rdf

Command Line Tool for RDF Analysis

This command line tool can be used to calculate the radial distribution function (RDF) of given trajectory file(s). This is an input file based tool, so that the input file can be used to specify the parameters of the RDF calculation. For more information on the general the RDF analysis and its input file options please visit PQAnalysis.analysis.rdf.rdf.RDF and PQAnalysis.analysis.rdf.rdf_input_file_reader

For the RDF analysis input file several keys are available of which some are required and some are optional. For more details on the grammar and syntax of the input file see Input File.

Required keys

Key - Value
traj_files - The trajectory files to read. This can be a single file or a list of files.
reference_selection - The selection string to select the reference atoms. For more details see Selection.
target_selection - The selection string to select the target atoms. For more details see Selection.
out_file - The output file to write the RDF data to.

Optional keys

Key - Value
r_max - The maximum radius to calculate the RDF for.
r_min - The minimum radius to calculate the RDF for.
delta_r - The delta radius to calculate the RDF for.
n_bins - The number of bins to calculate the RDF for.
log_file - The log file to write the log information to.
use_full_atom_info - Whether to use full atom information for the selections.
no_intra_molecular - Whether to exclude intra molecular pairs.
restart_file - The restart file to read the topology from.
moldescriptor_file - The moldescriptor file to read the reference residues from.

Note

Optional keys does not mean that they are optional for the analysis. They are optional in the input file, but they might be required for the analysis. This means that if an optional keyword is specified other keywords might be required. For example:

• If the no_intra_molecular key is specified,

the restart_file and moldescriptor_file keys are required in order to exclude intra molecular pairs. - If the moldescriptor_file key is specified, the restart_file key is required in order use the reference residues in any meaningful way. - In general, the r_max, n_bins and delta_r are mutual exclusive, meaning that they can’t be specified at the same time. Furthermore, at least one of <property object at 0x7fb2327fab60>' or :code:`<property object at 0x7fb2327faac0> is required (for more information see RDF).

Summary

Classes:

RDFCLI

Command Line Tool for RDF Analysis

Functions:

main	The main function of the RDF analysis command line tool, which is basically just a wrapper for the rdf function.

Reference

class RDFCLI

Bases: CLIBase

Command Line Tool for RDF Analysis

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 command line tool.

Parameters:

args (argparse.Namespace) – The arguments parsed by the parser.

main()

The main function of the RDF analysis command line tool, which is basically just a wrapper for the rdf function. For more information on the rdf function please visit PQAnalysis.analysis.rdf.api.rdf().