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 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 volume(atoms, grid_spacing, pdb="", verbose=True):
"""
Returns the volume of a list of atoms, and writes a PDB file of
fictious atoms to fill the volume.
"""
center = pdbatoms.get_center(atoms)
width = pdbatoms.get_width(atoms, center) + 4.0
grid = Grid(grid_spacing, width, center)
if verbose:
print "%d atoms, grid %d x %d x %d points, width %.2f angstroms" % \
(len(atoms), grid.n, grid.n, grid.n, grid.actual_width)
for atom in atoms:
grid.exclude_sphere(atom.pos, atom.radius)
d_volume = float(grid_spacing)**3
volume = grid.n_excluded() * d_volume
if verbose:
print "Volume %.1f angstroms^3 (%d x %.3f angstroms^3)" \
% (volume, grid.n_excluded(), d_volume)
if pdb:
if verbose:
print "Warning: there will probably be more residues/atoms " \
"than PDB can uniquely number"
print pdb
grid.write_pdb(pdb)
return volume
def volume(atoms, grid_spacing, pdb="",verbose=True):
"""
Returns the volume of a list of atoms, and writes a PDB file of
fictious atoms to fill the volume.
"""
center = pdbatoms.get_center(atoms)
width = pdbatoms.get_width(atoms, center) + 4.0
grid = Grid(grid_spacing, width, center)
if verbose:
print "%d atoms, grid %d x %d x %d points, width %.2f angstroms" % \
(len(atoms), grid.n, grid.n, grid.n, grid.actual_width)
for atom in atoms:
grid.exclude_sphere(atom.pos, atom.radius)
d_volume = float(grid_spacing)**3
volume = grid.n_excluded()*d_volume
if verbose:
print "Volume %.1f angstroms^3 (%d x %.3f angstroms^3)" \
% (volume, grid.n_excluded(), d_volume)
if pdb:
if verbose:
print "Warning: there will probably be more residues/atoms " \
"than PDB can uniquely number"
print pdb
grid.write_pdb(pdb)
return volume
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
