mehmetazizyirik / algorithmicgrouptheory Goto Github PK

When running MORGEN.jar with option -v, time should be given in seconds.
Seems like a minor detail, but important.

java -jar MORGEN.jar -f C10H16 -v
MORGEN is generating isomers of C10H16...
The number of structures is: 24938
Time: 2.277

should be "Time: 2.277 seconds"

When running MORGEN.jar, it say that the option -d is required, but the program runs without.

In usage use -f for molecular formula

Option -D should be replaced with -o and take a filename (plus optional path) as an argument.
Furthermore, it is important that "maygen.jar -o -" writes output to standard out (use "System.out" as filename).

Like: BufferedWriter log = new BufferedWriter(new OutputStreamWriter(System.out));

This means that the option "-o" just gets the hyphen as an argument. This is a general convention in Unix and allows one to do things like "java -jar maygen.jar -o - | gzip > mycalc.sdf.gz" when one expects many solutions and a large SDF. This command compresses the SDF on the fly and allows the generation of very large SDF files with small hard disk footprint.

With the current version, I cannot generate the isomers of C15H24 on a google machine with 10GB Harddisk space.

use the -o option to create a file instead of -d and then not requiring a directory but a file

The program should throw an error if something goes wrong instead of quietly failing.
Example is formula C2Be (Beryllium) leads to no output at all, but should throw an error.