propka.parameters¶
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. |
- 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
- 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
- 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.
- parse_to_number_dictionary(words)[source]¶
Parse field to number dictionary.
- Parameters
words – strings to parse.
- parse_to_string_dictionary(words)[source]¶
Parse field to string dictionary.
- Parameters
words – strings to parse