def apply(self, soup):
residue = soup.residue(self.i_res)
atoms = residue.atoms()
n_chi = get_n_chi(residue)
if self.mean_chis is None:
self.mean_chis = [calculate_chi(residue, i) for i in range(n_chi)]
rot_vels = [get_rot_vel_chi(residue, i) for i in range(n_chi)]
for atom in atoms:
v3.set_vector(atom.vel, 0.0, 0.0, 0.0)
for i_chi in reversed(range(n_chi)):
chi = calculate_chi(residue, i_chi)
delta_chi = v3.normalize_angle(chi - self.mean_chis[i_chi])
target_rot_vel = get_random_chi_rot_vel(residue, i_chi,
self.heating_temperature)
if abs(delta_chi) > self.max_delta_chi:
if delta_chi > self.max_delta_chi:
target_rot_vel = -target_rot_vel
else:
if rot_vels[i_chi] < 0.0:
target_rot_vel *= -target_rot_vel
add_rot_vel_to_chi(residue, i_chi, target_rot_vel)
anderson_velocity_scale(atoms, self.heating_temperature,
3 * len(atoms))
def apply(self, soup):
residue = soup.residue(self.i_res)
atoms = residue.atoms()
n_chi = get_n_chi(residue)
if self.mean_chis is None:
self.mean_chis = [calculate_chi(residue, i) for i in range(n_chi)]
rot_vels = [get_rot_vel_chi(residue, i) for i in range(n_chi)]
for atom in atoms:
v3.set_vector(atom.vel, 0.0, 0.0, 0.0)
for i_chi in reversed(range(n_chi)):
chi = calculate_chi(residue, i_chi)
delta_chi = v3.normalize_angle(chi - self.mean_chis[i_chi])
target_rot_vel = get_random_chi_rot_vel(
residue, i_chi, self.heating_temperature)
if abs(delta_chi) > self.max_delta_chi:
if delta_chi > self.max_delta_chi:
target_rot_vel = -target_rot_vel
else:
if rot_vels[i_chi] < 0.0:
target_rot_vel *= -target_rot_vel
add_rot_vel_to_chi(residue, i_chi, target_rot_vel)
anderson_velocity_scale(atoms, self.heating_temperature, 3*len(atoms))
def calculate_chi(residue, i_chi):
"""
Returns the angle for the i_chi dihedral angle of residue.
"""
res_chi_topology = data.get_res_chi_topology(residue.type)
if i_chi < len(res_chi_topology):
atom_types = res_chi_topology[i_chi]
crds = [residue.atom(t).pos for t in atom_types]
return v3.normalize_angle(v3.dihedral(*crds))
raise ValueError, "No Chi%d angle for residue %d" % (i_chi, i)
def calculate_chi(residue, i_chi):
"""
Returns the angle for the i_chi dihedral angle of residue.
"""
res_chi_topology = data.get_res_chi_topology(residue.type)
if i_chi < len(res_chi_topology):
atom_types = res_chi_topology[i_chi]
crds = [residue.atom(t).pos for t in atom_types]
return v3.normalize_angle(v3.dihedral(*crds))
raise ValueError, "No Chi%d angle for residue %d" % (i_chi, i)