def __init__(self,
m,
objects,
kt,
gamma=0.01,
maximum_time_step=1.0,
sf=None):
"""Setup MD
@param m The IMP Model
@param objects What to sample. Use flat list of particles or (deprecated) 'MD Sample Objects' from PMI1
@param kt Temperature
@param gamma Viscosity parameter
@param maximum_time_step MD max time step
"""
self.m = m
# check if using PMI1 objects dictionary, or just list of particles
try:
for obj in objects:
to_sample = obj.get_particles_to_sample(
)['Floppy_Bodies_SimplifiedModel'][0]
except:
to_sample = objects
self.ltstate = IMP.atom.LangevinThermostatOptimizerState(
self.m, to_sample, kt / 0.0019872041, gamma)
self.md = IMP.atom.MolecularDynamics(self.m)
self.md.set_maximum_time_step(maximum_time_step)
if sf:
self.md.set_scoring_function(sf)
else:
self.md.set_scoring_function(get_restraint_set(self.m))
self.md.add_optimizer_state(self.ltstate)
self.simulated_annealing = False
self.nframe = -1
def __init__(self,m,objects,kt,gamma=0.01,maximum_time_step=1.0):
"""Setup MD
@param m The IMP Model
@param objects What to sample. Use flat list of particles or (deprecated) 'MD Sample Objects' from PMI1
@param kt Temperature
@param gamma Viscosity parameter
@param maximum_time_step MD max time step
"""
self.m=m
# check if using PMI1 objects dictionary, or just list of particles
try:
for obj in objects:
to_sample=obj.get_particles_to_sample()['Floppy_Bodies_SimplifiedModel'][0]
except:
to_sample = objects
self.ltstate=IMP.atom.LangevinThermostatOptimizerState(self.m,to_sample,
kt/0.0019872041,
gamma)
self.md = IMP.atom.MolecularDynamics(self.m)
self.md.set_maximum_time_step(maximum_time_step)
self.md.set_scoring_function(get_restraint_set(self.m))
self.md.add_optimizer_state(self.ltstate)
self.simulated_annealing = False
self.nframe = -1
def __init__(self, m, objects, temp, filterbyname=None, dof=None):
"""Setup Monte Carlo sampling
@param m The IMP Model
@param objects Sample Objects. Alternatively pass the degrees of freedom object
@param temp The initial MC temperature
@param filterbyname Not implemented
@param dof DegreesOfFreedom object (replaces "objects")
"""
# check that the objects containts get_particles_to_sample methods
# and the particle type is supported
# list of particles to sample self.losp
self.losp = ["Rigid_Bodies", "Floppy_Bodies", "Nuisances", "X_coord", "Weights"]
self.simulated_annealing = False
self.selfadaptive = False
# that is -1 because mc has not yet run
self.nframe = -1
self.temp = temp
self.mvs = []
self.mvslabels = []
self.label = "None"
self.m = m
if dof is not None:
self.mvs = dof.get_all_movers()
else:
for ob in objects:
try:
ob.get_particles_to_sample()
except:
print("MonteCarlo: object ", ob, " doesn't have get_particles_to_sample() method")
pts = ob.get_particles_to_sample()
for k in pts.keys():
if "Rigid_Bodies" in k:
mvs = self.get_rigid_body_movers(pts[k][0], pts[k][1], pts[k][2])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "SR_Bodies" in k:
print(len(pts[k]))
mvs = self.get_super_rigid_body_movers(pts[k][0], pts[k][1], pts[k][2])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Floppy_Bodies" in k:
mvs = self.get_floppy_body_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "X_coord" in k:
mvs = self.get_X_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Nuisances" in k:
if not self.isd_available:
raise ValueError("isd module needed to use nuisances")
mvs = self.get_nuisance_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Weights" in k:
if not self.isd_available:
raise ValueError("isd module needed to use weights")
mvs = self.get_weight_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
# SerialMover
self.smv = IMP.core.SerialMover(self.mvs)
self.mc = IMP.core.MonteCarlo(self.m)
self.mc.set_scoring_function(get_restraint_set(self.m))
self.mc.set_return_best(False)
self.mc.set_kt(self.temp)
self.mc.add_mover(self.smv)
def __init__(self, m, objects):
self.m = m
self.nframe = -1
self.cg = IMP.core.ConjugateGradients(self.m)
self.cg.set_scoring_function(get_restraint_set(self.m))
def __init__(self, m, objects=None, temp=1.0, filterbyname=None):
"""Setup Monte Carlo sampling
@param m The IMP Model
@param objects What to sample. Use flat list of particles or
(deprecated) 'MC Sample Objects' from PMI1
@param temp The MC temperature
@param filterbyname Not used
"""
self.losp = [
"Rigid_Bodies", "Floppy_Bodies", "Nuisances", "X_coord", "Weights"
"Surfaces"
]
self.simulated_annealing = False
self.selfadaptive = False
# that is -1 because mc has not yet run
self.nframe = -1
self.temp = temp
self.mvs = []
self.mvslabels = []
self.label = "None"
self.m = m
self.movers_data = {}
# check if using PMI1 or just passed a list of movers
gather_objects = False
try:
objects[0].get_particles_to_sample()
gather_objects = True
except:
self.mvs = objects
print(gather_objects)
if gather_objects:
for ob in objects:
pts = ob.get_particles_to_sample()
for k in pts.keys():
if "Rigid_Bodies" in k:
mvs = self.get_rigid_body_movers(
pts[k][0], pts[k][1], pts[k][2])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "SR_Bodies" in k:
print(len(pts[k]))
mvs = self.get_super_rigid_body_movers(
pts[k][0], pts[k][1], pts[k][2])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Floppy_Bodies" in k:
mvs = self.get_floppy_body_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "X_coord" in k:
mvs = self.get_X_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Nuisances" in k:
if not self.isd_available:
raise ValueError(
"isd module needed to use nuisances")
mvs = self.get_nuisance_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Weights" in k:
if not self.isd_available:
raise ValueError(
"isd module needed to use weights")
mvs = self.get_weight_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Surfaces" in k:
mvs = self.get_surface_movers(pts[k][0], pts[k][1],
pts[k][2], pts[k][3])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
# SerialMover
self.smv = IMP.core.SerialMover(self.mvs)
self.mc = IMP.core.MonteCarlo(self.m)
self.mc.set_scoring_function(get_restraint_set(self.m))
self.mc.set_return_best(False)
self.mc.set_kt(self.temp)
self.mc.add_mover(self.smv)
def __init__(self, m, objects):
self.m = m
self.nframe = -1
self.cg = IMP.core.ConjugateGradients(self.m)
self.cg.set_scoring_function(get_restraint_set(self.m))
def __init__(self, m, objects=None, temp=1.0, filterbyname=None):
"""Setup Monte Carlo sampling
@param m The IMP Model
@param objects What to sample. Use flat list of particles or
(deprecated) 'MC Sample Objects' from PMI1
@param temp The MC temperature
@param filterbyname Not used
"""
self.losp = [
"Rigid_Bodies",
"Floppy_Bodies",
"Nuisances",
"X_coord",
"Weights"]
self.simulated_annealing = False
self.selfadaptive = False
# that is -1 because mc has not yet run
self.nframe = -1
self.temp = temp
self.mvs = []
self.mvslabels = []
self.label = "None"
self.m = m
# check if using PMI1 or just passed a list of movers
gather_objects = False
try:
objects[0].get_particles_to_sample()
gather_objects = True
except:
self.mvs = objects
if gather_objects:
for ob in objects:
pts = ob.get_particles_to_sample()
for k in pts.keys():
if "Rigid_Bodies" in k:
mvs = self.get_rigid_body_movers(
pts[k][0],
pts[k][1],
pts[k][2])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "SR_Bodies" in k:
print(len(pts[k]))
mvs = self.get_super_rigid_body_movers(
pts[k][0],
pts[k][1],
pts[k][2])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Floppy_Bodies" in k:
mvs = self.get_floppy_body_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "X_coord" in k:
mvs = self.get_X_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Nuisances" in k:
if not self.isd_available:
raise ValueError("isd module needed to use nuisances")
mvs = self.get_nuisance_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Weights" in k:
if not self.isd_available:
raise ValueError("isd module needed to use weights")
mvs = self.get_weight_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
# SerialMover
self.smv = IMP.core.SerialMover(self.mvs)
self.mc = IMP.core.MonteCarlo(self.m)
self.mc.set_scoring_function(get_restraint_set(self.m))
self.mc.set_return_best(False)
self.mc.set_kt(self.temp)
self.mc.add_mover(self.smv)
def __init__(self, m, objects, temp, filterbyname=None, dof=None):
"""Setup Monte Carlo sampling
@param m The IMP Model
@param objects Sample Objects. Alternatively pass the degrees of freedom object
@param temp The initial MC temperature
@param filterbyname Not implemented
@param dof DegreesOfFreedom object (replaces "objects")
"""
# check that the objects containts get_particles_to_sample methods
# and the particle type is supported
# list of particles to sample self.losp
self.losp = [
"Rigid_Bodies", "Floppy_Bodies", "Nuisances", "X_coord", "Weights"
]
self.simulated_annealing = False
self.selfadaptive = False
# that is -1 because mc has not yet run
self.nframe = -1
self.temp = temp
self.mvs = []
self.mvslabels = []
self.label = "None"
self.m = m
if dof is not None:
self.mvs = dof.get_all_movers()
else:
for ob in objects:
try:
ob.get_particles_to_sample()
except:
print("MonteCarlo: object ", ob,
" doesn't have get_particles_to_sample() method")
pts = ob.get_particles_to_sample()
for k in pts.keys():
if "Rigid_Bodies" in k:
mvs = self.get_rigid_body_movers(
pts[k][0], pts[k][1], pts[k][2])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "SR_Bodies" in k:
print(len(pts[k]))
mvs = self.get_super_rigid_body_movers(
pts[k][0], pts[k][1], pts[k][2])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Floppy_Bodies" in k:
mvs = self.get_floppy_body_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "X_coord" in k:
mvs = self.get_X_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Nuisances" in k:
if not self.isd_available:
raise ValueError(
"isd module needed to use nuisances")
mvs = self.get_nuisance_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
if "Weights" in k:
if not self.isd_available:
raise ValueError(
"isd module needed to use weights")
mvs = self.get_weight_movers(pts[k][0], pts[k][1])
for mv in mvs:
mv.set_name(k)
self.mvs += mvs
# SerialMover
self.smv = IMP.core.SerialMover(self.mvs)
self.mc = IMP.core.MonteCarlo(self.m)
self.mc.set_scoring_function(get_restraint_set(self.m))
self.mc.set_return_best(False)
self.mc.set_kt(self.temp)
self.mc.add_mover(self.smv)
