4.2.4. propka.parameters

4.2.4.1. Configuration file parameters

Holds parameters and settings that can be set in propka.cfg. The file format consists of lines of keyword value [value ...], blank lines, and comment lines (introduced with #).

The module attributes below list the names and types of all key words in configuration file.

Module Attributes

MATRICES	matrices
PAIR_WISE_MATRICES	pari-wise matrices
NUMBER_DICTIONARIES	dict containing numbers
LIST_DICTIONARIES	dict containing lists
STRING_DICTIONARIES	dict containing strings
STRING_LISTS	list containing strings
DISTANCES	distances (float)
PARAMETERS	other parameters

Classes

InteractionMatrix(name)	Interaction matrix class.
PairwiseMatrix(name)	Pairwise interaction matrix class.
Parameters()	PROPKA parameter class.

propka.parameters.DISTANCES = ['desolv_cutoff', 'buried_cutoff', 'coulomb_cutoff1', 'coulomb_cutoff2']

distances (float)

class propka.parameters.InteractionMatrix(name)

Interaction matrix class.

add(words)

Add values to matrix.

Parameters

words – values to add

get_value(item1, item2)

Get specific matrix value.

Parameters

• item1 – matrix row index

• item2 – matrix column index

Returns

matrix value or None

keys()

Get keys from matrix.

Returns

dictionary key list

propka.parameters.LIST_DICTIONARIES = ['backbone_NH_hydrogen_bond', 'backbone_CO_hydrogen_bond']

dict containing lists

propka.parameters.MATRICES = ['interaction_matrix']

matrices

propka.parameters.NUMBER_DICTIONARIES = ['VanDerWaalsVolume', 'charge', 'model_pkas', 'ions', 'valence_electrons', 'custom_model_pkas']

dict containing numbers

propka.parameters.PAIR_WISE_MATRICES = ['sidechain_cutoffs']

pari-wise matrices

propka.parameters.PARAMETERS = ['Nmin', 'Nmax', 'desolvationSurfaceScalingFactor', 'desolvationPrefactor', 'desolvationAllowance', 'coulomb_diel', 'COO_HIS_exception', 'OCO_HIS_exception', 'CYS_HIS_exception', 'CYS_CYS_exception', 'min_ligand_model_pka', 'max_ligand_model_pka', 'include_H_in_interactions', 'coupling_max_number_of_bonds', 'min_bond_distance_for_hydrogen_bonds', 'coupling_penalty', 'shared_determinants', 'common_charge_centre', 'hide_penalised_group', 'remove_penalised_group', 'max_intrinsic_pka_diff', 'min_interaction_energy', 'max_free_energy_diff', 'min_swap_pka_shift', 'min_pka', 'max_pka', 'sidechain_interaction']

other parameters

class propka.parameters.PairwiseMatrix(name)

Pairwise interaction matrix class.

add(words)

Add information to the matrix.

TODO - this function unnecessarily bundles arguments into a tuple

Parameters

words – tuple with assignment information and value

get_value(item1, item2)

Get specified value from matrix.

Parameters

• item1 – row index

• item2 – column index

Returns

matrix value (or default)

insert(key1, key2, value)

Insert value into matrix.

Parameters

• key1 – first matrix key (row)

• key2 – second matrix key (column)

• value – value to insert

keys()

Get keys from matrix.

Returns

dictionary key list

class propka.parameters.Parameters

PROPKA parameter class.

parse_distance(words)

Parse field to distance.

Parameters

words – strings to parse

parse_line(line)

Parse parameter file line.

parse_parameter(words)

Parse field to parameters.

Parameters

words – strings to parse

parse_string(words)

Parse field to strings.

Parameters

words – strings to parse

parse_to_list_dictionary(words)

Parse field to list dictionary.

Parameters

words – strings to parse.

parse_to_matrix(words)

Parse field to matrix.

Parameters

words – strings to parse

parse_to_number_dictionary(words)

Parse field to number dictionary.

Parameters

words – strings to parse.

parse_to_string_dictionary(words)

Parse field to string dictionary.

Parameters

words – strings to parse

parse_to_string_list(words)

Parse field to string list.

Parameters

words – strings to parse

print_interaction_parameters()

Print interaction parameters.

print_interaction_parameters_latex()

Print interaction parameters in LaTeX format.

print_interactions_latex()

Print interactions in LaTeX.

set_up_data_structures()

Set up internal data structures.

TODO - it would be better to make these assignments explicit in __init__.

propka.parameters.STRING_DICTIONARIES = ['protein_group_mapping']

dict containing strings

propka.parameters.STRING_LISTS = ['ignore_residues', 'angular_dependent_sidechain_interactions', 'acid_list', 'base_list', 'exclude_sidechain_interactions', 'backbone_reorganisation_list', 'write_out_order']

list containing strings