def checkRings(cycles):
"""This fixes a bug in figuras algorithm. Sometimes when
traversing through fused rings embedded in a larger ring
two paths are returned when only one should have been
This removes (most) of these cases"""
# XXX I've encountered this bug before in figueras algorithm
# I really need to investigate if further and see
# if CDK has the same issues.
res = []
set = kjSet()
sameSizes = {}
i = 0
for atoms, bonds in cycles:
size = len(bonds)
sameSizes[size] = sameSizes.get(size, []) + [(atoms, bonds)]
keys = sameSizes.keys()
keys.sort()
last = kjSet()
for size in keys:
cycles = sameSizes[size]
nextCycles = kjSet()
i = 0
if len(cycles) == 1:
res.append(cycles[0])
print "adding ring of size", cycles[0][1]
continue
dontAdd = {}
for atoms1, bonds1 in cycles:
s1 = kjSet(bonds1)
j = i + 1
for atom2, bonds2 in cycles[j:]:
s2 = kjSet(bonds2)
check = (s1-s2) + (s2-s1)
l = len(check)
if not (l and len(last & check) == l):
print "adding ring of size", len(bonds1)
res.append((atoms1, bonds1))
else:
if i not in dontAdd:
dontAdd[j] = 1
res.append((atoms1, bonds1))
print "adding ring of size", len(bonds1)
print "dropping ring of size", len(bonds2)
i += 1
nextCycles += s1
last += nextCycles
return res
def checkRings(cycles):
"""This fixes a bug in figuras algorithm. Sometimes when
traversing through fused rings embedded in a larger ring
two paths are returned when only one should have been
This removes (most) of these cases"""
# XXX I've encountered this bug before in figueras algorithm
# I really need to investigate if further and see
# if CDK has the same issues.
res = []
set = kjSet()
sameSizes = {}
i = 0
for atoms, bonds in cycles:
size = len(bonds)
sameSizes[size] = sameSizes.get(size, []) + [(atoms, bonds)]
keys = sameSizes.keys()
keys.sort()
last = kjSet()
for size in keys:
cycles = sameSizes[size]
nextCycles = kjSet()
i = 0
if len(cycles) == 1:
res.append(cycles[0])
print "adding ring of size", cycles[0][1]
continue
dontAdd = {}
for atoms1, bonds1 in cycles:
s1 = kjSet(bonds1)
j = i + 1
for atom2, bonds2 in cycles[j:]:
s2 = kjSet(bonds2)
check = (s1 - s2) + (s2 - s1)
l = len(check)
if not (l and len(last & check) == l):
print "adding ring of size", len(bonds1)
res.append((atoms1, bonds1))
else:
if i not in dontAdd:
dontAdd[j] = 1
res.append((atoms1, bonds1))
print "adding ring of size", len(bonds1)
print "dropping ring of size", len(bonds2)
i += 1
nextCycles += s1
last += nextCycles
return res
def factor(G):
from kjbuckets import kjSet, kjGraph
allnodes = kjSet(G.keys()) + kjSet(G.values())
allnodelist = allnodes.items()
allnodemap = map(None, allnodelist, range(len(allnodelist)))
nodetoindex = kjGraph(allnodemap)
pairs = G.items()
left = pairs[:]
right = left[:]
for i in xrange(len(left)):
(l, r) = pairs[i]
left[i], right[i] = nodetoindex[l], nodetoindex[r]
return (left, right), allnodelist
def factor(G):
from kjbuckets import kjSet, kjGraph
allnodes = kjSet(G.keys()) + kjSet(G.values())
allnodelist = allnodes.items()
allnodemap = map(None, allnodelist, range(len(allnodelist)))
nodetoindex = kjGraph(allnodemap)
pairs = G.items()
left = pairs[:]
right = left[:]
for i in xrange(len(left)):
(l, r) = pairs[i]
left[i], right[i] = nodetoindex[l], nodetoindex[r]
return (left, right), allnodelist
def tsort(list_of_pairs):
result = []
Graph = kjGraph(list_of_pairs)
notsource = (kjSet(Graph.values()) - kjSet(Graph.keys())).items()
while Graph:
sources = kjSet(Graph.keys())
dests = kjSet(Graph.values())
startingpoints = sources - dests
if not startingpoints:
raise LOOPERROR, "loop detected in Graph"
for node in startingpoints.items():
result.append(node)
del Graph[node]
return result + notsource
def tsort(list_of_pairs):
result = []
Graph = kjGraph(list_of_pairs)
notsource = (kjSet(Graph.values()) - kjSet(Graph.keys())).items()
while Graph:
sources = kjSet(Graph.keys())
dests = kjSet(Graph.values())
startingpoints = sources - dests
if not startingpoints:
raise LOOPERROR, "loop detected in Graph"
for node in startingpoints.items():
result.append(node)
del Graph[node]
return result + notsource
def tsort(pairs):
from kjbuckets import kjGraph, kjSet
G = kjGraph(pairs)
Gt = ~G # transpose
sources = kjSet(G.keys())
dests = kjSet(G.values())
all = (sources + dests).items()
total = len(all)
endpoints = dests - sources
for i in xrange(total - 1, -1, -1):
#print i, endpoints
if not endpoints:
raise LOOPERROR, "loop detected"
choice = endpoints.choose_key()
for n in Gt.neighbors(choice):
G.delete_arc(n, choice)
if not G.has_key(n):
endpoints[n] = n
del endpoints[choice]
all[i] = choice
return all
def calc_mincut( me, g, uncutables =(), exclude_selfrefs =True, count_multiples =True):
edge_cost = me.edge_cost = {}
for edge in g:
if edge in uncutables: cost = len(g)
else:
cost = count_multiples and g.count(edge) or 1
edge_cost[ edge] = cost
g = kj.kjGraph( g)
#prngraph( g & ~g.tclosure() ) #- core-cycle
if exclude_selfrefs:
# self_refs = kj.kjSet(g).ident() & g
# g = g - self_refs
g = g - kj.kjSet(g).ident()
me._find( g)
def calc_mincut(me,
g,
uncutables=(),
exclude_selfrefs=True,
count_multiples=True):
edge_cost = me.edge_cost = {}
for edge in g:
if edge in uncutables: cost = len(g)
else:
cost = count_multiples and g.count(edge) or 1
edge_cost[edge] = cost
g = kj.kjGraph(g)
#prngraph( g & ~g.tclosure() ) #- core-cycle
if exclude_selfrefs:
# self_refs = kj.kjSet(g).ident() & g
# g = g - self_refs
g = g - kj.kjSet(g).ident()
me._find(g)