def read_start(self, filobj):
## parse the mmCIF file
self.cif_file = mmCIF.mmCIFFile()
self.cif_file.load_file(filobj)
## for a mmCIF file for a structure, assume the first data item
## contains the structure; if there is no data in the mmCIF
## file, halt
try:
self.cif_data = self.cif_file[0]
except IndexError:
self.halt = True
return
self.set_atom_site_data_columns()
## maintain a map of atom_site.id -> atm
self.atom_site_id_map = {}
def read_start(self, filobj):
## parse the mmCIF file
self.cif_file = mmCIF.mmCIFFile()
self.cif_file.load_file(filobj)
## for an mmCIF file for a structure, assume the first data item
## contains the structure; if there is no data in the mmCIF
## file, halt
try:
self.cif_data = self.cif_file[0]
except IndexError:
self.halt = True
return
self.set_atom_site_data_columns()
## maintain a map of atom_site.id -> atm
self.atom_site_id_map = {}
def SaveStructure(**args):
"""Saves a Structure object into a supported file type.
file = <file object or path; required>
structure = <mmLib.Structure object to save; required>
format = <'PDB' or 'CIF'; defaults to 'PDB'>
"""
fil = get_file_arg(args)
if not args.has_key("format"):
args["format"] = get_file_extension(fil)
else:
args["format"] = args["format"].upper()
fileobj = open_fileobj(fil, "w")
try:
struct = args["struct"]
except KeyError:
try:
struct = args["structure"]
except KeyError:
raise TypeError, "LoadStructure(structure=) argument required"
if args["format"] == "PDB":
pdb_file = PDBFile()
PDBFileBuilder(struct, pdb_file)
pdb_file.save_file(fileobj)
return
elif args["format"] == "CIF":
cif_file = mmCIFFile()
mmCIFFileBuilder(struct, cif_file)
cif_file.save_file(fileobj)
return
raise FileIOUnsupportedFormat("Unsupported file format %s" % (str(fil)))
def SaveStructure(**args):
"""Saves a Structure object into a supported file type.
file = <file object or path; required>
structure = <mmLib.Structure object to save; required>
format = <'PDB' or 'CIF'; defaults to 'PDB'>
"""
fil = get_file_arg(args)
if not args.has_key("format"):
args["format"] = get_file_extension(fil)
else:
args["format"] = args["format"].upper()
fileobj = open_fileobj(fil, "w")
try:
struct = args["struct"]
except KeyError:
try:
struct = args["structure"]
except KeyError:
raise TypeError,"LoadStructure(structure=) argument required"
if args["format"] == "PDB":
pdb_file = PDBFile()
PDBFileBuilder(struct, pdb_file)
pdb_file.save_file(fileobj)
return
elif args["format"] == "CIF":
cif_file = mmCIFFile()
mmCIFFileBuilder(struct, cif_file)
cif_file.save_file(fileobj)
return
raise FileIOUnsupportedFormat("Unsupported file format %s" % (str(fil)))
def library_construct_monomer_desc(res_name):
"""Constructs the MonomerDesc object for the given residue name.
"""
## return None when the res_name is an empty string
if len(res_name) < 1:
return None
if ALT_RES_NAME_DICT.has_key(res_name):
lookup_name = ALT_RES_NAME_DICT[res_name]
else:
lookup_name = res_name.upper()
libfil = library_open_monomer_lib_file(lookup_name)
if libfil is None:
ConsoleOutput.warning("monomer description not found for '%s'" % (res_name))
return None
## generate monomer description
mon_desc = MonomerDesc()
## data from RCSB library
rcsb_cif_file = mmCIF.mmCIFFile()
rcsb_cif_file.load_file(libfil)
rcsb_cif_data = rcsb_cif_file[0]
libfil.close()
chem_comp = rcsb_cif_data.get_table("chem_comp")[0]
mon_desc.res_name = chem_comp.get_lower("res_name")
mon_desc.full_name = chem_comp.get_lower("name")
mon_desc.type = chem_comp.get_lower("type")
mon_desc.pdbx_type = chem_comp.get_lower("pdbx_type")
mon_desc.formula = chem_comp.get_lower("formula")
mon_desc.rcsb_class_1 = chem_comp.get_lower("rcsb_class_1")
chem_comp_atom = rcsb_cif_data.get_table("chem_comp_atom")
if chem_comp_atom is not None:
for cif_row in chem_comp_atom:
name = cif_row.getitem_lower("atom_id")
try:
symbol = cif_row.getitem_lower("type_symbol")
except KeyError:
## this should occur when an atom name does not match the ones
## found in a monomer file
symbol = name
msg = "unrecognized atom name: '%s' in residue '%s'" % (
symbol, res_name)
ConsoleOutput.warning(msg)
mon_desc.atom_list.append({"name": name, "symbol": symbol})
mon_desc.atom_dict[name] = symbol
try:
alt_name = cif_row.getitem_lower("alt_atom_id")
except KeyError:
pass
else:
mon_desc.alt_atom_dict[name] = alt_name
chem_comp_bond = rcsb_cif_data.get_table("chem_comp_bond")
if chem_comp_bond is not None:
for cif_row in chem_comp_bond:
atom1 = cif_row.getitem_lower("atom_id_1")
atom2 = cif_row.getitem_lower("atom_id_2")
mon_desc.bond_list.append({"atom1": atom1, "atom2": atom2})
## data from mmLib supplemental library in mmLib/Data/monomers.cif
mmlib_cif_data = MMLIB_MONOMERS_CIF.get_data(res_name)
if mmlib_cif_data is not None:
## get additional chemical information on amino acids
chem_comp = mmlib_cif_data.get_table("chem_comp")
if chem_comp is not None:
mon_desc.one_letter_code = chem_comp["one_letter_code"]
mon_desc.chem_type = chem_comp["chem_type"]
## get torsion angle definitions
torsion_angles = mmlib_cif_data.get_table("torsion_angles")
if torsion_angles is not None:
for cif_row in torsion_angles:
mon_desc.torsion_angle_dict[cif_row["name"]] = (
cif_row["atom1"], cif_row["atom2"],
cif_row["atom3"], cif_row["atom4"])
## set some derived flags on the monomer description
mon_type = mon_desc.type.upper()
if mon_type == "L-PEPTIDE LINKING":
mon_desc.amino_acid = True
elif mon_type == "DNA LINKING" or mon_type == "RNA LINKING":
mon_desc.nucleic_acid = True
elif mon_type == "HOH" or mon_type == "WAT":
mon_desc.water = True
return mon_desc
elif __file__:
MMLIB_PATH = os.path.dirname(__file__)
DATA_PATH = os.path.join(MMLIB_PATH, "Data")
ELEMENT_DATA_PATH = os.path.join(MMLIB_PATH, "Data", "elements.cif")
MMLIB_MONOMER_DATA_PATH = os.path.join(MMLIB_PATH, "Data", "monomers.cif")
RCSB_MONOMER_DATA_FILE = os.path.join(MMLIB_PATH, "Data", "Monomers.zip")
RCSB_MONOMER_DATA_PATH = os.path.join(MMLIB_PATH, "Data", "Monomers")
###############################################################################
## Caches
##
ELEMENT_CACHE = {}
MONOMER_RES_NAME_CACHE = {}
ELEMENT_CIF_FILE = mmCIF.mmCIFFile()
ELEMENT_CIF_FILE.load_file(open(ELEMENT_DATA_PATH, "r"))
MMLIB_MONOMERS_CIF = mmCIF.mmCIFFile()
MMLIB_MONOMERS_CIF.load_file(open(MMLIB_MONOMER_DATA_PATH, "r"))
RCSB_USE_ZIP = None
RCSB_ZIP = None
###############################################################################
## Constants
##
ELEMENT_SYMBOL_DICT = {
"H" : True, "h" : True,
"He": True, "he": True, "HE": True,
"Li": True, "li": True, "LI": True,
def library_construct_monomer_desc(res_name):
"""Constructs the MonomerDesc object for the given residue name.
"""
## return None when the res_name is an empty string
if len(res_name) < 1:
return None
if ALT_RES_NAME_DICT.has_key(res_name):
lookup_name = ALT_RES_NAME_DICT[res_name]
else:
lookup_name = res_name.upper()
libfil = library_open_monomer_lib_file(lookup_name)
if libfil is None:
ConsoleOutput.warning("monomer description not found for '%s'" %
(res_name))
return None
## generate monomer description
mon_desc = MonomerDesc()
## data from RCSB library
rcsb_cif_file = mmCIF.mmCIFFile()
rcsb_cif_file.load_file(libfil)
rcsb_cif_data = rcsb_cif_file[0]
libfil.close()
chem_comp = rcsb_cif_data.get_table("chem_comp")[0]
mon_desc.res_name = chem_comp.get_lower("res_name")
mon_desc.full_name = chem_comp.get_lower("name")
mon_desc.type = chem_comp.get_lower("type")
mon_desc.pdbx_type = chem_comp.get_lower("pdbx_type")
mon_desc.formula = chem_comp.get_lower("formula")
mon_desc.rcsb_class_1 = chem_comp.get_lower("rcsb_class_1")
chem_comp_atom = rcsb_cif_data.get_table("chem_comp_atom")
if chem_comp_atom is not None:
for cif_row in chem_comp_atom:
name = cif_row.getitem_lower("atom_id")
try:
symbol = cif_row.getitem_lower("type_symbol")
except KeyError:
## this should occur when an atom name does not match the ones
## found in a monomer file
symbol = name
msg = "unrecognized atom name: '%s' in residue '%s'" % (
symbol, res_name)
ConsoleOutput.warning(msg)
mon_desc.atom_list.append({"name": name, "symbol": symbol})
mon_desc.atom_dict[name] = symbol
try:
alt_name = cif_row.getitem_lower("alt_atom_id")
except KeyError:
pass
else:
mon_desc.alt_atom_dict[name] = alt_name
chem_comp_bond = rcsb_cif_data.get_table("chem_comp_bond")
if chem_comp_bond is not None:
for cif_row in chem_comp_bond:
atom1 = cif_row.getitem_lower("atom_id_1")
atom2 = cif_row.getitem_lower("atom_id_2")
mon_desc.bond_list.append({"atom1": atom1, "atom2": atom2})
## data from mmLib supplemental library in mmLib/Data/monomers.cif
mmlib_cif_data = MMLIB_MONOMERS_CIF.get_data(res_name)
if mmlib_cif_data is not None:
## get additional chemical information on amino acids
chem_comp = mmlib_cif_data.get_table("chem_comp")
if chem_comp is not None:
mon_desc.one_letter_code = chem_comp["one_letter_code"]
mon_desc.chem_type = chem_comp["chem_type"]
## get torsion angle definitions
torsion_angles = mmlib_cif_data.get_table("torsion_angles")
if torsion_angles is not None:
for cif_row in torsion_angles:
mon_desc.torsion_angle_dict[cif_row["name"]] = (
cif_row["atom1"], cif_row["atom2"], cif_row["atom3"],
cif_row["atom4"])
## set some derived flags on the monomer description
mon_type = mon_desc.type.upper()
if mon_type == "L-PEPTIDE LINKING":
mon_desc.amino_acid = True
elif mon_type == "DNA LINKING" or mon_type == "RNA LINKING":
mon_desc.nucleic_acid = True
elif mon_type == "HOH" or mon_type == "WAT":
mon_desc.water = True
return mon_desc
elif __file__:
MMLIB_PATH = os.path.dirname(__file__)
DATA_PATH = os.path.join(MMLIB_PATH, "Data")
ELEMENT_DATA_PATH = os.path.join(MMLIB_PATH, "Data", "elements.cif")
MMLIB_MONOMER_DATA_PATH = os.path.join(MMLIB_PATH, "Data", "monomers.cif")
RCSB_MONOMER_DATA_FILE = os.path.join(MMLIB_PATH, "Data", "Monomers.zip")
RCSB_MONOMER_DATA_PATH = os.path.join(MMLIB_PATH, "Data", "Monomers")
###############################################################################
## Caches
##
ELEMENT_CACHE = {}
MONOMER_RES_NAME_CACHE = {}
ELEMENT_CIF_FILE = mmCIF.mmCIFFile()
ELEMENT_CIF_FILE.load_file(open(ELEMENT_DATA_PATH, "r"))
MMLIB_MONOMERS_CIF = mmCIF.mmCIFFile()
MMLIB_MONOMERS_CIF.load_file(open(MMLIB_MONOMER_DATA_PATH, "r"))
RCSB_USE_ZIP = None
RCSB_ZIP = None
###############################################################################
## Constants
##
ELEMENT_SYMBOL_DICT = {
"H": True,
"h": True,
"He": True,
