tools Package — AChemKit v0.1 documentation

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# 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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