def testPdbWriteAltlocOptions(self):
""" Test PDB file writing with different altloc options """
pdbfile = read_PDB(self.pdb)
self._check4lzt(pdbfile)
output = StringIO()
pdbfile.write_pdb(output, renumber=False, altlocs='all')
output.seek(0)
pdbfile2 = read_PDB(output)
self._check4lzt(pdbfile2, check_meta=False)
self._compareInputOutputPDBs(pdbfile, pdbfile2)
# Check that 'first' option works
output = reset_stringio(output)
pdbfile.write_pdb(output, renumber=False, altlocs='first')
output.seek(0)
pdbfile3 = read_PDB(output)
self._check4lzt(pdbfile3, check_meta=False, has_altloc=False)
self._compareInputOutputPDBs(pdbfile, pdbfile3, altloc_option='first')
# Check that the 'occupancy' option works
output = reset_stringio(output)
write_PDB(pdbfile, output, renumber=False, altlocs='occupancy')
output.seek(0)
pdbfile4 = read_PDB(output)
self._check4lzt(pdbfile4, check_meta=False, has_altloc=False)
self._compareInputOutputPDBs(pdbfile, pdbfile4, altloc_option='occupancy')
# Double-check 'first' vs. 'occupancy'. Residue 85 (SER) has a conformer
# A that has an occupancy of 0.37 and conformer B with occupancy 0.63
self.assertEqual(pdbfile3.residues[84][4].xx, -4.162)
self.assertEqual(pdbfile4.residues[84][4].xx, -4.157)
def testPdbWriteXtal(self):
""" Test PDB file writing from a Xtal structure """
pdbfile = read_PDB(self.pdb)
self._check4lzt(pdbfile)
output = StringIO()
pdbfile.write_pdb(output, renumber=False)
output.seek(0)
pdbfile2 = read_PDB(output)
self._check4lzt(pdbfile2, check_meta=False)
self._compareInputOutputPDBs(pdbfile, pdbfile2)
output = reset_stringio(output)
write_PDB(pdbfile, output)
output.seek(0)
pdbfile3 = read_PDB(output)
self._check4lzt(pdbfile3, check_meta=False)
self._compareInputOutputPDBs(pdbfile, pdbfile3, True)
# Now check that renumbering is done correctly. 4lzt skips residues 130
# through 200
for res1, res2 in zip(pdbfile.residues, pdbfile3.residues):
if res1.idx < 129:
self.assertEqual(res1.number, res2.number)
elif res1.idx < 135:
self.assertEqual(res1.number, res2.number + 71)
else:
# Some residue numbers are skipped in the water numbering
self.assertGreaterEqual(res1.number, res2.number + 71 + 794)
def testPdbWriteModels(self):
""" Test PDB file writing from NMR structure with models """
pdbfile = read_PDB(self.models)
self.assertEqual(pdbfile.get_coordinates('all').shape, (20, 451, 3))
self.assertEqual(len(pdbfile.atoms), 451)
output = StringIO()
write_PDB(pdbfile, output)
output.seek(0)
pdbfile2 = read_PDB(output)
self.assertEqual(len(pdbfile2.atoms), 451)
self.assertEqual(pdbfile2.get_coordinates('all').shape, (20, 451, 3))
self._compareInputOutputPDBs(pdbfile, pdbfile2)
continue
new_b = list()
neighbor_list = pdb[matrix_idx[1][np.where(matrix_idx[0] == idx_1)]].atoms
for atom_2 in neighbor_list:
if atom_2.bfactor == 0.0:
continue
atom2_name = atom_2.name
if (atom2_name.startswith("H") \
or atom2_name.startswith("h")) \
and atom2_name != "HG":
continue
new_b.append(atom_2.occupancy + atom_2.bfactor)
norm_pdb[idx_1].bfactor /= np.array(new_b).mean()
std_pdb[idx_1].bfactor = (std_pdb[idx_1].bfactor -
np.array(new_b).mean()) / np.array(new_b).std()
pmd.write_PDB(norm_pdb, name + "_norm.pdb")
pmd.write_PDB(std_pdb, name + "_std.pdb")