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_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)

log_to_chem 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’

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