def calculate_residue_asas(soup):
residue_asas = []
atoms = []
for r in soup.residues():
atoms.extend(r.atoms())
pdbstruct.add_radii(atoms)
atom_asas = calculate_asa(atoms, 1.4)
for atom, asa in zip(atoms, atom_asas):
atom.asa = asa
for r in soup.residues():
atom_asas = [a.asa for a in r.atoms()]
residue_asas.append(sum(atom_asas))
return residue_asas
def calculate_residue_asas(soup):
residue_asas = []
atoms = []
for r in soup.residues():
atoms.extend(r.atoms())
pdbstruct.add_radii(atoms)
atom_asas = calculate_asa(atoms, 1.4)
for atom, asa in zip(atoms, atom_asas):
atom.asa = asa
for r in soup.residues():
atom_asas = [a.asa for a in r.atoms()]
residue_asas.append(sum(atom_asas))
return residue_asas
def main():
import sys
import getopt
import pdbstruct
opts, args = getopt.getopt(sys.argv[1:], "n:")
usage = \
"""
Copyright (c) 2007 Bosco Ho
Calculates the total Accessible Surface Area (ASA) of atoms in a
PDB file.
Usage: asa.py -n n_sphere in_pdb [out_pdb]
- out_pdb PDB file in which the atomic ASA values are written
to the b-factor column.
-n n_sphere number of points used in generating the spherical
dot-density for the calculation (default=960). The
more points, the more accurate (but slower) the
calculation.
"""
if len(args) == 0:
print usage
return
mol = pdbstruct.Molecule(args[0])
atoms = mol.atoms()
pdbstruct.add_radii(atoms)
n_sphere = 960
for o, a in opts:
if '-n' in o:
n_sphere = int(a)
print "Points on sphere: ", n_sphere
asas = calculate_asa(atoms, 1.4, n_sphere)
print "%.1f angstrom squared." % sum(asas)
if len(args) > 1:
for asa, atom in zip(asas, atoms):
atom.bfactor = asa
mol.write_pdb(args[1])
dot-density for the calculation (default=960). The
more points, the more accurate (but slower) the
calculation.
"""
import sys
import getopt
opts, args = getopt.getopt(sys.argv[1:], "n:")
if len(args) == 0:
print usage
sys.exit(1)
mol = pdbstruct.Molecule(args[0])
atoms = mol.atoms()
pdbstruct.add_radii(atoms)
n_sphere = 960
for o, a in opts:
if '-n' in o:
n_sphere = int(a)
print "Points on sphere: ", n_sphere
asas = calculate_asa(atoms, 1.4, n_sphere)
print "%.1f angstrom squared." % sum(asas)
if len(args) > 1:
for asa, atom in zip(asas, atoms):
atom.bfactor = asa
mol.write_pdb(args[1])
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)