tools Package

tools Package

AChemKit comes with a number of complete command-line driven tools for working with various file types.

These are intended to be used in automated pipelines, such as Makefiles.

These can be used as stand-alone programs, or examined as usage examples for the AChemKit API.

chem_linear Module

This is a command-line tool for generating .chem files using the Linear() random reaction network algorithm.

usage: chem_linear.py [options]

Options:

-h, --help show this help message and exit
-o OUTFILE, --outfile OUTFILE
 write to OUTFILE in .chem format (if ommited, use stdout)
-a NATOMS, --natoms NATOMS
 number of atoms
-l LENGTH, --length LENGTH
 maximum number of atoms per molecule
-f PFORM, --pform PFORM
 probability of bonding
-b PBREAK, --pbreak PBREAK
 probability of breaking
-u, --undirected
 undirected molecules
-d, --directed directed molecules
-t RATES, --rates RATES
 possible reaction rates
-s SEED, --seed SEED
 pseudo-random seed

chem_pp Module

A pretty-printer and syntax checker for .chem files

For information in .chem files see .chem Format.

Usage: chem_pp.py [options]

Options:

-h, --help show a help message and exit
-i INFILE, --infile=INFILE
 read from INFILE (if ommited, use stdin)
-o OUTFILE, --outfile=OUTFILE
 write to OUTFILE in .chem format (if ommited, use stdout)

chem_to_dot Module

Produces a .dot output from a provided .chem format input

The output files in .dot format are suitable for future processing using Graphviz tools. In particular, they are constructed using AChemKit.utils.simpledot.SimpleDot.

For information in .chem files see .chem Format.

Usage: chem_to_dot.py [options]

Options:

-h, --help Show a help message and exit
-i INFILE, --infile=INFILE
 Read from INFILE (if ommited, use stdin)
-o OUTFILE, --outfile=OUTFILE
 Write to OUTFILE in .chem format (if ommited, use stdout)
-n NAMES, --names
 Style of molecular species naming. One of ‘full’, ‘id’, ‘blank’

chem_to_pdf Module

Produces a .pdf output from a provided .chem format input

The output files in .pdf format produced using Graphviz tools. In particular, they are constructed using AChemKit.utils.simpledot.SimpleDot.

For information in .chem files see .chem Format.

Usage: chem_to_pdf.py [options]

Options:

-h, --help show a help message and exit
-i INFILE, --infile=INFILE
 read from INFILE (if ommited, use stdin)
-o OUTFILE, --outfile=OUTFILE
 write to OUTFILE in .pdf format (if ommited, use stdout)
-l LAYOUT, --layout=LAYOUT
 Graphviz layout to use (if ommited, use dot)

chem_uniform Module

This is a command-line tool for generating .chem files using the Uniform() random reaction network algorithm.

log_to_chem Module

Produces a .chem output from a provided .log format input

For information in .chem files see .chem Format.

Usage: chem_to_dot.py [options]

Options:

-h, --help Show a help message and exit
-i INFILE, --infile=INFILE
 Read from INFILE (if ommited, use stdin)
-o OUTFILE, --outfile=OUTFILE
 Write to OUTFILE in .chem format (if ommited, use stdout)
-n NAMES, --names
 Style of molecular species naming. One of ‘full’, ‘id’, ‘blank’

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