propka.group

Data structures for groups

Routines and classes for storing groups important to PROPKA calculations.

Changed in version 3.4.0: Removed initialize_atom_group() as reading PROPKA inputs is no longer supported.

Module Attributes

`EXPECTED_ATOMS_ACID_INTERACTIONS`	acids
`EXPECTED_ATOMS_BASE_INTERACTIONS`	bases

Functions

`is_group`(parameters, atom)	Identify whether the atom belongs to a group.
`is_ion_group`(parameters, atom)	Identify whether the atom belongs to an ion group.
`is_ligand_group_by_groups`(_, atom)	Identify whether the atom belongs to a ligand group by checking groups.
`is_ligand_group_by_marvin_pkas`(parameters, atom)	Identify whether the atom belongs to a ligand group by calculating 'Marvin pKas'.
`is_protein_group`(parameters, atom)	Identify whether the atom belongs to a protein group.

Classes

`AMDGroup`(atom)	Amide group.
`ARGGroup`(atom)	Arginine group.
`BBCGroup`(atom)	Backbone carbon group.
`BBNGroup`(atom)	Backbone nitrogen group.
`C2NGroup`(atom)	Amidinium group.
`CGGroup`(atom)	Guadinium group.
`COOGroup`(atom)	Carboxyl group.
`CYSGroup`(atom)	Cysteine group.
`ClGroup`(atom)	Chloride group.
`CtermGroup`(atom)	C-terminus group.
`FGroup`(atom)	Fluoride group.
`Group`(atom)	Class for storing groups important to pKa calculations.
`HISGroup`(atom)	Histidine group.
`IonGroup`(atom)	Ion group.
`LYSGroup`(atom)	Lysine group.
`N1Group`(atom)	Unknown group.
`N30Group`(atom)	Unknown group.
`N31Group`(atom)	Unknown group.
`N32Group`(atom)	Unknown group.
`N33Group`(atom)	Unknown group.
`NAMGroup`(atom)	Unknown group.
`NARGroup`(atom)	Unknown group.
`NP1Group`(atom)	Unknown group.
`NonTitratableLigandGroup`(atom)	Non-titratable ligand group.
`NtermGroup`(atom)	N-terminus group.
`O2Group`(atom)	Unknown group.
`O3Group`(atom)	Unknown group.
`OCOGroup`(atom)	Carboxyl group.
`OHGroup`(atom)	Hydroxide group.
`OPGroup`(atom)	Phosphate group.
`ROHGroup`(atom)	Alcohol group.
`SERGroup`(atom)	Serine group.
`SHGroup`(atom)	Sulfhydryl group.
`TRPGroup`(atom)	Tryptophan group.
`TYRGroup`(atom)	Tyrosine group.
`TitratableLigandGroup`(atom)	Titratable ligand group.

class propka.group.AMDGroup(atom)[source]

Amide group.

setup_atoms()[source]: Setup group.

class propka.group.ARGGroup(atom)[source]

Arginine group.

setup_atoms()[source]: Set up group.

class propka.group.BBCGroup(atom)[source]

Backbone carbon group.

setup_atoms()[source]: Set up atoms in group.

class propka.group.BBNGroup(atom)[source]

Backbone nitrogen group.

setup_atoms()[source]: Set up atoms in group.

class propka.group.C2NGroup(atom)[source]

Amidinium group.

setup_atoms()[source]: Set up atoms in this group.

class propka.group.CGGroup(atom)[source]

Guadinium group.

setup_atoms()[source]: Set up atoms in this group.

class propka.group.COOGroup(atom)[source]

Carboxyl group.

setup_atoms()[source]: Set up group.

class propka.group.CYSGroup(atom)[source]: Cysteine group.

class propka.group.ClGroup(atom)[source]: Chloride group.

class propka.group.CtermGroup(atom)[source]

C-terminus group.

setup_atoms()[source]: Set up atoms in group.

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

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

class propka.group.FGroup(atom)[source]: Fluoride group.

class propka.group.Group(atom: Atom)[source]

Class for storing groups important to pKa calculations.

Changed in version 3.4.0: Removed make_covalently_coupled_line() and make_non_covalently_coupled_line() as writing PROPKA inputs is no longer supported.

add_determinant(new_determinant: Determinant, type_: str) → None[source]

Add to current and creates non-present determinants.

Parameters:

new_determinant – new determinant to add
type – determinant type

calculate_charge(_, ph: float = 7.0, state: str = 'folded') → float[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

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

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.

calculate_total_pka()[source]: Calculate total pKa based on determinants associated with this group.

clone()[source]

Create a copy of this group.

Returns:: Copy of this group.

couple_covalently(other: Group) → None[source]

Couple this group with another group.

Parameters:: other – other group for coupling

couple_non_covalently(other: Group) → None[source]

Non-covalenthly couple this group with another group.

Parameters:: other – other group for coupling

get_covalently_coupled_groups()[source]

Get covalently coupled groups.

Returns:: list of covalently coupled groups.

get_determinant_for_string(type_, number)[source]

Return a string describing determinant.

Parameters:

type – determinant type
number – determinant index number

Returns:

string

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

get_interaction_atoms(interacting_group: Group) → List[Atom][source]

Get atoms involved in interaction with other group.

Parameters:: interacting_group – other group
Returns:: list of atoms

get_non_covalently_coupled_groups()[source]

Get non-covalently coupled groups.

Returns:: list of covalently coupled groups.

get_summary_string(remove_penalised_group: bool = False) → str[source]

Create summary string for this group.

Parameters:: remove_penalised_group – Boolean to ignore penalized groups
Returns:: string

remove_determinants(labels)[source]

Remove all determinants with specified labels.

Parameters:: labels – list of labels to remove

set_center(atoms)[source]

Set center of group based on atoms.

Parameters:: atoms – list of atoms

set_determinant(new_determinant: Determinant, type_: str) → None[source]

Overwrite current and create non-present determinants.

Parameters:

new_determinant – new determinant to add
type – determinant type

set_interaction_atoms(interaction_atoms_for_acids: List[Atom], interaction_atoms_for_bases: List[Atom])[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

setup()[source]: Set up a group.

setup_atoms()[source]

Set up atoms in group.

This method is overwritten for some types of groups

use_in_calculations() → bool[source]

Indicate whether group should be included in results report.

If –titrate_only option is specified, only residues that are titratable and are in that list are included; otherwise all titratable residues and CYS residues are included.

class propka.group.HISGroup(atom)[source]

Histidine group.

setup_atoms()[source]: Set up atoms in group.

class propka.group.IonGroup(atom)[source]: Ion group.

class propka.group.LYSGroup(atom)[source]: Lysine group.

class propka.group.N1Group(atom)[source]

Unknown group.

TODO - identify this group.

class propka.group.N30Group(atom)[source]

Unknown group.

TODO - identify this group.

setup_atoms()[source]: Set up atoms in this group.

class propka.group.N31Group(atom)[source]

Unknown group.

TODO - identify this group.

setup_atoms()[source]: Set up atoms in this group.

class propka.group.N32Group(atom)[source]

Unknown group.

TODO - identify this group.

setup_atoms()[source]: Set up atoms in this group.

class propka.group.N33Group(atom)[source]

Unknown group.

TODO - identify this group.

setup_atoms()[source]: Set up atoms in this group.

class propka.group.NAMGroup(atom)[source]

Unknown group.

TODO - identify this group.

setup_atoms()[source]: Set up atoms in this group.

class propka.group.NARGroup(atom)[source]

Unknown group.

TODO - identify this group.

setup_atoms()[source]: Set up atoms in group.

class propka.group.NP1Group(atom)[source]

Unknown group.

TODO - identify this group.

setup_atoms()[source]: Set up atoms in group.

class propka.group.NonTitratableLigandGroup(atom)[source]: Non-titratable ligand group.

class propka.group.NtermGroup(atom)[source]: N-terminus group.

class propka.group.O2Group(atom)[source]

Unknown group.

TODO - identify this group.

class propka.group.O3Group(atom)[source]

Unknown group.

TODO - identify this group.

class propka.group.OCOGroup(atom)[source]

Carboxyl group.

setup_atoms()[source]: Set up atoms in group.

class propka.group.OHGroup(atom)[source]

Hydroxide group.

setup_atoms()[source]: Set up atoms in this group.

class propka.group.OPGroup(atom)[source]

Phosphate group.

setup_atoms()[source]: Set up atoms in this group.

class propka.group.ROHGroup(atom)[source]: Alcohol group.

class propka.group.SERGroup(atom)[source]: Serine group.

class propka.group.SHGroup(atom)[source]: Sulfhydryl group.

class propka.group.TRPGroup(atom)[source]

Tryptophan group.

setup_atoms()[source]: Set up atoms in group.

class propka.group.TYRGroup(atom)[source]: Tyrosine group.

class propka.group.TitratableLigandGroup(atom)[source]: Titratable ligand group.

propka.group.is_group(parameters: Parameters, atom: Atom) → Group | None[source]

Identify whether the atom belongs to a group.

Parameters:

parameters – parameters for check
atom – atom to check

Returns:

group for atom or None

propka.group.is_ion_group(parameters, atom: Atom) → Group | None[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

propka.group.is_ligand_group_by_groups(_, atom: Atom) → Group | None[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

propka.group.is_ligand_group_by_marvin_pkas(parameters: Parameters, atom: Atom) → Group | None[source]

Identify whether the atom belongs to a ligand group by calculating ‘Marvin pKas’.

Parameters:

parameters – parameters for check
atom – atom to check

Returns:

group for atom or None

propka.group.is_protein_group(parameters, atom: Atom) → Group | None[source]

Identify whether the atom belongs to a protein group.

Parameters:

parameters – parameters for check
atom – atom to check

Returns:

group for atom or None