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# Copyright (C) 2002, Thomas Hamelryck ([email protected])
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""mmCIF parsers."""
import numpy
import warnings
from Bio.File import as_handle
from Bio.PDB.MMCIF2Dict import MMCIF2Dict
from Bio.PDB.StructureBuilder import StructureBuilder
from Bio.PDB.PDBExceptions import PDBConstructionException
from Bio.PDB.PDBExceptions import PDBConstructionWarning
class MMCIFParser:
"""Parse a mmCIF file and return a Structure object."""
def __init__(
self, structure_builder=None, auth_chains=True, auth_residues=True, QUIET=False
):
"""Create a PDBParser object.
The mmCIF parser calls a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instantiated by the
MMCIParser object itself, but if the user provides his/her own
StructureBuilder object, the latter is used instead.
Arguments:
- structure_builder - an optional user implemented StructureBuilder class.
- auth_chains - True by default. If true, use the author chain IDs.
If false, use the re-assigned mmCIF chain IDs.
- auth_residues - True by default. If true, use the author residue numbering.
If false, use the mmCIF "label" residue numbering, which has no insertion
codes, and strictly increments residue numbers.
NOTE: Non-polymers such as water don't have a "label" residue number,
and will be skipped.
- QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the mmCIF file!
"""
if structure_builder is not None:
self._structure_builder = structure_builder
else:
self._structure_builder = StructureBuilder()
self.header = None
# self.trailer = None
self.line_counter = 0
self.build_structure = None
self.auth_chains = bool(auth_chains)
self.auth_residues = bool(auth_residues)
self.QUIET = bool(QUIET)
# Public methods
def get_structure(self, structure_id, filename):
"""Return the structure.
Arguments:
- structure_id - string, the id that will be used for the structure
- filename - name of mmCIF file, OR an open text mode file handle
"""
with warnings.catch_warnings():
if self.QUIET:
warnings.filterwarnings("ignore", category=PDBConstructionWarning)
self._mmcif_dict = MMCIF2Dict(filename)
self._build_structure(structure_id)
self._structure_builder.set_header(self._get_header())
return self._structure_builder.get_structure()
# Private methods
def _mmcif_get(self, key, dict, deflt):
if key in dict:
rslt = dict[key][0]
if "?" != rslt:
return rslt
return deflt
def _update_header_entry(self, target_key, keys):
md = self._mmcif_dict
for key in keys:
val = md.get(key)
try:
item = val[0]
except (TypeError, IndexError):
continue
if item != "?":
self.header[target_key] = item
break
def _get_header(self):
self.header = {
"name": "",
"head": "",
"idcode": "",
"deposition_date": "",
"structure_method": "",
"resolution": None,
}
self._update_header_entry(
"idcode", ["_entry_id", "_exptl.entry_id", "_struct.entry_id"]
)
self._update_header_entry("name", ["_struct.title"])
self._update_header_entry(
"head", ["_struct_keywords.pdbx_keywords", "_struct_keywords.text"]
)
self._update_header_entry(
"deposition_date", ["_pdbx_database_status.recvd_initial_deposition_date"]
)
self._update_header_entry("structure_method", ["_exptl.method"])
self._update_header_entry(
"resolution",
[
"_refine.ls_d_res_high",
"_refine_hist.d_res_high",
"_em_3d_reconstruction.resolution",
],
)
if self.header["resolution"] is not None:
try:
self.header["resolution"] = float(self.header["resolution"])
except ValueError:
self.header["resolution"] = None
return self.header
def _build_structure(self, structure_id):
# two special chars as placeholders in the mmCIF format
# for item values that cannot be explicitly assigned
# see: pdbx/mmcif syntax web page
_unassigned = {".", "?"}
mmcif_dict = self._mmcif_dict
atom_serial_list = mmcif_dict["_atom_site.id"]
atom_id_list = mmcif_dict["_atom_site.label_atom_id"]
residue_id_list = mmcif_dict["_atom_site.label_comp_id"]
try:
element_list = mmcif_dict["_atom_site.type_symbol"]
except KeyError:
element_list = None
if self.auth_chains:
chain_id_list = mmcif_dict["_atom_site.auth_asym_id"]
else:
chain_id_list = mmcif_dict["_atom_site.label_asym_id"]
x_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_x"]]
y_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_y"]]
z_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_z"]]
alt_list = mmcif_dict["_atom_site.label_alt_id"]
icode_list = mmcif_dict["_atom_site.pdbx_PDB_ins_code"]
b_factor_list = mmcif_dict["_atom_site.B_iso_or_equiv"]
occupancy_list = mmcif_dict["_atom_site.occupancy"]
fieldname_list = mmcif_dict["_atom_site.group_PDB"]
try:
serial_list = [int(n) for n in mmcif_dict["_atom_site.pdbx_PDB_model_num"]]
except KeyError:
# No model number column
serial_list = None
except ValueError:
# Invalid model number (malformed file)
raise PDBConstructionException("Invalid model number") from None
try:
aniso_u11 = mmcif_dict["_atom_site_anisotrop.U[1][1]"]
aniso_u12 = mmcif_dict["_atom_site_anisotrop.U[1][2]"]
aniso_u13 = mmcif_dict["_atom_site_anisotrop.U[1][3]"]
aniso_u22 = mmcif_dict["_atom_site_anisotrop.U[2][2]"]
aniso_u23 = mmcif_dict["_atom_site_anisotrop.U[2][3]"]
aniso_u33 = mmcif_dict["_atom_site_anisotrop.U[3][3]"]
aniso_flag = 1
except KeyError:
# no anisotropic B factors
aniso_flag = 0
if self.auth_residues:
# if auth_seq_id is present, we use this.
# Otherwise label_seq_id is used.
if "_atom_site.auth_seq_id" in mmcif_dict:
seq_id_list = mmcif_dict["_atom_site.auth_seq_id"]
else:
seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
else:
seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
# Now loop over atoms and build the structure
current_chain_id = None
current_residue_id = None
current_resname = None
structure_builder = self._structure_builder
structure_builder.init_structure(structure_id)
structure_builder.init_seg(" ")
# Historically, Biopython PDB parser uses model_id to mean array index
# so serial_id means the Model ID specified in the file
current_model_id = -1
current_serial_id = -1
for i in range(0, len(atom_id_list)):
# set the line_counter for 'ATOM' lines only and not
# as a global line counter found in the PDBParser()
structure_builder.set_line_counter(i)
# Try coercing serial to int, for compatibility with PDBParser
# But do not quit if it fails. mmCIF format specs allow strings.
try:
serial = int(atom_serial_list[i])
except ValueError:
serial = atom_serial_list[i]
warnings.warn(
"PDBConstructionWarning: "
"Some atom serial numbers are not numerical",
PDBConstructionWarning,
)
x = x_list[i]
y = y_list[i]
z = z_list[i]
resname = residue_id_list[i]
chainid = chain_id_list[i]
altloc = alt_list[i]
if altloc in _unassigned:
altloc = " "
resseq = seq_id_list[i]
if resseq == ".":
# Non-existing residue ID
try:
msg_resseq = mmcif_dict["_atom_site.auth_seq_id"][i]
msg = "Non-existing residue ID in chain '{}', residue '{}'".format(
chainid, msg_resseq
)
except (KeyError, IndexError):
msg = f"Non-existing residue ID in chain '{chainid}'"
warnings.warn(
"PDBConstructionWarning: ",
msg,
PDBConstructionWarning,
)
continue
int_resseq = int(resseq)
icode = icode_list[i]
if icode in _unassigned:
icode = " "
name = atom_id_list[i]
# occupancy & B factor
try:
tempfactor = float(b_factor_list[i])
except ValueError:
raise PDBConstructionException("Invalid or missing B factor") from None
try:
occupancy = float(occupancy_list[i])
except ValueError:
raise PDBConstructionException("Invalid or missing occupancy") from None
fieldname = fieldname_list[i]
if fieldname == "HETATM":
if resname == "HOH" or resname == "WAT":
hetatm_flag = "W"
else:
hetatm_flag = "H"
else:
hetatm_flag = " "
resseq = (hetatm_flag, int_resseq, icode)
if serial_list is not None:
# model column exists; use it
serial_id = serial_list[i]
if current_serial_id != serial_id:
# if serial changes, update it and start new model
current_serial_id = serial_id
current_model_id += 1
structure_builder.init_model(current_model_id, current_serial_id)
current_chain_id = None
current_residue_id = None
current_resname = None
else:
# no explicit model column; initialize single model
structure_builder.init_model(current_model_id)
if current_chain_id != chainid:
current_chain_id = chainid
structure_builder.init_chain(current_chain_id)
current_residue_id = None
current_resname = None
if current_residue_id != resseq or current_resname != resname:
current_residue_id = resseq
current_resname = resname
structure_builder.init_residue(resname, hetatm_flag, int_resseq, icode)
coord = numpy.array((x, y, z), "f")
element = element_list[i].upper() if element_list else None
structure_builder.init_atom(
name,
coord,
tempfactor,
occupancy,
altloc,
name,
serial_number=serial,
element=element,
)
if aniso_flag == 1 and i < len(aniso_u11):
u = (
aniso_u11[i],
aniso_u12[i],
aniso_u13[i],
aniso_u22[i],
aniso_u23[i],
aniso_u33[i],
)
mapped_anisou = [float(_) for _ in u]
anisou_array = numpy.array(mapped_anisou, "f")
structure_builder.set_anisou(anisou_array)
# Now try to set the cell
try:
a = float(mmcif_dict["_cell.length_a"][0])
b = float(mmcif_dict["_cell.length_b"][0])
c = float(mmcif_dict["_cell.length_c"][0])
alpha = float(mmcif_dict["_cell.angle_alpha"][0])
beta = float(mmcif_dict["_cell.angle_beta"][0])
gamma = float(mmcif_dict["_cell.angle_gamma"][0])
cell = numpy.array((a, b, c, alpha, beta, gamma), "f")
spacegroup = mmcif_dict["_symmetry.space_group_name_H-M"][0]
spacegroup = spacegroup[1:-1] # get rid of quotes!!
if spacegroup is None:
raise Exception
structure_builder.set_symmetry(spacegroup, cell)
except Exception:
pass # no cell found, so just ignore
class FastMMCIFParser:
"""Parse an MMCIF file and return a Structure object."""
def __init__(
self, structure_builder=None, auth_chains=True, auth_residues=True, QUIET=False
):
"""Create a FastMMCIFParser object.
The mmCIF parser calls a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instantiated by the
parser object itself, but if the user provides his/her own
StructureBuilder object, the latter is used instead.
The main difference between this class and the regular MMCIFParser is
that only 'ATOM' and 'HETATM' lines are parsed here. Use if you are
interested only in coordinate information.
Arguments:
- structure_builder - an optional user implemented StructureBuilder class.
- auth_chains - True by default. If true, use the author chain IDs.
If false, use the re-assigned mmCIF chain IDs.
- auth_residues - True by default. If true, use the author residue numbering.
If false, use the mmCIF "label" residue numbering, which has no insertion
codes, and strictly increments residue numbers.
NOTE: Non-polymers such as water don't have a "label" residue number,
and will be skipped.
- QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the mmCIF file!
"""
if structure_builder is not None:
self._structure_builder = structure_builder
else:
self._structure_builder = StructureBuilder()
self.line_counter = 0
self.build_structure = None
self.auth_chains = bool(auth_chains)
self.auth_residues = bool(auth_residues)
self.QUIET = bool(QUIET)
# Public methods
def get_structure(self, structure_id, filename):
"""Return the structure.
Arguments:
- structure_id - string, the id that will be used for the structure
- filename - name of the mmCIF file OR an open filehandle
"""
with warnings.catch_warnings():
if self.QUIET:
warnings.filterwarnings("ignore", category=PDBConstructionWarning)
with as_handle(filename) as handle:
self._build_structure(structure_id, handle)
return self._structure_builder.get_structure()
# Private methods
def _build_structure(self, structure_id, filehandle):
# two special chars as placeholders in the mmCIF format
# for item values that cannot be explicitly assigned
# see: pdbx/mmcif syntax web page
_unassigned = {".", "?"}
# Read only _atom_site. and atom_site_anisotrop entries
read_atom, read_aniso = False, False
_fields, _records = [], []
_anisof, _anisors = [], []
for line in filehandle:
if line.startswith("_atom_site."):
read_atom = True
_fields.append(line.strip())
elif line.startswith("_atom_site_anisotrop."):
read_aniso = True
_anisof.append(line.strip())
elif read_atom and line.startswith("#"):
read_atom = False
elif read_aniso and line.startswith("#"):
read_aniso = False
elif read_atom:
_records.append(line.strip())
elif read_aniso:
_anisors.append(line.strip())
# Dumping the shlex module here since this particular
# category should be rather straightforward.
# Quite a performance boost..
_record_tbl = zip(*map(str.split, _records))
_anisob_tbl = zip(*map(str.split, _anisors))
mmcif_dict = dict(zip(_fields, _record_tbl))
mmcif_dict.update(dict(zip(_anisof, _anisob_tbl)))
# Build structure object
atom_serial_list = mmcif_dict["_atom_site.id"]
atom_id_list = mmcif_dict["_atom_site.label_atom_id"]
residue_id_list = mmcif_dict["_atom_site.label_comp_id"]
try:
element_list = mmcif_dict["_atom_site.type_symbol"]
except KeyError:
element_list = None
if self.auth_chains:
chain_id_list = mmcif_dict["_atom_site.auth_asym_id"]
else:
chain_id_list = mmcif_dict["_atom_site.label_asym_id"]
x_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_x"]]
y_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_y"]]
z_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_z"]]
alt_list = mmcif_dict["_atom_site.label_alt_id"]
icode_list = mmcif_dict["_atom_site.pdbx_PDB_ins_code"]
b_factor_list = mmcif_dict["_atom_site.B_iso_or_equiv"]
occupancy_list = mmcif_dict["_atom_site.occupancy"]
fieldname_list = mmcif_dict["_atom_site.group_PDB"]
try:
serial_list = [int(n) for n in mmcif_dict["_atom_site.pdbx_PDB_model_num"]]
except KeyError:
# No model number column
serial_list = None
except ValueError:
# Invalid model number (malformed file)
raise PDBConstructionException("Invalid model number") from None
try:
aniso_u11 = mmcif_dict["_atom_site_anisotrop.U[1][1]"]
aniso_u12 = mmcif_dict["_atom_site_anisotrop.U[1][2]"]
aniso_u13 = mmcif_dict["_atom_site_anisotrop.U[1][3]"]
aniso_u22 = mmcif_dict["_atom_site_anisotrop.U[2][2]"]
aniso_u23 = mmcif_dict["_atom_site_anisotrop.U[2][3]"]
aniso_u33 = mmcif_dict["_atom_site_anisotrop.U[3][3]"]
aniso_flag = 1
except KeyError:
# no anisotropic B factors
aniso_flag = 0
if self.auth_residues:
# if auth_seq_id is present, we use this.
# Otherwise label_seq_id is used.
if "_atom_site.auth_seq_id" in mmcif_dict:
seq_id_list = mmcif_dict["_atom_site.auth_seq_id"]
else:
seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
else:
seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
# Now loop over atoms and build the structure
current_chain_id = None
current_residue_id = None
current_resname = None
structure_builder = self._structure_builder
structure_builder.init_structure(structure_id)
structure_builder.init_seg(" ")
# Historically, Biopython PDB parser uses model_id to mean array index
# so serial_id means the Model ID specified in the file
current_model_id = -1
current_serial_id = -1
for i in range(0, len(atom_id_list)):
# set the line_counter for 'ATOM' lines only and not
# as a global line counter found in the PDBParser()
structure_builder.set_line_counter(i)
serial = atom_serial_list[i]
x = x_list[i]
y = y_list[i]
z = z_list[i]
resname = residue_id_list[i]
chainid = chain_id_list[i]
altloc = alt_list[i]
if altloc in _unassigned:
altloc = " "
resseq = seq_id_list[i]
if resseq == ".":
# Non-existing residue ID
try:
msg_resseq = mmcif_dict["_atom_site.auth_seq_id"][i]
msg = "Non-existing residue ID in chain '{}', residue '{}'".format(
chainid, msg_resseq
)
except (KeyError, IndexError):
msg = f"Non-existing residue ID in chain '{chainid}'"
warnings.warn(
"PDBConstructionWarning: ",
msg,
PDBConstructionWarning,
)
continue
int_resseq = int(resseq)
icode = icode_list[i]
if icode in _unassigned:
icode = " "
# Remove occasional " from quoted atom names (e.g. xNA)
name = atom_id_list[i].strip('"')
# occupancy & B factor
try:
tempfactor = float(b_factor_list[i])
except ValueError:
raise PDBConstructionException("Invalid or missing B factor") from None
try:
occupancy = float(occupancy_list[i])
except ValueError:
raise PDBConstructionException("Invalid or missing occupancy") from None
fieldname = fieldname_list[i]
if fieldname == "HETATM":
hetatm_flag = "H"
else:
hetatm_flag = " "
resseq = (hetatm_flag, int_resseq, icode)
if serial_list is not None:
# model column exists; use it
serial_id = serial_list[i]
if current_serial_id != serial_id:
# if serial changes, update it and start new model
current_serial_id = serial_id
current_model_id += 1
structure_builder.init_model(current_model_id, current_serial_id)
current_chain_id = None
current_residue_id = None
current_resname = None
else:
# no explicit model column; initialize single model
structure_builder.init_model(current_model_id)
if current_chain_id != chainid:
current_chain_id = chainid
structure_builder.init_chain(current_chain_id)
current_residue_id = None
current_resname = None
if current_residue_id != resseq or current_resname != resname:
current_residue_id = resseq
current_resname = resname
structure_builder.init_residue(resname, hetatm_flag, int_resseq, icode)
coord = numpy.array((x, y, z), "f")
element = element_list[i] if element_list else None
structure_builder.init_atom(
name,
coord,
tempfactor,
occupancy,
altloc,
name,
serial_number=serial,
element=element,
)
if aniso_flag == 1 and i < len(aniso_u11):
u = (
aniso_u11[i],
aniso_u12[i],
aniso_u13[i],
aniso_u22[i],
aniso_u23[i],
aniso_u33[i],
)
mapped_anisou = [float(_) for _ in u]
anisou_array = numpy.array(mapped_anisou, "f")
structure_builder.set_anisou(anisou_array)
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