Module protkit.structure.atom

Implements class Atom to represent an atom in a protein.

#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Authors:  Fred Senekal (FS)
# Contact:  fred@silicogenesis.com
# License:  GPLv3

"""
Implements class `Atom` to represent an atom in a protein.
"""

from __future__ import annotations
from typing import TYPE_CHECKING, Optional, Any
from copy import deepcopy

if TYPE_CHECKING:
    from protkit.structure.residue import Residue
    from protkit.structure.chain import Chain
    from protkit.structure.protein import Protein


class Atom:
    # ------------------------------------------------------------
    # Constructor
    # ------------------------------------------------------------
    def __init__(self,
                 # Core
                 element: str,
                 atom_type: str,
                 x: float,
                 y: float,
                 z: float,

                 is_hetero: bool = False,
                 is_disordered: bool = False,

                 # Optional
                 alt_loc: Optional[str] = None,
                 occupancy: Optional[float] = None,
                 temp_factor: Optional[float] = None,
                 assigned_charge: Optional[str] = None,

                 # Optional PQR attributes
                 calculated_charge: Optional[float] = None,
                 radius: Optional[float] = None,

                 residue: Optional[Residue] = None):
        """
        Constructor for the Atom class.

        Args:
            element (str): The element associated with the atom.
            atom_type (str): The atom type.
            x (float): The x coordinate of the atom.
            y (float): The y coordinate of the atom.
            z (float): The z coordinate of the atom.
            is_hetero (bool, optional): The hetero flag. Defaults to False.
            is_disordered (bool, optional): The disordered flag. Defaults to False.
            alt_loc (Optional[str], optional): The alt_loc identifier. Defaults to None.
            occupancy (Optional[float], optional): The occupancy. Defaults to None.
            temp_factor (Optional[float], optional): The temperature factor. Defaults to None.
            assigned_charge (Optional[str], optional): The assigned charge. Defaults to None.
            calculated_charge (Optional[float], optional): The calculated charge (PQR). Defaults to None.
            radius (Optional[float], optional): The radius (PQR). Defaults to None.
            residue (Optional[Residue], optional): The residue the atom forms part of. Defaults to None.

        Returns:
            None
        """

        # Core properties
        self._x: float = x
        self._y: float = y
        self._z: float = z
        self._element: str = element
        self._atom_type: str = atom_type

        # It could happen that the element is not set. For example, PQR files
        # do not have an element field.
        # In this case, the element is set to the first character of the atom type.
        # This should generally work, although some programs use naming conventions for
        # atom types that are not standard, for example starting a hydrogen with
        # a numerical value rather than H. There may also be complications for
        # two-letter element names. For example "CA" could be Calcium or Alpha Carbon.
        # Further improvements should be made to handle these cases.
        if self._element is None or self._element == "":
            if self._atom_type is not None and self._atom_type != "":
                self._element = self._atom_type[0]

        # Derived properties
        self._is_hetero: bool = is_hetero
        self._is_disordered: bool = is_disordered

        # Optional attributes
        if alt_loc is not None and alt_loc != "":
            self.set_attribute("alt_loc", alt_loc)
            # If alt_loc is set, occupancy is also set
            # There are examples where alt_loc is set, even though occupancy is 1.0.
            # In these cases, the if statement below will not set the occupancy
            # to 1.0, which is why it needs to be set here.
            self.set_attribute("occupancy", occupancy)
        if occupancy is not None and occupancy != 1.0:
            self.set_attribute("occupancy", occupancy)
        if temp_factor is not None:
            self.set_attribute("temp_factor", temp_factor)
        if assigned_charge is not None and assigned_charge != "":
            self.set_attribute("assigned_charge", assigned_charge)
        if calculated_charge is not None:
            self.set_attribute("calculated_charge", calculated_charge)
        if radius is not None:
            self.set_attribute("radius", radius)

        # If alt_loc is specified, the atom is disordered
        # Keep track of all disordered states.
        if self.get_attribute("alt_loc") is not None:
            self._is_disordered = True
            self._disordered_states = [{
                "alt_loc": self.get_attribute("alt_loc"),
                "occupancy": self.get_attribute("occupancy"),
                "temp_factor": self.get_attribute("temp_factor"),
                "x": self._x,
                "y": self._y,
                "z": self._z
            }]

        self._residue: Optional[Residue] = residue

    def copy(self):
        """
        Returns a deep copy of the atom, excluding the residue.

        Returns:
            Atom: A deep copy of the atom, excluding the residue.
        """
        residue = self._residue
        self._residue = None
        atom = deepcopy(self)
        self._residue = residue
        return atom

    # ------------------------------------------------------------
    # Methods for managing the atom's core properties.
    # - id (property)
    # - element (property)
    # - element (setter)
    # - atom_type (property)
    # - atom_type (setter)
    # - x (property)
    # - x (setter)
    # - y (property)
    # - y (setter)
    # - z (property)
    # - z (setter)
    # - is_hetero (property)
    # - is_disordered (property)
    # ------------------------------------------------------------

    @property
    def id(self) -> str:
        """
        Returns the atom's id, which is a combination of the
        residue id and the atom type.

        Returns:
            str: The atom's id.
        """
        if self._residue is None:
            return self._atom_type
        else:
            return self._residue.id + ":" + self._atom_type

    @property
    def element(self) -> str:
        """
        Returns the element associated with the atom.

        Returns:
            str: The element associated with the atom.
        """
        return self._element

    @element.setter
    def element(self, element: str) -> None:
        """
        Sets the element associated with the atom.

        Args:
            element (str): The element associated with the atom.

        Returns:
            None
        """
        self._element = element

    @property
    def atom_type(self) -> str:
        """
        Returns the atom type.

        Returns:
            str: The atom type.
        """
        return self._atom_type

    @atom_type.setter
    def atom_type(self, atom_type: str) -> None:
        """
        Sets the atom type.

        Args:
            atom_type (str): The atom type.

        Returns:
            None
        """
        self._atom_type = atom_type

    @property
    def x(self) -> float:
        """
        Returns the x coordinate of the atom.

        Returns:
            float: The x coordinate of the atom.
        """
        return self._x

    @x.setter
    def x(self, x: float) -> None:
        """
        Sets the x coordinate of the atom.

        Args:
            x (float): The x coordinate of the atom.

        Returns:
            None
        """
        self._x = x

    @property
    def y(self) -> float:
        """
        Returns the y coordinate of the atom.

        Returns:
            float: The y coordinate of the atom.
        """
        return self._y

    @y.setter
    def y(self, y: float) -> None:
        """
        Sets the y coordinate of the atom.

        Args:
            y (float): The y coordinate of the atom.

        Returns:
            None
        """
        self._y = y

    @property
    def z(self) -> float:
        """
        Returns the z coordinate of the atom.

        Returns:
            float: The z coordinate of the atom.
        """
        return self._z

    @z.setter
    def z(self, z: float) -> None:
        """
        Sets the z coordinate of the atom.

        Args:
            z (float): The z coordinate of the atom.

        Returns:
            None
        """
        self._z = z

    @property
    def is_hetero(self) -> bool:
        """
        Returns the hetero flag.

        Returns:
            bool: The hetero flag.
        """
        return self._is_hetero

    @property
    def is_disordered(self) -> bool:
        """
        Returns the disordered flag.

        Returns:
            bool: The disordered flag.

        """
        return self._is_disordered

    # ------------------------------------------------------------
    # Methods for managing the atom's residue, chain or protein
    # - residue (property)
    # - residue (setter)
    # - chain (property)
    # - chain_id (property)
    # - protein (property)
    # - pdb_id (property)
    # ------------------------------------------------------------

    @property
    def residue(self) -> Optional[Residue]:
        """
        Returns the residue the atom forms part of.

        Returns:
            Optional[Residue]: The residue the atom forms part of.
        """
        return self._residue

    @residue.setter
    def residue(self, residue: Residue) -> None:
        """
        Sets the residue the atom forms part of.

        Args:
            residue (Residue): The residue the atom forms part of.

        Returns:
            None
        """
        self._residue = residue

    @property
    def chain(self) -> Optional[Chain]:
        """
        Returns the chain the atom forms part of.

        Returns:
            Optional[Chain]: The chain the atom forms part of.
        """
        if self._residue is not None:
            return self._residue.chain

    @property
    def chain_id(self) -> Optional[str]:
        """
        Returns the chain ID the atom forms part of.

        Returns:
            Optional[str]: The chain ID the atom forms part of.
        """
        if self.chain is not None:
            return self.chain.chain_id

    @property
    def protein(self) -> Optional[Protein]:
        """
        Returns the protein the atom forms part of.

        Returns:
            Optional[Protein]: The protein the atom forms part of.
        """
        if self.chain is not None:
            return self.chain.protein

    @property
    def pdb_id(self) -> Optional[str]:
        """
        Returns the PDB ID the atom forms part of.

        Returns:
            Optional[str]: The PDB ID the atom forms part of.
        """
        if self.protein is not None:
            return self.protein.pdb_id

    # ------------------------------------------------------------
    # Disordered state
    # - merge_disordered_atom
    # - fix_disordered_atom
    # ------------------------------------------------------------

    def merge_disordered_atom(self, atom: Atom) -> None:
        """
        Merges the disordered atom with the current atom.
        Keep track of the additional disordered information
        from the atom that the merge is done with.

        Args:
            atom (Atom): The atom to merge with.

        Returns:
            None
        """
        self._disordered_states.append({
            "alt_loc": atom.get_attribute("alt_loc"),
            "occupancy": atom.get_attribute("occupancy"),
            "temp_factor": atom.get_attribute("temp_factor"),
            "x": atom.x,
            "y": atom.y,
            "z": atom.z
        })
        self._is_disordered = True

    def fix_disordered_atom(self) -> None:
        """
        Fixes the disordered atom by selecting the disordered
        state with the highest occupancy.

        Returns:
            None
        """
        if self._is_disordered:
            # Sort disordered states by occupancy
            self._disordered_states.sort(key=lambda dis_state: dis_state["occupancy"], reverse=True)

            # Select the disordered state with the highest occupancy
            state = self._disordered_states[0]

            # Set the atom's properties to the disordered state with the highest occupancy
            self.set_attribute("alt_loc", state["alt_loc"])
            self.set_attribute("occupancy", state["occupancy"])
            self.set_attribute("temp_factor", state["temp_factor"])
            self._x = state["x"]
            self._y = state["y"]
            self._z = state["z"]

            # Remove the disordered states
            self._disordered_states = None
            self._is_disordered = False

    # ------------------------------------------------------------
    # Methods for managing the atom's attributes.
    # - has_attribute
    # - get_attribute
    # - set_attribute
    # - delete_attribute
    # ------------------------------------------------------------

    def has_attribute(self, key: str) -> bool:
        """
        Returns True if the atom has the specified attribute.

        Args:
            key (str): The name of the attribute.

        Returns:
            bool: True if the atom has the specified attribute.
        """
        return hasattr(self, "_" + key)

    def get_attribute(self, key: str) -> Any:
        """
        current_residueReturns the value of the specified attribute.

        Args:
            key (str): The name of the attribute.

        Returns:
            Any: The value of the specified attribute.

        Raises:
            AttributeError: If the attribute does not exist.
        """
        if hasattr(self, "_" + key):
            return getattr(self, "_" + key)

    def set_attribute(self, key: str, value: Any) -> None:
        """"
        Sets the value of the specified attribute.

        Args:
            key (str): The name of the attribute.
            value (Any): The value of the attribute.

        Returns:
            None
        """
        if value is not None:
            setattr(self, "_" + key, value)

    def delete_attribute(self, key: str) -> None:
        """
        Deletes the specified attribute.

        Args:
            key (str): The name of the attribute.

        Returns:
            None
        """
        if hasattr(self, "_" + key):
            delattr(self, "_" + key)

Classes

class Atom (element: str, atom_type: str, x: float, y: float, z: float, is_hetero: bool = False, is_disordered: bool = False, alt_loc: Optional[str] = None, occupancy: Optional[float] = None, temp_factor: Optional[float] = None, assigned_charge: Optional[str] = None, calculated_charge: Optional[float] = None, radius: Optional[float] = None, residue: Optional[Residue] = None)

Constructor for the Atom class.

Args

element : str

The element associated with the atom.

atom_type : str

The atom type.

x : float

The x coordinate of the atom.

y : float

The y coordinate of the atom.

z : float

The z coordinate of the atom.

is_hetero : bool, optional

The hetero flag. Defaults to False.

is_disordered : bool, optional

The disordered flag. Defaults to False.

alt_loc : Optional[str], optional

The alt_loc identifier. Defaults to None.

occupancy : Optional[float], optional

The occupancy. Defaults to None.

temp_factor : Optional[float], optional

The temperature factor. Defaults to None.

assigned_charge : Optional[str], optional

The assigned charge. Defaults to None.

calculated_charge : Optional[float], optional

The calculated charge (PQR). Defaults to None.

radius : Optional[float], optional

The radius (PQR). Defaults to None.

residue : Optional[Residue], optional

The residue the atom forms part of. Defaults to None.

Returns

None

Expand source code

class Atom:
    # ------------------------------------------------------------
    # Constructor
    # ------------------------------------------------------------
    def __init__(self,
                 # Core
                 element: str,
                 atom_type: str,
                 x: float,
                 y: float,
                 z: float,

                 is_hetero: bool = False,
                 is_disordered: bool = False,

                 # Optional
                 alt_loc: Optional[str] = None,
                 occupancy: Optional[float] = None,
                 temp_factor: Optional[float] = None,
                 assigned_charge: Optional[str] = None,

                 # Optional PQR attributes
                 calculated_charge: Optional[float] = None,
                 radius: Optional[float] = None,

                 residue: Optional[Residue] = None):
        """
        Constructor for the Atom class.

        Args:
            element (str): The element associated with the atom.
            atom_type (str): The atom type.
            x (float): The x coordinate of the atom.
            y (float): The y coordinate of the atom.
            z (float): The z coordinate of the atom.
            is_hetero (bool, optional): The hetero flag. Defaults to False.
            is_disordered (bool, optional): The disordered flag. Defaults to False.
            alt_loc (Optional[str], optional): The alt_loc identifier. Defaults to None.
            occupancy (Optional[float], optional): The occupancy. Defaults to None.
            temp_factor (Optional[float], optional): The temperature factor. Defaults to None.
            assigned_charge (Optional[str], optional): The assigned charge. Defaults to None.
            calculated_charge (Optional[float], optional): The calculated charge (PQR). Defaults to None.
            radius (Optional[float], optional): The radius (PQR). Defaults to None.
            residue (Optional[Residue], optional): The residue the atom forms part of. Defaults to None.

        Returns:
            None
        """

        # Core properties
        self._x: float = x
        self._y: float = y
        self._z: float = z
        self._element: str = element
        self._atom_type: str = atom_type

        # It could happen that the element is not set. For example, PQR files
        # do not have an element field.
        # In this case, the element is set to the first character of the atom type.
        # This should generally work, although some programs use naming conventions for
        # atom types that are not standard, for example starting a hydrogen with
        # a numerical value rather than H. There may also be complications for
        # two-letter element names. For example "CA" could be Calcium or Alpha Carbon.
        # Further improvements should be made to handle these cases.
        if self._element is None or self._element == "":
            if self._atom_type is not None and self._atom_type != "":
                self._element = self._atom_type[0]

        # Derived properties
        self._is_hetero: bool = is_hetero
        self._is_disordered: bool = is_disordered

        # Optional attributes
        if alt_loc is not None and alt_loc != "":
            self.set_attribute("alt_loc", alt_loc)
            # If alt_loc is set, occupancy is also set
            # There are examples where alt_loc is set, even though occupancy is 1.0.
            # In these cases, the if statement below will not set the occupancy
            # to 1.0, which is why it needs to be set here.
            self.set_attribute("occupancy", occupancy)
        if occupancy is not None and occupancy != 1.0:
            self.set_attribute("occupancy", occupancy)
        if temp_factor is not None:
            self.set_attribute("temp_factor", temp_factor)
        if assigned_charge is not None and assigned_charge != "":
            self.set_attribute("assigned_charge", assigned_charge)
        if calculated_charge is not None:
            self.set_attribute("calculated_charge", calculated_charge)
        if radius is not None:
            self.set_attribute("radius", radius)

        # If alt_loc is specified, the atom is disordered
        # Keep track of all disordered states.
        if self.get_attribute("alt_loc") is not None:
            self._is_disordered = True
            self._disordered_states = [{
                "alt_loc": self.get_attribute("alt_loc"),
                "occupancy": self.get_attribute("occupancy"),
                "temp_factor": self.get_attribute("temp_factor"),
                "x": self._x,
                "y": self._y,
                "z": self._z
            }]

        self._residue: Optional[Residue] = residue

    def copy(self):
        """
        Returns a deep copy of the atom, excluding the residue.

        Returns:
            Atom: A deep copy of the atom, excluding the residue.
        """
        residue = self._residue
        self._residue = None
        atom = deepcopy(self)
        self._residue = residue
        return atom

    # ------------------------------------------------------------
    # Methods for managing the atom's core properties.
    # - id (property)
    # - element (property)
    # - element (setter)
    # - atom_type (property)
    # - atom_type (setter)
    # - x (property)
    # - x (setter)
    # - y (property)
    # - y (setter)
    # - z (property)
    # - z (setter)
    # - is_hetero (property)
    # - is_disordered (property)
    # ------------------------------------------------------------

    @property
    def id(self) -> str:
        """
        Returns the atom's id, which is a combination of the
        residue id and the atom type.

        Returns:
            str: The atom's id.
        """
        if self._residue is None:
            return self._atom_type
        else:
            return self._residue.id + ":" + self._atom_type

    @property
    def element(self) -> str:
        """
        Returns the element associated with the atom.

        Returns:
            str: The element associated with the atom.
        """
        return self._element

    @element.setter
    def element(self, element: str) -> None:
        """
        Sets the element associated with the atom.

        Args:
            element (str): The element associated with the atom.

        Returns:
            None
        """
        self._element = element

    @property
    def atom_type(self) -> str:
        """
        Returns the atom type.

        Returns:
            str: The atom type.
        """
        return self._atom_type

    @atom_type.setter
    def atom_type(self, atom_type: str) -> None:
        """
        Sets the atom type.

        Args:
            atom_type (str): The atom type.

        Returns:
            None
        """
        self._atom_type = atom_type

    @property
    def x(self) -> float:
        """
        Returns the x coordinate of the atom.

        Returns:
            float: The x coordinate of the atom.
        """
        return self._x

    @x.setter
    def x(self, x: float) -> None:
        """
        Sets the x coordinate of the atom.

        Args:
            x (float): The x coordinate of the atom.

        Returns:
            None
        """
        self._x = x

    @property
    def y(self) -> float:
        """
        Returns the y coordinate of the atom.

        Returns:
            float: The y coordinate of the atom.
        """
        return self._y

    @y.setter
    def y(self, y: float) -> None:
        """
        Sets the y coordinate of the atom.

        Args:
            y (float): The y coordinate of the atom.

        Returns:
            None
        """
        self._y = y

    @property
    def z(self) -> float:
        """
        Returns the z coordinate of the atom.

        Returns:
            float: The z coordinate of the atom.
        """
        return self._z

    @z.setter
    def z(self, z: float) -> None:
        """
        Sets the z coordinate of the atom.

        Args:
            z (float): The z coordinate of the atom.

        Returns:
            None
        """
        self._z = z

    @property
    def is_hetero(self) -> bool:
        """
        Returns the hetero flag.

        Returns:
            bool: The hetero flag.
        """
        return self._is_hetero

    @property
    def is_disordered(self) -> bool:
        """
        Returns the disordered flag.

        Returns:
            bool: The disordered flag.

        """
        return self._is_disordered

    # ------------------------------------------------------------
    # Methods for managing the atom's residue, chain or protein
    # - residue (property)
    # - residue (setter)
    # - chain (property)
    # - chain_id (property)
    # - protein (property)
    # - pdb_id (property)
    # ------------------------------------------------------------

    @property
    def residue(self) -> Optional[Residue]:
        """
        Returns the residue the atom forms part of.

        Returns:
            Optional[Residue]: The residue the atom forms part of.
        """
        return self._residue

    @residue.setter
    def residue(self, residue: Residue) -> None:
        """
        Sets the residue the atom forms part of.

        Args:
            residue (Residue): The residue the atom forms part of.

        Returns:
            None
        """
        self._residue = residue

    @property
    def chain(self) -> Optional[Chain]:
        """
        Returns the chain the atom forms part of.

        Returns:
            Optional[Chain]: The chain the atom forms part of.
        """
        if self._residue is not None:
            return self._residue.chain

    @property
    def chain_id(self) -> Optional[str]:
        """
        Returns the chain ID the atom forms part of.

        Returns:
            Optional[str]: The chain ID the atom forms part of.
        """
        if self.chain is not None:
            return self.chain.chain_id

    @property
    def protein(self) -> Optional[Protein]:
        """
        Returns the protein the atom forms part of.

        Returns:
            Optional[Protein]: The protein the atom forms part of.
        """
        if self.chain is not None:
            return self.chain.protein

    @property
    def pdb_id(self) -> Optional[str]:
        """
        Returns the PDB ID the atom forms part of.

        Returns:
            Optional[str]: The PDB ID the atom forms part of.
        """
        if self.protein is not None:
            return self.protein.pdb_id

    # ------------------------------------------------------------
    # Disordered state
    # - merge_disordered_atom
    # - fix_disordered_atom
    # ------------------------------------------------------------

    def merge_disordered_atom(self, atom: Atom) -> None:
        """
        Merges the disordered atom with the current atom.
        Keep track of the additional disordered information
        from the atom that the merge is done with.

        Args:
            atom (Atom): The atom to merge with.

        Returns:
            None
        """
        self._disordered_states.append({
            "alt_loc": atom.get_attribute("alt_loc"),
            "occupancy": atom.get_attribute("occupancy"),
            "temp_factor": atom.get_attribute("temp_factor"),
            "x": atom.x,
            "y": atom.y,
            "z": atom.z
        })
        self._is_disordered = True

    def fix_disordered_atom(self) -> None:
        """
        Fixes the disordered atom by selecting the disordered
        state with the highest occupancy.

        Returns:
            None
        """
        if self._is_disordered:
            # Sort disordered states by occupancy
            self._disordered_states.sort(key=lambda dis_state: dis_state["occupancy"], reverse=True)

            # Select the disordered state with the highest occupancy
            state = self._disordered_states[0]

            # Set the atom's properties to the disordered state with the highest occupancy
            self.set_attribute("alt_loc", state["alt_loc"])
            self.set_attribute("occupancy", state["occupancy"])
            self.set_attribute("temp_factor", state["temp_factor"])
            self._x = state["x"]
            self._y = state["y"]
            self._z = state["z"]

            # Remove the disordered states
            self._disordered_states = None
            self._is_disordered = False

    # ------------------------------------------------------------
    # Methods for managing the atom's attributes.
    # - has_attribute
    # - get_attribute
    # - set_attribute
    # - delete_attribute
    # ------------------------------------------------------------

    def has_attribute(self, key: str) -> bool:
        """
        Returns True if the atom has the specified attribute.

        Args:
            key (str): The name of the attribute.

        Returns:
            bool: True if the atom has the specified attribute.
        """
        return hasattr(self, "_" + key)

    def get_attribute(self, key: str) -> Any:
        """
        current_residueReturns the value of the specified attribute.

        Args:
            key (str): The name of the attribute.

        Returns:
            Any: The value of the specified attribute.

        Raises:
            AttributeError: If the attribute does not exist.
        """
        if hasattr(self, "_" + key):
            return getattr(self, "_" + key)

    def set_attribute(self, key: str, value: Any) -> None:
        """"
        Sets the value of the specified attribute.

        Args:
            key (str): The name of the attribute.
            value (Any): The value of the attribute.

        Returns:
            None
        """
        if value is not None:
            setattr(self, "_" + key, value)

    def delete_attribute(self, key: str) -> None:
        """
        Deletes the specified attribute.

        Args:
            key (str): The name of the attribute.

        Returns:
            None
        """
        if hasattr(self, "_" + key):
            delattr(self, "_" + key)

Instance variables

var atom_type : str

Returns the atom type.

Returns

str

The atom type.

Expand source code

@property
def atom_type(self) -> str:
    """
    Returns the atom type.

    Returns:
        str: The atom type.
    """
    return self._atom_type

var chain : Optional[Chain]

Returns the chain the atom forms part of.

Returns

Optional[Chain]

The chain the atom forms part of.

Expand source code

@property
def chain(self) -> Optional[Chain]:
    """
    Returns the chain the atom forms part of.

    Returns:
        Optional[Chain]: The chain the atom forms part of.
    """
    if self._residue is not None:
        return self._residue.chain

var chain_id : Optional[str]

Returns the chain ID the atom forms part of.

Returns

Optional[str]

The chain ID the atom forms part of.

Expand source code

@property
def chain_id(self) -> Optional[str]:
    """
    Returns the chain ID the atom forms part of.

    Returns:
        Optional[str]: The chain ID the atom forms part of.
    """
    if self.chain is not None:
        return self.chain.chain_id

var element : str

Returns the element associated with the atom.

Returns

str

The element associated with the atom.

Expand source code

@property
def element(self) -> str:
    """
    Returns the element associated with the atom.

    Returns:
        str: The element associated with the atom.
    """
    return self._element

var id : str

Returns the atom's id, which is a combination of the residue id and the atom type.

Returns

str

The atom's id.

Expand source code

@property
def id(self) -> str:
    """
    Returns the atom's id, which is a combination of the
    residue id and the atom type.

    Returns:
        str: The atom's id.
    """
    if self._residue is None:
        return self._atom_type
    else:
        return self._residue.id + ":" + self._atom_type

var is_disordered : bool

Returns the disordered flag.

Returns

bool

The disordered flag.

Expand source code

@property
def is_disordered(self) -> bool:
    """
    Returns the disordered flag.

    Returns:
        bool: The disordered flag.

    """
    return self._is_disordered

var is_hetero : bool

Returns the hetero flag.

Returns

bool

The hetero flag.

Expand source code

@property
def is_hetero(self) -> bool:
    """
    Returns the hetero flag.

    Returns:
        bool: The hetero flag.
    """
    return self._is_hetero

var pdb_id : Optional[str]

Returns the PDB ID the atom forms part of.

Returns

Optional[str]

The PDB ID the atom forms part of.

Expand source code

@property
def pdb_id(self) -> Optional[str]:
    """
    Returns the PDB ID the atom forms part of.

    Returns:
        Optional[str]: The PDB ID the atom forms part of.
    """
    if self.protein is not None:
        return self.protein.pdb_id

var protein : Optional[Protein]

Returns the protein the atom forms part of.

Returns

Optional[Protein]

The protein the atom forms part of.

Expand source code

@property
def protein(self) -> Optional[Protein]:
    """
    Returns the protein the atom forms part of.

    Returns:
        Optional[Protein]: The protein the atom forms part of.
    """
    if self.chain is not None:
        return self.chain.protein

var residue : Optional[Residue]

Returns the residue the atom forms part of.

Returns

Optional[Residue]

The residue the atom forms part of.

Expand source code

@property
def residue(self) -> Optional[Residue]:
    """
    Returns the residue the atom forms part of.

    Returns:
        Optional[Residue]: The residue the atom forms part of.
    """
    return self._residue

var x : float

Returns the x coordinate of the atom.

Returns

float

The x coordinate of the atom.

Expand source code

@property
def x(self) -> float:
    """
    Returns the x coordinate of the atom.

    Returns:
        float: The x coordinate of the atom.
    """
    return self._x

var y : float

Returns the y coordinate of the atom.

Returns

float

The y coordinate of the atom.

Expand source code

@property
def y(self) -> float:
    """
    Returns the y coordinate of the atom.

    Returns:
        float: The y coordinate of the atom.
    """
    return self._y

var z : float

Returns the z coordinate of the atom.

Returns

float

The z coordinate of the atom.

Expand source code

@property
def z(self) -> float:
    """
    Returns the z coordinate of the atom.

    Returns:
        float: The z coordinate of the atom.
    """
    return self._z

Methods

def copy(self)

Returns a deep copy of the atom, excluding the residue.

Returns

Atom

A deep copy of the atom, excluding the residue.

Expand source code

def copy(self):
    """
    Returns a deep copy of the atom, excluding the residue.

    Returns:
        Atom: A deep copy of the atom, excluding the residue.
    """
    residue = self._residue
    self._residue = None
    atom = deepcopy(self)
    self._residue = residue
    return atom

def delete_attribute(self, key: str) ‑> None

Deletes the specified attribute.

Args

key : str

The name of the attribute.

Returns

None

Expand source code

def delete_attribute(self, key: str) -> None:
    """
    Deletes the specified attribute.

    Args:
        key (str): The name of the attribute.

    Returns:
        None
    """
    if hasattr(self, "_" + key):
        delattr(self, "_" + key)

def fix_disordered_atom(self) ‑> None

Fixes the disordered atom by selecting the disordered state with the highest occupancy.

Returns

None

Expand source code

def fix_disordered_atom(self) -> None:
    """
    Fixes the disordered atom by selecting the disordered
    state with the highest occupancy.

    Returns:
        None
    """
    if self._is_disordered:
        # Sort disordered states by occupancy
        self._disordered_states.sort(key=lambda dis_state: dis_state["occupancy"], reverse=True)

        # Select the disordered state with the highest occupancy
        state = self._disordered_states[0]

        # Set the atom's properties to the disordered state with the highest occupancy
        self.set_attribute("alt_loc", state["alt_loc"])
        self.set_attribute("occupancy", state["occupancy"])
        self.set_attribute("temp_factor", state["temp_factor"])
        self._x = state["x"]
        self._y = state["y"]
        self._z = state["z"]

        # Remove the disordered states
        self._disordered_states = None
        self._is_disordered = False

def get_attribute(self, key: str) ‑> Any

current_residueReturns the value of the specified attribute.

Args

key : str

The name of the attribute.

Returns

Any

The value of the specified attribute.

Raises

AttributeError

If the attribute does not exist.

Expand source code

def get_attribute(self, key: str) -> Any:
    """
    current_residueReturns the value of the specified attribute.

    Args:
        key (str): The name of the attribute.

    Returns:
        Any: The value of the specified attribute.

    Raises:
        AttributeError: If the attribute does not exist.
    """
    if hasattr(self, "_" + key):
        return getattr(self, "_" + key)

def has_attribute(self, key: str) ‑> bool

Returns True if the atom has the specified attribute.

Args

key : str

The name of the attribute.

Returns

bool

True if the atom has the specified attribute.

Expand source code

def has_attribute(self, key: str) -> bool:
    """
    Returns True if the atom has the specified attribute.

    Args:
        key (str): The name of the attribute.

    Returns:
        bool: True if the atom has the specified attribute.
    """
    return hasattr(self, "_" + key)

def merge_disordered_atom(self, atom: Atom) ‑> None

Merges the disordered atom with the current atom. Keep track of the additional disordered information from the atom that the merge is done with.

Args

atom : Atom

The atom to merge with.

Returns

None

Expand source code

def merge_disordered_atom(self, atom: Atom) -> None:
    """
    Merges the disordered atom with the current atom.
    Keep track of the additional disordered information
    from the atom that the merge is done with.

    Args:
        atom (Atom): The atom to merge with.

    Returns:
        None
    """
    self._disordered_states.append({
        "alt_loc": atom.get_attribute("alt_loc"),
        "occupancy": atom.get_attribute("occupancy"),
        "temp_factor": atom.get_attribute("temp_factor"),
        "x": atom.x,
        "y": atom.y,
        "z": atom.z
    })
    self._is_disordered = True

def set_attribute(self, key: str, value: Any) ‑> None

" Sets the value of the specified attribute.

Args

key : str

The name of the attribute.

value : Any

The value of the attribute.

Returns

None

Expand source code

def set_attribute(self, key: str, value: Any) -> None:
    """"
    Sets the value of the specified attribute.

    Args:
        key (str): The name of the attribute.
        value (Any): The value of the attribute.

    Returns:
        None
    """
    if value is not None:
        setattr(self, "_" + key, value)