Example #1
0
    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
Example #2
0
  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
Example #3
0
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
Example #4
0
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
Example #5
0
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
Example #6
0
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