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 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 change_vels(self):
# calculate the vel diff vector
self.old_kinetic_energy = kinetic_energy(self.move_atoms)
vel_target = self.target_val*self.axis2to1
if self.is_first_domain_only:
change_sets = [(self.atoms1, vel_target)]
else:
change_sets = [
(self.atoms1, 0.5*vel_target),
(self.atoms2, -0.5*vel_target)]
# now change velocities of movable atoms
for move_atoms, vel_target in change_sets:
for a in move_atoms:
vel_axis = v3.parallel(a.vel, self.axis2to1)
vel_diff = vel_target - vel_axis
a.vel += vel_diff
self.kinetic_energy = kinetic_energy(self.move_atoms)
