pqanalysis_input_file_reader

A module for reading the input file for the PQAnalysis.

Summary

Classes:

PQAnalysisInputFileReader

A class to read the input file for the PQAnalysis.

Reference

class PQAnalysisInputFileReader(filename: str)

Bases: _FileMixin, _SelectionMixin, _PositionsMixin

A class to read the input file for the PQAnalysis. It inherits from _FileMixin, _SelectionMixin and _PositionsMixin.

The main idea of this class is work as a super class for all command line tools of PQAnalysis, but it can also be used as a standalone class. But if for example an analysis tool needs only few input file keywords, it is recommended to inherit from this class.

Attention

As this class is not intended to be used as a standalone class, it does not check if all required keys are set in the input file, thus also no information/documentation of the values of the keywords is given, so that they can be used accordingly in the implementing subclasses.

It sets the format to InputFileFormat.PQANALYSIS and the filename to the given filename. It also creates a InputFileParser with the given filename.

Parameters:

filename (str) – the filename of the input file

check_known_keys(

known_keys: list[str] | None = None,

)

Checks if all keys in the input file are known.

Parameters:

known_keys (List[str] | None, optional) – the known keys, by default None

Warns:

InputFileWarning – if unknown keys were set in the input file

check_required_keys(

required_keys: list[str],

)

Checks if all required keys are set in the input file.

Parameters:

required_keys (List[str]) – the required keys

Raises:

InputFileError – if not all required keys are set in the input file

read()

Reads the input file and parses it. It also sets the raw_input_file and the dictionary.

property delta_r: PositiveReal | None

The radius step size of the PQAnalysis.

Type:

PositiveReal | None

delta_r_key = 'delta_r'

known_keys = ['r_max', 'r_min', 'delta_r', 'n_bins', 'traj_files', 'selection', 'reference_selection', 'target_selection', 'use_full_atom_info', 'out_file', 'log_file', 'no_intra_molecular', 'moldescriptor_file', 'restart_file']

property log_file: str | None

The log file of the simulation.

Type:

str | None

log_file_key = 'log_file'

logger = <CustomLogger PQAnalysis.PQAnalysisInputFileReader (INFO)>

property moldescriptor_file: str | None

The moldescriptor file of the simulation.

Type:

str | None

moldescriptor_file_key = 'moldescriptor_file'

property n_bins: PositiveInt | None

The number of bins of the PQAnalysis.

Type:

PositiveInt | None

n_bins_key = 'n_bins'

property no_intra_molecular: bool | None

Whether intra molecular interactions should be excluded.

Type:

bool | None

no_intra_molecular_key = 'no_intra_molecular'

property out_file: str | None

The out file of the simulation.

Type:

str | None

out_file_key = 'out_file'

property r_max: PositiveReal | None

The maximum radius of the PQAnalysis.

Type:

PositiveReal | None

r_max_key = 'r_max'

property r_min: PositiveReal | None

The minimum radius of the PQAnalysis.

Type:

PositiveReal | None

r_min_key = 'r_min'

property reference_selection: str | None

The reference selection of the simulation.

Type:

str | None

reference_selection_key = 'reference_selection'

property restart_file: str | None

The restart file of the simulation.

Type:

str | None

restart_file_key = 'restart_file'

property selection: str | None

The selection of the simulation.

Type:

str | None

selection_key = 'selection'

property target_selection: str | None

The target selection of the simulation.

Type:

str | None

target_selection_key = 'target_selection'

property traj_files: list[str] | None

The trajectory files of the simulation.

Type:

List[str] | None

traj_files_key = 'traj_files'

property use_full_atom_info: bool | None

Whether the full atom information should be used.

Type:

bool | None

use_full_atom_info_key = 'use_full_atom_info'