######################################################################
# BioSimSpace: Making biomolecular simulation a breeze!
#
# Copyright: 2017-2024
#
# Authors: Lester Hedges <lester.hedges@gmail.com>
#
# BioSimSpace is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# BioSimSpace is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with BioSimSpace. If not, see <http://www.gnu.org/licenses/>.
#####################################################################
"""
A thin wrapper around Sire.Mol.Atom. This is an internal package and should
not be directly exposed to the user.
"""
__author__ = "Lester Hedges"
__email__ = "lester.hedges@gmail.com"
__all__ = ["Atom"]
from sire.legacy import Mol as _SireMol
from ..Types import Coordinate as _Coordinate
from ..Types import Length as _Length
from ._sire_wrapper import SireWrapper as _SireWrapper
[docs]
class Atom(_SireWrapper):
"""A class for storing an atom."""
[docs]
def __init__(self, atom):
"""
Constructor.
Parameters
----------
atom : Sire.Mol.Atom, :class:`Atom <BioSimSpace._SireWrappers.Atom>`
A Sire or BioSimSpace Atom object.
"""
# Check that the atom is valid.
# A Sire Atom object.
if isinstance(atom, _SireMol._Mol.Atom):
sire_object = atom
# Another BioSimSpace Atom object.
elif isinstance(atom, Atom):
sire_object = atom._sire_object
# Invalid type.
else:
raise TypeError(
"'atom' must be of type 'Sire.Mol.Atom' "
"or 'BioSimSpace._SireWrappers.Atom'."
)
# Call the base class constructor.
super().__init__(sire_object)
def __str__(self):
"""Return a human readable string representation of the object."""
return "<BioSimSpace.Atom: name=%r, molecule=%d, index=%d>" % (
self.name(),
self.moleculeNumber(),
self.index(),
)
def __repr__(self):
"""Return a string showing how to instantiate the object."""
return "<BioSimSpace.Atom: name=%r, molecule=%d, index=%d>" % (
self.name(),
self.moleculeNumber(),
self.index(),
)
[docs]
def name(self):
"""
Return the name of the atom.
Returns
-------
name : str
The name of the atom.
"""
return self._sire_object.name().value()
[docs]
def index(self):
"""
Return the index of the atom.
Returns
-------
index : int
The index of the atom.
"""
return self._sire_object.index().value()
[docs]
def moleculeNumber(self):
"""
Return the number of the molecule to which this atom belongs.
Returns
-------
number : int
The number of the molecule to which the atom belongs.
"""
return self._sire_object.molecule().number().value()
[docs]
def coordinates(self, property_map={}):
"""
Return the coordinates of the atom.
Parameters
----------
property_map : dict
A dictionary that maps system "properties" to their user defined
values. This allows the user to refer to properties with their
own naming scheme, e.g. { "charge" : "my-charge" }
Returns
-------
coordinates : class:`Coordinate <BioSimSpace.Types.Coordinate>`
The coordinates of the atom.
"""
prop = property_map.get("coordinates", "coordinates")
# Get the "coordinates" property from the atom.
try:
sire_coord = self._sire_object.property(prop)
coordinates = _Coordinate(
_Length(sire_coord[0], "Angstrom"),
_Length(sire_coord[1], "Angstrom"),
_Length(sire_coord[2], "Angstrom"),
)
except:
return None
# Return the coordinates.
return coordinates
[docs]
def element(self, property_map={}):
"""
Return the element.
Parameters
----------
property_map : dict
A dictionary that maps system "properties" to their user defined
values. This allows the user to refer to properties with their
own naming scheme, e.g. { "charge" : "my-charge" }
Returns
-------
element : str
The element.
"""
prop = property_map.get("element", "element")
# Get the element property from the atom.
try:
element = self._sire_object.property(prop).toString()
except:
element = ""
# Return the element.
return element
[docs]
def toMolecule(self):
"""
Convert a single Atom to a Molecule.
Returns
-------
system : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
"""
return _Molecule(
_SireMol.PartialMolecule(self._sire_object).extract().molecule()
)
# Import at bottom of module to avoid circular dependency.
from ._molecule import Molecule as _Molecule