Use maven to build a jar with dependencies:
mvn package -DskipTests
and then run :
java -cp target/moleculegen-1.0-jar-with-dependencies.jar app.AMG -e "C4H11N" -O SMI
NC(C)(C)C
NCC(C)C
NC(C)CC
NCCCC
N(C)C(C)C
N(C)CCC
N(CC)CC
N(C)(C)CC
For a full list of commands, run with -h or no arguments:
java -cp target/moleculegen-1.0-jar-with-dependencies.jar app.AMG
Usage: java -jar AMG.jar -e <formula>
Basic options :
-c Compare the output to the input file
-e <formula> Elemental Formula
-h Print help
-i <path> Input Filepath
-I <format> Input Format (SMI, SIG, SDF, MOL)
-n Number output lines
-o <path> Output Filepath
-O <format> Output Format (SMI, SIG, SDF, MOL)
-p Show parent of each molecule
-r <min:max> Range of input file to use
-t Time the run
-z Compress (zip) the output
Advanced options :
--augmentation=<method> Augmentation method (ATOM, BOND)
An implementation of a molecule generation algorithm similar to that of the Open Molecule Generator (OMG) Source here. There are a couple of differences:
- OMG uses nauty (a fast c-library for graph automorphism and canonical labelling computation), this uses signatures.
- OMG augments by bond while this augments by vertex.
- There is an alterntative listing method for candidate children of a parent molecule, that uses the automorphism group of the parent to eliminate symmetric duplicates.
It is, however, slower than OMG - which is slower than molgen. So it should be considered as a proof-of-concept rather than a useable tool (for now...). Comments and suggestions are welcome.