Copyright 2019 Mehmet Aziz Yirik

Algorithmic group theory functions shared in this repository, are especially developed for the implementations in mathematical chemistry.These algorithms are for the molecular structure generation problem.

This is an ongoing project for molecular structure generation. Already tested functions are regularly shared on this repository. The prototype algorithm, the MORGEN class, is the main class of the jar file. The theoretical basis and the outlines of the functions can be found in [1,2]. The current version needs some optimization to overcome stackOverFlow issues and this is the ongoing work in this project.

The main class of the current jar file is MORGEN class. The file can be downloaded from here

It is assumed that users have git on their system and have initialised their local directory. For more information set-up-git

To download AlgorithmicGroupTheory source code:

$ git clone https://github.com/MehmetAzizYirik/AlgorithmicGroupTheory.git

To compile AlgorithmicGroupTheory, Apache Maven and Java 1.8 (or later) are required.

AlgorithmicGroupTheory/$ mvn package

This command will create jar file named as "MORGEN-jar-with-dependencies" under target folder.

MORGEN.jar can be run from command line with the specified arguments. An example command is given below.

The definitions of the arguments are given below:

usage: java -jar MORGEN.jar -f <arg> [-v] -d <arg>

Generates molecular structures for a given molecular formula. The input is 
a molecular formula string. For example 'C2OH4'. Besides molecular formula, the
directory is needed to be specified for the output file.

 -f,--molecularFormula <arg>   Molecular formula as a string (required)
 
 -v,--verbose                  Print messages about structure generation
 
 -d,--filedir <arg>            Creates and store the output txt file 
                               in the directory (required)

Please report issues at https://github.com/MehmetAzizYirik/AlgorithmicGroupTheory

java -jar MORGEN.jar -f C2OH4 -v -d C:\Users\UserName\Desktop\

This project is licensed under the MIT License - see the LICENSE.md file for details

• Mehmet Aziz Yirik - MehmetAzizYirik

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This project relies on the Chemistry Development Project (CDK), hosted under CDK GitHub. Please refer to these pages for updated information and the latest version of the CDK. CDK's API documentation is available though our Github site.

1- Kerber, A., Laue, R., Meringer, M., Rücker, C. and Schymanski, E., 2013. Mathematical chemistry and chemoinformatics: structure generation, elucidation and quantitative structure-property relationships. Walter de Gruyter.

2- Grund, R. and Müller, R., 1995. Konstruktion molekularer Graphen mit gegebenen Hybridisierungen und überlappungsfreien Fragmenten. Lehrstuhl II für Mathematik.