add_molecules

Command Line Tool for Converting Restart Files to XYZ Files

This command line tool can be used to add molecules to a restart file.

The molecules are added by fitting the molecule to the restart file. The fitting is done randomly by rotating the molecule and translating it to a random position. After the fitting, the molecule is added to the restart file. The class can add multiple molecules to the restart file.

This tool provides also the possibility of not only extending the restart file with the molecule but also the topology file. Therefore, the topology file of the restart file and the topology file of the molecule file have to be provided as well as the desired output topology file.

Summary

Classes:

AddMoleculesCLI

Command Line Tool for Adding Molecules to Restart Files

Functions:

main	Main function of the add_molecules command line tool, which is basically just a wrapper for the add_molecules function.

Reference

class AddMoleculesCLI

Bases: CLIBase

Command Line Tool for Adding Molecules to Restart Files

classmethod add_arguments(

parser: _ArgumentParser,

) → None

Adds the arguments to the parser.

Parameters:

parser (_ArgumentParser) – The parser to which the arguments should be added.

classmethod program_name() → str

Returns the name of the program.

Returns:

The name of the program.

Return type:

str

classmethod run(args)

Runs the add_molecules function.

Parameters:

args (argparse.Namespace) – The parsed arguments.

main()

Main function of the add_molecules command line tool, which is basically just a wrapper for the add_molecules function. For more information on the add_molecules function please visit PQAnalysis.tools.add_molecule().