Source code for BioSimSpace._SireWrappers._search_result
######################################################################
# 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.SelectResult. This is an internal package and should
not be directly exposed to the user.
"""
__author__ = "Lester Hedges"
__email__ = "lester.hedges@gmail.com"
__all__ = ["SearchResult"]
import sire.legacy as _Sire
[docs]
class SearchResult:
"""A thin wrapper around Sire.Mol.SelectResult."""
[docs]
def __init__(self, select_result):
"""
Constructor.
Parameters
----------
select_result : Output of a Sire search
The Sire result object.
"""
# Note that the type of a sire search will now be
# whatever makes most sense for the result, e.g.
# SelectorMol if this is a list of molecules,
# SelectorBond if this is a list of bonds etc.
# Store the Sire select result.
self._sire_object = select_result.__deepcopy__()
# Store the number of results.
self._num_results = len(self._sire_object)
# Initialise the iterator count.
self._iter_count = 0
def __str__(self):
"""Return a human readable string representation of the object."""
return "<BioSimSpace.SearchResult: nResults=%d>" % self.nResults()
def __repr__(self):
"""Return a string showing how to instantiate the object."""
return "<BioSimSpace.SearchResult: nResults=%d>" % self.nResults()
def __len__(self):
"""
Return the number of results.
Returns
-------
num_results : int
The number of search results.
"""
return self._num_results
def __eq__(self, other):
"""Equals to operator."""
# Compare to another object of the same type.
if type(other) is type(self):
return self._sire_object == other._sire_object
else:
return False
def __ne__(self, other):
"""Not equals to operator."""
# Compare to another object of the same type.
if type(other) is type(self):
return self._sire_object != other._sire_object
else:
return False
def __hash__(self):
"""Hash operator."""
return hash(self._sire_object)
def __getitem__(self, key):
"""Get a search result from the container."""
# Slice.
if type(key) is slice:
# Create a list to hold the results.
results = []
# Iterate over the slice.
for x in range(*key.indices(self._num_results)):
results.append(self[x])
# Return the results.
return results
# Index.
else:
try:
key = int(key)
except:
raise TypeError("'key' must be of type 'int'")
if key < -self._num_results or key > self._num_results - 1:
raise IndexError("SearchResult index is out of range.")
if key < 0:
key = key + self._num_results
# Extract the result from the Sire object.
result = self._sire_object[key]
# Atom.
if isinstance(result, _Sire.Mol._Mol.Atom):
return _Atom(result)
# Residue.
elif isinstance(result, _Sire.Mol._Mol.Residue):
return _Residue(result)
# Molecule.
elif isinstance(result, _Sire.Mol._Mol.Molecule):
return _Molecule(result)
# Bond
elif isinstance(result, _Sire.MM._MM.Bond):
return _Bond(result)
# Unsupported.
else:
print(f"WARNING: Type {type(result)} is not supported.")
return None
def __setitem__(self, key, value):
"""Set a molecule in the container."""
raise TypeError("'SearchResult' object does not support assignment.")
def __iter__(self):
"""An iterator for the object."""
# Reset the iterator counter and return the object.
self._iter_count = 0
return self
def __next__(self):
"""An iterator for the object."""
# Stop if we've reached the end of the container.
if self._iter_count == self._num_results:
raise StopIteration
# Extract the next result in the container.
result = self[self._iter_count]
# Update the iterator counter.
self._iter_count += 1
# Return the result.
return result
[docs]
def copy(self):
"""
Create a copy of this object.
Returns
-------
search_result : :class:`SearchResult <BioSimSpace._SireWrappers.SearchResult>`
A copy of the object.
"""
return SearchResult(self)
[docs]
def atoms(self):
"""
Return all of the atoms that contain the results of this
search.
Returns
-------
search_result : :class:`SearchResult <BioSimSpace._SireWrappers.SearchResult>`
A copy of the object viewed via its atoms.
"""
return SearchResult(self._sire_object.atoms())
[docs]
def residues(self):
"""
Return all of the residues that contain the results of this
search.
Returns
-------
search_result : :class:`SearchResult <BioSimSpace._SireWrappers.SearchResult>`
A copy of the object viewed via its residues.
"""
return SearchResult(self._sire_object.residues())
[docs]
def chains(self):
"""
Return all of the chains that contain the results of this
search.
Returns
-------
search_result : :class:`SearchResult <BioSimSpace._SireWrappers.SearchResult>`
A copy of the object viewed via its chains.
"""
return SearchResult(self._sire_object.chains())
[docs]
def segments(self):
"""
Return all of the segments that contain the results of this
search.
Returns
-------
search_result : :class:`SearchResult <BioSimSpace._SireWrappers.SearchResult>`
A copy of the object viewed via its segments.
"""
return SearchResult(self._sire_object.segments())
[docs]
def molecules(self):
"""
Return all of the molecules that contain the results of this
search.
Returns
-------
search_result : :class:`SearchResult <BioSimSpace._SireWrappers.SearchResult>`
A copy of the object viewed via its molecules.
"""
try:
return SearchResult(self._sire_object.molecules())
except Exception:
# this is a single molecule view
from sire.mol import SelectorMol
return SearchResult(SelectorMol(self._sire_object.molecule()))
[docs]
def bonds(self):
"""
Return all of the bonds in this result.
Returns
-------
search_result : :class:`SearchResult <BioSimSpace._SireWrappers.SearchResult>`
A copy of the object viewed via its bonds.
"""
try:
from sire.mm import SelectorMBond
return SearchResult(SelectorMBond(self._sire_object))
except Exception:
from sire.mm import SelectorBond
return SearchResult(SelectorBond(self._sire_object))
[docs]
def nResults(self):
"""
Return the number of results.
Returns
-------
num_results : int
The number of search results.
"""
return self._num_results
[docs]
def getResult(self, index):
"""
Return the result at the given index.
Parameters
----------
index : int
The index of the result.
Returns
-------
molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`
The requested molecule.
result : :class:`Atom <BioSimSpace._SireWrappers.Atom>`, \
:class:`Residue <BioSimSpace._SireWrappers.Residue>`, \
:class:`Molecule <BioSimSpace._SireWrappers.Molecule>`, \
:class:`Bond <BioSimSpace._SireWrappers.Bond>`
"""
return self[index]
def _getSireObject(self):
"""
Return the underlying Sire object.
Returns
-------
object : Sire.Mol.SelectResult
"""
return self._sire_object
# Import at bottom of module to avoid circular dependency.
from ._atom import Atom as _Atom
from ._molecule import Molecule as _Molecule
from ._residue import Residue as _Residue
from ._bond import Bond as _Bond