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.
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)
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’
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)
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’