def __init__(self, filename, id=None):
# Extract the protein id from file
assert (isinstance(filename, str))
if id is None or id is '':
id = os.path.basename(filename).split('.')[0]
ProteinEntity.__init__(self, 'STRUCTURE', id)
# Use new PDBCoordsParser instance to parse out and build protein protein model
all_models = PDBCoordsParser().get_models(filename)
for model in all_models:
self.add_model(model)
# Remove water "residues" (HOH)
for chain in self.chains():
chain.remove_waters()
# Use PDBInfo to parse out and store protein meta-information
self.__info = PDBInfo(filename)
def __init__(self, filename, id=None):
# Extract the protein id from file
assert(isinstance(filename, str))
if id is None or id is '':
id = os.path.basename(filename).split('.')[0]
ProteinEntity.__init__(self, 'STRUCTURE', id)
# Use new PDBCoordsParser instance to parse out and build protein protein model
all_models = PDBCoordsParser().get_models(filename)
for model in all_models:
self.add_model(model)
# Remove water "residues" (HOH)
for chain in self.chains():
chain.remove_waters()
# Use PDBInfo to parse out and store protein meta-information
self.__info = PDBInfo(filename)
class Structure(ProteinEntity):
"""
The Structure class contains a collection of Model instances.
"""
def __init__(self, filename, id=None):
# Extract the protein id from file
assert(isinstance(filename, str))
if id is None or id is '':
id = os.path.basename(filename).split('.')[0]
ProteinEntity.__init__(self, 'STRUCTURE', id)
# Use new PDBCoordsParser instance to parse out and build protein protein model
all_models = PDBCoordsParser().get_models(filename)
for model in all_models:
self.add_model(model)
# Remove water "residues" (HOH)
for chain in self.chains():
chain.remove_waters()
# Use PDBInfo to parse out and store protein meta-information
self.__info = PDBInfo(filename)
def __repr__(self):
return "<Structure id=%s>" % self.id()
def show_info(self):
print(self.__info)
def info(self, hash_key=None):
if hash_key is None:
return self.__info.full_description()
else:
return self.__info[hash_key]
def info_keys(self):
return self.__info.keys()
# Sub-entity manipulation methods
def add_model(self, model):
self.add_child(model, model.id())
def has_model_with_id(self, id):
return self.has_child_with_id(id)
def remove_model_with_id(self, id):
self.remove_child_with_id(id)
# Hierarchy Identity Methods
def models(self, hash_key=None):
return self.children(hash_key)
def chains(self):
chains = []
for m in self.models():
chains += m.chains()
return chains
def residues(self):
residues = []
for c in self.chains():
residues += c.residues()
return residues
def atoms(self):
atoms = []
for r in self.residues():
atoms += r.atoms()
return atoms
class Structure(ProteinEntity):
"""
The Structure class contains a collection of Model instances.
"""
def __init__(self, filename, id=None):
# Extract the protein id from file
assert (isinstance(filename, str))
if id is None or id is '':
id = os.path.basename(filename).split('.')[0]
ProteinEntity.__init__(self, 'STRUCTURE', id)
# Use new PDBCoordsParser instance to parse out and build protein protein model
all_models = PDBCoordsParser().get_models(filename)
for model in all_models:
self.add_model(model)
# Remove water "residues" (HOH)
for chain in self.chains():
chain.remove_waters()
# Use PDBInfo to parse out and store protein meta-information
self.__info = PDBInfo(filename)
def __repr__(self):
return "<Structure id=%s>" % self.id()
def show_info(self):
print(self.__info)
def info(self, hash_key=None):
if hash_key is None:
return self.__info.full_description()
else:
return self.__info[hash_key]
def info_keys(self):
return self.__info.keys()
# Sub-entity manipulation methods
def add_model(self, model):
self.add_child(model, model.id())
def has_model_with_id(self, id):
return self.has_child_with_id(id)
def remove_model_with_id(self, id):
self.remove_child_with_id(id)
# Hierarchy Identity Methods
def models(self, hash_key=None):
return self.children(hash_key)
def chains(self):
chains = []
for m in self.models():
chains += m.chains()
return chains
def residues(self):
residues = []
for c in self.chains():
residues += c.residues()
return residues
def atoms(self):
atoms = []
for r in self.residues():
atoms += r.atoms()
return atoms