MD

Last Update: Victorien Delannée, 2020-06-02