def get_molecule(pdb):
txt = open(pdb, 'r').read()
txt = pdbtext.strip_other_nmr_models(txt)
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('ANISOU'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('CONECT'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('MASTER'))
txt = pdbtext.strip_alternative_atoms(txt)
bare_fname = util.temp_fname('.pdb')
open(bare_fname, 'w').write(txt)
mol = pdbstruct.Molecule(bare_fname)
if os.path.isfile(bare_fname):
os.remove(bare_fname)
return mol
def make_mol(self, res_type, atom_type):
mol = pdbstruct.Molecule()
element = ""
for c in atom_type[:2]:
if not c.isdigit() and c != " ":
element += c
i_res = 1
for i in range(self.n):
for j in range(self.n):
for k in range(self.n):
if not (self.is_excluded_or_drilled(i, j, k)):
hollow_atom = pdbstruct.Atom()
hollow_atom.pos = self.pos(i, j, k)
hollow_atom.type = atom_type
hollow_atom.element = element
hollow_atom.res_type = res_type
hollow_atom.res_num = i_res
hollow_atom.num = i_res
mol.insert_atom(hollow_atom)
i_res += 1
return mol
def make_mol(self, res_type, atom_type):
mol = pdbstruct.Molecule()
element = ""
for c in atom_type[:2]:
if not c.isdigit() and c != " ":
element += c
i_res = 1
for i in range(self.n):
for j in range(self.n):
for k in range(self.n):
l = i * self.n_sq + j * self.n + k
if self.array[l]:
hollow_atom = pdbstruct.Atom()
hollow_atom.pos = self.pos(i, j, k)
hollow_atom.type = atom_type
hollow_atom.element = element
hollow_atom.res_type = res_type
hollow_atom.res_num = i_res
hollow_atom.num = i_res
mol.insert_atom(hollow_atom)
i_res += 1
return mol
-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.
"""
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
if __name__ == "__main__":
usage = \
"""
Calculates the volume of the atoms in a PDB file.
Copyright (c) 2007 Bosco Ho.
Usage: volume.py in_pdb [spacing]
-spacing the spacing in the grid used to calculate the
volume grid (default=0.5). The smaller value,
the more accurate, but slower.
"""
import sys
if len(sys.argv) < 2:
print usage
sys.exit(1)
spacing = 0.5
if len(sys.argv) > 2:
spacing = float(sys.argv[2])
load_psyco_if_in_system()
mol = pdbstruct.Molecule(sys.argv[1])
atoms = mol.atoms()
pdbstruct.add_radii(atoms)
print "%d atoms in input pdb file" % len(atoms)
volume(atoms, spacing, sys.argv[1].replace('.pdb', '.grid.pdb'))