def get_rmsd(pdb1, pdb2, segments1, segments2, atom_types): polymer1 = pdbstruct.Polymer(pdb1) atoms1 = get_superposable_atoms(polymer1, segments1, atom_types) polymer2 = pdbstruct.Polymer(pdb2) atoms2 = get_superposable_atoms(polymer2, segments2, atom_types) center1 = pdbstruct.get_center(atoms1) polymer1.transform(vector3d.Translation(-center1)) polymer2.transform(vector3d.Translation(-pdbstruct.get_center(atoms2))) crds1 = get_crds(atoms1) crds2 = get_crds(atoms2) return rmsd(crds1, crds2)
def get_best_alignment(pdb1, pdb2, segments1, segments2, atom_types): """Returns rmsd and filename of transformed pdb2.""" polymer1 = pdbstruct.Polymer(pdb1) atoms1 = get_superposable_atoms(polymer1, segments1, atom_types) polymer2 = pdbstruct.Polymer(pdb2) atoms2 = get_superposable_atoms(polymer2, segments2, atom_types) center1 = pdbstruct.get_center(atoms1) polymer1.transform(vector3d.Translation(-center1)) polymer2.transform(vector3d.Translation(-pdbstruct.get_center(atoms2))) polymer2.transform(calculate_superposition_matrix(atoms1, atoms2)) rmsd = sum_rmsd(atoms1, atoms2) temp_pdb2 = util.fname_variant(pdb2) polymer2.transform(vector3d.Translation(center1)) polymer2.write_pdb(temp_pdb2) return rmsd, temp_pdb2
def volume(atoms, grid_spacing, out_fname=""):
center = pdbstruct.get_center(atoms)
width = pdbstruct.get_width(atoms, center) + 4.0
grid = Grid(grid_spacing, width, center)
print "Grid %d x %d x %d; Width %.2f Å" % \
(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
print u"Volume %.1f Å^3 (%d x %.3f Å^3)" \
% (volume, grid.n_excluded(), d_volume)
if out_fname:
atoms = grid.make_mol("HOH", "O").atoms()
pdbstruct.save_atoms(atoms, out_fname)
def make_hollow_spheres(pdb,
out_pdb="",
grid_spacing=defaults.grid_spacing,
size_interior_probe=defaults.interior_probe,
is_skip_waters=defaults.is_skip_waters,
size_surface_probe=defaults.surface_probe,
constraint_file="",
size_bfactor_probe=defaults.bfactor_probe):
# load protein and get protein parameters
print "Loading", pdb
mol = get_molecule(pdb)
atoms = mol.atoms()
if is_skip_waters:
print "Skipping water molecules"
atoms = [a for a in atoms if a.res_type != "HOH"]
pdbstruct.add_radii(atoms)
# setup constraints and grid size in width
timer = util.Timer()
if not constraint_file:
center = pdbstruct.get_center(atoms)
width = pdbstruct.get_width(atoms, center)
else:
print "Loading constraints from %s" % constraint_file
constraints = util.read_parameters(constraint_file)
if constraints.type == 'sphere':
atom1 = find_atom(atoms, constraints.chain1, constraints.res_num1,
constraints.atom1)
radius = constraints.radius
constraint_fn = get_sphere_constraint_fn(atom1.pos, radius)
center = atom1.pos
width = 2.0 * constraints.radius + 2.0 * grid_spacing
radius = radius - 3.0 * grid_spacing
inner_constraint_fn = get_sphere_constraint_fn(atom1.pos, radius)
elif constraints.type == 'cylinder':
atom1 = find_atom(atoms, constraints.chain1, constraints.res_num1,
constraints.atom1)
atom2 = find_atom(atoms, constraints.chain2, constraints.res_num2,
constraints.atom2)
axis12 = atom2.pos - atom1.pos
offset1 = -axis12.normal_vec()
offset1.scale(constraints.axis_offset1)
center1 = atom1.pos + offset1
offset2 = axis12.normal_vec()
offset2.scale(constraints.axis_offset2)
center2 = atom2.pos + offset2
center = center1 + center2
center.scale(0.5)
radius = constraints.radius
constraint_fn = get_cylinder_constraint_fn(center1, center2,
radius)
half_length = vector3d.pos_distance(center, center1)
width = 2.0 * grid_spacing + 2.0 * \
math.sqrt(half_length*half_length \
+ constraints.radius*constraints.radius)
border_length = 3.0 * grid_spacing
center1 = center1 + axis12.normal_vec().scaled_vec(border_length)
center2 = center2 - axis12.normal_vec().scaled_vec(border_length)
radius = radius - border_length
inner_constraint_fn = get_cylinder_constraint_fn(
center1, center2, radius)
else:
raise ValueError("Don't understand constraint type")
# Make the grid
n_point = width / grid_spacing
print "Setting up grid: %d x %d x %d, spacing %.3f, width %.1f" \
% (n_point, n_point, n_point, grid_spacing, width)
grid = Grid(grid_spacing, width, center)
print_time(timer)
print "Excluding protein bulk from grid with %.1f angstrom probe" \
% size_interior_probe
timer.start()
exclude_atoms_from_grid(grid, atoms, size_interior_probe)
print_time(timer)
if constraint_file:
# Eliminate all grid points outside constraints
print "Excluding grid points outside constraint"
timer.start()
grid.exclude_points_in_constraint(constraint_fn)
print_time(timer)
is_calculate_asa_shell = True
if constraint_file:
if not constraints.remove_asa_shell:
is_calculate_asa_shell = False
if is_calculate_asa_shell:
print "Calculating asa of atoms in protein"
# Roll large ball over surface residues to eliminate
# grid points over surface, then drill in from the
# edge to eliminate the rest
timer.start()
add_asa(atoms, 1.4)
print_time(timer)
print "Excluding surface shell from grid with %.1f angstrom probe" \
% size_surface_probe
timer.start()
exclude_surface(grid, atoms, size_surface_probe)
print_time(timer)
print "Excluding edges"
grid.exclude_edge_to_interior()
print "Excluding surrounded points"
timer.start()
hole_size = int(1.5 * 1.4 / grid_spacing)
grid.exclude_surrounded(hole_size)
print_time(timer)
# Make hollow spheres from grid-points
if not out_pdb:
out_pdb = pdb.replace('.pdb', '-hollow.pdb')
print "Saving hollow spheres to", out_pdb
grid_chain = grid.make_mol(defaults.res_type, defaults.atom_type)
if size_bfactor_probe:
print "Averaging nearby protein b-factors for each hollow atom"
timer.start()
if constraint_file:
atoms = [a for a in atoms if constraint_fn(a.pos)]
calculate_average_bfactor(grid_chain, atoms, size_bfactor_probe)
print_time(timer)
if constraint_file:
for atom in grid_chain.atoms():
if inner_constraint_fn(atom.pos):
atom.occupancy = 1.0
else:
atom.occupancy = 0.0
is_hetatm = not defaults.atom_field.startswith("ATOM")
pdbstruct.save_atoms(grid_chain.atoms(), out_pdb, is_hetatm)