def parser(g):
for node in g.nodes():
g.nodes[node]['charge'] = int(lit_ev(g.nodes[node]['charge']))
g.nodes[node]['chem'] = int(lit_ev(g.nodes[node]['chem']))
g.nodes[node]['symbol'] = lit_ev(g.nodes[node]['symbol']).strip()
real_2Dcoords = [
float(lit_ev(g.nodes[node]['x'])),
float(lit_ev(g.nodes[node]['y']))
]
g.nodes[node]['coords'] = numpy.reshape(numpy.asarray(real_2Dcoords),
(2, ))
{g.nodes[node].pop(k) for k in ['y', 'x']}
def parser(g):
for node in g.nodes():
# list_labels = list(map(lambda x: lit_ev(x), g.nodes[node].values()))
g.nodes[node]['charge'] = int(lit_ev(g.nodes[node]['charge']))
g.nodes[node]['chem'] = int(lit_ev(g.nodes[node]['chem']))
g.nodes[node]['symbol'] = lit_ev(g.nodes[node]['symbol']).strip()
real_2Dcoords = [
float(lit_ev(g.nodes[node]['x'])),
float(lit_ev(g.nodes[node]['y']))
]
# g.nodes[node]['coords'] = reshape(asarray(real_2Dcoords), (1, 2)) ?
g.nodes[node]['coords'] = reshape(asarray(real_2Dcoords), (2, ))
{g.nodes[node].pop(k) for k in ['y', 'x']}
def parser(g):
for node in g.nodes():
list_labels = list(
map(lambda x: float(lit_ev(x)), g.nodes[node].values()))
g.nodes[node]['coords'] = reshape(asarray(list_labels), (1, 2))
{g.nodes[node].pop(k) for k in ['y', 'x']}
def parser(g):
# GREC has particular attributes on edges which are not common to all graphs in dataset.
# In order to manage this issue, when an attribute is not found, it will be added to the graph
# with empty strings or 0's depending on its type.
# Since NetworkX edges/nodes are dict structure a try/except workaround is employed, then when
# missing key (KeyError) error occurs, the parser manages the exception adding the key to the edge labels
# Vertex Attributes:
# -type(string)
# -coords (x,y real values)
# Edge attributes:
# -frequency (real)
# -type0,1 (strings)
# -angle0,1 (real)
for node in g.nodes():
g.nodes[node]['type'] = g.nodes[node]['type']
real_2Dcoords = [
float(lit_ev(g.nodes[node]['x'])),
float(lit_ev(g.nodes[node]['y']))
]
g.nodes[node]['coords'] = reshape(asarray(real_2Dcoords), (2, ))
{g.nodes[node].pop(k) for k in ['y', 'x']}
for edge in g.edges():
u = edge[0]
v = edge[1]
try:
g.edges[u, v]['angle0'] = float(lit_ev(g.edges[u, v]['angle0']))
except KeyError:
g.edges[u, v]['angle0'] = 0
try:
g.edges[u, v]['angle1'] = float(lit_ev(g.edges[u, v]['angle1']))
except KeyError:
g.edges[u, v]['angle1'] = 0
try:
g.edges[u, v]['type0'] = g.edges[u, v]['type0']
except KeyError:
g.edges[u, v]['type0'] = ""
try:
g.edges[u, v]['type1'] = g.edges[u, v]['type1']
except KeyError:
g.edges[u, v]['type1'] = ""
g.edges[u, v]['frequency'] = float(lit_ev(g.edges[u, v]['frequency']))
def parser(g):
# Vertex Attributes:
# -aaLength - (unsigned int)
# -sequence - (string)
# -type - (unsigned int)
# Edge attributes:
# -distance0 (real)
# -distance1 (real)
# -frequency (unsigned inte)
# -type0 (strings)
# -type1 (strings)
for node in g.nodes():
# temp- they can still be strings
g.nodes[node]['type'] = int(g.nodes[node]['type'])
g.nodes[node]['sequence'] = g.nodes[node]['sequence']
# g.nodes[node]['aaLength']=int(g.nodes[node]['aaLength'])
for edge in g.edges():
u = edge[0]
v = edge[1]
try:
g.edges[u,
v]['distance0'] = float(lit_ev(g.edges[u, v]['distance0']))
except KeyError:
g.edges[u, v]['distance0'] = 0
try:
g.edges[u,
v]['distance1'] = float(lit_ev(g.edges[u, v]['distance1']))
except KeyError:
g.edges[u, v]['distance1'] = 0
try:
g.edges[u, v]['type0'] = g.edges[u, v]['type0']
except KeyError:
g.edges[u, v]['type0'] = ""
try:
g.edges[u, v]['type1'] = g.edges[u, v]['type1']
except KeyError:
g.edges[u, v]['type1'] = ""
g.edges[u, v]['frequency'] = int(g.edges[u, v]['frequency'])
g.addEdge(0, 4)
g.addEdge(1, 0)
g.addEdge(1, 2)
g.addEdge(2, 3)
g.addEdge(3, 2)
g.addEdge(3, 4)
g.addEdge(4, 3)
placeA = sys.argv[1]
placeB = sys.argv[2]
indexA = df.loc[df['place'] == placeA].index[0]
indexB = df.loc[df['place'] == placeB].index[0]
g.printAllPaths(indexA, indexB)
paths = [lit_ev(path) for path in g.paths]
distances = []
routes = []
for path in paths:
dist = 0
route = []
for a, b in zip(path[:-1], path[1:]):
A = df.iloc[a]['place']
B = df.iloc[b]['place']
d = distance(A, B)
dist += d
route.append(A)
distances.append(dist)
route.append(placeB)
routes.append(route)
