topology

A module containing the Topology class and related functions.

Summary

Classes:

Topology

A class for representing a topology.

Reference

class Topology(

atoms: Atoms | None = None,

residue_ids: Np1DIntArray | None = None,

reference_residues: Residues | None = None,

check_residues: bool = True,

bonded_topology: BondedTopology | None = None,

)

Bases: object

A class for representing a topology.

A topology is a collection of atoms, residues and residue ids. It is used to represent the topology of a system.

Examples

>>> import numpy as np
>>> import warnings
>>> from PQAnalysis.topology import Topology
>>> from PQAnalysis.core import Atom, Residue
>>> atoms = [Atom("H", 1), Atom("O", 8), Atom("H", 1), Atom("H", 1)]
>>> residue_ids = np.array([1, 1, 2, 2])
>>> residue1 = Residue("HO", 1, 0, ["H", "O"], np.array([1, 2]), np.array([0, 0]))
>>> residue2 = Residue("H2", 2, 0, ["H", "H"], np.array([1, 2]), np.array([0, 0]))
>>> residues = [residue1, residue2]
>>> with warnings.catch_warnings():
...     warnings.simplefilter("ignore")
...     topology = Topology(atoms=atoms, residue_ids=residue_ids, reference_residues=residues)

All of the parameters are optional, if they are not given, they are initialized with empty values. It checks if the residue ids are compatible and contiguous regarding the given residues if the list is not empty.

It is also possible to initialize a Topology object with residues that are not referenced within the residue_ids. This means that it is possible to have a Topology object with residues that are not used in the system.

Parameters:

• atoms (Atoms | None, optional) – a list of atoms, by default None (empty list)

• residue_ids (Np1DIntArray | None, optional) – a list of residue ids, by default None (empty list)

• reference_residues (Residues | None, optional) – a list of residues, by default None (empty list)

• check_residues (bool, optional) – If the residues should be checked, by default True

• bonded_topology (BondedTopology | None, optional) – Contains the bonded topology information, by default None

Raises:

TopologyError – If the number of atoms does not match the number of residue ids.

Warns:

UserWarning – If the bonded topology is not None. There is no check yet if the bonded topology is compatible with the topology. Please make sure that the bonded topology is compatible with the topology!

__eq__(other: Any) → bool

Checks whether the Topology is equal to another Topology.

Parameters:

other (Topology) – The other Topology to compare to.

Returns:

Whether the Topology is equal to the other Topology.

Return type:

bool

__getitem__(

indices: Np1DIntArray | int,

) → Topology

Returns a new Topology with the given indices.

Parameters:

indices (Np1DIntArray | int) – The indices of the atoms to return.

Returns:

The new Topology with the given indices.

Return type:

Topology

__repr__() → str

Returns a string representation of the Topology.

Returns:

The string representation of the Topology.

Return type:

str

__str__() → str

Returns a string representation of the Topology.

Returns:

The string representation of the Topology.

Return type:

str

get_atom_indices_from_residue_names(

residue_name: str,

) → Np1DIntArray

Returns the atom indices for the given residue name.

Parameters:

residue_name (str) – The name of the residue to get the atom indices for.

Returns:

The atom indices for the given residue name.

Return type:

Np1DIntArray

get_atom_indices_from_residue_numbers(

residue_numbers: Np1DIntArray,

) → Np1DIntArray

Returns the atom indices for the given residue numbers.

Parameters:

residue_numbers (Np1DIntArray) – The residue numbers to get the atom indices for.

Returns:

The atom indices for the given residue numbers.

Return type:

Np1DIntArray

setup_residues(

residue_ids: Np1DIntArray,

) → None

A method to set up the residues of the topology.

Parameters:

residue_ids (Np1DIntArray) – The residue ids of the topology.

Raises:

• ResidueError – If the residue ids are not contiguous.

• ResidueError – If the reference residues are not empty and residue_ids with 0 don’t have any element information. This problem can be avoided by setting ‘check_residues’ to False.

property atoms: Atoms

The atoms of the topology.

Type:

Atoms

property atomtype_names: list[str]

The atomtype names of the topology.

Type:

List[str]

property check_residues: bool

Whether the residues should be checked.

Type:

bool

logger = <CustomLogger PQAnalysis.Topology (INFO)>

property n_atoms: int

The number of atoms in the topology.

Type:

int

property n_atoms_per_residue: Np1DIntArray

The number of atoms per residue.

Type:

Np1DIntArray

property n_mm_residues: int

The number of MM residues in the topology.

Type:

int

property n_qm_residues: int

The number of QM residues in the topology.

Type:

int

property n_residues: int

The number of residues in the topology.

Type:

int

property n_unique_residues: int

The number of unique residues in the topology.

Type:

int

property reference_residue_ids: Np1DIntArray

The residue ids of the reference residues.

Type:

Np1DIntArray

property reference_residues: Residues

The reference residues of the topology.

Type:

Residues

property residue_atom_indices: list[Np1DIntArray]

The residue atom indices of the topology.

Type:

List[Np1DIntArray]

property residue_ids: Np1DIntArray

The residue ids of the topology.

Type:

Np1DIntArray

property residue_ids_per_residue: Np1DIntArray

The residue ids per residue.

Type:

List[Np1DIntArray]

property residue_numbers: Np1DIntArray

The residue numbers of the topology.

Type:

Np1DIntArray

property residues: Residues

The residues of the topology.

Type:

Residues