def get_pdb_transform(pdb, center_res, top_res):
"""
Returns a transformation matrix that centers pdb to
center_res on the z-axis and moves top_res above center_res
on the y-axis
"""
soup = pdbatoms.Soup(pdb)
atoms = soup.atoms()
soup_center = pdbatoms.get_center(atoms)
translation = v3.translation(-soup_center)
soup.transform(translation)
result = translation
center_atom = find_ca_of_resname(soup.atoms(), center_res)
view = v3.vector(0, 0, 1)
axis = v3.cross(view, center_atom.pos)
angle = v3.vec_dihedral(view, axis, center_atom.pos)
rotation = v3.rotation(axis, angle)
soup.transform(rotation)
result = v3.combine(rotation, result)
top_atom = find_ca_of_resname(soup.atoms(), top_res)
top_dir = v3.vector(0, 1, 0)
axis = view.copy()
angle = v3.vec_dihedral(top_dir, axis, top_atom.pos)
rotation2 = v3.rotation(axis, angle)
result = v3.combine(rotation2, result)
del soup
return result
def get_pdb_transform(pdb, center_res, top_res): """ Returns a transformation matrix that centers pdb to center_res on the z-axis and moves top_res above center_res on the y-axis """ soup = pdbatoms.Soup(pdb) atoms = soup.atoms() soup_center = pdbatoms.get_center(atoms) translation = v3.translation(-soup_center) soup.transform(translation) result = translation center_atom = find_ca_of_resname(soup.atoms(), center_res) view = v3.vector(0, 0, 1) axis = v3.cross(view, center_atom.pos) angle = v3.vec_dihedral(view, axis, center_atom.pos) rotation = v3.rotation(axis, angle) soup.transform(rotation) result = v3.combine(rotation, result) top_atom = find_ca_of_resname(soup.atoms(), top_res) top_dir = v3.vector(0, 1, 0) axis = view.copy() angle = v3.vec_dihedral(top_dir, axis, top_atom.pos) rotation2 = v3.rotation(axis, angle) result = v3.combine(rotation2, result) del soup return result
def add_rotational_velocity(atoms, rot_vel, axis, anchor):
"""
Adds the rot_vel to the vel vector of atoms with respect
to the rotation around axis and attached to anchor.
"""
for atom in atoms:
r_perp = v3.perpendicular(atom.pos - anchor, axis)
v_tang_dir = v3.cross(axis, r_perp)
v_tang_dir_len = v3.mag(v_tang_dir)
if v3.is_similar_mag(v_tang_dir_len, 0):
v_tang = v3.vector()
else:
v_new_len = rot_vel * v3.mag(r_perp)
v_tang = v3.scale(v_tang_dir, v_new_len / v_tang_dir_len)
atom.vel += v_tang
def add_rotational_velocity(atoms, rot_vel, axis, anchor):
"""
Adds the rot_vel to the vel vector of atoms with respect
to the rotation around axis and attached to anchor.
"""
for atom in atoms:
r_perp = v3.perpendicular(atom.pos - anchor, axis)
v_tang_dir = v3.cross(axis, r_perp)
v_tang_dir_len = v3.mag(v_tang_dir)
if v3.is_similar_mag(v_tang_dir_len, 0):
v_tang = v3.vector()
else:
v_new_len = rot_vel * v3.mag(r_perp)
v_tang = v3.scale(v_tang_dir, v_new_len/v_tang_dir_len)
atom.vel += v_tang
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