======Introduction====== MARS, Molecular Assembling and Representation Suite, is a program for general purpose computer aided molecular design. This program uses an integer arry data structure to store the information of atom type, atom connectivity, and bond order of a molecule. There are also subroutines that can be used to modify the data structure in order to generate new molecules. This program is espicially useful for computer molecular design problems. The program consists of 4 header files and 5 cpp files ATOM.h MATRIX.h MOLECULE.h OPT.h MARS.cpp ATOM.cpp MATRIX.cpp MOLECULE.cpp OPT.cpp There are additional 4 text files for running examples molecular operations on butane, methane, and phenol butane.gjf methane.gjf phenol.gjf example.in ======Compile the program====== This program is written in C++. In Linux/Unix environment, run ./compile or make to create the executable (MARS) for the program ======Usage====== 1. basic use (generate new molecules using butane and phenol) use the example files provided and execute ./MARS example.in The input file, example.in, contain the filenames of two molecules, butane and phenol. The program will expect the 3D coordinates of these two molecules (butane.gjf and phenol.gjf in Gaussian input file format) to be in the same folder as the example.in file. The program will perform molecular operations on these two molecules. The results will be produced in 6 output files combination.txt crossover.txt subtraction.txt addition.txt exchange.txt ring.txt These files contain all possible molecules that can be generated from each corresponding molecular operation. The results are shown in SMILES format. The structure of the generated molecules can be visualized using other programs, such as Avogadro (https://avogadro.cc/). Furthermore, the program also generates benzene from methane. The intermediate molecules are produced in benzene.txt. A log file, named molecule.log, will be produced to note any warning and error encountered during the molecular operations. A Warning message is produced when a certain operation cannot be performed successfully. A Error message is produced when the program needs to stop because of wrong usage (e.g., missing input files) 2. Advanced usage The program accept keywords, gen3d and genmds (both optional), to request the generation of 3D coordinates and MDS structure in the output files. For example, ./MARS example.in gen3d ./MARS example.in genmds ./MARS example.in gen3d genmds ======Developers====== This program is developed by Hsuan Hao Hsu, Chen Hsuan Huang, and Shiang Tai Lin. Computational Molecular Engineering Laboratory Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan stlin@ntu.edu.tw
hsuhsuanhao/MARS
MARS, Molecular Assembling and Representation Suite, is a program for general purpose computer aided molecular design. This program uses an integer arry data structure to store the information of atom type, atom connectivity, and bond order of a molecule. There are also subroutines that can be used to modify the data structure in order to generate new molecules. This program is espicially useful for computer molecular design problems.
C++GPL-3.0