def setup_domains(self):
# scale the temperature (necessary at high pulling speeds)
if self.temperature:
atoms = self.soup.atoms()
anderson_velocity_scale(atoms, self.temperature, 3*len(atoms))
# select the atoms from the domains definition
selection = ['CA'] if self.is_backbone_only else None
self.atoms1 = get_atoms_of_residues(self.soup, self.domain1, selection)
self.atoms2 = get_atoms_of_residues(self.soup, self.domain2, selection)
# get direction vectors based on domains
self.disp2to1 = pdbatoms.get_center(self.atoms1) \
- pdbatoms.get_center(self.atoms2)
self.axis2to1 = v3.norm(self.disp2to1)
# calculate relative velocities between domains
self.vel2to1 = average_vel(self.atoms1) - average_vel(self.atoms2)
self.axis_vel2to1 = v3.parallel(self.vel2to1, self.axis2to1)
self.vel = v3.dot(self.axis_vel2to1, self.axis2to1)
if self.is_first_domain_only:
self.move_atoms = self.atoms1
else:
self.move_atoms = self.atoms1 + self.atoms2
def setup_domains(self):
# scale the temperature (necessary at high pulling speeds)
if self.temperature:
atoms = self.soup.atoms()
anderson_velocity_scale(atoms, self.temperature, 3 * len(atoms))
# select the atoms from the domains definition
selection = data.backbone_atoms if self.is_backbone_only else None
self.atoms1 = get_atoms_of_residues(self.soup, self.domain1, selection)
self.atoms2 = get_atoms_of_residues(self.soup, self.domain2, selection)
# get direction vectors based on domains
self.disp2to1 = pdbatoms.get_center(self.atoms1) \
- pdbatoms.get_center(self.atoms2)
self.axis2to1 = v3.norm(self.disp2to1)
# calculate relative velocities between domains
self.vel2to1 = average_vel(self.atoms1) - average_vel(self.atoms2)
self.axis_vel2to1 = v3.parallel(self.vel2to1, self.axis2to1)
self.vel = v3.dot(self.axis_vel2to1, self.axis2to1)
if self.is_first_domain_only:
self.move_atoms = self.atoms1
else:
self.move_atoms = self.atoms1 + self.atoms2
def add_vel_to_atoms(atoms, vel_diff):
"""
Adds vel_diff to the vel vector of atoms.
"""
for a in atoms:
a.vel_last = a.vel
a.vel += vel_diff
a.work_delta = \
v3.dot(vel_diff, a.vel) * a.mass * timestep_in_ps * \
work_DaAngSqPerPsSq_to_pNAng
def add_vel_to_atoms(atoms, vel_diff):
"""
Adds vel_diff to the vel vector of atoms.
"""
for a in atoms:
a.vel_last = a.vel
a.vel += vel_diff
a.work_delta = \
v3.dot(vel_diff, a.vel) * a.mass * timestep_in_ps * \
work_DaAngSqPerPsSq_to_pNAng
def change_vels(self):
# calculate the vel diff vector to apply
diff_vel = self.target_val * self.dt
diff_axis_vel2to1 = v3.scale(self.axis2to1, diff_vel)
self.vel_diff = v3.dot(diff_axis_vel2to1, self.axis2to1)
if self.is_first_domain_only:
add_vel_to_atoms(self.atoms1, diff_axis_vel2to1)
else:
# apply half of vel_diff to each domain
diff_axis_vel2to1 = v3.scale(diff_axis_vel2to1, 0.5)
add_vel_to_atoms(self.atoms1, diff_axis_vel2to1)
add_vel_to_atoms(self.atoms2, -diff_axis_vel2to1)
def change_vels(self):
# calculate the vel diff vector to apply
diff_vel = self.target_val * self.dt
diff_axis_vel2to1 = v3.scale(self.axis2to1, diff_vel)
self.vel_diff = v3.dot(diff_axis_vel2to1, self.axis2to1)
if self.is_first_domain_only:
add_vel_to_atoms(self.atoms1, diff_axis_vel2to1)
else:
# apply half of vel_diff to each domain
diff_axis_vel2to1 = v3.scale(diff_axis_vel2to1, 0.5)
add_vel_to_atoms(self.atoms1, diff_axis_vel2to1)
add_vel_to_atoms(self.atoms2, -diff_axis_vel2to1)
def change_vels(self):
# calculate the vel diff vector
target_axis_vel2to1 = v3.scale(self.axis2to1, self.target_val)
diff_axis_vel2to1 = target_axis_vel2to1 - self.axis_vel2to1
self.vel_diff = v3.dot(diff_axis_vel2to1, self.axis2to1)
# now change velocities of movable atoms
self.old_kinetic_energy = kinetic_energy(self.move_atoms)
if self.is_first_domain_only:
add_vel_to_atoms(self.atoms1, diff_axis_vel2to1)
else:
# apply half of vel_diff to each domain
v3.scale(diff_axis_vel2to1, 0.5)
add_vel_to_atoms(self.atoms1, diff_axis_vel2to1)
add_vel_to_atoms(self.atoms2, -diff_axis_vel2to1)
self.kinetic_energy = kinetic_energy(self.move_atoms)
def change_vels(self):
# calculate the vel diff vector
target_axis_vel2to1 = v3.scale(self.axis2to1, self.target_val)
diff_axis_vel2to1 = target_axis_vel2to1 - self.axis_vel2to1
self.vel_diff = v3.dot(diff_axis_vel2to1, self.axis2to1)
# now change velocities of movable atoms
self.old_kinetic_energy = kinetic_energy(self.move_atoms)
if self.is_first_domain_only:
add_vel_to_atoms(self.atoms1, diff_axis_vel2to1)
else:
# apply half of vel_diff to each domain
v3.scale(diff_axis_vel2to1, 0.5)
add_vel_to_atoms(self.atoms1, diff_axis_vel2to1)
add_vel_to_atoms(self.atoms2, -diff_axis_vel2to1)
self.kinetic_energy = kinetic_energy(self.move_atoms)
def rotational_velocity(atom, axis, anchor):
"""
Returns the rotational velocity (rad/ps) of the atom connected
to anchor around axis.
"""
r = atom.pos - anchor
r_perp = v3.perpendicular(r, axis)
vel_perp = v3.perpendicular(atom.vel, axis)
vel_tang = v3.perpendicular(vel_perp, r_perp)
pos_ref = v3.cross(axis, r_perp)
if v3.dot(vel_tang, pos_ref) < 0.0:
sign = -1.0
else:
sign = 1.0
if v3.is_similar_mag(v3.mag(r_perp), 0):
result = 0.0
else:
result = sign * v3.mag(vel_tang) / v3.mag(r_perp)
return result
def rotational_velocity(atom, axis, anchor):
"""
Returns the rotational velocity (rad/ps) of the atom connected
to anchor around axis.
"""
r = atom.pos - anchor
r_perp = v3.perpendicular(r, axis)
vel_perp = v3.perpendicular(atom.vel, axis)
vel_tang = v3.perpendicular(vel_perp, r_perp)
pos_ref = v3.cross(axis, r_perp)
if v3.dot(vel_tang, pos_ref) < 0.0:
sign = -1.0
else:
sign = 1.0
if v3.is_similar_mag(v3.mag(r_perp), 0):
result = 0.0
else:
result = sign * v3.mag(vel_tang) / v3.mag(r_perp)
return result
