4.1.3. propka.group¶
4.1.3.1. Data structures for groups¶
Routines and classes for storing groups important to PROPKA calculations.
Module Attributes
acids |
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bases |
Functions
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Initialize an atom group. |
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Identify whether the atom belongs to a group. |
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Identify whether the atom belongs to an ion group. |
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Identify whether the atom belongs to a ligand group by checking groups. |
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Identify whether the atom belongs to a ligand group by calculating ‘Marvin pKas’. |
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Identify whether the atom belongs to a protein group. |
Classes
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Amide group. |
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Arginine group. |
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Backbone carbon group. |
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Backbone nitrogen group. |
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Amidinium group. |
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Guadinium group. |
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Carboxyl group. |
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Cysteine group. |
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Chloride group. |
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C-terminus group. |
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Fluoride group. |
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Class for storing groups important to pKa calculations. |
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Histidine group. |
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Ion group. |
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Lysine group. |
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Unknown group. |
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Unknown group. |
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Unknown group. |
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Unknown group. |
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Unknown group. |
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Unknown group. |
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Unknown group. |
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Unknown group. |
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Non-titratable ligand group. |
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N-terminus group. |
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Unknown group. |
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Unknown group. |
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Carboxyl group. |
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Hydroxide group. |
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Phosphate group. |
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Alcohol group. |
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Serine group. |
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Sulfhydryl group. |
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Tryptophan group. |
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Tyrosine group. |
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Titratable ligand group. |
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propka.group.
EXPECTED_ATOMS_ACID_INTERACTIONS
= {'AMD': {'H': 2, 'N': 1}, 'ARG': {'H': 5, 'N': 3}, 'BBC': {'O': 1}, 'BBN': {'H': 1, 'N': 1}, 'C-': {'O': 2}, 'C2N': {'H': 4, 'N': 2}, 'CG': {'H': 5, 'N': 3}, 'COO': {'O': 2}, 'CYS': {'S': 1}, 'Cl': {'Cl': 1}, 'F': {'F': 1}, 'HIS': {'H': 2, 'N': 2}, 'LYS': {'N': 1}, 'N+': {'N': 1}, 'N1': {'N': 1}, 'N30': {'H': 4, 'N': 1}, 'N31': {'H': 3, 'N': 1}, 'N32': {'H': 2, 'N': 1}, 'N33': {'H': 1, 'N': 1}, 'NAM': {'H': 1, 'N': 1}, 'NAR': {'H': 1, 'N': 1}, 'NP1': {'H': 2, 'N': 1}, 'O2': {'O': 1}, 'O3': {'O': 1}, 'OCO': {'O': 2}, 'OH': {'H': 1, 'O': 1}, 'OP': {'O': 1}, 'ROH': {'O': 1}, 'SH': {'S': 1}, 'TRP': {'H': 1, 'N': 1}, 'TYR': {'O': 1}}¶ acids
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propka.group.
EXPECTED_ATOMS_BASE_INTERACTIONS
= {'AMD': {'O': 1}, 'ARG': {'N': 3}, 'BBC': {'O': 1}, 'BBN': {'H': 1, 'N': 1}, 'C-': {'O': 2}, 'C2N': {'N': 2}, 'CG': {'N': 3}, 'COO': {'O': 2}, 'CYS': {'S': 1}, 'Cl': {'Cl': 1}, 'F': {'F': 1}, 'HIS': {'N': 2}, 'LYS': {'N': 1}, 'N+': {'N': 1}, 'N1': {'N': 1}, 'N30': {'N': 1}, 'N31': {'N': 1}, 'N32': {'N': 1}, 'N33': {'N': 1}, 'NAM': {'H': 1, 'N': 1}, 'NAR': {'H': 1, 'N': 1}, 'NP1': {'N': 1}, 'O2': {'O': 1}, 'O3': {'O': 1}, 'OCO': {'O': 2}, 'OH': {'H': 1, 'O': 1}, 'OP': {'O': 1}, 'ROH': {'O': 1}, 'SH': {'S': 1}, 'TRP': {'N': 1}, 'TYR': {'O': 1}}¶ bases
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class
propka.group.
Group
(atom)[source]¶ Class for storing groups important to pKa calculations.
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add_determinant
(new_determinant, type_)[source]¶ Add to current and creates non-present determinants.
- Parameters
new_determinant – new determinant to add
type – determinant type
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calculate_charge
(_, ph=7.0, state='folded')[source]¶ Calculate the charge of the specified state at the specified pH.
- Parameters
_ – parameters for calculation
ph – pH value
state – “folded” or “unfolded”
- Returns
float with charge
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calculate_folding_energy
(parameters, ph=None, reference=None)[source]¶ Return the electrostatic energy of this residue at specified pH.
- Parameters
parameters – parameters for energy calculation
ph – pH value for calculation
reference – reference state for calculation
- Returns
float describing energy
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calculate_intrinsic_pka
()[source]¶ Calculate the intrinsic pKa values from the desolvation determinants, back-bone hydrogen bonds, and side-chain hydrogen bonds to non-titratable residues.
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calculate_total_pka
()[source]¶ Calculate total pKa based on determinants associated with this group.
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couple_covalently
(other)[source]¶ Couple this group with another group.
- Parameters
other – other group for coupling
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couple_non_covalently
(other)[source]¶ Non-covalenthly couple this group with another group.
- Parameters
other – other group for coupling
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get_covalently_coupled_groups
()[source]¶ Get covalently coupled groups.
- Returns
list of covalently coupled groups.
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get_determinant_for_string
(type_, number)[source]¶ Return a string describing determinant.
- Parameters
type – determinant type
number – determinant index number
- Returns
string
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get_determinant_string
(remove_penalised_group=False)[source]¶ Create a string to identify this determinant.
- Parameters
remove_penalised_group – Boolean flag to remove penalized groups
- Returns
string
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get_interaction_atoms
(interacting_group)[source]¶ Get atoms involved in interaction with other group.
- Parameters
interacting_group – other group
- Returns
list of atoms
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get_non_covalently_coupled_groups
()[source]¶ Get non-covalently coupled groups.
- Returns
list of covalently coupled groups.
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get_summary_string
(remove_penalised_group=False)[source]¶ Create summary string for this group.
- Parameters
remove_penalised_group – Boolean to ignore penalized groups
- Returns
string
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remove_determinants
(labels)[source]¶ Remove all determinants with specified labels.
- Parameters
labels – list of labels to remove
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set_determinant
(new_determinant, type_)[source]¶ Overwrite current and create non-present determinants.
- Parameters
new_determinant – new determinant to add
type – determinant type
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set_interaction_atoms
(interaction_atoms_for_acids, interaction_atoms_for_bases)[source]¶ Set interacting atoms and group types.
- Parameters
interaction_atoms_for_acids – list of atoms for acid interactions
interaction_atoms_for_base – list of atoms for base interactions
Add determinant to this group’s list of determinants.
- Parameters
new_determinant – determinant to add
type – type of determinant
Share determinants between this group and others.
- Parameters
others – list of other groups
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propka.group.
initialize_atom_group
(atom)[source]¶ Initialize an atom group.
- Parameters
atom – atom to initialize
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propka.group.
is_group
(parameters, atom)[source]¶ Identify whether the atom belongs to a group.
- Parameters
parameters – parameters for check
atom – atom to check
- Returns
group for atom or None
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propka.group.
is_ion_group
(parameters, atom)[source]¶ Identify whether the atom belongs to an ion group.
- Parameters
parameters – parameters for check
atom – atom to check
- Returns
group for atom or None
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propka.group.
is_ligand_group_by_groups
(_, atom)[source]¶ Identify whether the atom belongs to a ligand group by checking groups.
- Parameters
_ – parameters for check
atom – atom to check
- Returns
group for atom or None