def __init__(self, cif_block):
crystal_symmetry_builder.__init__(self, cif_block)
self.hierarchy = hierarchy.root()
# These items are mandatory for the _atom_site loop, all others are optional
type_symbol = self._wrap_loop_if_needed(cif_block,
"_atom_site.type_symbol")
atom_labels = self._wrap_loop_if_needed(cif_block,
"_atom_site.auth_atom_id")
if atom_labels is None:
atom_labels = self._wrap_loop_if_needed(
cif_block, "_atom_site.label_atom_id"
) # corresponds to chem comp atom name
alt_id = self._wrap_loop_if_needed(
cif_block, "_atom_site.label_alt_id") # alternate conformer id
label_asym_id = self._wrap_loop_if_needed(
cif_block, "_atom_site.label_asym_id") # chain id
auth_asym_id = self._wrap_loop_if_needed(cif_block,
"_atom_site.auth_asym_id")
if label_asym_id is None: label_asym_id = auth_asym_id
if auth_asym_id is None: auth_asym_id = label_asym_id
comp_id = self._wrap_loop_if_needed(cif_block,
"_atom_site.auth_comp_id")
if comp_id is None:
comp_id = self._wrap_loop_if_needed(
cif_block, "_atom_site.label_comp_id") # residue name
entity_id = self._wrap_loop_if_needed(cif_block,
"_atom_site.label_entity_id")
seq_id = self._wrap_loop_if_needed(cif_block, "_atom_site.auth_seq_id")
if seq_id is None:
seq_id = self._wrap_loop_if_needed(
cif_block, "_atom_site.label_seq_id") # residue number
assert [atom_labels, alt_id, auth_asym_id, comp_id, entity_id,
seq_id].count(None) == 0, "someting is not present"
assert type_symbol is not None
atom_site_fp = cif_block.get('_atom_site.phenix_scat_dispersion_real')
atom_site_fdp = cif_block.get('_atom_site.phenix_scat_dispersion_imag')
pdb_ins_code = cif_block.get(
"_atom_site.pdbx_PDB_ins_code") # insertion code
model_ids = cif_block.get("_atom_site.pdbx_PDB_model_num")
atom_site_id = cif_block.get("_atom_site.id")
# only permitted values are ATOM or HETATM
group_PDB = cif_block.get("_atom_site.group_PDB")
# TODO: read esds
B_iso_or_equiv = flex.double(
self._wrap_loop_if_needed(cif_block, "_atom_site.B_iso_or_equiv"))
cart_x = flex.double(
self._wrap_loop_if_needed(cif_block, "_atom_site.Cartn_x"))
cart_y = flex.double(
self._wrap_loop_if_needed(cif_block, "_atom_site.Cartn_y"))
cart_z = flex.double(
self._wrap_loop_if_needed(cif_block, "_atom_site.Cartn_z"))
occu = flex.double(
self._wrap_loop_if_needed(cif_block, "_atom_site.occupancy"))
formal_charge = self._wrap_loop_if_needed(
cif_block, "_atom_site.pdbx_formal_charge")
# anisotropic b-factors
# TODO: read esds
anisotrop_id = self._wrap_loop_if_needed(cif_block,
"_atom_site_anisotrop.id")
adps = None
if anisotrop_id is not None:
u_ij = [
self._wrap_loop_if_needed(
cif_block,
"_atom_site_anisotrop.U[%s][%s]" % (ij[0], ij[1]))
for ij in ("11", "22", "33", "12", "13", "23")
]
assert u_ij.count(None) in (0, 6)
if u_ij.count(None) == 0:
adps = u_ij
else:
assert u_ij.count(None) == 6
b_ij = [
self._wrap_loop_if_needed(
cif_block,
"_atom_site_anisotrop.B[%s][%s]" % (ij[0], ij[1]))
for ij in ("11", "22", "33", "12", "13", "23")
]
assert b_ij.count(None) in (0, 6)
if b_ij.count(None) == 0:
adps = adptbx.b_as_u(b_ij)
assert not (u_ij.count(None) and b_ij.count(None)
) # illegal for both to be present
if adps is not None:
try:
adps = [flex.double(adp) for adp in adps]
except ValueError, e:
raise CifBuilderError("Error interpreting ADPs: " + str(e))
adps = flex.sym_mat3_double(*adps)
def __init__(self, cif_block):
crystal_symmetry_builder.__init__(self, cif_block)
self.hierarchy = hierarchy.root()
# These items are mandatory for the _atom_site loop, all others are optional
type_symbol = self._wrap_loop_if_needed(cif_block,
"_atom_site.type_symbol")
atom_labels = self._wrap_loop_if_needed(cif_block,
"_atom_site.auth_atom_id")
if atom_labels is None:
atom_labels = self._wrap_loop_if_needed(
cif_block, "_atom_site.label_atom_id"
) # corresponds to chem comp atom name
alt_id = self._wrap_loop_if_needed(
cif_block, "_atom_site.label_alt_id") # alternate conformer id
label_asym_id = self._wrap_loop_if_needed(
cif_block, "_atom_site.label_asym_id") # chain id
auth_asym_id = self._wrap_loop_if_needed(cif_block,
"_atom_site.auth_asym_id")
if label_asym_id is None: label_asym_id = auth_asym_id
if auth_asym_id is None: auth_asym_id = label_asym_id
comp_id = self._wrap_loop_if_needed(cif_block,
"_atom_site.auth_comp_id")
if comp_id is None:
comp_id = self._wrap_loop_if_needed(
cif_block, "_atom_site.label_comp_id") # residue name
entity_id = self._wrap_loop_if_needed(cif_block,
"_atom_site.label_entity_id")
seq_id = self._wrap_loop_if_needed(cif_block, "_atom_site.auth_seq_id")
if seq_id is None:
seq_id = self._wrap_loop_if_needed(
cif_block, "_atom_site.label_seq_id") # residue number
assert [atom_labels, alt_id, auth_asym_id, comp_id, entity_id,
seq_id].count(None) == 0, "someting is not present"
assert type_symbol is not None
atom_site_fp = cif_block.get('_atom_site.phenix_scat_dispersion_real')
atom_site_fdp = cif_block.get('_atom_site.phenix_scat_dispersion_imag')
pdb_ins_code = cif_block.get(
"_atom_site.pdbx_PDB_ins_code") # insertion code
model_ids = cif_block.get("_atom_site.pdbx_PDB_model_num")
atom_site_id = cif_block.get("_atom_site.id")
# only permitted values are ATOM or HETATM
group_PDB = cif_block.get("_atom_site.group_PDB")
# TODO: read esds
B_iso_or_equiv = flex.double(
self._wrap_loop_if_needed(cif_block, "_atom_site.B_iso_or_equiv"))
cart_x = flex.double(
self._wrap_loop_if_needed(cif_block, "_atom_site.Cartn_x"))
cart_y = flex.double(
self._wrap_loop_if_needed(cif_block, "_atom_site.Cartn_y"))
cart_z = flex.double(
self._wrap_loop_if_needed(cif_block, "_atom_site.Cartn_z"))
occu = flex.double(
self._wrap_loop_if_needed(cif_block, "_atom_site.occupancy"))
formal_charge = self._wrap_loop_if_needed(
cif_block, "_atom_site.pdbx_formal_charge")
# anisotropic b-factors
# TODO: read esds
anisotrop_id = self._wrap_loop_if_needed(cif_block,
"_atom_site_anisotrop.id")
adps = None
if anisotrop_id is not None:
u_ij = [
self._wrap_loop_if_needed(
cif_block,
"_atom_site_anisotrop.U[%s][%s]" % (ij[0], ij[1]))
for ij in ("11", "22", "33", "12", "13", "23")
]
assert u_ij.count(None) in (0, 6)
if u_ij.count(None) == 0:
adps = u_ij
else:
assert u_ij.count(None) == 6
b_ij = [
self._wrap_loop_if_needed(
cif_block,
"_atom_site_anisotrop.B[%s][%s]" % (ij[0], ij[1]))
for ij in ("11", "22", "33", "12", "13", "23")
]
assert b_ij.count(None) in (0, 6)
if b_ij.count(None) == 0:
adps = adptbx.b_as_u(b_ij)
assert not (u_ij.count(None) and b_ij.count(None)
) # illegal for both to be present
if adps is not None:
try:
adps = [flex.double(adp) for adp in adps]
except ValueError as e:
raise CifBuilderError("Error interpreting ADPs: " + str(e))
adps = flex.sym_mat3_double(*adps)
py_adps = {}
if anisotrop_id is not None and adps is not None:
for an_id, adp in zip(list(anisotrop_id), list(adps)):
py_adps[an_id] = adp
current_model_id = None
current_label_asym_id = None
current_auth_asym_id = None
current_residue_id = None
current_ins_code = None
for i_atom in range(atom_labels.size()):
# model(s)
last_model_id = current_model_id
current_model_id = model_ids[i_atom]
assert current_model_id is not None
if current_model_id != last_model_id:
model = hierarchy.model(id=current_model_id)
self.hierarchy.append_model(model)
# chain(s)
last_label_asym_id = current_label_asym_id
current_label_asym_id = label_asym_id[i_atom]
assert current_label_asym_id is not None
last_auth_asym_id = current_auth_asym_id
current_auth_asym_id = auth_asym_id[i_atom]
assert current_auth_asym_id not in [".", "?", " "], "mmCIF file contains " + \
"record with empty auth_asym_id, which is wrong."
assert current_label_asym_id is not None
if (current_auth_asym_id != last_auth_asym_id
or current_model_id != last_model_id):
chain = hierarchy.chain(id=current_auth_asym_id)
model.append_chain(chain)
else:
assert current_auth_asym_id == last_auth_asym_id
# residue_group(s)
# defined by residue id and insertion code
last_residue_id = current_residue_id
current_residue_id = seq_id[i_atom]
assert current_residue_id is not None
last_ins_code = current_ins_code
if pdb_ins_code is not None:
current_ins_code = pdb_ins_code[i_atom]
if current_ins_code in ("?", ".", None): current_ins_code = " "
if (current_residue_id != last_residue_id
or current_ins_code != last_ins_code
or current_auth_asym_id != last_auth_asym_id
or current_model_id != last_model_id):
try:
resseq = hy36encode(width=4, value=int(current_residue_id))
except ValueError as e:
resseq = current_residue_id
assert len(resseq) == 4
residue_group = hierarchy.residue_group(resseq=resseq,
icode=current_ins_code)
chain.append_residue_group(residue_group)
atom_groups = OrderedDict() # reset atom_groups cache
# atom_group(s)
# defined by resname and altloc id
current_altloc = alt_id[i_atom]
if current_altloc == "." or current_altloc == "?":
current_altloc = "" # Main chain atoms
current_resname = comp_id[i_atom]
if (current_altloc, current_resname) not in atom_groups:
atom_group = hierarchy.atom_group(altloc=current_altloc,
resname=current_resname)
atom_groups[(current_altloc, current_resname)] = atom_group
if current_altloc == "":
residue_group.insert_atom_group(0, atom_group)
else:
residue_group.append_atom_group(atom_group)
else:
atom_group = atom_groups[(current_altloc, current_resname)]
# atom(s)
atom = hierarchy.atom()
atom_group.append_atom(atom)
atom.set_element(type_symbol[i_atom])
atom.set_name(
format_pdb_atom_name(atom_labels[i_atom], type_symbol[i_atom]))
atom.set_xyz(new_xyz=(cart_x[i_atom], cart_y[i_atom],
cart_z[i_atom]))
atom.set_b(B_iso_or_equiv[i_atom])
atom.set_occ(occu[i_atom])
# hy36encode should go once the pdb.hierarchy has been
# modified to no longer store fixed-width strings
atom.set_serial(
hy36encode(width=5, value=int(atom_site_id[i_atom])))
# some code relies on an empty segid being 4 spaces
atom.set_segid(" ")
if group_PDB is not None and group_PDB[i_atom] == "HETATM":
atom.hetero = True
if formal_charge is not None:
charge = formal_charge[i_atom]
if charge not in ("?", "."):
if charge.endswith("-") or charge.startswith("-"):
sign = "-"
else:
sign = "+"
charge = charge.strip(" -+")
charge = int(charge)
if charge == 0: sign = ""
atom.set_charge("%i%s" % (charge, sign))
if atom_site_fp is not None:
fp = atom_site_fp[i_atom]
if fp not in ("?", "."):
atom.set_fp(new_fp=float(fp))
if atom_site_fdp is not None:
fdp = atom_site_fdp[i_atom]
if fdp not in ("?", "."):
atom.set_fdp(new_fdp=float(fdp))
if anisotrop_id is not None and adps is not None:
py_u_ij = py_adps.get(atom.serial.strip(), None)
if py_u_ij is not None:
atom.set_uij(py_u_ij)
if len(self.hierarchy.models()) == 1:
# for compatibility with single-model PDB files
self.hierarchy.models()[0].id = ""
def __init__(self, cif_block):
crystal_symmetry_builder.__init__(self, cif_block)
self.hierarchy = hierarchy.root()
# These items are mandatory for the _atom_site loop, all others are optional
type_symbol = cif_block.get("_atom_site.type_symbol")
atom_labels = cif_block.get("_atom_site.auth_atom_id")
if atom_labels is None:
atom_labels = cif_block.get("_atom_site.label_atom_id") # corresponds to chem comp atom name
alt_id = cif_block.get("_atom_site.label_alt_id") # alternate conformer id
label_asym_id = cif_block.get("_atom_site.label_asym_id") # chain id
auth_asym_id = cif_block.get("_atom_site.auth_asym_id")
if label_asym_id is None: label_asym_id = auth_asym_id
if auth_asym_id is None: auth_asym_id = label_asym_id
comp_id = cif_block.get("_atom_site.auth_comp_id")
if comp_id is None:
comp_id = cif_block.get("_atom_site.label_comp_id") # residue name
entity_id = cif_block.get("_atom_site.label_entity_id")
seq_id = cif_block.get("_atom_site.auth_seq_id")
if seq_id is None:
seq_id = cif_block.get("_atom_site.label_seq_id") # residue number
assert [atom_labels, alt_id, auth_asym_id, comp_id, entity_id, seq_id].count(None) == 0
assert type_symbol is not None
atom_site_fp = cif_block.get('_atom_site.phenix_scat_dispersion_real')
atom_site_fdp = cif_block.get('_atom_site.phenix_scat_dispersion_imag')
pdb_ins_code = cif_block.get("_atom_site.pdbx_PDB_ins_code") # insertion code
model_ids = cif_block.get("_atom_site.pdbx_PDB_model_num")
atom_site_id = cif_block.get("_atom_site.id")
# only permitted values are ATOM or HETATM
group_PDB = cif_block.get("_atom_site.group_PDB")
# TODO: read esds
B_iso_or_equiv = flex.double(cif_block.get("_atom_site.B_iso_or_equiv"))
cart_x = flex.double(cif_block.get("_atom_site.Cartn_x"))
cart_y = flex.double(cif_block.get("_atom_site.Cartn_y"))
cart_z = flex.double(cif_block.get("_atom_site.Cartn_z"))
occu = flex.double(cif_block.get("_atom_site.occupancy"))
formal_charge = cif_block.get("_atom_site.pdbx_formal_charge")
# anisotropic b-factors
# TODO: read esds
anisotrop_id = cif_block.get("_atom_site_anisotrop.id")
adps = None
if anisotrop_id is not None:
u_ij = [cif_block.get("_atom_site_anisotrop.U[%s][%s]" %(ij[0], ij[1]))
for ij in ("11", "22", "33", "12", "13", "23")]
assert u_ij.count(None) in (0, 6)
if u_ij.count(None) == 0:
adps = u_ij
else:
assert u_ij.count(None) == 6
b_ij = [cif_block.get("_atom_site_anisotrop.B[%s][%s]" %(ij[0], ij[1]))
for ij in ("11", "22", "33", "12", "13", "23")]
assert b_ij.count(None) in (0, 6)
if b_ij.count(None) == 0:
adps = adptbx.b_as_u(b_ij)
assert not (u_ij.count(None) and b_ij.count(None)) # illegal for both to be present
if adps is not None:
try:
adps = [flex.double(adp) for adp in adps]
except ValueError, e:
raise CifBuilderError("Error interpreting ADPs: " + str(e))
adps = flex.sym_mat3_double(*adps)