def build_cgmodel(rosetta_scoring):
# Set values for the parameters in our coarse grained model:
polymer_length = 2
backbone_lengths = [1]
sidechain_lengths = [1]
sidechain_positions = [0]
include_bond_forces = False # NOTE: By default bonds are constrained to their equilibrium lengths, even when this variable is set to False, unless 'constrain_bonds'=False
constrain_bonds = True
include_bond_angle_forces = False
include_nonbonded_forces = True
include_torsion_forces = False
# Particle properties
mass = 100.0 * unit.amu
masses = {'backbone_bead_masses': mass, 'sidechain_bead_masses': mass}
bond_length = 1.0 * unit.angstrom
bond_lengths = {
'bb_bb_bond_length': bond_length,
'bb_sc_bond_length': bond_length,
'sc_sc_bond_length': bond_length
}
bond_force_constant = 0.0 * unit.kilocalorie_per_mole / unit.nanometer / unit.nanometer
bond_force_constants = {
'bb_bb_bond_k': bond_force_constant,
'bb_sc_bond_k': bond_force_constant,
'sc_sc_bond_k': bond_force_constant
}
r_min = bond_length
sigma = r_min / (2.0**(1 / 6))
sigmas = {'bb_sigma': sigma, 'sc_sigma': sigma}
epsilon = 0.2 * unit.kilocalorie_per_mole
epsilons = {'bb_eps': epsilon, 'sc_eps': epsilon}
exclusions = True
# Get positions from a local PDB file written by PyRosetta, and modified (by hand) to have a geometry where the nonbonded interactions are easy to evaluate
cgmodel = CGModel(polymer_length=polymer_length,
backbone_lengths=backbone_lengths,
sidechain_lengths=sidechain_lengths,
sidechain_positions=sidechain_positions,
masses=masses,
sigmas=sigmas,
epsilons=epsilons,
bond_lengths=bond_lengths,
include_nonbonded_forces=include_nonbonded_forces,
include_bond_forces=include_bond_forces,
include_bond_angle_forces=include_bond_angle_forces,
include_torsion_forces=include_torsion_forces,
rosetta_scoring=rosetta_scoring,
exclusions=exclusions,
constrain_bonds=constrain_bonds)
pyrosetta_sequence = ''.join([
str('X[' + str(monomer['monomer_name']) + ']')
for monomer in cgmodel.sequence
])
pose = pyrosetta.pose_from_sequence(pyrosetta_sequence)
pose.dump_pdb("test_pyrosetta.pdb")
cgmodel.positions = PDBFile("test_pyrosetta.pdb").getPositions()
cgmodel.topology = build_topology(cgmodel)
return (cgmodel, pose)
def build_cgmodel(rosetta_scoring):
# Set values for the parameters in our coarse grained model:
polymer_length = 2
backbone_lengths = [1]
sidechain_lengths = [1]
sidechain_positions = [0]
include_bond_forces = False # NOTE: By default bonds are constrained to their equilibrium lengths, even when this variable is set to False, unless 'constrain_bonds'=False
constrain_bonds = True
include_bond_angle_forces = True
include_nonbonded_forces = True
include_torsion_forces = True
# Particle properties
mass = 100.0 * unit.amu
masses = {'backbone_bead_masses': mass, 'sidechain_bead_masses': mass}
bond_length = 1.0 * unit.angstrom
bond_lengths = {
'bb_bb_bond_length': bond_length,
'bb_sc_bond_length': bond_length,
'sc_sc_bond_length': bond_length
}
bond_force_constant = 0.0 * unit.kilocalorie_per_mole / unit.nanometer / unit.nanometer
bond_force_constants = {
'bb_bb_bond_k': bond_force_constant,
'bb_sc_bond_k': bond_force_constant,
'sc_sc_bond_k': bond_force_constant
}
r_min = bond_length
sigma = r_min / (2.0**(1 / 6))
sigmas = {'bb_sigma': sigma, 'sc_sigma': sigma}
epsilon = 10.0 * unit.kilocalorie_per_mole
epsilons = {'bb_eps': epsilon, 'sc_eps': epsilon}
exclusions = True
# Bond angle properties
bond_angle_force_constant = 2 * unit.kilocalorie_per_mole / unit.radian / unit.radian
bond_angle_force_constants = {
'bb_bb_sc_angle_k': bond_angle_force_constant
}
equil_bond_angle = 90.0 * (3.141 / 180.0)
equil_bond_angles = {'bb_bb_sc_angle_0': equil_bond_angle}
# Torsion properties
torsion_force_constant = 3 * unit.kilocalorie_per_mole / unit.radian / unit.radian
torsion_force_constants = {'sc_bb_bb_sc_torsion_k': torsion_force_constant}
torsion_periodicity = 1
torsion_periodicities = {'sc_bb_bb_sc_period': torsion_periodicity}
equil_torsion_angle = 0.0 * (3.141 / 180.0)
equil_torsion_angles = {'sc_bb_bb_sc_torsion_0': equil_torsion_angle}
# Get positions from a local PDB file written by PyRosetta, and modified (by hand) to have a geometry where the nonbonded interactions are easy to evaluate
cgmodel = CGModel(polymer_length=polymer_length,
backbone_lengths=backbone_lengths,
sidechain_lengths=sidechain_lengths,
sidechain_positions=sidechain_positions,
masses=masses,
sigmas=sigmas,
epsilons=epsilons,
bond_lengths=bond_lengths,
include_nonbonded_forces=include_nonbonded_forces,
include_bond_forces=include_bond_forces,
include_bond_angle_forces=include_bond_angle_forces,
include_torsion_forces=include_torsion_forces,
rosetta_scoring=rosetta_scoring,
exclusions=exclusions,
constrain_bonds=constrain_bonds,
equil_torsion_angles=equil_torsion_angles,
torsion_force_constants=torsion_force_constants,
torsion_periodicities=torsion_periodicities,
equil_bond_angles=equil_bond_angles,
bond_angle_force_constants=bond_angle_force_constants)
pyrosetta_sequence = ''.join([
str('X[' + str(monomer['monomer_name']) + ']')
for monomer in cgmodel.sequence
])
res_file_list = list(
set([
str(str(monomer['monomer_name']) + ".params")
for monomer in cgmodel.sequence
]))
res_file_list = " ".join(res_file_list)
assign_mm_atom_properties_with_cgopenmm_cgmodel(cgmodel)
exit()
pose = pyrosetta.pose_from_sequence(pyrosetta_sequence)
for residue_index in range(pose.total_residue()):
print(pose.residue(residue_index))
exit()
pose.dump_pdb("test_pyrosetta.pdb")
cgmodel.positions = PDBFile("test_pyrosetta.pdb").getPositions()
cgmodel.topology = build_topology(cgmodel)
return (cgmodel, pose)
def build_cgmodel():
# Set values for the parameters in our coarse grained model:
polymer_length = 3
backbone_lengths = [1]
sidechain_lengths = [1]
sidechain_positions = [0]
include_bond_forces = False # NOTE: Bonds are constrained to their equilibrium lengths, by default, even when this variable is set to False.
include_bond_angle_forces = False
include_nonbonded_forces = True
include_torsion_forces = False
rosetta_scoring = True
# Particle properties
mass = 100.0 * unit.amu
masses = {'backbone_bead_masses': mass, 'sidechain_bead_masses': mass}
bond_length = 1.0 * unit.angstrom
bond_lengths = {
'bb_bb_bond_length': bond_length,
'bb_sc_bond_length': bond_length,
'sc_sc_bond_length': bond_length
}
bond_force_constant = 0.0 * unit.kilocalorie_per_mole / unit.nanometer / unit.nanometer
bond_force_constants = {
'bb_bb_bond_k': bond_force_constant,
'bb_sc_bond_k': bond_force_constant,
'sc_sc_bond_k': bond_force_constant
}
r_min = bond_length
sigma = r_min / (2.0**(1 / 6))
sigmas = {'bb_bb_sigma': sigma, 'sc_sc_sigma': sigma}
epsilon = 0.2 * unit.kilocalorie_per_mole
epsilons = {'bb_bb_eps': epsilon, 'sc_sc_eps': epsilon}
# Bond angle properties
bond_angle_force_constant = 2 * unit.kilocalorie_per_mole / unit.radian / unit.radian
bond_angle_force_constants = {
'bb_bb_bb_angle_k': bond_angle_force_constant,
'bb_bb_sc_angle_k': bond_angle_force_constant
}
equil_bond_angle = 120.0 * (3.141 / 180.0)
equil_bond_angles = {
'bb_bb_bb_angle_0': equil_bond_angle,
'bb_bb_sc_angle_0': equil_bond_angle
}
# Torsion properties
torsion_force_constant = 3
torsion_force_constants = {
'bb_bb_bb_bb_torsion_k': torsion_force_constant,
'sc_bb_bb_sc_torsion_k': 0.0,
'bb_bb_bb_sc_torsion_k': 0.0,
'sc_bb_bb_bb_torsion_k': 0.0
}
torsion_periodicity = 3
torsion_periodicities = {
'bb_bb_bb_bb_period': torsion_periodicity,
'sc_bb_bb_sc_period': 0,
'bb_bb_bb_sc_period': 0,
'sc_bb_bb_bb_period': 0
}
equil_torsion_angle = 0.0 * (3.141 / 180.0)
equil_torsion_angles = {
'bb_bb_bb_bb_torsion_0': equil_torsion_angle,
'sc_bb_bb_sc_torsion_0': 0.0,
'bb_bb_bb_sc_torsion_0': 0.0,
'sc_bb_bb_bb_torsion_0': 0.0
}
# Build a coarse grained model
cgmodel = CGModel(polymer_length=polymer_length,
backbone_lengths=backbone_lengths,
sidechain_lengths=sidechain_lengths,
sidechain_positions=sidechain_positions,
masses=masses,
sigmas=sigmas,
epsilons=epsilons,
bond_lengths=bond_lengths,
bond_force_constants=bond_force_constants,
bond_angle_force_constants=bond_angle_force_constants,
torsion_force_constants=torsion_force_constants,
equil_bond_angles=equil_bond_angles,
equil_torsion_angles=equil_torsion_angles,
include_nonbonded_forces=include_nonbonded_forces,
include_bond_forces=include_bond_forces,
include_bond_angle_forces=include_bond_angle_forces,
include_torsion_forces=include_torsion_forces,
rosetta_scoring=rosetta_scoring,
torsion_periodicities=torsion_periodicities)
# Get positions by building a pose with PyRosetta
pyrosetta_sequence = ''.join([
str('X[' + str(monomer['monomer_name']) + ']')
for monomer in cgmodel.sequence
])
pose = pyrosetta.pose_from_sequence(pyrosetta_sequence)
pose.dump_pdb("init.pdb")
cgmodel.positions = PDBFile("init.pdb").getPositions()
cgmodel.topology = build_topology(cgmodel)
return (cgmodel)
