def read_geom_angle(self, bond_map):
"""Read bond information form the geom_angle section.
"""
for t in self.cif.tables:
if "geom_angle_atom_site_label_1" in t.columns:
table = t
break
else:
warning("read_atoms: no geom_angle section found")
return
for row in range(len(table.rows)):
name1 = table.get_value("geom_angle_atom_site_label_1", row)
atom1 = self.atom_site_name_map[name1]
name2 = table.get_value("geom_angle_atom_site_label_2", row)
atom2 = self.atom_site_name_map[name2]
name3 = table.get_value("geom_angle_atom_site_label_3", row)
atom3 = self.atom_site_name_map[name3]
if id(atom1) < id(atom2):
bnd = (atom1, atom2)
else:
bnd = (atom2, atom1)
bond_map[bnd] = {}
if id(atom2) < id(atom3):
bnd = (atom2, atom3)
else:
bnd = (atom3, atom2)
bond_map[bnd] = {}
def read_geom_angle(self, bond_map):
"""Read bond information form the geom_angle section.
"""
for t in self.cif.tables:
if "geom_angle_atom_site_label_1" in t.columns:
table = t
break
else:
warning("read_atoms: no geom_angle section found")
return
for row in range(len(table.rows)):
name1 = table.get_value("geom_angle_atom_site_label_1", row)
atom1 = self.atom_site_name_map[name1]
name2 = table.get_value("geom_angle_atom_site_label_2", row)
atom2 = self.atom_site_name_map[name2]
name3 = table.get_value("geom_angle_atom_site_label_3", row)
atom3 = self.atom_site_name_map[name3]
if id(atom1) < id(atom2):
bnd = (atom1, atom2)
else:
bnd = (atom2, atom1)
bond_map[bnd] = {}
if id(atom2) < id(atom3):
bnd = (atom2, atom3)
else:
bnd = (atom3, atom2)
bond_map[bnd] = {}
def read_start(self, filobj):
## parse the CIF file
cif_file = CIF.CIFFile()
cif_file.load_file(filobj)
if len(cif_file.data_blocks) != 1:
warning("read_start: only single-structure CIF files supported")
self.halt = True
return
self.cif = cif_file.data_blocks[0]
self.get_cell_parameters()
self.atom_site_name_map = {}
def read_start(self, filobj):
## parse the CIF file
cif_file = CIF.CIFFile()
cif_file.load_file(filobj)
if len(cif_file.data_blocks) != 1:
warning("read_start: only single-structure CIF files supported")
self.halt = True
return
self.cif = cif_file.data_blocks[0]
self.get_cell_parameters()
self.atom_site_name_map = {}
def read_atoms(self):
"""Read atom information form the atom_site section.
"""
for t in self.cif.tables:
if "atom_site_label" in t.columns:
table = t
break
else:
warning("read_atoms: no atom_site section found")
self.halt = True
return
for i in range(len(table.rows)):
atm_map = {
"res_name": self.cif.name,
"fragment_id": "1",
"chain_id": " ",
}
add_string(atm_map, "name", table, "atom_site_label", i)
add_string(atm_map, "element", table, "atom_site_type_symbol", i)
add_number(atm_map, "fractx", table, "atom_site_fract_x", i)
add_number(atm_map, "fracty", table, "atom_site_fract_y", i)
add_number(atm_map, "fractz", table, "atom_site_fract_z", i)
add_number(atm_map, "temp_factor", table,
"atom_site_U_iso_or_equiv", i)
add_number(atm_map, "occupancy", table, "atom_site_occupancy", i)
try:
fx = atm_map["fractx"]
fy = atm_map["fracty"]
fz = atm_map["fractz"]
except KeyError:
warning("read_atoms: missing coordinates")
else:
fc = [fx, fy, fz]
xyz = [0.0, 0.0, 0.0]
for i in range(3):
sum = 0.0
for j in range(3):
sum += self.xform[i][j] * fc[j]
xyz[i] = sum
atm_map["x"] = xyz[0]
atm_map["y"] = xyz[1]
atm_map["z"] = xyz[2]
atm = self.load_atom(atm_map)
self.atom_site_name_map[atm_map["name"]] = atm
#print "%d atoms" % len(self.atom_site_name_map)
## load the bonds
bond_map = {}
self.read_geom_bond(bond_map)
self.read_geom_angle(bond_map)
self.load_bonds(bond_map)
def read_atoms(self):
"""Read atom information form the atom_site section.
"""
for t in self.cif.tables:
if "atom_site_label" in t.columns:
table = t
break
else:
warning("read_atoms: no atom_site section found")
self.halt = True
return
for i in range(len(table.rows)):
atm_map = {
"res_name": self.cif.name,
"fragment_id": "1",
"chain_id": " ",
}
add_string(atm_map, "name", table, "atom_site_label", i)
add_string(atm_map, "element", table, "atom_site_type_symbol", i)
add_number(atm_map, "fractx", table, "atom_site_fract_x", i)
add_number(atm_map, "fracty", table, "atom_site_fract_y", i)
add_number(atm_map, "fractz", table, "atom_site_fract_z", i)
add_number(atm_map, "temp_factor",
table, "atom_site_U_iso_or_equiv", i)
add_number(atm_map, "occupancy", table, "atom_site_occupancy", i)
try:
fx = atm_map["fractx"]
fy = atm_map["fracty"]
fz = atm_map["fractz"]
except KeyError:
warning("read_atoms: missing coordinates")
else:
fc = [ fx, fy, fz ]
xyz = [ 0.0, 0.0, 0.0 ]
for i in range(3):
sum = 0.0
for j in range(3):
sum += self.xform[i][j] * fc[j]
xyz[i] = sum
atm_map["x"] = xyz[0]
atm_map["y"] = xyz[1]
atm_map["z"] = xyz[2]
atm = self.load_atom(atm_map)
self.atom_site_name_map[atm_map["name"]] = atm
#print "%d atoms" % len(self.atom_site_name_map)
## load the bonds
bond_map = {}
self.read_geom_bond(bond_map)
self.read_geom_angle(bond_map)
self.load_bonds(bond_map)
def read_geom_bond(self, bond_map):
"""Read bond information form the geom_bond section.
"""
for t in self.cif.tables:
if "geom_bond_atom_site_label_1" in t.columns:
table = t
break
else:
warning("read_atoms: no geom_bond section found")
return
for row in range(len(table.rows)):
name1 = table.get_value("geom_bond_atom_site_label_1", row)
try:
atom1 = self.atom_site_name_map[name1]
except KeyError:
warning("read_atoms: bond references non-existent atom '%s'" %
name1)
continue
name2 = table.get_value("geom_bond_atom_site_label_2", row)
try:
atom2 = self.atom_site_name_map[name2]
except KeyError:
warning("read_atoms: bond references non-existent atom '%s'" %
name2)
continue
if id(atom1) < id(atom2):
bnd = (atom1, atom2)
else:
bnd = (atom2, atom1)
bond_map[bnd] = {}
def read_geom_bond(self, bond_map):
"""Read bond information form the geom_bond section.
"""
for t in self.cif.tables:
if "geom_bond_atom_site_label_1" in t.columns:
table = t
break
else:
warning("read_atoms: no geom_bond section found")
return
for row in range(len(table.rows)):
name1 = table.get_value("geom_bond_atom_site_label_1", row)
try:
atom1 = self.atom_site_name_map[name1]
except KeyError:
warning("read_atoms: bond references non-existent atom '%s'"
% name1)
continue
name2 = table.get_value("geom_bond_atom_site_label_2", row)
try:
atom2 = self.atom_site_name_map[name2]
except KeyError:
warning("read_atoms: bond references non-existent atom '%s'"
% name2)
continue
if id(atom1) < id(atom2):
bnd = (atom1, atom2)
else:
bnd = (atom2, atom1)
bond_map[bnd] = {}
