Go package to calculate Assembly Numbers for Molecules.
Make sure go is installed, the instructions for that can be found on the (golang docs)[https://go.dev/doc/install]
Confirm you've installed go correctly by running go version (a version later than 1.15 should be shown)
after that building the command line tool is easy just run go build cmd/app/main.go -o assembly
Currently basic usage is as follows - note flags (preceded by a dash) can be in any order
filename as argument at the end of the command, outputs assembly index only:
./assembly my_mol.mol
verbose flag will result in more detailed pathway output. In this usage, my_mol.mol must be at the end:
./assembly -verbose my_mol.mol
filename can also be passed as a flag - this takes priority over putting the filename at the end if both are done
./assembly -file=my_mol.mol -verbose
number of workers in the worker pool and the buffer size of the jobs queue. Currently defaults both to 100 (yet to test how optimal the default is).
./assembly -file=my_mol.mol -workers=500 -buffer=500
The -molfile flag defaults to true to read input as a mol file. Switch to false to read input as custom graph txt file. This is a basic format that was used in testing and development as is simply 5 lines, those being name, list of vertex indices, list of associated edges (will be read in pairs, e.g. 1 2 2 3 is edges {1, 2} and {2, 3}), vertex colours, edge colours. Vertex and edge colours interpreted as strings, delineated by spaces. If there are no vertex or edge colours, replace the corresponding line with an exclamation mark "!"
Square graph (name - this line can be anything)
1 2 3 4 5
1 2 2 3 3 4 4 5
A B A B B
Red Blue Red Blue
./assembly -file=my_graph.txt -molfile=false
The -log flag is a boolean, and if present will log the pathway output to a file (default log.txt)
To specify a log file use e.g. -logfile my_log_file.txt (must also have log flag to do anything)
Here's an example with aspirin:
./assembly file=aspirin.mol -verbose
Which produces this output:
Running on file: aspirin.mol
ORIGINAL GRAPH
+++++++++++++++
Vertices [0 1 2 3 4 5 6 7 8 9 10 11 12]
Edges [[0 1] [2 0] [0 3] [1 4] [5 2] [2 6] [3 10] [4 7] [7 5] [6 8] [6 9] [10 11] [10 12]]
VertexColours [C C C O C C C C O O C O C]
EdgeColours [double single single single double single single double single double single double single]
+++++++++++++++
PATHWAY
Pathway Graphs
======
Vertices [2 0 5]
Edges [[2 0] [5 2]]
VertexColours [C C C]
EdgeColours [single double]
======
======
Vertices [3 10 11 12]
Edges [[3 10] [10 11] [10 12]]
VertexColours [O C O C]
EdgeColours [single double single]
======
======
Vertices [13 1 14]
Edges [[13 1] [1 14]]
VertexColours [C C C]
EdgeColours [double single]
======
----------
Remnant Graph
Vertices [0 3 2 6 8 9 4 7 5]
Edges [[0 3] [2 6] [6 8] [6 9] [4 7] [7 5]]
VertexColours [C O C C O O C C C]
EdgeColours [single single double single double single]
----------
Duplicated Edges
[0 2]
[1 4 5]
[1 2]
+++++++++++++++
Assembly Index: 8
Time: 0.0449225
Sample build command from repo root
go build -o bin\assembly.exe GoAssembly/cmd/app