__all__ = [
"get_alignment",
"is_water",
"selection_to_atoms",
"Atom",
"AtomIdx",
"AtomMapping",
"AtomMatch",
"AtomMatchM",
"AtomName",
"AtomNum",
"BondOrder",
"Chain",
"ChainIdx",
"ChainName",
"Cursor",
"Cursors",
"CursorsM",
"Dynamics",
"Element",
"Minimisation",
"ResIdx",
"ResName",
"ResNum",
"Residue",
"MolIdx",
"Molecule",
"MolName",
"MolNum",
"SegIdx",
"Segment",
"SegName",
"Selector_Atom_",
"Selector_Chain_",
"Selector_Residue_",
"Selector_Segment_",
"SelectorM_Atom_",
"SelectorM_Chain_",
"SelectorM_Residue_",
"SelectorM_Segment_",
"SelectorMol",
"Stereochemistry",
"TrajectoryIterator",
]
from ..legacy import Mol as _Mol
from .. import use_new_api as _use_new_api
# Imported as we need to ensure that Base is pythonized before
# loading the rest of this module
from ..legacy import Base as _Base # noqa: F401
from ..legacy.Mol import (
AtomName,
AtomNum,
AtomIdx,
AtomID,
ResName,
ResNum,
ResIdx,
ResID,
ChainName,
ChainIdx,
ChainID,
SegName,
SegIdx,
SegID,
MolName,
MolNum,
MolIdx,
BondID,
AngleID,
DihedralID,
ImproperID,
Atom,
Selector_Atom_,
SelectorM_Atom_,
CutGroup,
Selector_CutGroup_,
SelectorM_CutGroup_,
Residue,
Selector_Residue_,
SelectorM_Residue_,
Chain,
Selector_Chain_,
SelectorM_Chain_,
Segment,
Selector_Segment_,
SelectorM_Segment_,
Molecule,
SelectorMol,
MoleculeView,
Select,
BondOrder,
Stereochemistry,
AtomCoords,
AtomMapping,
AtomMatch,
AtomMatchM,
)
from ._cursor import Cursor, Cursors, CursorsM
from ._minimisation import Minimisation
from ._dynamics import Dynamics
from ._trajectory import TrajectoryIterator
from ._element import Element
from ._view import view as _viewfunc
from ._smiles import (
_to_smiles,
_to_smarts,
_view2d,
_selector_to_smiles,
_selector_to_smarts,
_selector_view2d,
)
# Imported to make sure that Vector has units attached
from ..maths import Vector as _Vector # noqa: F401
_use_new_api()
try:
get_alignment = _Mol.getAlignment
except AttributeError:
get_alignment = _Mol.get_alignment
[docs]
def selection_to_atoms(mols, atoms):
"""
Convert the passed selection to a list of atoms.
Parameters
----------
mols : A molecule view or collection
The molecule container from which to select the atoms.
atoms : str, int, list, molecule view/collection etc.
Any valid search string, atom index, list of atom indicies,
or molecule view/container that can be used to select
atoms from ``mols``
Returns
-------
atoms : A SelectorM_Atoms_ or Selector_Atom_ containing the list
of atoms.
Examples
--------
>>> import sire as sr
>>> mols = sr.load(sr.expand(sr.tutorial_url, "ala.top", "ala.crd"))
>>> sr.mol.selection_to_atoms(mols, "atomname CA")
Selector<SireMol::Atom>( size=1
0: Atom( CA:9 [ 16.54, 5.03, 15.81] )
)
>>> sr.mol.selection_to_atoms(mols, "resname ALA")
Selector<SireMol::Atom>( size=10
0: Atom( N:7 [ 17.22, 4.31, 14.71] )
1: Atom( H:8 [ 16.68, 3.62, 14.22] )
2: Atom( CA:9 [ 16.54, 5.03, 15.81] )
3: Atom( HA:10 [ 17.29, 5.15, 16.59] )
4: Atom( CB:11 [ 16.05, 6.39, 15.26] )
5: Atom( HB1:12 [ 15.63, 6.98, 16.07] )
6: Atom( HB2:13 [ 16.90, 6.89, 14.80] )
7: Atom( HB3:14 [ 15.24, 6.18, 14.55] )
8: Atom( C:15 [ 15.37, 4.19, 16.43] )
9: Atom( O:16 [ 14.94, 3.17, 15.88] )
)
>>> sr.mol.selection_to_atoms(mols, [0, 1, 2, 3])
SireMol::SelectorM<SireMol::Atom>( size=4
0: MolNum(641) Atom( HH31:1 [ 18.45, 3.49, 12.44] )
1: MolNum(641) Atom( CH3:2 [ 18.98, 3.45, 13.39] )
2: MolNum(641) Atom( HH32:3 [ 20.05, 3.63, 13.29] )
3: MolNum(641) Atom( HH33:4 [ 18.80, 2.43, 13.73] )
)
>>> sr.mol.selection_to_atoms(mols, mols[0])
Selector<SireMol::Atom>( size=22
0: Atom( HH31:1 [ 18.45, 3.49, 12.44] )
1: Atom( CH3:2 [ 18.98, 3.45, 13.39] )
2: Atom( HH32:3 [ 20.05, 3.63, 13.29] )
3: Atom( HH33:4 [ 18.80, 2.43, 13.73] )
4: Atom( C:5 [ 18.48, 4.55, 14.35] )
...
17: Atom( H:18 [ 15.34, 5.45, 17.96] )
18: Atom( CH3:19 [ 13.83, 3.94, 18.35] )
19: Atom( HH31:20 [ 14.35, 3.41, 19.15] )
20: Atom( HH32:21 [ 13.19, 4.59, 18.94] )
21: Atom( HH33:22 [ 13.21, 3.33, 17.69] )
)
"""
if hasattr(atoms, "atoms"):
return atoms.atoms()
from ..legacy.Base import NumberProperty, IntegerArrayProperty
if type(atoms) is int or type(atoms) is list:
return mols.atoms()[atoms]
elif type(atoms) is NumberProperty or type(atoms) is IntegerArrayProperty:
atoms = [x.as_integer() for x in atoms.as_array()]
return mols.atoms()[atoms]
else:
return mols[atoms].atoms()
[docs]
def is_water(mol, map=None):
"""
Return whether or not the passed molecule (or collection of molecules)
are water. This returns a single True or False if a single molecule
is passed, or a list of True/False values if a molecule collection
is passed.
"""
from ..base import create_map
map = create_map(map)
try:
return _Mol.is_water(mol, map)
except Exception:
pass
if hasattr(type(mol), "molecules"):
return _Mol.is_water(mol.molecules(), map)
raise TypeError(f"Cannot convert {mol} to a molecule view or molecule collection.")
# Here I will define some functions that make accessing
# things from moleculeviews more convenient
def __is_molecule_class(obj):
mro = type(obj).mro()
return Molecule in mro or SelectorMol in mro
def __is_bond_class(obj):
mro = type(obj).mro()
from sire.mm import Bond, SelectorBond
return Bond in mro or SelectorBond in mro
def __is_angle_class(obj):
mro = type(obj).mro()
from sire.mm import Angle, SelectorAngle
return Angle in mro or SelectorAngle in mro
def __is_dihedral_class(obj):
mro = type(obj).mro()
from sire.mm import Dihedral, SelectorDihedral
return Dihedral in mro or SelectorDihedral in mro
def __is_improper_class(obj):
mro = type(obj).mro()
from sire.mm import Improper, SelectorImproper
return Improper in mro or SelectorImproper in mro
def __is_atom_class(obj):
mro = type(obj).mro()
return Atom in mro or Selector_Atom_ in mro or SelectorM_Atom_ in mro
def __is_residue_class(obj):
mro = type(obj).mro()
return Residue in mro or Selector_Residue_ in mro or SelectorM_Residue_ in mro
def __is_chain_class(obj):
mro = type(obj).mro()
return Chain in mro or Selector_Chain_ in mro or SelectorM_Chain_ in mro
def __is_segment_class(obj):
mro = type(obj).mro()
return Segment in mro or Selector_Segment_ in mro or SelectorM_Segment_ in mro
def __is_cutgroup_class(obj):
mro = type(obj).mro()
return CutGroup in mro or Selector_CutGroup_ in mro or SelectorM_CutGroup_ in mro
def __is_selector_class(obj):
try:
t = obj.what()
return t.find("SireMol::Selector") != -1 or t.find("SireMM::Selector") != -1
except Exception:
return False
def __is_internal_class(obj):
from ..mm import Bond, Angle, Dihedral, Improper
return type(obj) in [Bond, Angle, Dihedral, Improper]
def __is_list_class(obj):
if type(obj) is list:
return True
else:
try:
return obj.what().find("::Selector") != -1
except Exception:
return False
def __fix_obj(obj):
"""This is needed because MolViewPtr objects that hold Selector_T_ types
do not convert properly.
"""
w = obj.what()
if w == Molecule.typename():
return obj
elif w == Selector_Atom_.typename():
return obj.atoms()
elif w == Selector_Residue_.typename():
return obj.residues()
elif w == Selector_Chain_.typename():
return obj.chains()
elif w == Selector_Segment_.typename():
return obj.segments()
elif w == Selector_CutGroup_.typename():
return obj.cutgroups()
else:
return obj
def __from_select_result(obj):
"""Convert the passed SelectResult from a search into the
most appropriate MoleculeView-derived class
"""
if hasattr(obj, "listCount") and not hasattr(obj, "list_count"):
# Sometimes the SelectResult hasn't been converted, i.e. because
# it has come from an old api or mixed version of Sire, or
# BioSimSpace has done something weird...
raise SystemError(
"Something has gone wrong with sire. Despite being loaded "
"with the new or mixed API, it is being passed the object "
f"'{obj}' of type {type(obj)} which only has the old API active. "
"Has Sire been loaded with support for old module names?"
)
if obj.list_count() == 0:
raise KeyError("Nothing matched the search.")
typ = obj.get_common_type()
if obj.list_count() == 1:
obj = __fix_obj(obj.list_at(0))
if obj.what() in [
"SireMM::SelectorBond",
"SireMM::SelectorAngle",
"SireMM::SelectorDihedral",
"SireMM::SelectorImproper",
]:
if obj.count() == 1:
obj = obj[0]
elif obj.what() != typ:
if typ == Molecule.typename():
return obj.molecule()
elif typ == Segment.typename():
return obj.segments(auto_reduce=True)
elif typ == Chain.typename():
return obj.chains(auto_reduce=True)
elif typ == Residue.typename():
return obj.residues(auto_reduce=True)
elif typ == Atom.typename():
return obj.atoms(auto_reduce=True)
return obj
if Atom.typename() != "SireMol::Atom":
raise AssertionError(
"The typename of an atom should be 'SireMol::Atom', but it "
f"is instead {Atom.typename()}. The mro is {Atom.mro()}. "
"This suggests something is broken with the boost wrappers, "
"and that further strange bugs will be present!"
)
if typ == Molecule.typename():
return SelectorMol(obj)
elif typ == Atom.typename():
return SelectorM_Atom_(obj)
elif typ == Residue.typename():
return SelectorM_Residue_(obj)
elif typ == Chain.typename():
return SelectorM_Chain_(obj)
elif typ == Segment.typename():
return SelectorM_Segment_(obj)
elif typ == CutGroup.typename():
return SelectorM_CutGroup_(obj)
elif typ == AtomMatch.typename():
return AtomMatchM(obj)
else:
from ..mm import SelectorBond, SelectorMBond
if SelectorBond in type(obj.list_at(0)).mro():
return SelectorMBond(obj)
from ..mm import SelectorAngle, SelectorMAngle
if SelectorAngle in type(obj.list_at(0)).mro():
return SelectorMAngle(obj)
from ..mm import SelectorDihedral, SelectorMDihedral
if SelectorDihedral in type(obj.list_at(0)).mro():
return SelectorMDihedral(obj)
from ..mm import SelectorImproper, SelectorMImproper
if SelectorImproper in type(obj.list_at(0)).mro():
return SelectorMImproper(obj)
# We really shouldn't get here, and if we do, then difficult
# to diagnose errors will propogate
from ..utils import Console
Console.warning(
f"Unrecognised type {typ}. "
"Expecting an Atom, Residue or other MoleculeView "
"type. Something may be wrong with the wrappers, and "
"further bugs from this point onwards are likely. "
f"Here is the container: {type(obj)}"
)
# return this as a raw list
return obj.to_list()
def __select_call__(obj, molecules, map=None):
"""Search for the desired objects in the passed molecules,
optionally passing in a property map to identify the properties
"""
from ..system import System
if type(molecules) is System:
molecules = molecules._system
from ..base import create_map
map = create_map(map)
return __from_select_result(obj.__orig_call__(molecules, map))
if not hasattr(Select, "__orig_call__"):
Select.__orig_call__ = Select.__call__
Select.__call__ = __select_call__
def __fixed__getitem__(obj, key):
map = None
from ..base import create_map
try:
if len(key) == 2:
map = create_map(key[1])
key = key[0]
except Exception:
# the second value is not a property map
pass
if type(key) is int:
if __is_selector_class(obj):
return obj.__orig__getitem__(key)
elif __is_chain_class(obj):
return obj.residue(key)
elif __is_internal_class(obj):
return obj.atom(obj.id()[key])
else:
return obj.atom(key)
elif type(key) is str:
# is this a search object - if so, then return whatever is
# most relevant from the search
if map is None:
map = create_map(map)
try:
# try to search for the object - this will raise
# a SyntaxError if this is not a search term
# (and is instead a name)
return __from_select_result(obj.search(key, map=map))
except SyntaxError:
# ignore SyntaxErrors as this is a name
pass
elif AtomID in type(key).mro():
return obj.atoms(key, auto_reduce=True)
elif ResID in type(key).mro():
return obj.residues(key, auto_reduce=True)
elif ChainID in type(key).mro():
return obj.chains(key, auto_reduce=True)
elif SegID in type(key).mro():
return obj.segments(key, auto_reduce=True)
elif BondID in type(key).mro():
return obj.bonds(key, auto_reduce=True)
elif AngleID in type(key).mro():
return obj.angles(key, auto_reduce=True)
elif DihedralID in type(key).mro():
return obj.dihedrals(key, auto_reduce=True)
elif ImproperID in type(key).mro():
return obj.impropers(key, auto_reduce=True)
elif Atom in type(key).mro():
atoms = obj.atoms(key, auto_reduce=True)
if __is_selector_class(atoms) and len(atoms) == 1:
return atoms[0]
else:
return atoms
elif Residue in type(key).mro():
res = obj.residues(key, auto_reduce=True)
if __is_selector_class(res) and len(res) == 1:
return res[0]
else:
return res
elif Chain in type(key).mro():
chains = obj.chains(key, auto_reduce=True)
if __is_selector_class(chains) and len(chains) == 1:
return chains[0]
else:
return chains
elif Segment in type(key).mro():
segs = obj.segments(key, auto_reduce=True)
if __is_selector_class(segs) and len(segs) == 1:
return segs[0]
else:
return segs
elif Molecule in type(key).mro():
mols = obj.molecules(key, auto_reduce=True)
if __is_selector_class(mols) and len(mols) == 1:
return mols[0]
else:
return mols
elif __is_selector_class(key):
if len(key) == 0:
raise KeyError("Nothing matched the search.")
elif len(key) == 1:
return __fixed__getitem__(obj, key[0])
T = type(key[0])
if Atom in T.mro():
return obj.atoms(key, auto_reduce=True)
elif Residue in T.mro():
return obj.residues(key, auto_reduce=True)
elif Chain in T.mro():
return obj.chains(key, auto_reduce=True)
elif Segment in T.mro():
return obj.segments(key, auto_reduce=True)
elif Molecule in T.mro():
return obj.molecules(key, auto_reduce=True)
else:
raise TypeError(f"You cannot search using an index of type {T}")
if __is_selector_class(obj):
return obj.__orig__getitem__(key)
elif __is_chain_class(obj):
return obj.residues(key, auto_reduce=True)
else:
return obj.atoms(key, auto_reduce=True)
def __idx_to_atoms(obj, idx, map):
if hasattr(idx, "atoms"):
atoms = obj.atoms()
return atoms[atoms.find(idx.atoms())]
else:
return obj.atoms(idx, map=map)
def __fixed__atoms__(
obj, idx=None, auto_reduce=False, error_on_missing: bool = False, map=None
):
from ..base import create_map
if idx is None:
result = obj.__orig__atoms()
elif type(idx) is range:
result = obj.__orig__atoms(list(idx), map=create_map(map))
elif hasattr(idx, "atoms"):
atoms = obj.atoms()
idxs = atoms.find(idx.atoms())
return atoms.__orig__atoms(idxs, map=create_map(map))
else:
result = obj.__orig__atoms(idx, map=create_map(map))
if auto_reduce and len(result) == 1:
return result[0]
elif error_on_missing and len(result) == 0:
raise KeyError("There is no matching atom in this view.")
else:
return result
def __fixed__atom__(obj, idx=None, map=None):
if isinstance(idx, int):
return obj.__orig__atom(idx)
atoms = __fixed__atoms__(obj, idx, auto_reduce=False, map=map)
if len(atoms) == 0:
raise KeyError("There is no matching atom in this view.")
elif len(atoms) > 1:
raise KeyError(
f"More than one atom matches. Number of matches is {len(atoms)}."
)
return atoms[0]
def __fixed__bonds__(
obj,
idx=None,
idx1=None,
auto_reduce=False,
error_on_missing: bool = False,
map=None,
):
if idx is None and idx1 is not None:
idx = idx1
idx1 = None
from . import MoleculeView
from ..base import create_map
map = create_map(map)
if issubclass(type(obj), MoleculeView):
# this is a single-molecule view
from ..mm import SelectorBond
C = SelectorBond
def _fromBondID(obj, bondid):
return SelectorBond(obj, bondid, map=map)
else:
# this is a multi-molecule container
from ..mm import SelectorMBond
C = SelectorMBond
def _fromBondID(obj, bondid):
return SelectorMBond(obj.to_select_result(), bondid, map=map)
if idx is None:
try:
result = C(obj, map=map)
except Exception:
result = C(obj.to_select_result(), map=map)
elif idx1 is None:
if BondID in type(idx).mro():
result = _fromBondID(obj, idx)
else:
result = C(__idx_to_atoms(obj, idx, map), map=map)
else:
result = C(
__idx_to_atoms(obj, idx, map),
__idx_to_atoms(obj, idx1, map),
map=map,
)
if auto_reduce and len(result) == 1:
return result[0]
elif error_on_missing and len(result) == 0:
raise KeyError("There is no matching bond in this view.")
else:
return result
def __fixed__angles__(
obj,
idx=None,
idx1=None,
idx2=None,
auto_reduce=False,
error_on_missing: bool = False,
map=None,
):
if idx1 is None and idx2 is not None:
idx1 = idx2
idx2 = None
if idx is None and idx1 is not None:
idx = idx1
idx1 = None
from . import MoleculeView
from ..base import create_map
map = create_map(map)
if issubclass(type(obj), MoleculeView):
# this is a single-molecule view
from ..mm import SelectorAngle
C = SelectorAngle
def _fromAngleID(obj, angid):
return SelectorAngle(obj, angid, map=map)
else:
# this is a multi-molecule container
from ..mm import SelectorMAngle
C = SelectorMAngle
def _fromAngleID(obj, angid):
return SelectorMAngle(obj.to_select_result(), angid, map=map)
if idx is None:
try:
result = C(obj, map=map)
except Exception:
result = C(obj.to_select_result(), map=map)
elif idx1 is None:
if AngleID in type(idx).mro():
result = _fromAngleID(obj, idx)
else:
result = C(__idx_to_atoms(obj, idx, map), map=map)
elif idx2 is None:
result = C(
__idx_to_atoms(obj, idx, map),
__idx_to_atoms(obj, idx1, map),
map=map,
)
else:
result = C(
__idx_to_atoms(obj, idx, map),
__idx_to_atoms(obj, idx1, map),
__idx_to_atoms(obj, idx2, map),
map=map,
)
if auto_reduce and len(result) == 1:
return result[0]
elif error_on_missing and len(result) == 0:
raise KeyError("There is no matching angle in this view.")
else:
return result
def __fixed__dihedrals__(
obj,
idx=None,
idx1=None,
idx2=None,
idx3=None,
auto_reduce=False,
error_on_missing: bool = False,
map=None,
):
if idx2 is None and idx3 is not None:
idx2 = idx3
idx3 = None
if idx1 is None and idx2 is not None:
idx1 = idx2
idx2 = None
if idx is None and idx1 is not None:
idx = idx1
idx1 = None
from . import MoleculeView
from ..base import create_map
map = create_map(map)
if issubclass(type(obj), MoleculeView):
# this is a single-molecule view
from ..mm import SelectorDihedral
C = SelectorDihedral
def _fromDihedralID(obj, dihid):
return SelectorDihedral(obj, dihid, map=map)
else:
# this is a multi-molecule container
from ..mm import SelectorMDihedral
C = SelectorMDihedral
def _fromDihedralID(obj, dihid):
return SelectorMDihedral(obj.to_select_result(), dihid, map=map)
if idx is None:
try:
result = C(obj, map=create_map(map))
except Exception:
result = C(obj.to_select_result(), map=map)
elif idx1 is None:
if DihedralID in type(idx).mro():
result = _fromDihedralID(obj, idx)
else:
result = C(__idx_to_atoms(obj, idx, map), map=map)
elif idx2 is None:
result = C(
__idx_to_atoms(obj, idx, map),
__idx_to_atoms(obj, idx1, map),
map=map,
)
elif idx3 is None:
result = C(
__idx_to_atoms(obj, idx, map),
__idx_to_atoms(obj, idx1, map),
__idx_to_atoms(obj, idx2, map),
map=map,
)
else:
result = C(
__idx_to_atoms(obj, idx, map),
__idx_to_atoms(obj, idx1, map),
__idx_to_atoms(obj, idx2, map),
__idx_to_atoms(obj, idx3, map),
map=map,
)
if auto_reduce and len(result) == 1:
return result[0]
elif error_on_missing and len(result) == 0:
raise KeyError("There is no matching dihedral in this view.")
else:
return result
def __fixed__impropers__(
obj,
idx=None,
idx1=None,
idx2=None,
idx3=None,
auto_reduce=False,
error_on_missing: bool = False,
map=None,
):
if idx2 is None and idx3 is not None:
idx2 = idx3
idx3 = None
if idx1 is None and idx2 is not None:
idx1 = idx2
idx2 = None
if idx is None and idx1 is not None:
idx = idx1
idx1 = None
from . import MoleculeView
from ..base import create_map
map = create_map(map)
if issubclass(type(obj), MoleculeView):
# this is a single-molecule view
from ..mm import SelectorImproper
C = SelectorImproper
def _fromImproperID(obj, impid):
return SelectorImproper(obj, impid, map=map)
else:
# this is a multi-molecule container
from ..mm import SelectorMImproper
C = SelectorMImproper
def _fromImproperID(obj, impid):
return SelectorMImproper(obj.to_select_result(), impid, map=map)
if idx is None:
try:
result = C(obj, map=map)
except Exception:
result = C(obj.to_select_result(), map=map)
elif idx1 is None:
if ImproperID in type(idx).mro():
result = _fromImproperID(obj, idx)
else:
result = C(__idx_to_atoms(obj, idx, map), map=map)
elif idx2 is None:
result = C(
__idx_to_atoms(obj, idx, map),
__idx_to_atoms(obj, idx1, map),
map=map,
)
elif idx3 is None:
result = C(
__idx_to_atoms(obj, idx, map),
__idx_to_atoms(obj, idx1, map),
__idx_to_atoms(obj, idx2, map),
map=map,
)
else:
result = C(
__idx_to_atoms(obj, idx, map),
__idx_to_atoms(obj, idx1, map),
__idx_to_atoms(obj, idx2, map),
__idx_to_atoms(obj, idx3, map),
map=map,
)
if auto_reduce and len(result) == 1:
return result[0]
elif error_on_missing and len(result) == 0:
raise KeyError("There is no matching improper in this view.")
else:
return result
def __fixed__bond__(obj, idx=None, idx1=None, map=None):
bonds = __fixed__bonds__(obj, idx, idx1, auto_reduce=False, map=map)
if len(bonds) == 0:
raise KeyError("There is no matching bond in this view.")
elif len(bonds) > 1:
raise KeyError(
f"More than one bond matches. Number of matches is {len(bonds)}."
)
return bonds[0]
def __fixed__angle__(obj, idx=None, idx1=None, idx2=None, map=None):
angles = __fixed__angles__(obj, idx, idx1, idx2, auto_reduce=False, map=map)
if len(angles) == 0:
raise KeyError("There is no matching angle in this view.")
elif len(angles) > 1:
raise KeyError(
f"More than one angle matches. Number of matches is {len(angles)}."
)
return angles[0]
def __fixed__dihedral__(obj, idx=None, idx1=None, idx2=None, idx3=None, map=None):
dihedrals = __fixed__dihedrals__(
obj, idx, idx1, idx2, idx3, auto_reduce=False, map=map
)
if len(dihedrals) == 0:
raise KeyError("There is no matching dihedral in this view.")
elif len(dihedrals) > 1:
raise KeyError(
"More than one dihedral matches. Number of " f"matches is {len(dihedrals)}."
)
return dihedrals[0]
def __fixed__improper__(obj, idx=None, idx1=None, idx2=None, idx3=None, map=None):
impropers = __fixed__impropers__(
obj, idx, idx1, idx2, idx3, auto_reduce=False, map=map
)
if len(impropers) == 0:
raise KeyError("There is no matching improper in this view.")
elif len(impropers) > 1:
raise KeyError(
"More than one improper matches. Number of " f"matches is {len(impropers)}."
)
return impropers[0]
def __fixed__residues__(
obj, idx=None, auto_reduce=False, error_on_missing: bool = False, map=None
):
from ..base import create_map
if idx is None:
result = obj.__orig__residues()
elif type(idx) is range:
result = obj.__orig__residues(list(idx), map=create_map(map))
elif hasattr(idx, "residues"):
residues = obj.residues()
idxs = residues.find(idx.residues())
return residues.__orig__residues(idxs, map=create_map(map))
else:
result = obj.__orig__residues(idx, map=create_map(map))
if auto_reduce and len(result) == 1:
return result[0]
elif error_on_missing and len(result) == 0:
raise KeyError("There is no matching residue in this view.")
else:
return result
def __fixed__chains__(
obj, idx=None, auto_reduce=False, error_on_missing: bool = False, map=None
):
from ..base import create_map
if idx is None:
result = obj.__orig__chains()
elif type(idx) is range:
result = obj.__orig__chains(list(idx), map=create_map(map))
elif hasattr(idx, "chains"):
chains = obj.chains()
idxs = chains.find(idx.chains())
return chains.__orig__chains(idxs, map=create_map(map))
else:
result = obj.__orig__chains(idx, map=create_map(map))
if auto_reduce and len(result) == 1:
return result[0]
elif error_on_missing and len(result) == 0:
raise KeyError("There is no matching chain in this view.")
else:
return result
def __fixed__segments__(
obj, idx=None, auto_reduce=False, error_on_missing: bool = False, map=None
):
from ..base import create_map
if idx is None:
result = obj.__orig__segments()
elif type(idx) is range:
result = obj.__orig__segments(list(idx), map=create_map(map))
elif hasattr(idx, "segments"):
segments = obj.segments()
idxs = segments.find(idx.segments())
return segments.__orig__segments(idxs, map=create_map(map))
else:
from ..base import create_map
result = obj.__orig__segments(idx, map=create_map(map))
if auto_reduce and len(result) == 1:
return result[0]
elif error_on_missing and len(result) == 0:
raise KeyError("There is no matching segment in this view.")
else:
return result
def __fixed__molecules__(
obj, idx=None, auto_reduce=False, error_on_missing: bool = False, map=None
):
from ..base import create_map
if idx is None:
result = obj.__orig__molecules()
elif type(idx) is range:
result = obj.__orig__molecules(list(idx), map=create_map(map))
elif hasattr(idx, "molecules"):
molecules = obj.molecules()
idxs = molecules.find(idx.molecules())
return molecules.__orig__molecules(idxs, map=create_map(map))
else:
result = obj.__orig__molecules(idx, map=create_map(map))
if auto_reduce and len(result) == 1:
return result[0]
elif error_on_missing and len(result) == 0:
raise KeyError("There is no matching molecule in this view.")
else:
return result
def __fix_getitem(C):
if not hasattr(C, "__orig__getitem__"):
C.__orig__getitem__ = C.__getitem__
if not hasattr(C, "__orig_atom"):
C.__orig__atom = C.atom
if not hasattr(C, "__orig__atoms"):
C.__orig__atoms = C.atoms
if not hasattr(C, "__orig__residues"):
C.__orig__residues = C.residues
if not hasattr(C, "__orig__chains"):
C.__orig__chains = C.chains
if not hasattr(C, "__orig__segments"):
C.__orig__segments = C.segments
C.__getitem__ = __fixed__getitem__
C.atom = __fixed__atom__
C.atoms = __fixed__atoms__
C.residues = __fixed__residues__
C.chains = __fixed__chains__
C.segments = __fixed__segments__
C.count = C.__len__
if hasattr(C, "measure"):
# make sure we use the right `size` function
C.size = C.measure
else:
C.size = C.__len__
if hasattr(C, "molecules"):
if not hasattr(C, "__orig__molecules"):
C.__orig__molecules = C.molecules
C.molecules = __fixed__molecules__
C.bonds = __fixed__bonds__
C.bond = __fixed__bond__
C.angles = __fixed__angles__
C.angle = __fixed__angle__
C.dihedrals = __fixed__dihedrals__
C.dihedral = __fixed__dihedral__
C.impropers = __fixed__impropers__
C.improper = __fixed__improper__
try:
Residue.__len__ = Residue.nAtoms
Chain.__len__ = Chain.nResidues
Segment.__len__ = Segment.nAtoms
CutGroup.__len__ = CutGroup.nAtoms
Molecule.__len__ = Molecule.nAtoms
except AttributeError:
Residue.__len__ = Residue.num_atoms
Chain.__len__ = Chain.num_residues
Segment.__len__ = Segment.num_atoms
CutGroup.__len__ = CutGroup.num_atoms
Molecule.__len__ = Molecule.num_atoms
for C in [
Atom,
CutGroup,
Residue,
Chain,
Segment,
Molecule,
Selector_Atom_,
Selector_Residue_,
Selector_Chain_,
Selector_Segment_,
Selector_CutGroup_,
SelectorMol,
SelectorM_Atom_,
SelectorM_Residue_,
SelectorM_Chain_,
SelectorM_Segment_,
SelectorM_CutGroup_,
]:
__fix_getitem(C)
def _atom_coordinates(atom, map=None):
if map is None:
return atom.property("coordinates")
from ..base import create_map
map = create_map(map)
return atom.property(map["coordinates"])
Atom.element = lambda x: x.property("element")
Atom.lj = lambda x: x.property("LJ")
Atom.coordinates = _atom_coordinates
Atom.coords = Atom.coordinates
Atom.x = lambda atom, map=None: atom.coordinates(map=map).x()
Atom.y = lambda atom, map=None: atom.coordinates(map=map).y()
Atom.z = lambda atom, map=None: atom.coordinates(map=map).z()
def __atomcoords__str__(obj):
n = len(obj)
if n == 0:
return "AtomCoords::empty"
parts = []
if n <= 10:
for i in range(0, n):
parts.append(f"{i}: {obj[i]}")
else:
for i in range(0, 5):
parts.append(f"{i}: {obj[i]}")
parts.append("...")
for i in range(n - 5, n):
parts.append(f"{i}: {obj[i]}")
joined = "\n".join(parts)
return f"AtomCoords( size={n}\n{joined}\n)"
AtomCoords.__str__ = __atomcoords__str__
AtomCoords.__repr__ = __atomcoords__str__
def _add_evals(obj):
from ..base import create_map
obj.mass = lambda x, map=None: x.evaluate().mass(map=create_map(map))
obj.charge = lambda x, map=None: x.evaluate().charge(map=create_map(map))
obj.coordinates = lambda x, map=None: x.evaluate().center_of_mass(
map=create_map(map)
)
obj.coords = obj.coordinates
obj.x = lambda x, map=None: x.coordinates(map=map).x()
obj.y = lambda x, map=None: x.coordinates(map=map).y()
obj.z = lambda x, map=None: x.coordinates(map=map).z()
def _get_container_property(x, key):
vals = []
from ..base import ProgressBar
with ProgressBar(len(x), "Extract property") as bar:
for v in x:
prop = _get_property(v, key)
if type(prop) is list:
vals += prop
else:
vals.append(prop)
bar.tick()
return vals
def _get_property(x, key):
if hasattr(x, "__orig__property"):
# get the property directly
try:
return x.__orig__property(key)
except Exception as e:
saved_exception = e
else:
saved_exception = None
# we couldn't get the property directly, so get
# the property at the molecule level...
try:
mol = x.molecule()
except Exception:
# this must be a SelectorMol or other container
return _get_container_property(x, key)
prop = mol.property(key)
# Now extract the bits we want
import sire
if issubclass(prop.__class__, sire.legacy.Mol.AtomProp):
vals = []
for atom in x.atoms():
vals.append(atom.property(key))
return vals
elif issubclass(prop.__class__, sire.legacy.Mol.ResProp):
vals = []
for res in x.residues():
vals.append(res.property(key))
return vals
elif issubclass(prop.__class__, sire.legacy.Mol.ChainProp):
vals = []
for chain in x.chains():
vals.append(chain.property(key))
return vals
elif issubclass(prop.__class__, sire.legacy.Mol.SegProp):
vals = []
for seg in x.segments():
vals.append(seg.property(key))
return vals
elif issubclass(prop.__class__, sire.legacy.Mol.MolViewProperty):
return prop
elif saved_exception is not None:
raise saved_exception
else:
raise KeyError(f"Could not find property {key} in {x}")
def _apply(objs, func, *args, **kwargs):
"""
Call the passed function on all views in the container,
appending the result to a list of results, which
is returned.
The function can be either;
1. a string containing the name of the function to call, or
2. an actual function (either a normal function or a lambda expression)
You can optionally pass in positional and keyword arguments
here that will be passed to the function.
Args:
objs (self): The container itself (this is self)
func (str or function): The function to be called, or the name
of the function to be called.
Returns:
list: A list of the results, with one result per view in the container.
"""
result = []
from ..base import ProgressBar
if str(func) == func:
# we calling a named function
with ProgressBar(total=len(objs), text="Looping through views") as progress:
for i, obj in enumerate(objs):
result.append(getattr(obj, func)(*args, **kwargs))
progress.set_progress(i + 1)
else:
# we have been passed the function to call
with ProgressBar(total=len(objs), text="Looping through views") as progress:
for i, obj in enumerate(objs):
result.append(func(obj, *args, **kwargs))
progress.set_progress(i + 1)
return result
def _apply_reduce(objs, func, reduction_func=None, *args, **kwargs):
"""
Call the passed function on all views in the container,
reducing the result into a single value via the 'reduce' function.
This is equivalent to calling
```
reduce(reduction_func, objs.apply(func, *args, **kwargs))
The function can be either;
1. a string containing the name of the function to call, or
2. an actual function (either a normal function or a lambda expression)
The reduction function should be a function that can be passed
to `reduce`. If this isn't passed, then it is assumed to
be operator.add.
You can optionally pass in positional and keyword arguments
here that will be passed to the applied function.
Args:
objs (self): The container itself (this is self)
func (str or function): The function to be called, or the name
of the function to be called.
reduction_func: The function used to reduce the result. This
is operator.add by default.
Returns:
result: The reduced result
"""
if reduction_func is None:
from operator import add
reduction_func = add
from functools import reduce
return reduce(reduction_func, objs.apply(func, *args, **kwargs))
def _add_apply_func(obj):
if hasattr(obj, "apply"):
return
obj.apply = _apply
obj.apply_reduce = _apply_reduce
def _add_property_func(obj):
if hasattr(obj, "__orig__property"):
return
if hasattr(obj, "property"):
obj.__orig__property = obj.property
obj.property = _get_property
for C in [
MoleculeView,
SelectorMol,
SelectorM_Atom_,
SelectorM_Residue_,
SelectorM_Chain_,
SelectorM_CutGroup_,
SelectorM_Segment_,
]:
_add_evals(C)
_add_property_func(C)
_add_apply_func(C)
for C in [Residue, Chain, Segment]:
_add_property_func(C)
def _molecule(obj, id=None):
"""
Return the molecule that contains this view. If 'id' is specified
then this will check that the ID matches this molecule before
returning it. This will raise an exception if the ID doesn't match.
Returns
-------
sire.mol.Molecule: The molecule containing this view
"""
if id is None:
return obj.__orig__molecule()
else:
from . import SelectorMol
return SelectorMol(obj).molecule(id)
def _molecules(obj, id=None):
"""
Return the molecule that contains this view as a list of molecules,
containing just a single molecule.
If 'id' is specified then this checks that this molecule matches
the ID before returning it. This will raise an exception if the
ID doesn't match.
Returns
-------
sire.mol.SelectorMol: A collection containing only a single molecule
that contains this view.
"""
from . import SelectorMol
if id is None:
return SelectorMol(obj).molecules()
else:
return SelectorMol(obj).molecules(id)
if not hasattr(MoleculeView, "__orig__molecule"):
MoleculeView.__orig__molecule = MoleculeView.molecule
MoleculeView.molecule = _molecule
MoleculeView.molecules = _molecules
def _get_atom_mass(x):
if x.has_property("mass"):
return x.property("mass")
elif x.has_property("element"):
return x.property("element").mass()
else:
return 0
Atom.mass = _get_atom_mass
def _get_atom_charge(x):
if x.has_property("charge"):
return x.property("charge")
elif x.has_property("formal_charge"):
return x.property("formal_charge")
else:
return 0
Atom.charge = _get_atom_charge
Molecule.connectivity = lambda x: x.property("connectivity")
def __molecule__add__(mol0, mol1):
"""
Combine two molecules together into a system.
"""
from ..system import System
mols = System()
mols.add(mol0)
mols.add(mol1)
from ..vol import Cartesian
mols.set_space(Cartesian())
mols.set_time(0)
return mols
Molecule.__add__ = __molecule__add__
# Here are some extra classes / functions defined as part of the
# public API
def _cursor(view, map=None):
"""
Return a Cursor that can be used to edit the properties
of this view
"""
from ..base import create_map
return Cursor(view, map=create_map(map))
Atom.cursor = _cursor
Residue.cursor = _cursor
Chain.cursor = _cursor
Segment.cursor = _cursor
Molecule.cursor = _cursor
def _dynamics(
view,
cutoff=None,
cutoff_type=None,
timestep=None,
save_frequency=None,
energy_frequency=None,
frame_frequency=None,
save_velocities=None,
constraint=None,
perturbable_constraint=None,
include_constrained_energies: bool = True,
integrator=None,
schedule=None,
lambda_value=None,
swap_end_states=None,
ignore_perturbations=None,
temperature=None,
pressure=None,
vacuum=None,
shift_delta=None,
shift_coulomb=None,
coulomb_power=None,
restraints=None,
fixed=None,
platform=None,
device=None,
precision=None,
com_reset_frequency=None,
barostat_frequency=None,
dynamic_constraints: bool = True,
map=None,
):
"""
Return a Dynamics object that can be used to perform
dynamics of the molecule(s) in this view
cutoff: Length
The size of the non-bonded cutoff
cutoff_type: str
The type of cutoff to use, e.g. "PME", "RF" etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options
timestep: time
The size of the dynamics timestep
save_frequency: time
The amount of simulation time between saving energies and frames.
This can be overridden using `energy_frequency` or `frame_frequency`,
or by these options in individual dynamics runs. Set this
to zero if you don't want any saves.
energy_frequency: time
The amount of time between saving energies. This overrides the
value in `save_frequency`. Set this to zero if you don't want
to save energies during the trajectory. This can be overridden
by setting energy_frequency during an individual run.
frame_frequency: time
The amount of time between saving frames. This overrides the
value in `save_frequency`. Set this to zero if you don't want
to save frames during the trajectory. This can be overridden
by setting frame_frequency during an individual run.
save_velocities: bool
Whether or not to save velocities when saving trajectory frames
during the simulation. This defaults to False, as velocity
trajectories aren't often needed, and they double the amount
of space that is required for a trajectory.
constraint: str
The type of constraint to use for bonds and/or angles, e.g.
`h-bonds`, `bonds` etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options. This will be automatically
guessed from the timestep if it isn't set.
perturbable_constraint: str
The type of constraint to use for perturbable bonds and/or angles,
e.g. `h-bonds`, `bonds` etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options. This equal the value of `constraint`
if it isn't set.
include_constrained_energies: bool
Whether or not to include the energies of the constrained bonds
and angles. If this is False, then the internal bond or angle
energy of the constrained degrees of freedom are not included
in the total energy, and their forces are not evaluated.
integrator: str
The type of integrator to use, e.g. `langevin`, `verlet` etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options. This will be automatically
set to `langevin_middle` (NVT/NPT) or `verlet` (NVE) depending
on the ensemble if this is not set (or is set to `auto`)
schedule: sire.cas.LambdaSchedule
The schedule used to control how perturbable forcefield parameters
should be morphed as a function of lambda. If this is not set
then a sire.cas.LambdaSchedule.standard_morph() is used.
lambda_value: float
The value of lambda at which to run dynamics. This only impacts
perturbable molecules, whose forcefield parameters will be
scaled according to the lambda schedule for the specified
value of lambda.
swap_end_states: bool
Whether or not to swap the end states. If this is True, then
the perturbation will run from the perturbed back to the
reference molecule (the perturbed molecule will be at lambda=0,
while the reference molecule will be at lambda=1). This will
use the coordinates of the perturbed molecule as the
starting point.
ignore_perturbations: bool
Whether or not to ignore perturbations. If this is True, then
the perturbation will be ignored, and the simulation will
be run using the properties of the reference molecule
(or the perturbed molecule if swap_end_states is True). This
is useful if you just want to run standard molecular dynamics
of the reference or perturbed states.
temperature: temperature
The temperature at which to run the simulation. A
microcanonical (NVE) simulation will be run if you don't
specify the temperature.
pressure: pressure
The pressure at which to run the simulation. A
microcanonical (NVE) or canonical (NVT) simulation will be
run if the pressure is not set.
vacuum: bool (optional)
Whether or not to run the simulation in vacuum. If this is
set to `True`, then the simulation space automatically be
replaced by a `sire.vol.Cartesian` space, and the
simulation run in vacuum.
shift_delta: length
The shift_delta parameter that controls the Lennard-Jones
softening potential that smooths the
creation and deletion of ghost atoms during a potential.
This defaults to 2.0 A.
shift_coulomb: length
The shift_coulomb parameter that controls the electrostatic
softening potential that smooths the creation and deletion
of ghost atoms during a potential. This defaults to 1.0 A.
coulomb_power: int
The coulomb power parmeter that controls the electrostatic
softening potential that smooths the creation and deletion
of ghost atoms during a potential. This defaults to 0.
restraints: sire.mm.Restraints or list[sire.mm.Restraints]
A single set of restraints, or a list of sets of
restraints that will be applied to the atoms during
the simulation.
fixed: molecule(s) view, search string, int, list[int] etc
Anything that can be used to identify the atom or atoms
that should be fixed in place during the simulation. These
atoms will not be moved by dynamics.
platform: str
The name of the OpenMM platform on which to run the dynamics,
e.g. "CUDA", "OpenCL", "Metal" etc.
device: str or int
The ID of the GPU (or accelerator) used to accelerate
the simulation. This would be CUDA_DEVICE_ID or similar
if CUDA was used. This can be any valid OpenMM device string
precision: str
The desired precision for the simulation (e.g. `single`,
`mixed` or `double`)
com_reset_frequency:
Either the number of steps between center-of-mass resets,
or the time between resets. If this is unset, then
the center-of-mass is not reset during the simulation.
barostat_frequency:
Either the number of steps between MC moves to apply the
barostat, of the time between moves. If this is unset,
then the default of every 25 steps is used.
dynamic_constraints: bool
Whether or not to update the length of constraints of
perturbable bonds with lambda. This defaults to True,
meaning that changing lambda will change any constraint
on a perturbable bond to equal to the value of r0 at
that lambda value. If this is false, then the constraint
is set based on the current length.
map: dict
A dictionary of additional options. Note that any options
set in this dictionary that are also specified via one of
the arguments above will be overridden by the argument
value
"""
from ..base import create_map
from ..system import System
from .. import u
map = create_map(map)
if vacuum is True:
from ..vol import Cartesian
map.set("space", Cartesian())
view = view.clone()
try:
view.set_property("space", Cartesian())
except Exception:
pass
if not map.specified("space"):
map = create_map(map, {"space": "space"})
if (
System.is_system(view)
and map.specified("space")
and not map["space"].has_value()
and not view.shared_properties().has_property(map["space"])
):
# space is not a shared property, so may be lost when we
# convert to molecules. Make sure this doesn't happen by
# adding the space directly to the property map
try:
map.set("space", view.property(map["space"]))
except Exception:
from ..vol import Cartesian
map.set("space", Cartesian())
# Set default values if these have not been set
if cutoff is None and not map.specified("cutoff"):
from ..units import angstrom
cutoff = 7.5 * angstrom
if cutoff_type is None and not map.specified("cutoff_type"):
cutoff_type = "auto"
if timestep is None and not map.specified("timestep"):
from ..units import femtosecond
timestep = 1 * femtosecond
elif timestep is not None:
timestep = u(timestep)
else:
timestep = u(map["timestep"].value())
if save_frequency is None and not map.specified("save_frequency"):
from ..units import picosecond
map.set("save_frequency", 25 * picosecond)
elif save_frequency is not None:
map.set("save_frequency", u(save_frequency))
if energy_frequency is not None:
map.set("energy_frequency", u(energy_frequency))
if frame_frequency is not None:
map.set("frame_frequency", u(frame_frequency))
if save_velocities is not None:
map.set("save_velocities", save_velocities)
if constraint is None and not map.specified("constraint"):
constraint = "auto"
if perturbable_constraint is not None:
perturbable_constraint = str(perturbable_constraint).lower()
if temperature is not None:
temperature = u(temperature)
map.set("temperature", temperature)
if pressure is not None:
pressure = u(pressure)
map.set("pressure", pressure)
if device is not None:
map.set("device", str(device))
if precision is not None:
map.set("precision", str(precision).lower())
if include_constrained_energies is not None:
map.set("include_constrained_energies", include_constrained_energies)
if platform is not None:
map.set("platform", str(platform))
if integrator is not None:
map.set("integrator", str(integrator))
if dynamic_constraints is not None:
if dynamic_constraints:
map.set("dynamic_constraints", True)
else:
map.set("dynamic_constraints", False)
if barostat_frequency is not None:
barostat_frequency = u(barostat_frequency)
elif map.specified("barostat_frequency"):
barostat_frequency = u(map["barostat_frequency"].value())
if barostat_frequency is None:
map.unset("barostat_frequency")
else:
if barostat_frequency.is_dimensionless():
barostat_frequency = int(barostat_frequency.value())
if barostat_frequency != 0:
map.set("barostat_frequency", barostat_frequency)
else:
map.unset("barostat_frequency")
else:
if not barostat_frequency.has_same_units(timestep):
raise ValueError("The units of barostat_frequency must match timestep")
barostat_frequency = int((barostat_frequency / timestep).value())
if barostat_frequency != 0:
map.set("barostat_frequency", barostat_frequency)
else:
map.unset("barostat_frequency")
if com_reset_frequency is not None:
com_reset_frequency = u(com_reset_frequency)
elif map.specified("com_reset_frequency"):
com_reset_frequency = u(map["com_reset_frequency"].value())
if com_reset_frequency is None:
map.unset("com_reset_frequency")
else:
if com_reset_frequency.is_dimensionless():
com_reset_frequency = int(com_reset_frequency.value())
if com_reset_frequency != 0:
map.set("com_reset_frequency", com_reset_frequency)
else:
map.unset("com_reset_frequency")
else:
if not com_reset_frequency.has_same_units(timestep):
raise ValueError("The units of com_reset_frequency must match timestep")
com_reset_frequency = int((com_reset_frequency / timestep).value())
if com_reset_frequency != 0:
map.set("com_reset_frequency", com_reset_frequency)
else:
map.unset("com_reset_frequency")
return Dynamics(
view,
cutoff=cutoff,
cutoff_type=cutoff_type,
timestep=timestep,
constraint=str(constraint),
perturbable_constraint=perturbable_constraint,
schedule=schedule,
lambda_value=lambda_value,
shift_delta=shift_delta,
shift_coulomb=shift_coulomb,
coulomb_power=coulomb_power,
swap_end_states=swap_end_states,
ignore_perturbations=ignore_perturbations,
restraints=restraints,
fixed=fixed,
map=map,
)
def _minimisation(
view,
cutoff=None,
cutoff_type=None,
constraint=None,
perturbable_constraint=None,
include_constrained_energies: bool = True,
schedule=None,
lambda_value=None,
swap_end_states=None,
ignore_perturbations=None,
vacuum=None,
shift_delta=None,
shift_coulomb=None,
coulomb_power=None,
platform=None,
device=None,
precision=None,
restraints=None,
fixed=None,
dynamic_constraints: bool = True,
map=None,
):
"""
Return a Minimisation object that can be used to perform
minimisation of the molecule(s) in this view
cutoff: Length
The size of the non-bonded cutoff
cutoff_type: str
The type of cutoff to use, e.g. "PME", "RF" etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options
constraint: str
The type of constraint to use for bonds and/or angles, e.g.
`h-bonds`, `bonds` etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options. This is `none` if it is not set.
perturbable_constraint: str
The type of constraint to use for perturbable bonds and/or angles,
e.g. `h-bonds`, `bonds` etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options. This equal the value of `constraint`
if it isn't set.
include_constrained_energies: bool
Whether or not to include the energies of the perturbable bonds
and angles. If this is False, then the internal bond or angle
energy of the perturbable degrees of freedom are not included
in the total energy, and their forces are not evaluated.
schedule: sire.cas.LambdaSchedule
The schedule used to control how perturbable forcefield parameters
should be morphed as a function of lambda. If this is not set
then a sire.cas.LambdaSchedule.standard_morph() is used.
lambda_value: float
The value of lambda at which to run minimisation. This only impacts
perturbable molecules, whose forcefield parameters will be
scaled according to the lambda schedule for the specified
value of lambda.
swap_end_states: bool
Whether or not to swap the end states. If this is True, then
the perturbation will run from the perturbed back to the
reference molecule (the perturbed molecule will be at lambda=0,
while the reference molecule will be at lambda=1). This will
use the coordinates of the perturbed molecule as the
starting point.
ignore_perturbations: bool
Whether or not to ignore perturbations. If this is True, then
the perturbation will be ignored, and the simulation will
be run using the properties of the reference molecule
(or the perturbed molecule if swap_end_states is True). This
is useful if you just want to run standard molecular dynamics
of the reference or perturbed states.
vacuum: bool (optional)
Whether or not to run the simulation in vacuum. If this is
set to `True`, then the simulation space automatically be
replaced by a `sire.vol.Cartesian` space, and the
simulation run in vacuum.
shift_delta: length
The shift_delta parameter that controls the Lennard-Jones
softening potential that smooths the
creation and deletion of ghost atoms during a potential.
This defaults to 2.0 A.
shift_coulomb: length
The shift_coulomb parameter that controls the electrostatic
softening potential that smooths the creation and deletion
of ghost atoms during a potential. This defaults to 1.0 A.
coulomb_power: int
The coulomb power parmeter that controls the electrostatic
softening potential that smooths the creation and deletion
of ghost atoms during a potential. This defaults to 0.
restraints: sire.mm.Restraints or list[sire.mm.Restraints]
A single set of restraints, or a list of sets of
restraints that will be applied to the atoms during
the simulation.
fixed: molecule(s) view, search string, int, list[int] etc
Anything that can be used to identify the atom or atoms
that should be fixed in place during the simulation. These
atoms will not be moved by minimisation.
platform: str
The name of the OpenMM platform on which to run the dynamics,
e.g. "CUDA", "OpenCL", "Metal" etc.
device: str or int
The ID of the GPU (or accelerator) used to accelerate
minimisation. This would be CUDA_DEVICE_ID or similar
if CUDA was used. This can be any valid OpenMM device string
precision: str
The desired precision for the simulation (e.g. `single`,
`mixed` or `double`)
dynamic_constraints: bool
Whether or not to update the length of constraints of
perturbable bonds with lambda. This defaults to True,
meaning that changing lambda will change any constraint
on a perturbable bond to equal to the value of r0 at
that lambda value. If this is false, then the constraint
is set based on the current length.
map: dict
A dictionary of additional options. Note that any options
set in this dictionary that are also specified via one of
the arguments above will be overridden by the argument
value
"""
from ..base import create_map
from ..system import System
map = create_map(map)
if vacuum is True:
from ..vol import Cartesian
map.set("space", Cartesian())
view = view.clone()
try:
view.set_property("space", Cartesian())
except Exception:
pass
if not map.specified("space"):
map = create_map(map, {"space": "space"})
if (
System.is_system(view)
and map.specified("space")
and not map["space"].has_value()
and not view.shared_properties().has_property(map["space"])
):
# space is not a shared property, so may be lost when we
# convert to molecules. Make sure this doens't happen by
# adding the space directly to the property map
try:
map.set("space", view.property(map["space"]))
except Exception:
from ..vol import Cartesian
map.set("space", Cartesian())
# Set default values if these have not been set
if cutoff is None and not map.specified("cutoff"):
from ..units import angstrom
cutoff = 7.5 * angstrom
if cutoff_type is None and not map.specified("cutoff_type"):
cutoff_type = "auto"
if device is not None:
map.set("device", str(device))
if precision is not None:
map.set("precision", str(precision).lower())
if constraint is not None:
map.set("constraint", str(constraint).lower())
if perturbable_constraint is not None:
map.set("perturbable_constraint", str(perturbable_constraint).lower())
if include_constrained_energies is not None:
map.set("include_constrained_energies", include_constrained_energies)
if dynamic_constraints is not None:
if dynamic_constraints:
map.set("dynamic_constraints", True)
else:
map.set("dynamic_constraints", False)
if platform is not None:
map.set("platform", str(platform))
return Minimisation(
view,
cutoff=cutoff,
cutoff_type=cutoff_type,
schedule=schedule,
lambda_value=lambda_value,
swap_end_states=swap_end_states,
ignore_perturbations=ignore_perturbations,
shift_delta=shift_delta,
shift_coulomb=shift_coulomb,
coulomb_power=coulomb_power,
restraints=restraints,
fixed=fixed,
map=map,
)
MoleculeView.dynamics = _dynamics
SelectorM_Atom_.dynamics = _dynamics
SelectorM_Residue_.dynamics = _dynamics
SelectorM_Chain_.dynamics = _dynamics
SelectorM_Segment_.dynamics = _dynamics
SelectorM_CutGroup_.dynamics = _dynamics
SelectorMol.dynamics = _dynamics
MoleculeView.minimisation = _minimisation
SelectorM_Atom_.minimisation = _minimisation
SelectorM_Residue_.minimisation = _minimisation
SelectorM_Chain_.minimisation = _minimisation
SelectorM_Segment_.minimisation = _minimisation
SelectorM_CutGroup_.minimisation = _minimisation
SelectorMol.minimisation = _minimisation
def _cursors(views, map=None):
"""Return the Cursors object that contains cursors for all
of the views in this collection. Note that the `parent`
cursor of this list will be the molecule
"""
cursor = views.molecule().cursor(map=map)
return cursor._from_views(views)
Selector_Atom_.cursor = _cursors
Selector_Residue_.cursor = _cursors
Selector_Chain_.cursor = _cursors
Selector_Segment_.cursor = _cursors
def _trajectory(
obj, align=None, smooth=None, wrap=None, mapping=None, frame=None, map=None
):
"""
Return an iterator over the trajectory of frames of this view.
align:
Pass in a selection string to select atoms against which
every frame will be aligned. These atoms will be moved
to the center of the periodic box (if a periodic box
is used). If "True" is passed, then this will attempt
to align *ALL* of the coordinates in the view.
You can also choose to pass in a molecular container,
and it will align against the atoms in that container,
assuming they are contained in this view. If not, then
you need to supply a mapping that maps from the
atoms in the align container, to the atoms in this view.
frame:
The frame of the trajectory against which the alignment
should be based. For example, `frame=3` would align based
on the coordinates of the aligned atoms in frame 3 of
the trajectory. If this is `None` (the default) then the
first frame will be used.
mapping: AtomMapping
An AtomMapping object that maps from atoms in the alignment
container to atoms in this view. You only need to supply
this if all of the alignment atoms are not contained
in this view.
smooth:
Pass in the number of frames to smooth (average) the view
over. If 'True' is passed, then the recommended number
of frames will be averaged over
wrap: bool
Whether or not to wrap the coordinates into the periodic box
"""
from ._trajectory import TrajectoryIterator
return TrajectoryIterator(
obj,
align=align,
frame=frame,
smooth=smooth,
wrap=wrap,
mapping=mapping,
map=map,
)
MoleculeView.trajectory = _trajectory
SelectorM_Atom_.trajectory = _trajectory
SelectorM_Residue_.trajectory = _trajectory
SelectorM_Chain_.trajectory = _trajectory
SelectorM_Segment_.trajectory = _trajectory
SelectorM_CutGroup_.trajectory = _trajectory
SelectorMol.trajectory = _trajectory
def _cursorsm(obj, map=None):
from ._cursor import CursorsM
return CursorsM(parent=obj, map=map)
SelectorM_Atom_.cursor = _cursorsm
SelectorM_Residue_.cursor = _cursorsm
SelectorM_Chain_.cursor = _cursorsm
SelectorM_Segment_.cursor = _cursorsm
SelectorM_CutGroup_.cursor = _cursorsm
SelectorMol.cursor = _cursorsm
def _to_molecules(obj):
if obj is None:
return None
if hasattr(obj, "to_molecule_group"):
return obj.to_molecule_group().molecules()
else:
from ..legacy.Mol import Molecules
m = Molecules(obj)
return m
def _energy(obj, other=None, map=None):
"""
Calculate the total energy of the molecule view(s) in this
collection.
other: (view or views, optional)
An optional second view (or collection of views).
If this is passed, then the energy between the
views in this collections and others will be calculated.
map: (dictionary, optional)
An optional property map that will be used to find
or map the properties used for this energy calculation.
Returns
-------
sire.units.GeneralUnit (energy per quantity):
Returns an energy, with attached components for the
sub-components (if any) for this energy.
"""
from ..system import calculate_energy
if map is None:
if other is None:
return calculate_energy(obj)
else:
return calculate_energy(obj, _to_molecules(other))
elif other is None:
return calculate_energy(obj, map=map)
else:
return calculate_energy(obj, _to_molecules(other), map=map)
def _energies(obj, other=None, map=None):
"""
Calculate the total energy of the molecule view(s) in this
collection.
other: (view or views, optional)
An optional second view (or collection of views).
If this is passed, then the energy between the
views in this collections and others will be calculated.
map: (dictionary, optional)
An optional property map that will be used to find
or map the properties used for this energy calculation.
Returns
-------
sire.units.GeneralUnit (energy per quantity):
Returns an energy, with attached components for the
sub-components (if any) for this energy.
"""
return obj.apply("energy", other=other, map=map)
def _atom_energy(obj, other=None, map=None):
"""
Calculate the total energy of the molecule view(s) in this
collection.
other: (view or views, optional)
An optional second view (or collection of views).
If this is passed, then the energy between the
views in this collections and others will be calculated.
map: (dictionary, optional)
An optional property map that will be used to find
or map the properties used for this energy calculation.
Returns
-------
sire.units.GeneralUnit (energy per quantity):
Returns an energy, with attached components for the
sub-components (if any) for this energy.
"""
if other is None:
from ..units import GeneralUnit
return GeneralUnit(0)
elif map is None:
from ..system import calculate_energy
return calculate_energy(obj, _to_molecules(other))
else:
from ..system import calculate_energy
return calculate_energy(obj, _to_molecules(other), map=map)
def _total_energy(obj, other=None, map=None):
"""
Calculate the total energy of the molecule view(s) in this
collection.
other: (view or views, optional)
An optional second view (or collection of views).
If this is passed, then the energy between the
views in this collections and others will be calculated.
map: (dictionary, optional)
An optional property map that will be used to find
or map the properties used for this energy calculation.
Returns
-------
sire.units.GeneralUnit (energy per quantity):
Returns an energy, with attached components for the
sub-components (if any) for this energy.
"""
if hasattr(obj, "to_molecule_group"):
mols = obj.to_molecule_group()
else:
from ..legacy.Mol import MoleculeGroup
mols = MoleculeGroup("all")
mols.add(obj)
from ..system import calculate_energy
if map is None:
if other is None:
return calculate_energy(mols.molecules())
else:
return calculate_energy(mols.molecules(), _to_molecules(other))
elif other is None:
return calculate_energy(mols.molecules(), map=map)
else:
return calculate_energy(mols.molecules(), _to_molecules(other), map=map)
Atom.energy = _atom_energy
Residue.energy = _energy
Chain.energy = _energy
Segment.energy = _energy
CutGroup.energy = _energy
Molecule.energy = _energy
SelectorMol.energy = _total_energy
Selector_Atom_.energy = _total_energy
Selector_Residue_.energy = _total_energy
Selector_Chain_.energy = _total_energy
Selector_Segment_.energy = _total_energy
Selector_CutGroup_.energy = _total_energy
SelectorM_Atom_.energy = _total_energy
SelectorM_Residue_.energy = _total_energy
SelectorM_Chain_.energy = _total_energy
SelectorM_Segment_.energy = _total_energy
SelectorM_CutGroup_.energy = _total_energy
SelectorMol.energies = _energies
Selector_Atom_.energies = _energies
Selector_Residue_.energies = _energies
Selector_Chain_.energies = _energies
Selector_Segment_.energies = _energies
Selector_CutGroup_.energies = _energies
SelectorM_Atom_.energies = _energies
SelectorM_Residue_.energies = _energies
SelectorM_Chain_.energies = _energies
SelectorM_Segment_.energies = _energies
SelectorM_CutGroup_.energies = _energies
MoleculeView.view = _viewfunc
MoleculeView.smiles = _to_smiles
MoleculeView.smarts = _to_smarts
MoleculeView.view2d = _view2d
SelectorMol.view = _viewfunc
SelectorMol.view2d = _selector_view2d
SelectorMol.smiles = _selector_to_smiles
SelectorMol.smarts = _selector_to_smarts
Selector_Atom_.view = _viewfunc
Selector_Residue_.view = _viewfunc
Selector_Chain_.view = _viewfunc
Selector_Segment_.view = _viewfunc
Selector_CutGroup_.view = _viewfunc
SelectorM_Atom_.view = _viewfunc
SelectorM_Atom_.view2d = _selector_view2d
SelectorM_Atom_.smiles = _selector_to_smiles
SelectorM_Atom_.smiles = _selector_to_smarts
SelectorM_Residue_.view = _viewfunc
SelectorM_Residue_.view2d = _selector_view2d
SelectorM_Residue_.smiles = _selector_to_smiles
SelectorM_Residue_.smiles = _selector_to_smarts
SelectorM_Chain_.view = _viewfunc
SelectorM_Chain_.view2d = _selector_view2d
SelectorM_Chain_.smiles = _selector_to_smiles
SelectorM_Chain_.smiles = _selector_to_smarts
SelectorM_Segment_.view = _viewfunc
SelectorM_Segment_.view2d = _selector_view2d
SelectorM_Segment_.smiles = _selector_to_smiles
SelectorM_Segment_.smiles = _selector_to_smarts
SelectorM_CutGroup_.view = _viewfunc
SelectorM_CutGroup_.view2d = _selector_view2d
SelectorM_CutGroup_.smiles = _selector_to_smiles
SelectorM_CutGroup_.smiles = _selector_to_smarts
if not hasattr(SelectorMol, "__orig__find__"):
def __find__(obj, views):
"""
Find the index(es) of the passed view(s) in this container.
This returns a single index if a single view is passed,
or a list of indexes if multiple views are passed
(in the same order as the passed views).
This raises an IndexError if any of the views are
not in this container.
"""
matches = obj.__orig__find__(views)
if matches is None:
raise IndexError("Cannot find the passed view in the container.")
if views.is_selector():
if len(matches) != len(views):
raise IndexError(
"Could not find all of the passed views "
"in the container. We only found "
f"{len(matches)} of the required "
f"{len(views)}."
)
return matches
else:
if len(matches) != 1:
raise IndexError(
"We matched too many indexes? "
f"{matches}. Only expected to match one?"
)
return matches[0]
def __fix__find(CLASS):
CLASS.__orig__find__ = CLASS.find
CLASS.find = __find__
for C in [
Selector_Atom_,
Selector_Residue_,
Selector_Chain_,
Selector_CutGroup_,
Selector_Segment_,
SelectorMol,
SelectorM_Atom_,
SelectorM_Residue_,
SelectorM_Chain_,
SelectorM_CutGroup_,
SelectorM_Segment_,
]:
__fix__find(C)
if not hasattr(AtomMapping, "__orig_find__"):
def __mapping_find__(obj, atoms, container, find_all: bool = True):
from ..system import System
if System.is_system(container):
container = container.atoms()
return obj.__orig_find__(atoms, container, find_all=find_all)
def __mapping_map__(obj, atoms, container, match_all: bool = True):
from ..system import System
if System.is_system(container):
container = container.atoms()
return obj.__orig_map__(atoms, container, find_all=match_all)
AtomMapping.__orig_find__ = AtomMapping.find
AtomMapping.__orig_map__ = AtomMapping.map
AtomMapping.find = __mapping_find__
AtomMapping.map = __mapping_map__
if not hasattr(Molecule, "perturbation"):
def __molecule_perturbation(mol, map=None):
"""
Return an interface to the perturbable properties of
this molecule. Note that the molecule must be
perturbable to call this function
"""
from ..morph._perturbation import Perturbation
return Perturbation(mol, map=map)
def __molecule_is_perturbable(mol):
"""
Return whether or not this molecule is perturbable
(can be morphed with a lambda coordinate)
"""
if mol.has_property("is_perturbable"):
return mol.property("is_perturbable").as_boolean()
else:
return False
Molecule.perturbation = __molecule_perturbation
Molecule.is_perturbable = __molecule_is_perturbable
# Remove some temporary variables
del C
# also initialise sire.mm (it can sometimes be uninitialised if
# sire.mol is loaded first)
from ..mm import _fix_siremm
_fix_siremm()