def __call__(self, f):
Universe = context.application.plugins.get_node("Universe")
universe = Universe()
Folder = context.application.plugins.get_node("Folder")
folder = Folder()
Atom = context.application.plugins.get_node("Atom")
counter = 1
atom_index = 0
for line in f:
#if len(line) != 81:
# raise FilterError("Each line in a PDB file must count 80 characters, error at line %i, len=%i" % (counter, len(line)-1))
if line.startswith("ATOM"):
extra = {"index": atom_index}
atom_info = periodic[line[76:78].strip()]
try:
t = numpy.array([
float(line[30:38].strip()),
float(line[38:46].strip()),
float(line[46:54].strip())
]) * angstrom
except ValueError:
raise FilterError(
"Error while reading PDB file: could not read coordinates at line %i."
% counter)
atom = Atom(name=line[12:16].strip(),
number=atom_info.number,
transformation=Translation(t),
extra=extra)
universe.add(atom)
atom_index += 1
elif line.startswith("CRYST1"):
space_group = line[55:66].strip().upper()
if space_group != "P 1":
raise FilterError(
"Error while reading PDB file: only unit cells with space group P 1 are supported."
)
a = float(line[6:15].strip()) * angstrom
b = float(line[15:24].strip()) * angstrom
c = float(line[24:33].strip()) * angstrom
alpha = float(line[33:40].strip()) * numpy.pi / 180
beta = float(line[40:47].strip()) * numpy.pi / 180
gamma = float(line[47:54].strip()) * numpy.pi / 180
universe.set_cell(
UnitCell.from_parameters3([a, b, c], [alpha, beta, gamma]))
counter += 1
return [universe, folder]
def __call__(self, f):
Universe = context.application.plugins.get_node("Universe")
universe = Universe()
Folder = context.application.plugins.get_node("Folder")
folder = Folder()
Atom = context.application.plugins.get_node("Atom")
counter = 1
atom_index = 0
for line in f:
#if len(line) != 81:
# raise FilterError("Each line in a PDB file must count 80 characters, error at line %i, len=%i" % (counter, len(line)-1))
if line.startswith("ATOM"):
extra = {"index": atom_index}
atom_info = periodic[line[76:78].strip()]
try:
t = numpy.array([
float(line[30:38].strip()),
float(line[38:46].strip()),
float(line[46:54].strip())
]) * angstrom
except ValueError:
raise FilterError("Error while reading PDB file: could not read coordinates at line %i." % counter)
atom = Atom(
name=line[12:16].strip(), number=atom_info.number,
transformation=Translation(t), extra=extra
)
universe.add(atom)
atom_index += 1
elif line.startswith("CRYST1"):
space_group = line[55:66].strip().upper()
if space_group != "P 1":
raise FilterError("Error while reading PDB file: only unit cells with space group P 1 are supported.")
a = float(line[6:15].strip())*angstrom
b = float(line[15:24].strip())*angstrom
c = float(line[24:33].strip())*angstrom
alpha = float(line[33:40].strip())*numpy.pi/180
beta = float(line[40:47].strip())*numpy.pi/180
gamma = float(line[47:54].strip())*numpy.pi/180
universe.set_cell(UnitCell.from_parameters3([a, b, c], [alpha, beta, gamma]))
counter += 1
return [universe, folder]
def convert_to_value(self, representation):
lengths, angles = ComposedInTable.convert_to_value(
self, representation)
return UnitCell.from_parameters3(lengths, angles)
def convert_to_value(self, representation):
lengths, angles = ComposedInTable.convert_to_value(self, representation)
return UnitCell.from_parameters3(lengths, angles)
