def __init__(self,
obj1,
obj2,
distance,
force_constant,
nb_exclusion=False):
"""
:param obj1: the object defining center-of-mass 1
:type obj1: :class:`~MMTK.Collections.GroupOfAtoms`
:param obj2: the object defining center-of-mass 2
:type obj2: :class:`~MMTK.Collections.GroupOfAtoms`
:param distance: the distance between cm 1 and cm2 at which
the restraint is zero
:type distance: float
:param force_constant: the force constant of the restraint term.
The functional form of the restraint is
force_constant*((cm1-cm2).length()-distance)**2,
where cm1 and cm2 are the centrer-of-mass
positions of the two objects.
:type force_constant: float
:param nb_exclussion: if True, non-bonded interactions between
the restrained atoms are suppressed, as
for a chemical bond
:type nb_exclussion: bool
"""
if isinstance(obj1, int) and isinstance(obj2, int):
# Older MMTK versions admitted only single atoms and
# stored single indices. Support this mode for opening
# trajectories made with those versions
self.atom_indices_1 = [obj1]
self.atom_indices_2 = [obj2]
if isChemicalObject(obj1) or isCollection(obj1):
obj1 = obj1.atomList()
if isChemicalObject(obj2) or isCollection(obj2):
obj2 = obj2.atomList()
self.atom_indices_1 = self.getAtomParameterIndices(obj1)
self.atom_indices_2 = self.getAtomParameterIndices(obj2)
if nb_exclusion and (len(self.atom_indices_1) > 1
or len(self.atom_indices_2) > 1):
raise ValueError("Non-bonded exclusion possible only "
"between single-atom objects")
self.arguments = (self.atom_indices_1, self.atom_indices_2, distance,
force_constant, nb_exclusion)
self.distance = distance
self.force_constant = force_constant
self.nb_exclusion = nb_exclusion
ForceField.__init__(self, 'harmonic distance restraint')
def get_chemical_objects_dict(universe):
d = {}
for obj in universe.objectList():
if isChemicalObject(obj):
d.setdefault(obj.name, []).append(obj)
return d
def run_step(self, index):
"""
Runs a single step of the job.\n
:Parameters:
#. index (int): The index of the step.
:Returns:
#. index (int): The index of the step.
#. None
"""
# get the Frame index
frameIndex = self.configuration['frames']['value'][index]
universe = self.configuration['trajectory']['instance'].universe
# The configuration corresponding to this index is set to the universe.
universe.setFromTrajectory(self.configuration['trajectory']['instance'], frameIndex)
# Case of the first frame.
if self._refCoords is None:
self._refCoords = universe._realToBoxPointArray(universe.configuration().array)
for obj in universe.objectList():
if not isChemicalObject(obj):
continue
if isinstance(obj,Atom):
continue
if not obj in self._chemicalObjects:
continue
atoms = obj.atomList()[:]
contiguous_configuration(atoms[0],atoms,self._refCoords)
# Case of the other frames.
else:
currentCoords = universe._realToBoxPointArray(universe.configuration().array)
diff = currentCoords - self._refCoords
self._refCoords = numpy.where(numpy.abs(diff)>0.5,currentCoords-numpy.round(diff),currentCoords)
corrCoords = universe._boxToRealPointArray(self._refCoords)
universe.configuration().array = corrCoords
# The times corresponding to the running index.
t = self.configuration['frames']['time'][index]
# Write the step.
self.snapshot(data = {'time' : t})
return index, None
def atomindex_to_moleculeindex(universe):
d = {}
for i,obj in enumerate(universe.objectList()):
if isChemicalObject(obj):
for at in obj.atomList():
d[at.index] = i
return d
def __init__(self, obj1, obj2, distance, force_constant,
nb_exclusion=False):
"""
:param obj1: the object defining center-of-mass 1
:type obj1: :class:`~MMTK.Collections.GroupOfAtoms`
:param obj2: the object defining center-of-mass 2
:type obj2: :class:`~MMTK.Collections.GroupOfAtoms`
:param distance: the distance between cm 1 and cm2 at which
the restraint is zero
:type distance: float
:param force_constant: the force constant of the restraint term.
The functional form of the restraint is
force_constant*((cm1-cm2).length()-distance)**2,
where cm1 and cm2 are the centrer-of-mass
positions of the two objects.
:type force_constant: float
:param nb_exclussion: if True, non-bonded interactions between
the restrained atoms are suppressed, as
for a chemical bond
:type nb_exclussion: bool
"""
if isinstance(obj1, int) and isinstance(obj2, int):
# Older MMTK versions admitted only single atoms and
# stored single indices. Support this mode for opening
# trajectories made with those versions
self.atom_indices_1 = [obj1]
self.atom_indices_2 = [obj2]
if isChemicalObject(obj1) or isCollection(obj1):
obj1 = obj1.atomList()
if isChemicalObject(obj2) or isCollection(obj2):
obj2 = obj2.atomList()
self.atom_indices_1 = self.getAtomParameterIndices(obj1)
self.atom_indices_2 = self.getAtomParameterIndices(obj2)
if nb_exclusion and (len(self.atom_indices_1) > 1
or len(self.atom_indices_2) > 1):
raise ValueError("Non-bonded exclusion possible only "
"between single-atom objects")
self.arguments = (self.atom_indices_1, self.atom_indices_2,
distance, force_constant, nb_exclusion)
self.distance = distance
self.force_constant = force_constant
self.nb_exclusion = nb_exclusion
ForceField.__init__(self, 'harmonic distance restraint')
def get_chemical_objects_size(universe):
d = {}
for obj in universe.objectList():
if isChemicalObject(obj):
if d.has_key(obj.name):
continue
d[obj.name] = obj.numberOfAtoms()
return d
def addObject(self, object):
"""
Add objects to the collection.
:param object: the object(s) to be added. If it is another collection
or a list, all of its elements are added
"""
from MMTK.ChemicalObjects import isChemicalObject
if isChemicalObject(object):
self.addChemicalObject(object)
elif isCollection(object):
self.addChemicalObjectList(object.objectList())
elif Utility.isSequenceObject(object):
if object and isChemicalObject(object[0]):
self.addChemicalObjectList(list(object))
else:
for o in object:
self.addObject(o)
else:
raise TypeError('Wrong object type in collection')
def addObject(self, object):
"""
Add objects to the collection.
:param object: the object(s) to be added. If it is another collection
or a list, all of its elements are added
"""
from MMTK.ChemicalObjects import isChemicalObject
if isChemicalObject(object):
self.addChemicalObject(object)
elif isCollection(object):
self.addChemicalObjectList(object.objectList())
elif Utility.isSequenceObject(object):
if object and isChemicalObject(object[0]):
self.addChemicalObjectList(list(object))
else:
for o in object:
self.addObject(o)
else:
raise TypeError('Wrong object type in collection')
def get_chemical_objects_number(universe):
d = {}
for obj in universe.objectList():
if isChemicalObject(obj):
if d.has_key(obj.name):
d[obj.name] += 1
else:
d[obj.name] = 1
return d
def map(self, function):
"""
Apply a function to all objects in the collection and
return the list of the results. If the results are chemical
objects, a Collection object is returned instead of a list.
:param function: the function to be applied
:type function: callable
:returns: the list or collection of the results
"""
from MMTK.ChemicalObjects import isChemicalObject
list = [function(o) for o in self.objectList()]
if list and isChemicalObject(list[0]):
return Collection(list)
else:
return list
def map(self, function):
"""
Apply a function to all objects in the collection and
return the list of the results. If the results are chemical
objects, a Collection object is returned instead of a list.
:param function: the function to be applied
:type function: callable
:returns: the list or collection of the results
"""
from MMTK.ChemicalObjects import isChemicalObject
list = [function(o) for o in self.objectList()]
if list and isChemicalObject(list[0]):
return Collection(list)
else:
return list
def __init__(self, obj, center, force_constant):
"""
:param obj: the object on whose center of mass the force field acts
:type obj: :class:`~MMTK.Collections.GroupOfAtoms`
:param center: the point to which the atom is attached by
the harmonic potential
:type center: Scientific.Geometry.Vector
:param force_constant: the force constant of the harmonic potential
:type force_constant: float
"""
if isChemicalObject(obj):
obj = obj.atomList()
self.atom_indices = self.getAtomParameterIndices(obj)
self.arguments = (self.atom_indices, center, force_constant)
ForceField.__init__(self, 'harmonic_trap')
self.center = center
self.force_constant = force_constant
def __init__(self, obj, center, force_constant):
"""
:param obj: the object on whose center of mass the force field acts
:type obj: :class:`~MMTK.Collections.GroupOfAtoms`
:param center: the point to which the atom is attached by
the harmonic potential
:type center: Scientific.Geometry.Vector
:param force_constant: the force constant of the harmonic potential
:type force_constant: float
"""
if isChemicalObject(obj):
obj = obj.atomList()
self.atom_indices = self.getAtomParameterIndices(obj)
self.arguments = (self.atom_indices, center, force_constant)
ForceField.__init__(self, 'harmonic_trap')
self.center = center
self.force_constant = force_constant
def write(self, object, configuration=None, distance=None):
from MMTK.ChemicalObjects import isChemicalObject
from MMTK.Universe import InfiniteUniverse
if distance is None:
try:
distance = object.universe().distanceVector
except AttributeError:
distance = InfiniteUniverse().distanceVector
if not isChemicalObject(object):
for o in object:
self.write(o, configuration, distance)
else:
for bu in object.bondedUnits():
for a in bu.atomList():
self.writeAtom(a, configuration)
if hasattr(bu, 'bonds'):
for b in bu.bonds:
self.writeBond(b, configuration, distance)
def write(self, object, configuration = None, distance = None):
from MMTK.ChemicalObjects import isChemicalObject
from MMTK.Universe import InfiniteUniverse
if distance is None:
try:
distance = object.universe().distanceVector
except AttributeError:
distance = InfiniteUniverse().distanceVector
if not isChemicalObject(object):
for o in object:
self.write(o, configuration, distance)
else:
for bu in object.bondedUnits():
for a in bu.atomList():
self.writeAtom(a, configuration)
if hasattr(bu, 'bonds'):
for b in bu.bonds:
self.writeBond(b, configuration, distance)
def removeObject(self, object):
"""
Remove an object or a list or collection of objects from the
collection. The object(s) to be removed must be elements of the
collection.
:param object: the object to be removed, or a list or collection
of objects whose elements are to be removed
:raises ValueError: if the object is not an element of the collection
"""
from MMTK.ChemicalObjects import isChemicalObject
if isChemicalObject(object):
self.removeChemicalObject(object)
elif isCollection(object) or Utility.isSequenceObject(object):
for o in object:
self.removeObject(o)
else:
raise ValueError('Object not in this collection')
def removeObject(self, object):
"""
Remove an object or a list or collection of objects from the
collection. The object(s) to be removed must be elements of the
collection.
:param object: the object to be removed, or a list or collection
of objects whose elements are to be removed
:raises ValueError: if the object is not an element of the collection
"""
from MMTK.ChemicalObjects import isChemicalObject
if isChemicalObject(object):
self.removeChemicalObject(object)
elif isCollection(object) or Utility.isSequenceObject(object):
for o in object:
self.removeObject(o)
else:
raise ValueError('Object not in this collection')
def find_atoms_in_molecule(universe, moleculeName, atomNames, indexes=False):
molecules = []
for obj in universe.objectList():
if isChemicalObject(obj):
if obj.name == moleculeName:
molecules.append(obj)
match = []
for mol in molecules:
atoms = mol.atomList()
names = [at.name for at in mol.atomList()]
l = [atoms[names.index(atName)] for atName in atomNames]
match.append(l)
if indexes is True:
match = [[at.index for at in atList] for atList in match]
return match
def resolve_undefined_molecules_name(universe):
for obj in universe.objectList():
if isChemicalObject(obj):
if not obj.name.strip():
obj.name = brute_formula(obj,sep="")