def __init__(self, ind1, ind2, ind3, X1, Y1, Z1, phi, theta, omega, \
hwidth_spatial = 0.1, \
k_spatial = 200.0, \
hwidth_angular = np.pi/4., \
k_angular = 200.0):
"""
@param input: [index1, index2, index3, X1, Y1, Z1, phi, theta, omega]
ind1 - index of atom 1
ind2 - index of atom 2
ind3 - index of atom 3
The next 6 variables are the center of the flat-bottom harmonic bias
X1 - x coordinate of atom 1
X2 - x coordinate of atom 2
X3 - x coordinate of atom 3
phi, theta, omega - angular degrees of freedom, in radians
hwidth_spatial - the half width of the spatial flat-bottom harmonic terms (nm)
k_spatial - the spring constant on the spatial flat-bottom harmonic terms (kJ/nm)
hwidth_angular - the half width of the angular flat-bottom harmonic terms (radians)
k_angular - the spring constant on the angular flat-bottom harmonic terms (kJ/nm)
"""
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'external restraint')
# Store the parameters for later use.
self.params = OrderedDict()
for key in [\
'ind1', 'ind2', 'ind3', 'X1', 'Y1', 'Z1', 'phi', 'theta', 'omega', \
'hwidth_spatial', 'k_spatial', 'hwidth_angular', 'k_angular']:
self.params[key] = locals()[key]
def __init__(self, ind1, ind2, ind3, X1, Y1, Z1, phi, theta, omega, \
hwidth_spatial = 0.0, \
k_spatial = 200.0, \
hwidth_angular = 0.0, \
k_angular = 200.0):
"""
@param input: [index1, index2, index3, X1, Y1, Z1, phi, theta, omega]
ind1 - index of atom 1
ind2 - index of atom 2
ind3 - index of atom 3
The next 6 variables are the center of the flat-bottom harmonic bias
X1 - x coordinate of atom 1
X2 - x coordinate of atom 2
X3 - x coordinate of atom 3
phi, theta, omega - angular degrees of freedom, in radians
hwidth_spatial - the half width of the spatial flat-bottom harmonic terms (nm)
k_spatial - the spring constant on the spatial flat-bottom harmonic terms (kJ/nm)
hwidth_angular - the half width of the angular flat-bottom harmonic terms (radians)
k_angular - the spring constant on the angular flat-bottom harmonic terms (kJ/nm)
"""
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'external restraint')
# Store the parameters for later use.
self.params = OrderedDict()
for key in [\
'ind1', 'ind2', 'ind3', 'X1', 'Y1', 'Z1', 'phi', 'theta', 'omega', \
'hwidth_spatial', 'k_spatial', 'hwidth_angular', 'k_angular']:
self.params[key] = locals()[key]
def __init__(self, origin, direction, max_Z, max_R, name='cylinder'):
"""
@param origin: the origin of the principal axis of the cylinder
@type origin: {numpy.array}
@param direction: the direction of the principal axis of the cylinder
@type direction: {numpy.array}
@param max_Z: the maximal value of the projection along the principal axis
@type max_Z: C{float}
@param max_R: the maximal value orthogonal to the principal axis
@type max_R: C{float}
"""
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (origin, direction, max_Z, max_R)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, name)
# Store the parameters for later use.
self.origin = origin
self.direction = direction
self.max_Z = max_Z
self.max_R = max_R
self.name = name
if not ((self.direction[0] == 0.0) and
(self.direction[1] == 0.0) and
(self.direction[2] == 1.0)):
raise Exception("For efficiency, principal axis must be along (0,0,1)")
# Calculate the cylinder volume
self.volume = N.pi*(self.max_R*self.max_R)*(self.max_Z - self.origin[2])
def __init__(self, atom, center, force_constant):
"""
@param atom: the atom on which the force field acts
@type atom: L{MMTK.ChemicalObjects.Atom}
@param center: the point to which the atom is attached by
the harmonic potential
@type center: L{Scientific.Geometry.Vector}
@param force_constant: the force constant of the harmonic potential
@type force_constant: C{float}
"""
# Get the internal index of the atom if the argument is an
# atom object. It is the index that is stored internally,
# and when the force field is recreated from a specification
# in a trajectory file, it is the index that is passed instead
# of the atom object itself. Calling this method takes care
# of all the necessary checks and conversions.
self.atom_index = self.getAtomParameterIndices([atom])[0]
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (self.atom_index, center, force_constant)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'harmonic_oscillator')
# Store the parameters for later use.
self.center = center
self.force_constant = force_constant
def __init__(self, atom, xc,yc,zc, force_constant):
"""
@param atom: the atom on which the force field acts
@type atom: L{MMTK.ChemicalObjects.Atom}
@param center: the point to which the atom is attached by
the harmonic potential
@type center: L{Scientific.Geometry.Vector}
@param force_constant: the force constant of the harmonic potential
@type force_constant: C{float}
"""
# Get the internal index of the atom if the argument is an
# atom object. It is the index that is stored internally,
# and when the force field is recreated from a specification
# in a trajectory file, it is the index that is passed instead
# of the atom object itself. Calling this method takes care
# of all the necessary checks and conversions.
self.atom_index = self.getAtomParameterIndices([atom])[0]
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
# Store the parameters for later use.
self.x = xc
self.y = yc
self.z = zc
self.forceconstant = force_constant
self.arguments = (self.atom_index, self.x,self.y,self.z, self.forceconstant)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'HarmonicWell')
def __init__(self, atom1, atom2, atom3, atom4, dihedral, force_constant):
"""
:param atom1: first atom
:type atom1: :class:`~MMTK.ChemicalObjects.Atom`
:param atom2: second (axis) atom
:type atom2: :class:`~MMTK.ChemicalObjects.Atom`
:param atom3: third (axis)atom
:type atom3: :class:`~MMTK.ChemicalObjects.Atom`
:param atom4: fourth atom
:type atom4: :class:`~MMTK.ChemicalObjects.Atom`
:param dihedral: the dihedral angle at which the restraint is zero
:type dihedral: float
:param force_constant: the force constant of the restraint term.
The functional form of the restraint is
force_constant*(phi-abs(dihedral))**2, where
phi is the dihedral angle
atom1-atom2-atom3-atom4.
"""
self.index1, self.index2, self.index3, self.index4 = \
self.getAtomParameterIndices((atom1, atom2, atom3, atom4))
self.dihedral = dihedral
self.force_constant = force_constant
self.arguments = (self.index1, self.index2, self.index3, self.index4,
dihedral, force_constant)
ForceField.__init__(self, 'harmonic dihedral restraint')
def __init__(self, FN, strength, scaling_property, scaling_prefactor=None, inv_power=-2., grid_name='trilinear transformed grid', max_val=-1.0):
"""
@param strength: the electric field vector
@type strength: L{float}
@scaling_property: the name of the atomic property in the database
that is used to retrieve the atomic scaling_factor.
The default is 'amber_charge', the charge property
for Amber94 and Amber99.
@type scaling_property: C{str}
@param inv_power: the inverse of the power by which grid points are transformed
@grid_name: a name for the grid
@max_val: the maximum allowed value for a point on the grid.
A negative value means that there is no max.
"""
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (FN, strength,
scaling_property, scaling_prefactor,
inv_power, grid_name, max_val)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, grid_name)
# Store the parameters for later use.
self.FN = FN
self.strength = strength
self.scaling_property = scaling_property
self.inv_power = float(inv_power)
self.grid_name = grid_name
self.max_val = max_val
# Load the grid
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
self.grid_data = IO_Grid.read(self.FN, multiplier=0.1)
if not (self.grid_data['origin']==0.0).all():
raise Exception('Trilinear grid origin in %s not at (0, 0, 0)!'%self.FN)
# Make sure all grid values are positive
if (self.grid_data['vals']>0).any():
if (self.grid_data['vals']<0).any():
raise Exception('All of the grid points do not have the same sign')
else:
neg_vals = False
else:
neg_vals = True
self.grid_data['vals'] = -1*self.grid_data['vals']
# Transform the grid
nonzero = self.grid_data['vals']!=0
self.grid_data['vals'][nonzero] = self.grid_data['vals'][nonzero]**(1./self.inv_power)
import numpy as np
# "Cap" the grid values
if max_val>0.0:
self.grid_data['vals'] = max_val*np.tanh(self.grid_data['vals']/max_val)
if scaling_prefactor is not None:
self.scaling_prefactor = scaling_prefactor
else:
self.scaling_prefactor = -1. if neg_vals else 1.
def __init__(self, input_table):
"""
First 2 entries for external dofs:
[index1, index2, index3, X, Y, Z, bbot, abot]
[b0, kb, theta0, ka, n, gamma, dbot, kd]
Internal torsional dofs:
@param input_table: [index1, index2, index3, X, Y, Z, bbot, abot]
[b0, kb, theta0, ka, n, gamma, dbot, kd]
[4 atom indices, periodicity, gamma, bottom, force K] x internal dofs
@type atom: L{L{MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
double, double, double, double, double},
L{double, double, double, double,
int, double, double, double},
L{MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
inp, dobule, double, double} x #of internal dofs}
"""
# Internal dofs arguments
self.externalArgs = input_table[:2]
self.internalArgs = input_table[2:]
# Halve the flat bottoms
self.externalArgs[0][6] /= 2
self.externalArgs[0][7] /= 2
for ia in self.internalArgs:
ia[6] /= 2
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'pose')
def __init__(self, atom1, atom2, atom3):
self.index1, self.index2, self.index3 = self.getAtomParameterIndices(
[atom1, atom2, atom3])
self.arguments = (self.index1, self.index2, self.index3)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'HeCO2Trans')
def __init__(self, atom1, atom2, atom3, atom4, dihedral, force_constant):
"""
:param atom1: first atom
:type atom1: :class:`~MMTK.ChemicalObjects.Atom`
:param atom2: second (axis) atom
:type atom2: :class:`~MMTK.ChemicalObjects.Atom`
:param atom3: third (axis)atom
:type atom3: :class:`~MMTK.ChemicalObjects.Atom`
:param atom4: fourth atom
:type atom4: :class:`~MMTK.ChemicalObjects.Atom`
:param dihedral: the dihedral angle at which the restraint is zero
:type dihedral: float
:param force_constant: the force constant of the restraint term.
The functional form of the restraint is
force_constant*(phi-abs(dihedral))**2, where
phi is the dihedral angle
atom1-atom2-atom3-atom4.
"""
self.index1, self.index2, self.index3, self.index4 = \
self.getAtomParameterIndices((atom1, atom2, atom3, atom4))
self.dihedral = dihedral
self.force_constant = force_constant
self.arguments = (self.index1, self.index2, self.index3, self.index4,
dihedral, force_constant)
ForceField.__init__(self, 'harmonic dihedral restraint')
def __init__(self, atom1, atom2):
self.atom_index1, self.atom_index2 = self.getAtomParameterIndices((atom1,atom2))
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (self.atom_index1, self.atom_index2)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'NoPot')
def __init__(self, atom1, atom2, atom3, atom4, atom5, atom6):
self.atom_index1, self.atom_index2, self.atom_index3, self.atom_index4, self.atom_index5, self.atom_index6 = self.getAtomParameterIndices((atom1,atom2, atom3, atom4, atom5, atom6))
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (self.atom_index1, self.atom_index2, self.atom_index3, self.atom_index4, self.atom_index5, self.atom_index6)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'Dipole')
def __init__(self, atoms, D_r, c1, c2, c3, r_eq):
self.atom_indices = map(lambda x: self.getAtomParameterIndices([x])[0],atoms)
self.D_r = D_r
self.c1 = c1
self.c2 = c2
self.c3 = c3
self.r_eq = r_eq
self.arguments = (self.atom_indices,D_r,c1,c2,c3,r_eq)
ForceField.__init__(self, 'quartic_bond')
def __init__(self, universe,fraction,o_charge):
#Take the list of objects (molecules) and create a new list where each element in the
#list is another list containing the indices of all the atoms in the molecule
waters = universe.objectList()
water_atoms = map(lambda x: map(lambda y: self.getAtomParameterIndices([y])[0],x.atomList()), waters)
self.atom_indices = water_atoms
self.fraction = fraction
self.o_charge = o_charge
self.arguments = (self.atom_indices,self.fraction,self.o_charge)
ForceField.__init__(self, 'electrostatics')
def __init__(self,
FN,
strength,
scaling_property,
scaling_prefactor=None,
grid_name='trilinear grid',
max_val=-1.0,
Ethresh=-1.0):
"""
@param strength: the electric field vector
@type strength: L{float}
@scaling_property: the name of the atomic property in the database
that is used to retrieve the atomic scaling_factor.
The default is 'amber_charge', the charge property
for Amber94 and Amber99.
@grid_name: a name for the grid
@max_val: the maximum allowed value for a point on the grid.
A negative value means that there is no max.
@Ethresh: the maximum allowed value for the energy at any point.
A negative value means that there is no max.
@type scaling_property: C{str}
"""
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (FN, strength, scaling_property, scaling_prefactor,
grid_name, max_val)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, grid_name)
# Store the parameters for later use.
self.FN = FN
self.strength = strength
self.scaling_property = scaling_property
self.grid_name = grid_name
self.max_val = max_val
self.Ethresh = Ethresh
# Load the grid
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
self.grid_data = IO_Grid.read(self.FN, multiplier=0.1)
if not (self.grid_data['origin'] == 0.0).all():
raise Exception('Trilinear grid origin in %s not at (0, 0, 0)!' %
self.FN)
import numpy as np
# "Cap" the grid values
if max_val > 0.0:
self.grid_data['vals'] = max_val * np.tanh(
self.grid_data['vals'] / max_val)
if scaling_prefactor is not None:
self.scaling_prefactor = scaling_prefactor
else:
self.scaling_prefactor = 1.
def __init__(self, universe, epsilon, sigma):
#Get atom indices for oxygens
waters = universe.objectList()
oxygens = map(lambda x: x.atomList()[2],waters) #Oxygen is 2 in atom list
atom_indices = map(lambda x: self.getAtomParameterIndices([x])[0],oxygens)
self.atom_indices = atom_indices
self.epsilon = epsilon
self.sigma = sigma
self.arguments = (self.atom_indices,self.epsilon,self.sigma)
ForceField.__init__(self, 'lennard_jones')
def __init__(self,
FN,
strength,
scaling_property,
scaling_prefactor=None,
grid_name='trilinear transformed grid',
max_val=-1.0):
"""
@param strength: the electric field vector
@type strength: L{float}
@scaling_property: the name of the atomic property in the database
that is used to retrieve the atomic scaling_factor.
The default is 'amber_charge', the charge property
for Amber94 and Amber99.
@type scaling_property: C{str}
@grid_name: a name for the grid
@max_val: the maximum allowed value for a point on the grid.
A negative value means that there is no max.
"""
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (FN, strength, scaling_property, grid_name, max_val)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, grid_name)
# Store the parameters for later use.
self.FN = FN
self.strength = strength
self.scaling_property = scaling_property
self.grid_name = grid_name
self.max_val = max_val
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
self.grid_data = IO_Grid.read(self.FN, multiplier=0.1)
if not (self.grid_data['origin'] == 0.0).all():
raise Exception('Trilinear grid origin in %s not at (0, 0, 0)!' %
self.FN)
# Make sure all grid values are positive
n_positive = sum(self.grid_data['vals'] > 0)
n_negative = sum(self.grid_data['vals'] < 0)
if n_positive > 0 and n_negative > 0:
raise Exception('All of the grid points do not have the same sign')
if n_negative > 0:
self.grid_data['vals'] = -1 * self.grid_data['vals']
if scaling_prefactor is not None:
self.scaling_prefactor = scaling_prefactor
else:
self.scaling_prefactor = -1. if n_negative > 0 else 1.
def __init__(self, cutoff = None, scale_factor = 1.):
"""
:param cutoff: the cutoff for pair interactions. Pair interactions
in periodic systems are calculated using
the minimum-image convention; the cutoff should
therefore never be larger than half the smallest
edge length of the elementary cell.
:type cutoff: float
:param scale_factor: a global scaling factor
:type scale_factor: float
"""
ForceField.__init__(self, 'anisotropic_network')
self.arguments = (cutoff,)
self.cutoff = cutoff
self.scale_factor = scale_factor
def __init__(self, cutoff=None, scale_factor=1.):
"""
:param cutoff: the cutoff for pair interactions. Pair interactions
in periodic systems are calculated using
the minimum-image convention; the cutoff should
therefore never be larger than half the smallest
edge length of the elementary cell.
:type cutoff: float
:param scale_factor: a global scaling factor
:type scale_factor: float
"""
ForceField.__init__(self, 'anisotropic_network')
self.arguments = (cutoff, )
self.cutoff = cutoff
self.scale_factor = scale_factor
def __init__(self, FN, strength,
scaling_property, scaling_prefactor=None,
grid_name='trilinear grid', max_val=-1.0, Ethresh=-1.0):
"""
@param strength: the electric field vector
@type strength: L{float}
@scaling_property: the name of the atomic property in the database
that is used to retrieve the atomic scaling_factor.
The default is 'amber_charge', the charge property
for Amber94 and Amber99.
@grid_name: a name for the grid
@max_val: the maximum allowed value for a point on the grid.
A negative value means that there is no max.
@Ethresh: the maximum allowed value for the energy at any point.
A negative value means that there is no max.
@type scaling_property: C{str}
"""
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (FN, strength,
scaling_property, scaling_prefactor, grid_name, max_val)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, grid_name)
# Store the parameters for later use.
self.FN = FN
self.strength = strength
self.scaling_property = scaling_property
self.grid_name = grid_name
self.max_val = max_val
self.Ethresh = Ethresh
# Load the grid
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
self.grid_data = IO_Grid.read(self.FN, multiplier=0.1)
if not (self.grid_data['origin']==0.0).all():
raise Exception('Trilinear grid origin in %s not at (0, 0, 0)!'%self.FN)
import numpy as np
# "Cap" the grid values
if max_val>0.0:
self.grid_data['vals'] = max_val*np.tanh(self.grid_data['vals']/max_val)
if scaling_prefactor is not None:
self.scaling_prefactor = scaling_prefactor
else:
self.scaling_prefactor = 1.
def __init__(self, prmtopFN, \
prmtop_atom_order, inv_prmtop_atom_order, implicitSolvent='OpenMM_OBC2'):
"""
@name: a name for the grid
@implicitSolvent: the type of implicit solvent, which can be ['OpenMM_Gas','OpenMM_GBn', 'OpenMM_GBn2', 'OpenMM_HCT', 'OpenMM_OBC1', 'OpenMM_OBC2'].
"""
if not implicitSolvent in \
['OpenMM_Gas','OpenMM_GBn', 'OpenMM_GBn2', \
'OpenMM_HCT', 'OpenMM_OBC1', 'OpenMM_OBC2']:
raise Exception('Implicit solvent not recognized')
ForceField.__init__(self, implicitSolvent) # Initialize the ForceField class
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (prmtopFN, prmtop_atom_order, inv_prmtop_atom_order, implicitSolvent)
def __init__(self, prmtopFN,
prmtop_atom_order, inv_prmtop_atom_order):
"""
@param prmtopFN: an AMBER parameter and topology file
@type strength: C{str}
"""
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'OBC')
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (prmtopFN, prmtop_atom_order, inv_prmtop_atom_order)
self.prmtopFN = prmtopFN
self.prmtop_atom_order = prmtop_atom_order
self.inv_prmtop_atom_order = inv_prmtop_atom_order
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 __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 __init__(self, strength, charge_property='amber_charge'):
"""
@param strength: the electric field vector
@type strength: L{Scientific.Geometry.Vector}
@charge_property: the name of the atomic property in the database
that is used to retrieve the atomic charges.
The default is 'amber_charge', the charge property
for Amber94 and Amber99.
@type charge_property: C{str}
"""
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (strength, charge_property)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'electric_field')
# Store the parameters for later use.
self.strength = strength
self.charge_property = charge_property
def __init__(self, strength, charge_property='amber_charge'):
"""
@param strength: the electric field vector
@type strength: L{Scientific.Geometry.Vector}
@charge_property: the name of the atomic property in the database
that is used to retrieve the atomic charges.
The default is 'amber_charge', the charge property
for Amber94 and Amber99.
@type charge_property: C{str}
"""
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (strength, charge_property)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'electric_field')
# Store the parameters for later use.
self.strength = strength
self.charge_property = charge_property
def __init__(self, center, max_R, name='Sphere'):
"""
@param center: the center of the principal axis of the sphere
@type center: {numpy.array}
@param max_R: the maximal value orthogonal to the principal axis
@type max_R: C{float}
"""
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (center, max_R)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, name)
# Store the parameters for later use.
self.center = center
self.max_R = max_R
self.name = name
# Calculate the sphere volume
self.volume = 4. / 3. * N.pi * (self.max_R * self.max_R * self.max_R)
def __init__(self, center, max_R, name='Sphere'):
"""
@param center: the center of the principal axis of the sphere
@type center: {numpy.array}
@param max_R: the maximal value orthogonal to the principal axis
@type max_R: C{float}
"""
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (center, max_R)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, name)
# Store the parameters for later use.
self.center = center
self.max_R = max_R
self.name = name
# Calculate the sphere volume
self.volume = 4./3.*N.pi*(self.max_R*self.max_R*self.max_R)
def __init__(self, torsions, \
k = 200.0):
"""
Internal torsional dofs:
@param input: [4 atom indices, gamma] x internal dofs
@type atom: L{MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
double} x # of internal dofs}
"""
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'internal dihedral restraint')
# Store the parameters for later use
self.params = OrderedDict()
for key in ['torsions', 'k']:
self.params[key] = locals()[key]
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 __init__(self, FN, strength, scaling_property, scaling_prefactor=None, grid_name='trilinear transformed grid', max_val=-1.0):
"""
@param strength: the electric field vector
@type strength: L{float}
@scaling_property: the name of the atomic property in the database
that is used to retrieve the atomic scaling_factor.
The default is 'amber_charge', the charge property
for Amber94 and Amber99.
@type scaling_property: C{str}
@grid_name: a name for the grid
@max_val: the maximum allowed value for a point on the grid.
A negative value means that there is no max.
"""
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (FN, strength, scaling_property, grid_name, max_val)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, grid_name)
# Store the parameters for later use.
self.FN = FN
self.strength = strength
self.scaling_property = scaling_property
self.grid_name = grid_name
self.max_val = max_val
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
self.grid_data = IO_Grid.read(self.FN, multiplier=0.1)
if not (self.grid_data['origin']==0.0).all():
raise Exception('Trilinear grid origin in %s not at (0, 0, 0)!'%self.FN)
# Make sure all grid values are positive
n_positive = sum(self.grid_data['vals']>0)
n_negative = sum(self.grid_data['vals']<0)
if n_positive>0 and n_negative>0:
raise Exception('All of the grid points do not have the same sign')
if n_negative>0:
self.grid_data['vals'] = -1*self.grid_data['vals']
if scaling_prefactor is not None:
self.scaling_prefactor = scaling_prefactor
else:
self.scaling_prefactor = -1. if n_negative>0 else 1.
def __init__(self, torsions, \
k = 200.0):
"""
Internal torsional dofs:
@param input: [4 atom indices, gamma] x internal dofs
@type atom: L{MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
MMTK.ChemicalObjects.Atom.index,
double} x # of internal dofs}
"""
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'internal dihedral restraint')
# Store the parameters for later use
self.params = OrderedDict()
for key in ['torsions', 'k']:
self.params[key] = locals()[key]
def __init__(self,
prmtopFN=None,
inv_prmtop_atom_order=None,
desolvationGridFN=None,
r_min=0.14,
r_max=1.0,
strength=1.0):
"""
@param prmtopFN: an AMBER parameter and topology file
@type strength: C{str}
r_min and r_max should be in units of nanometers
"""
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'OBC')
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (prmtopFN, inv_prmtop_atom_order, \
desolvationGridFN, r_min, r_max, strength)
# Load the desolvation grid
if desolvationGridFN is not None:
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
self.grid_data = IO_Grid.read(desolvationGridFN, multiplier=0.1)
if not (self.grid_data['origin'] == 0.0).all():
raise Exception(
'Trilinear grid origin in %s not at (0, 0, 0)!' % FN)
self.useDesolvationGrid = True
else:
self.grid_data = {'spacing':np.array([0., 0., 0.]), \
'counts':np.array([0, 0, 0]), \
'vals':np.array([])}
self.useDesolvationGrid = False
# Store arguments as class variables
self.prmtopFN = prmtopFN
self.inv_prmtop_atom_order = inv_prmtop_atom_order
self.desolvationGridFN = desolvationGridFN
self.r_min = r_min
self.r_max = r_max
self.strength = strength
def __init__(self, fc_length=0.7, cutoff=1.2, factor=46402.):
"""
:param fc_length: a range parameter
:type fc_length: float
:param cutoff: the cutoff for pair interactions, should be
at least 2.5 nm. Pair interactions in periodic
systems are calculated using the minimum-image
convention; the cutoff should therefore never be
larger than half the smallest edge length of the
elementary cell.
:type cutoff: float
:param factor: a global scaling factor
:type factor: float
"""
self.arguments = (fc_length, cutoff, factor)
ForceField.__init__(self, 'deformation')
self.arguments = (fc_length, cutoff, factor)
self.fc_length = fc_length
self.cutoff = cutoff
self.factor = factor
def __init__(self, fc_length = 0.7, cutoff = 1.2, factor = 46402.):
"""
:param fc_length: a range parameter
:type fc_length: float
:param cutoff: the cutoff for pair interactions, should be
at least 2.5 nm. Pair interactions in periodic
systems are calculated using the minimum-image
convention; the cutoff should therefore never be
larger than half the smallest edge length of the
elementary cell.
:type cutoff: float
:param factor: a global scaling factor
:type factor: float
"""
self.arguments = (fc_length, cutoff, factor)
ForceField.__init__(self, 'deformation')
self.arguments = (fc_length, cutoff, factor)
self.fc_length = fc_length
self.cutoff = cutoff
self.factor = factor
def __init__(self,
prmtopFN=None,
inv_prmtop_atom_order=None,
desolvationGridFN=None,
r_min = 0.14,
r_max = 1.0,
strength=1.0):
"""
@param prmtopFN: an AMBER parameter and topology file
@type strength: C{str}
r_min and r_max should be in units of nanometers
"""
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'OBC')
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (prmtopFN, inv_prmtop_atom_order, \
desolvationGridFN, r_min, r_max, strength)
# Load the desolvation grid
if desolvationGridFN is not None:
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
self.grid_data = IO_Grid.read(desolvationGridFN, multiplier=0.1)
if not (self.grid_data['origin']==0.0).all():
raise Exception('Trilinear grid origin in %s not at (0, 0, 0)!'%FN)
self.useDesolvationGrid = True
else:
self.grid_data = {'spacing':np.array([0., 0., 0.]), \
'counts':np.array([0, 0, 0]), \
'vals':np.array([])}
self.useDesolvationGrid = False
# Store arguments as class variables
self.prmtopFN = prmtopFN
self.inv_prmtop_atom_order = inv_prmtop_atom_order
self.desolvationGridFN = desolvationGridFN
self.r_min = r_min
self.r_max = r_max
self.strength = strength
def __init__(self, atom1, atom2, atom3, angle, force_constant):
"""
:param atom1: first atom
:type atom1: :class:`~MMTK.ChemicalObjects.Atom`
:param atom2: second (central) atom
:type atom2: :class:`~MMTK.ChemicalObjects.Atom`
:param atom3: third atom
:type atom3: :class:`~MMTK.ChemicalObjects.Atom`
:param angle: the angle at which the restraint is zero
:type angle: float
:param force_constant: the force constant of the restraint term.
The functional form of the restraint is
force_constant*(phi-angle)**2, where
phi is the angle atom1-atom2-atom3.
"""
self.index1, self.index2, self.index3 = \
self.getAtomParameterIndices((atom1, atom2, atom3))
self.arguments = (self.index1, self.index2, self.index3, angle,
force_constant)
self.angle = angle
self.force_constant = force_constant
ForceField.__init__(self, 'harmonic angle restraint')
def __init__(self, atom1, atom2, atom3, angle, force_constant):
"""
:param atom1: first atom
:type atom1: :class:`~MMTK.ChemicalObjects.Atom`
:param atom2: second (central) atom
:type atom2: :class:`~MMTK.ChemicalObjects.Atom`
:param atom3: third atom
:type atom3: :class:`~MMTK.ChemicalObjects.Atom`
:param angle: the angle at which the restraint is zero
:type angle: float
:param force_constant: the force constant of the restraint term.
The functional form of the restraint is
force_constant*(phi-angle)**2, where
phi is the angle atom1-atom2-atom3.
"""
self.index1, self.index2, self.index3 = \
self.getAtomParameterIndices((atom1, atom2, atom3))
self.arguments = (self.index1, self.index2, self.index3,
angle, force_constant)
self.angle = angle
self.force_constant = force_constant
ForceField.__init__(self, 'harmonic angle restraint')
def __init__(self, FN,
name='Interpolation',
interpolation_type='Trilinear',
strength=1.0,
scaling_property='amber_charge',
scaling_prefactor=None,
inv_power=None,
grid_thresh=-1.0,
energy_thresh=-1.0):
"""
@FN: the file name.
@name: a name for the grid
@interpolation_type: the type of interpolation, which can be
['Trilinear','BSpline','CatmullRom', or 'Tricubic'].
@param strength: scaling factor for all the energies and gradients.
@type strength: L{float}
@scaling_property: the name of the atomic property in the database.
that is used to retrieve the atomic scaling_factor.
The default is 'amber_charge'.
@scaling_prefactor: the atomic scaling_factor is scaled by this value.
@inv_power: the inverse of the power by which grid points are transformed.
@grid_thresh: the maximum allowed value for a point on the grid.
A negative value means that there is no max.
@energy_thresh: the maximum allowed value for the energy at any point.
A negative value means that there is no max.
@type scaling_property: C{str}
"""
if not interpolation_type in \
['Trilinear','BSpline', 'CatmullRom', 'Tricubic']:
raise Exception('Interpolation type not recognized')
ForceField.__init__(self, name) # Initialize the ForceField class
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (FN, name, interpolation_type, strength, \
scaling_property, scaling_prefactor, \
inv_power, grid_thresh, energy_thresh)
self.params = OrderedDict()
for key in ['FN','name','interpolation_type','strength','scaling_property',\
'scaling_prefactor','inv_power','grid_thresh','energy_thresh']:
self.params[key] = locals()[key]
# Load the grid
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
self.grid_data = IO_Grid.read(FN, multiplier=0.1)
if not (self.grid_data['origin']==0.0).all():
raise Exception('Trilinear grid origin in %s not at (0, 0, 0)!'%FN)
# Transform the grid
neg_vals = False
if inv_power is not None:
# Make sure all grid values are positive
if (self.grid_data['vals']>0).any():
if (self.grid_data['vals']<0).any():
raise Exception('All of the grid points do not have the same sign')
else:
neg_vals = True
self.grid_data['vals'] = -1*self.grid_data['vals']
# Transform all nonzero elements
nonzero = self.grid_data['vals']!=0
self.grid_data['vals'][nonzero] = self.grid_data['vals'][nonzero]**(1./inv_power)
import numpy as np
# "Cap" the grid values
if grid_thresh>0.0:
self.grid_data['vals'] = grid_thresh*np.tanh(self.grid_data['vals']/grid_thresh)
if scaling_prefactor is None:
self.params['scaling_prefactor'] = -1. if neg_vals else 1.
def __init__(self, universe):
self.atoms = map(lambda x: self.getAtomParameterIndices([x])[0],
universe.atomList())
self.arguments = (self.atoms)
ForceField.__init__(self, 'mbpol_potential')
def __init__(self, name):
ForceField.__init__(self, name)
self.type = 'bonded'
def __init__(self, atom1, atom2):
self.id1, self.id2 = self.getAtomParameterIndices([atom1, atom2])
self.arguments = (self.id1, self.id2)
#self.arguments = (self.id1, self.id2, beads)
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'hehe')
def __init__(self, atom1):
self.atom_index = self.getAtomParameterIndices([atom1])[0]
self.arguments = (self.atom_index, )
# Initialize the ForceField class, giving a name to this one.
ForceField.__init__(self, 'h2h2o')
def __init__(self, atoms, r_eq, k_r):
self.atom_indices = map(lambda x: self.getAtomParameterIndices([x])[0],atoms)
self.r_eq = r_eq
self.k_r = k_r
self.arguments = (self.atom_indices,r_eq,k_r)
ForceField.__init__(self, 'harmonic_bond')
def __init__(self,
FN,
name='Interpolation',
interpolation_type='Trilinear',
strength=1.0,
scaling_property='amber_charge',
scaling_prefactor=None,
inv_power=None,
grid_thresh=-1.0,
energy_thresh=-1.0):
"""
@FN: the file name.
@name: a name for the grid
@interpolation_type: the type of interpolation, which can be
['Trilinear','BSpline','CatmullRom', or 'Tricubic'].
@param strength: scaling factor for all the energies and gradients.
@type strength: L{float}
@scaling_property: the name of the atomic property in the database.
that is used to retrieve the atomic scaling_factor.
The default is 'amber_charge'.
@scaling_prefactor: the atomic scaling_factor is scaled by this value.
@inv_power: the inverse of the power by which grid points are transformed.
@grid_thresh: the maximum allowed value for a point on the grid.
A negative value means that there is no max.
@energy_thresh: the maximum allowed value for the energy at any point.
A negative value means that there is no max.
@type scaling_property: C{str}
"""
if not interpolation_type in \
['Trilinear','BSpline', 'CatmullRom', 'Tricubic']:
raise Exception('Interpolation type not recognized')
ForceField.__init__(self, name) # Initialize the ForceField class
# Store arguments that recreate the force field from a pickled
# universe or from a trajectory.
self.arguments = (FN, name, interpolation_type, strength, \
scaling_property, scaling_prefactor, \
inv_power, grid_thresh, energy_thresh)
self.params = OrderedDict()
for key in ['FN','name','interpolation_type','strength','scaling_property',\
'scaling_prefactor','inv_power','grid_thresh','energy_thresh']:
self.params[key] = locals()[key]
# Load the grid
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
self.grid_data = IO_Grid.read(FN, multiplier=0.1)
if not (self.grid_data['origin'] == 0.0).all():
raise Exception('Trilinear grid origin in %s not at (0, 0, 0)!' %
FN)
# Transform the grid
neg_vals = False
if inv_power is not None:
# Make sure all grid values are positive
if (self.grid_data['vals'] > 0).any():
if (self.grid_data['vals'] < 0).any():
raise Exception(
'All of the grid points do not have the same sign')
else:
neg_vals = True
self.grid_data['vals'] = -1 * self.grid_data['vals']
# Transform all nonzero elements
nonzero = self.grid_data['vals'] != 0
self.grid_data['vals'][nonzero] = self.grid_data['vals'][
nonzero]**(1. / inv_power)
import numpy as np
# "Cap" the grid values
if grid_thresh > 0.0:
self.grid_data['vals'] = grid_thresh * np.tanh(
self.grid_data['vals'] / grid_thresh)
if scaling_prefactor is not None:
self.params['scaling_prefactor'] = scaling_prefactor
else:
self.params['scaling_prefactor'] = -1. if neg_vals else 1.
def __init__(self, name):
ForceField.__init__(self, name)
self.type = 'nonbonded'
def __init__(self, atoms, theta_eq, k_theta):
self.atom_indices = map(lambda x: self.getAtomParameterIndices([x])[0],atoms)
self.theta_eq = theta_eq
self.k_theta = k_theta
self.arguments = (self.atom_indices,theta_eq,k_theta)
ForceField.__init__(self, 'harmonic_angle')
