def load_unit_cell(self, ucell_map):
"""Called by the implementation of load_metadata to load the
unit cell pararameters for the structure.
"""
for key in ("a", "b", "c", "alpha", "beta", "gamma"):
if not ucell_map.has_key(key):
ConsoleOutput.debug("ucell_map missing: %s" % (key))
return
if ucell_map.has_key("space_group"):
self.struct.unit_cell = UnitCell.UnitCell(
a=ucell_map["a"],
b=ucell_map["b"],
c=ucell_map["c"],
alpha=ucell_map["alpha"],
beta=ucell_map["beta"],
gamma=ucell_map["gamma"],
space_group=ucell_map["space_group"])
else:
self.struct.unit_cell = UnitCell.UnitCell(a=ucell_map["a"],
b=ucell_map["b"],
c=ucell_map["c"],
alpha=ucell_map["alpha"],
beta=ucell_map["beta"],
gamma=ucell_map["gamma"])
def load_unit_cell(self, ucell_map):
"""Called by the implementation of load_metadata to load the unit cell
parameters for the structure.
"""
for key in ("a", "b", "c", "alpha", "beta", "gamma"):
if not ucell_map.has_key(key):
ConsoleOutput.debug("ucell_map missing: %s" % (key))
return
if ucell_map.has_key("space_group"):
self.struct.unit_cell = UnitCell.UnitCell(
a = ucell_map["a"],
b = ucell_map["b"],
c = ucell_map["c"],
alpha = ucell_map["alpha"],
beta = ucell_map["beta"],
gamma = ucell_map["gamma"],
space_group = ucell_map["space_group"])
else:
self.struct.unit_cell = UnitCell.UnitCell(
a = ucell_map["a"],
b = ucell_map["b"],
c = ucell_map["c"],
alpha = ucell_map["alpha"],
beta = ucell_map["beta"],
gamma = ucell_map["gamma"])
def read_end_finalize(self):
"""Called for final cleanup after structure source reading is done.
Currently, this method does nothing but may be used in future versions.
"""
ConsoleOutput.debug("read_end_finalize()")
## calculate sequences for all chains
if self.calc_sequence is True:
for model in self.struct.iter_models():
for chain in model.iter_chains():
if len(chain.sequence) == 0:
chain.sequence.set_from_fragments(chain.iter_fragments())
## build bonds as defined in the monomer library
if self.library_bonds is True:
self.struct.add_bonds_from_library()
## build bonds by covalent distance calculations
if self.distance_bonds is True:
self.struct.add_bonds_from_covalent_distance()
def read_end_finalize(self):
"""Called for final cleanup after structure source reading is done.
Currently, this method does nothing but may be used in future versions.
"""
ConsoleOutput.debug("read_end_finalize()")
## calculate sequences for all chains
if self.calc_sequence is True:
for model in self.struct.iter_models():
for chain in model.iter_chains():
if len(chain.sequence) == 0:
chain.sequence.set_from_fragments(
chain.iter_fragments())
## build bonds as defined in the monomer library
if self.library_bonds is True:
self.struct.add_bonds_from_library()
## build bonds by covalent distance calculations
if self.distance_bonds is True:
self.struct.add_bonds_from_covalent_distance()
def name_service(self):
"""Runs the name service on all atoms needing to be named. This is
a complicated function which corrects most commonly found errors and
omitions from PDB files.
"""
if len(self.name_service_list) == 0:
return
## returns the next available chain_id in self.struct
## XXX: it's possible to run out of chain IDs!
def next_chain_id(suggest_chain_id):
if suggest_chain_id != "":
chain = self.struct.get_chain(suggest_chain_id)
if not chain:
return suggest_chain_id
for chain_id in "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789":
chain = self.struct.get_chain(chain_id)
if not chain:
return chain_id
raise StructureBuilderError("name_service exhausted new chain_ids")
## NAME SERVICE FOR POLYMER ATOMS
## what if we are given a list of atoms with res_name, frag_id,
## and model_id where the frag_id are sequental? they can be
## sequental several ways using insertion codes, but large breaks
## often denote chain breaks
## I need to handle the special case of a list of polymer residues
## which do not have chain_ids. This requires a first pass over
## the atom list usind different rules than what I use for sorting
## out non-polymers
current_polymer_type = None
current_polymer_model_id = None
current_polymer_chain_id = None
current_polymer_frag_id = None
current_polymer_res_name = None
current_polymer_name_dict = None
polymer_model_dict = {}
current_frag = None
current_frag_list = None
for atm in self.name_service_list[:]:
## determine the polymer type of the atom
if Library.library_is_amino_acid(atm.res_name):
polymer_type = "protein"
elif Library.library_is_nucleic_acid(atm.res_name):
polymer_type = "dna"
else:
## if the atom is not a polymer, we definately have a break
## in this chain
current_polymer_type = None
current_polymer_model_id = None
current_polymer_chain_id = None
current_polymer_frag_id = None
current_polymer_res_name = None
current_polymer_name_dict = None
current_frag = None
current_frag_list = None
continue
fragment_id = Structure.FragmentID(atm.fragment_id)
## now we deal with conditions which can terminate the current
## polymer chain
if polymer_type!=current_polymer_type or \
atm.model_id!=current_polymer_model_id or \
atm.chain_id!=current_polymer_chain_id or \
fragment_id<current_polymer_frag_id:
current_polymer_type = polymer_type
current_polymer_model_id = atm.model_id
current_polymer_chain_id = atm.chain_id
current_polymer_frag_id = Structure.FragmentID(atm.fragment_id)
current_polymer_res_name = atm.res_name
current_polymer_name_dict = {atm.name: True}
## create new fragment
current_frag = [atm]
current_frag_list = [current_frag]
## create new fragment list (chain)
try:
model = polymer_model_dict[atm.model_id]
except KeyError:
model = [current_frag_list]
polymer_model_dict[atm.model_id] = model
else:
model.append(current_frag_list)
## we have now dealt with the atom, so it can be removed
## from the name service list
self.name_service_list.remove(atm)
continue
## if we get here, then we know this atom is destine for the
## current chain, and the algorithm needs to place the atom
## in the current fragment, or create a new fragment for it
## to go into; the conditions for it going into the current
## fragment are: it has it have the same res_name, and its
## atom name cannot conflict with the names of atoms already in
## in the fragment
if atm.res_name != current_polymer_res_name or current_polymer_name_dict.has_key(
atm.name):
current_polymer_res_name = atm.res_name
current_polymer_name_dict = {atm.name: True}
## create new fragment and add it to the current fragment list
current_frag = [atm]
current_frag_list.append(current_frag)
## we have now dealt with the atom, so it can be removed
## from the name service list
self.name_service_list.remove(atm)
continue
## okay, put it in the current fragment
current_frag.append(atm)
self.name_service_list.remove(atm)
## now assign chain_ids and add the atoms to the structure
model_ids = polymer_model_dict.keys()
model_ids.sort()
model_list = [polymer_model_dict[model_id] for model_id in model_ids]
num_chains = 0
for frag_list in polymer_model_dict.itervalues():
num_chains = max(num_chains, len(frag_list))
for chain_index in xrange(num_chains):
## get next availible chain_id
chain_id = next_chain_id("")
## assign the chain_id to all the atoms in the chain
## TODO: check fragment_id too
for model in model_list:
frag_list = model[chain_index]
for frag in frag_list:
for atm in frag:
atm.chain_id = chain_id
self.struct.add_atom(atm, True)
## free the memory used by the polymer naming service
del polymer_model_dict
del model_list
## NAME SERVICE FOR NON-POLYMER ATOMS
## cr = (chain_id, res_name)
##
## cr_dict[cr_key] = model_dict
##
## model_dict[model] = frag_list
##
## frag_list = [ frag1, frag2, frag3, ...]
##
## frag = [atm1, atm2, atm3, ...]
cr_dict = {}
cr_key_list = []
frag_id = None
frag = None
name_dict = {}
## split atoms into fragments
for atm in self.name_service_list:
atm_id = (atm.name, atm.alt_loc)
atm_frag_id = (atm.model_id, atm.chain_id, atm.fragment_id,
atm.res_name)
## if the atom fragment id matches the current fragment id
## and doesn't conflict with any other atom name in the fragment
## then add it to the fragment
if atm_frag_id == frag_id and not name_dict.has_key(atm_id):
frag.append(atm)
name_dict[atm_id] = True
else:
cr_key = (atm.chain_id, atm.res_name)
### debug
if frag:
ConsoleOutput.debug(
"name_service: fragment detected in cr=%s" %
(str(cr_key)))
for a in frag:
ConsoleOutput.debug(" " + str(a))
### /debug
try:
model_dict = cr_dict[cr_key]
except KeyError:
model_dict = cr_dict[cr_key] = {}
cr_key_list.append(cr_key)
try:
frag_list = model_dict[atm.model_id]
except KeyError:
frag_list = model_dict[atm.model_id] = []
name_dict = {atm_id: True}
frag_id = atm_frag_id
frag = [atm]
frag_list.append(frag)
## free self.name_service_list and other vars to save some memory
del self.name_service_list
new_chain_id = None
fragment_id_num = None
for cr_key in cr_key_list:
### debug
ConsoleOutput.debug("name_service: chain_id / res_name keys")
ConsoleOutput.debug(" cr_key: chain_id='%s' res_name='%s'" %
(cr_key[0], cr_key[1]))
### /debug
## get the next chain ID, use the cfr group's
## loaded chain_id if possible
chain_id = next_chain_id(cr_key[0])
## if we are not out of chain IDs, use the new chain ID and
## reset the fragment_id
if chain_id != None:
new_chain_id = chain_id
fragment_id_num = 0
elif new_chain_id == None or fragment_id_num == None:
ConsoleOutput.fatal(
"name_service: unable to assign any chain ids")
## get model dictionary
model_dict = cr_dict[cr_key]
## inspect the model dictionary to determine the number
## of fragments in each model -- they should be the same
## and have a 1:1 cooraspondance; if not, match up the
## fragments as much as possible
max_frags = -1
for (model, frag_list) in model_dict.iteritems():
frag_list_len = len(frag_list)
if max_frags == -1:
max_frags = frag_list_len
continue
if max_frags != frag_list_len:
strx = "name_service: model fragments not identical"
ConsoleOutput.debug(strx)
ConsoleOutput.warning(strx)
max_frags = max(max_frags, frag_list_len)
## now iterate through the fragment lists in parallel and assign
## the new chain_id and fragment_id
for i in xrange(max_frags):
fragment_id_num += 1
for frag_list in model_dict.itervalues():
try:
frag = frag_list[i]
except IndexError:
continue
## assign new chain_id and fragment_id, than place the
## atom in the structure
for atm in frag:
atm.chain_id = new_chain_id
atm.fragment_id = str(fragment_id_num)
self.struct.add_atom(atm, True)
## logging
ConsoleOutput.warning(
"name_service(): added chain_id=%s, res_name=%s, num_residues=%d"
% (new_chain_id, cr_key[1], fragment_id_num))
def name_service(self):
"""Runs the name service on all atoms needing to be named. This is a
complicated function which corrects most commonly found errors and
omissions from PDB files.
"""
if len(self.name_service_list) == 0:
return
## returns the next available chain_id in self.struct
## XXX: it's possible to run out of chain IDs!
def next_chain_id(suggest_chain_id):
if suggest_chain_id != "":
chain = self.struct.get_chain(suggest_chain_id)
if not chain:
return suggest_chain_id
## TODO: Add the following alphanumeric string to Constants.py, 2010-09-21
for chain_id in "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789":
chain = self.struct.get_chain(chain_id)
if not chain:
return chain_id
raise StructureBuilderError("name_service exhausted new chain_ids")
## NAME SERVICE FOR POLYMER ATOMS
## What if we are given a list of atoms with res_name, frag_id, and
## model_id where the frag_id are sequential? They can be sequential
## several ways using insertion codes, but large breaks often denote
## chain breaks.
## We need to handle the special case of a list of polymer residues
## which do not have chain_ids. This requires a first pass over the
## atom list using different rules than what we use for sorting out
## non-polymers.
current_polymer_type = None
current_polymer_model_id = None
current_polymer_chain_id = None
current_polymer_frag_id = None
current_polymer_res_name = None
current_polymer_name_dict = None
polymer_model_dict = {}
current_frag = None
current_frag_list = None
for atm in self.name_service_list[:]:
## determine the polymer type of the atom
if Library.library_is_amino_acid(atm.res_name):
polymer_type = "protein"
elif Library.library_is_nucleic_acid(atm.res_name):
polymer_type = "dna"
else:
## if the atom is not a polymer, we definitely have a break
## in this chain
current_polymer_type = None
current_polymer_model_id = None
current_polymer_chain_id = None
current_polymer_frag_id = None
current_polymer_res_name = None
current_polymer_name_dict = None
current_frag = None
current_frag_list = None
continue
fragment_id = Structure.FragmentID(atm.fragment_id)
## now we deal with conditions which can terminate the current
## polymer chain
if polymer_type!=current_polymer_type or \
atm.model_id!=current_polymer_model_id or \
atm.chain_id!=current_polymer_chain_id or \
fragment_id<current_polymer_frag_id:
current_polymer_type = polymer_type
current_polymer_model_id = atm.model_id
current_polymer_chain_id = atm.chain_id
current_polymer_frag_id = Structure.FragmentID(atm.fragment_id)
current_polymer_res_name = atm.res_name
current_polymer_name_dict = {atm.name: True}
## create new fragment
current_frag = [atm]
current_frag_list = [current_frag]
## create new fragment list (chain)
try:
model = polymer_model_dict[atm.model_id]
except KeyError:
model = [current_frag_list]
polymer_model_dict[atm.model_id] = model
else:
model.append(current_frag_list)
## we have now dealt with the atom, so it can be removed from
## the name service list
self.name_service_list.remove(atm)
continue
## if we get here, then we know this atom is destine for the
## current chain, and the algorithm needs to place the atom
## in the current fragment, or create a new fragment for it
## to go into; the conditions for it going into the current
## fragment are: it has it have the same res_name, and its
## atom name cannot conflict with the names of atoms already in
## in the fragment
if atm.res_name != current_polymer_res_name or current_polymer_name_dict.has_key(atm.name):
current_polymer_res_name = atm.res_name
current_polymer_name_dict = {atm.name: True}
## create new fragment and add it to the current fragment list
current_frag = [atm]
current_frag_list.append(current_frag)
## we have now dealt with the atom, so it can be removed
## from the name service list
self.name_service_list.remove(atm)
continue
## okay, put it in the current fragment
current_frag.append(atm)
self.name_service_list.remove(atm)
## now assign chain_ids and add the atoms to the structure
model_ids = polymer_model_dict.keys()
model_ids.sort()
model_list = [polymer_model_dict[model_id] for model_id in model_ids]
num_chains = 0
for frag_list in polymer_model_dict.itervalues():
num_chains = max(num_chains, len(frag_list))
for chain_index in xrange(num_chains):
## get next available chain_id
chain_id = next_chain_id("")
## assign the chain_id to all the atoms in the chain
## TODO: check fragment_id too, 2010-09-22
for model in model_list:
frag_list = model[chain_index]
for frag in frag_list:
for atm in frag:
atm.chain_id = chain_id
self.struct.add_atom(atm, True)
## free the memory used by the polymer naming service
del polymer_model_dict
del model_list
## NAME SERVICE FOR NON-POLYMER ATOMS
## cr = (chain_id, res_name)
##
## cr_dict[cr_key] = model_dict
##
## model_dict[model] = frag_list
##
## frag_list = [ frag1, frag2, frag3, ...]
##
## frag = [atm1, atm2, atm3, ...]
cr_dict = {}
cr_key_list = []
frag_id = None
frag = None
name_dict = {}
## split atoms into fragments
for atm in self.name_service_list:
atm_id = (atm.name, atm.alt_loc)
atm_frag_id = (atm.model_id, atm.chain_id, atm.fragment_id, atm.res_name)
## if the atom fragment id matches the current fragment id
## and doesn't conflict with any other atom name in the fragment
## then add it to the fragment
if atm_frag_id==frag_id and not name_dict.has_key(atm_id):
frag.append(atm)
name_dict[atm_id] = True
else:
cr_key = (atm.chain_id, atm.res_name)
### debug
if frag:
msg = "name_service: fragment detected in cr=%s" % (
str(cr_key))
ConsoleOutput.debug(msg)
for a in frag:
ConsoleOutput.debug(" " + str(a))
### /debug
try:
model_dict = cr_dict[cr_key]
except KeyError:
model_dict = cr_dict[cr_key] = {}
cr_key_list.append(cr_key)
try:
frag_list = model_dict[atm.model_id]
except KeyError:
frag_list = model_dict[atm.model_id] = []
name_dict = {atm_id: True}
frag_id = atm_frag_id
frag = [atm]
frag_list.append(frag)
## free self.name_service_list and other vars to save some memory
del self.name_service_list
new_chain_id = None
fragment_id_num = None
for cr_key in cr_key_list:
### debug
msg = "name_service: chain_id / res_name keys\n"
msg += " cr_key: chain_id='%s' res_name='%s'" % (
cr_key[0], cr_key[1])
ConsoleOutput.debug(msg)
### /debug
## get the next chain ID, use the cfr group's
## loaded chain_id if possible
chain_id = next_chain_id(cr_key[0])
## if we are not out of chain IDs, use the new chain ID and
## reset the fragment_id
if chain_id != None:
new_chain_id = chain_id
fragment_id_num = 0
elif new_chain_id == None or fragment_id_num == None:
ConsoleOutput.fatal("name_service: unable to assign any chain ids")
## get model dictionary
model_dict = cr_dict[cr_key]
## inspect the model dictionary to determine the number of
## fragments in each model -- they should be the same
## and have a 1:1 correspondence; if not, match up the
## fragments as much as possible
max_frags = -1
for (model, frag_list) in model_dict.iteritems():
frag_list_len = len(frag_list)
if max_frags == -1:
max_frags = frag_list_len
continue
if max_frags != frag_list_len:
strx = "name_service: model fragments not identical"
ConsoleOutput.debug(strx)
ConsoleOutput.warning(strx)
max_frags = max(max_frags, frag_list_len)
## now iterate through the fragment lists in parallel and assign
## the new chain_id and fragment_id
for i in xrange(max_frags):
fragment_id_num += 1
for frag_list in model_dict.itervalues():
try:
frag = frag_list[i]
except IndexError:
continue
## assign new chain_id and fragment_id, than place the
## atom in the structure
for atm in frag:
atm.chain_id = new_chain_id
atm.fragment_id = str(fragment_id_num)
self.struct.add_atom(atm, True)
## logging
ConsoleOutput.warning("name_service(): added chain_id=%s, res_name=%s, num_residues=%d" % (
new_chain_id, cr_key[1], fragment_id_num))