def __init__(self, sequence_name, sequence, vectorizer, structure):
self.sequence_name = sequence_name
self.sequence = sequence
self.vectorizer = vectorizer
self.structure = structure
# create a base_graph , expand
base_graph = conv.sequence_dotbracket_to_graph(seq_info=sequence, seq_struct=structure)
self.base_graph = vectorizer._edge_to_vertex_transform(base_graph)
# get an expanded abstract graph
abstract_graph = forgi.get_abstr_graph(structure)
abstract_graph = vectorizer._edge_to_vertex_transform(abstract_graph)
# connect edges to nodes in the abstract graph
self.abstract_graph = edge_parent_finder(abstract_graph, self.base_graph)
# we are forced to set a label .. for eden reasons
def name_edges(graph, what=''):
for n, d in graph.nodes(data=True):
if 'edge' in d:
d['label'] = what
# in the abstract graph , all the edge nodes need to have a contracted attribute.
# originaly this happens naturally but since we make multiloops into one loop there are some left out
def setset(graph):
for n, d in graph.nodes(data=True):
if 'contracted' not in d:
d['contracted'] = set()
name_edges(self.abstract_graph)
setset(self.abstract_graph)
def abstract_graph(self):
'''
we need to make an abstraction Ooo
'''
if self._abstract_graph is None:
# create the abstract graph and populate the contracted set
abstract_graph = forgi.get_abstr_graph(
self.structure, ignore_inserts=self.ignore_inserts)
abstract_graph = self.vectorizer._edge_to_vertex_transform(
abstract_graph)
self._abstract_graph = forgi.edge_parent_finder(
abstract_graph, self._base_graph)
# eden is forcing us to set a label and a contracted attribute.. lets do this
for n, d in self._abstract_graph.nodes(data=True):
if 'edge' in d:
d['label'] = 'e'
# in the abstract graph , all the edge nodes need to have a contracted attribute.
# originaly this happens naturally but since we make multiloops into one loop
# there are some left out
for n, d in self._abstract_graph.nodes(data=True):
if 'contracted' not in d:
d['contracted'] = set()
return self._abstract_graph
def abstract_graph(self):
'''
we need to make an abstraction Ooo
'''
# create the abstract graph and populate the contracted set
abstract_graph = forgi.get_abstr_graph(self.structure, ignore_inserts=self.ignore_inserts)
abstract_graph = self.vectorizer._edge_to_vertex_transform(abstract_graph)
completed_abstract_graph = forgi.edge_parent_finder(abstract_graph, self._base_graph)
# eden is forcing us to set a label and a contracted attribute.. lets do this
for n, d in completed_abstract_graph.nodes(data=True):
if 'edge' in d:
d['label'] = 'e'
# in the abstract graph , all the edge nodes need to have a contracted attribute.
# originaly this happens naturally but since we make multiloops into one loop
# there are some left out
for n, d in completed_abstract_graph.nodes(data=True):
if 'contracted' not in d:
d['contracted'] = set()
return completed_abstract_graph
