INSTRUCTIONS.txt

BASIC USAGE
-----------

There are a number of ways to run AMG:

WARNING : only use very small formulae to test at first.

1) Just count the number of structures for a formula : "AMG -e C4H8". 
2) Print the structures to stdout: "AMG -e C4H8 -O SMI"
3) Augment a set of structures, from a file : "AMG -e C4H8 -O SMI -i myFile.sdf -I SDF"

This last way can be used as a crude form of parallelism. First, pick a number of initial
structures to generate, and write these to a file (SDF or signatures):

  AMG -e C5 -o master_list.txt -O SIG

Then, run AMG on chunks of this input list, possibly using the "-r" option:

  AMG -e C7H12 -i master_list.txt -I SIG -o result_1_10.txt -O SMI -r 1:10
  AMG -e C7H12 -i master_list.txt -I SIG -o result_10_20.txt -O SMI -r 10:20
  AMG -e C7H12 -i master_list.txt -I SIG -o result_20_30.txt -O SMI -r 20:30
  ...
  
Each run will take a different chunk of the master list, and produce a non-overlapping set of
results in each of the results files.

DEBUG OPTIONS
-------------

Some of the basic flags (-t, -n, -p) are used for debugging, so they can be ignored by most users. Timing with
(-t) is obviously for speed checks, and only works when no output format is given. Numbering the output lines
(with -n) is just an alternative to using the nl utility. Printing the parent structure (with -p) does exactly that, and is basically just for me.

Also, the "ACP" output format gives an exact string-form for the atom and bonds of a structure, which is near-
readable. So "C0C1O2 0:1(3),0:2(1),1:2(1)" has two carbons and on oxygen, and three bonds (triple, single, 
single) between the numbered atoms. It cannot currently be used as an input format.

ADVANCED OPTIONS
----------------

There are some advanced options available, for those that know what they are doing:

1) augmentation=ATOM or augmentation=BOND : augment molecules by adding atoms or by bonds.
2) lister=FILTER or lister=SYMMETRIC : the method used to list candidate children of a parent.
3) validator=REFINER or validator=SIGNATURE : the canonical checking algorithm.

These options are really only useful at the moment for testing the behaviour of the different algorithms.