libcli

Shared operations for client interfaces.

This module contains functions and classes that are shared amongst the client interfaces. It contains also others used to enhance the user experience.

class taurenmd.libs.libcli.CustomParser(prog=None, usage=None, description=None, epilog=None, parents=[], formatter_class=<class 'argparse.HelpFormatter'>, prefix_chars='-', fromfile_prefix_chars=None, argument_default=None, conflict_handler='error', add_help=True, allow_abbrev=True)

Custom Parser class.

error(message)

Present error message.

class taurenmd.libs.libcli.ParamsToDict(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)

Convert command-line parameters in an argument to a dictionary.

Example

Where -x is an optional argument of the command-line client interface.

>>> par1=1 par2='my name' par3=[1,2,3]
>>> {'par1': 1, 'par2': 'my name', 'par3': [1, 2, 3]}

class taurenmd.libs.libcli.ProgressBar(total, prefix='', suffix='', decimals=1, bar_length=None)

Contextualizes a Progress Bar.

Parameters

• total (int convertable) – The total number o iteractions expected.

• prefix (str) – Some prefix to enhance readability.

• suffix (str) – Some suffix to enhance readability.

• decimals (int-convertable) – The demicals to show in percentage. Defaults to 1.

• bar_length (int, float, -convertable) – The length of the bar. If not provided (None), uses half of the terminal window.

• Thanks to for the initial template function

• https (//dev.to/natamacm/progressbar-in-python-a3n)

Examples

>>> with ProgressBar(5000, suffix='frames') as PB:
>>>     for i in trajectory:
>>>         # do something
>>>         PB.increment()

increment()

Print next progress bar increment.

taurenmd.libs.libcli.add_angle_unit_arg(parser)

Add angle unit selectiona argument to parser.

Is defined by -a and --aunit.

Wether angles are to be calculated in degrees or radians.

Parameters

parser (argparse.ArgumentParser) – The argument parser to add the topology positionl argument.

taurenmd.libs.libcli.add_atom_selection_arg(parser)

Add selection optional argument.

Selection argument is a string that defines the atom selection, this is defined by -l and --selection, and defaults to all.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the selection argument.

taurenmd.libs.libcli.add_atom_selections_arg(parser)

Add selections optional argument.

Selections argument is a string that defines a list of atom selections, this is defined by -g and --selections, and defaults to all.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the selections argument.

taurenmd.libs.libcli.add_data_export_arg(parser)

Add export argument.

Export argument configures data export to a text file in table format.

Is defined by -x and --export.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the export argument.

taurenmd.libs.libcli.add_frame_list_arg(parser)

Add frame list argument.

Registers a list of frame numbers, is defined by -t and --flist.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the flist argument.

taurenmd.libs.libcli.add_insort_arg(parser)

Sort input by trail int.

Applies taurenmd.libs.libio.sort_numbered_input().

Parameters

parser (argparse.ArgumentParser) – The argument parser to add the insort argument.

taurenmd.libs.libcli.add_inverted_array(parser)

Add inverted selections optional argument.

Saves an array of 0s and 1s to invert the order of selections.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the selections argument.

taurenmd.libs.libcli.add_output_dir_arg(parser)

Add output dir to client.

Client gains –odir option.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the export argument.

taurenmd.libs.libcli.add_plane_selection_arg(parser)

Add plane selection argument.

Plane selection is a selection of three regions separated by ‘or’ operator.

Is defined by -z and --plane-selection.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the plane-selection argument.

taurenmd.libs.libcli.add_plot_arg(parser)

Add plot parameters.

Plot kwargs that will be passed to the plotting function.

Defined by --plot.

If given, plot results. Additional arguments can be given to specify the plot parameters.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the plot argument.

taurenmd.libs.libcli.add_reference_frame_arg(parser)

Add a reference frame argument.

Reference frame is the frame to compute the parameter against.

Depending on the client logic the reference frame might have different meanings.

Is defined by -r and --ref-frame.

Defaults to 0.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the refence-frame argument.

taurenmd.libs.libcli.add_slice_arg(parser)

Add start, stop and step slicing arguments.

Slicing arguments are according to Python Slice object

Parameters

parser (argparse.ArgumentParser) – The argument parser to add the trajectory positionl argument.

taurenmd.libs.libcli.add_subparser(parser, module)

Add a subcommand to a parser.

Parameters

• parser (argparse.add_suparsers object) – The parser to add the subcommand to.

• module – A python module containing the characteristics of a taurenmd client interface. Client interface modules require the following attributes: __doc__ which feeds the description argument of add_parser, _help which feeds help, ap which is an ArgumentParser, and a main function, which executes the main logic of the interface.

taurenmd.libs.libcli.add_top_output_arg(parser)

Add argument to export first frame as topology PDB file.

Defined by -o and --top-output.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the topology output argument.

taurenmd.libs.libcli.add_topology_arg(parser)

Add topology positional argument to parser.

Parameters

parser (argparse.ArgumentParser) – The argument parser to add the topology positionl argument.

taurenmd.libs.libcli.add_traj_output_arg(parser)

Add argument to export trajectory after client modifications.

Defined by -d and --traj-output.

Parameters

parser (argparse.ArgumentParser) – The argument parser to which add the trajectory output argument.

taurenmd.libs.libcli.add_trajectories_arg(parser)

Add trajectory positional argument to parser.

Accepts multiple trajectory files.

Parameters

parser (argparse.ArgumentParser) – The argument parser to add the trajectory positionl argument.

taurenmd.libs.libcli.add_trajectory_arg(parser)

Add trajectory positional argument to parser.

Accepts a single trajectory file.

Parameters

parser (argparse.ArgumentParser) – The argument parser to add the trajectory positionl argument.

taurenmd.libs.libcli.add_version_arg(parser)

Add version -v option to parser.

Displays a message informing the current version. Also accessible via --version.

Parameters

parser (argparse.ArgumentParser) – The argument parser to add the version argument.

taurenmd.libs.libcli.load_args(ap)

Load user arguments.

taurenmd.libs.libcli.maincli(ap, main)

Client main function.

Operates when client is called directly outside the taurenmd client interface.

• Reads input parameters

• saves inpu command to log file

• runs client main function

• saves references to log file

Returns

The result value from client main function.

taurenmd.libs.libcli.represent_argument(arg)

Represent argument in a string.

If argument has spaces represents string with quotation marks “.

taurenmd.libs.libcli.save_command(fname, *args)

Append the execution command to a log file.

Parameters

• fname (string or Path) – The file name of the log file where to append the command.

• *args (strings) – String parts that compose the command.

taurenmd.libs.libcli.save_references()

Save used references to log file.