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 |
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pari-wise matrices |
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distances ( |
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other parameters |
Classes
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Interaction matrix class. |
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Pairwise interaction matrix class. |
PROPKA parameter class. |
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propka.parameters.
DISTANCES
= ['desolv_cutoff', 'buried_cutoff', 'coulomb_cutoff1', 'coulomb_cutoff2']¶ distances (
float
)
-
class
propka.parameters.
InteractionMatrix
(name)[source]¶ Interaction matrix class.
-
propka.parameters.
LIST_DICTIONARIES
= ['backbone_NH_hydrogen_bond', 'backbone_CO_hydrogen_bond']¶ dict
containing lists
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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)[source]¶ Pairwise interaction matrix class.
-
add
(words)[source]¶ Add information to the matrix.
TODO - this function unnecessarily bundles arguments into a tuple
- Parameters
words – tuple with assignment information and value
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get_value
(item1, item2)[source]¶ Get specified value from matrix.
- Parameters
item1 – row index
item2 – column index
- Returns
matrix value (or default)
-
-
class
propka.parameters.
Parameters
[source]¶ PROPKA parameter class.
-
parse_to_list_dictionary
(words)[source]¶ Parse field to list dictionary.
- Parameters
words – strings to parse.
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parse_to_number_dictionary
(words)[source]¶ Parse field to number dictionary.
- Parameters
words – strings to parse.
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parse_to_string_dictionary
(words)[source]¶ Parse field to string dictionary.
- Parameters
words – strings to parse
-
-
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