277 lines
8.0 KiB
Python
277 lines
8.0 KiB
Python
config.ilp.solver="CPLEX"
|
|
#import mod
|
|
#from mod import *
|
|
import networkx as nx
|
|
|
|
# import Graph class from graph.py
|
|
from graph import GraphObj
|
|
|
|
#ethylen = Graph.fromGMLString(
|
|
"""graph [
|
|
node [ id 0 label "H" ]
|
|
node [ id 1 label "H" ]
|
|
node [ id 2 label "C" ]
|
|
node [ id 3 label "C" ]
|
|
node [ id 4 label "H" ]
|
|
node [ id 5 label "H" ]
|
|
edge [ source 0 target 2 label "-" ]
|
|
edge [ source 1 target 2 label "-" ]
|
|
edge [ source 2 target 3 label "=" ]
|
|
edge [ source 3 target 4 label "-" ]
|
|
edge [ source 3 target 5 label "-" ]
|
|
]"""
|
|
#, name="Ethylen")
|
|
|
|
butadien = Graph.fromGMLString(
|
|
"""graph [
|
|
node [ id 0 label "C" ]
|
|
node [ id 1 label "C" ]
|
|
node [ id 2 label "C" ]
|
|
node [ id 3 label "C" ]
|
|
node [ id 4 label "H" ]
|
|
node [ id 5 label "H" ]
|
|
node [ id 6 label "H" ]
|
|
node [ id 7 label "H" ]
|
|
node [ id 8 label "H" ]
|
|
node [ id 9 label "H" ]
|
|
edge [ source 0 target 1 label "=" ]
|
|
edge [ source 1 target 2 label "-" ]
|
|
edge [ source 2 target 3 label "=" ]
|
|
edge [ source 0 target 4 label "-" ]
|
|
edge [ source 0 target 5 label "-" ]
|
|
edge [ source 1 target 6 label "-" ]
|
|
edge [ source 2 target 7 label "-" ]
|
|
edge [ source 3 target 8 label "-" ]
|
|
edge [ source 3 target 9 label "-" ]
|
|
]"""
|
|
, name="Butadien")
|
|
|
|
#benzene = Graph.fromSMILES('c1=cc=cc=c1')
|
|
|
|
#benzene = Graph.fromGMLString(
|
|
"""graph [
|
|
node [ id 0 label "C" ]
|
|
node [ id 1 label "H" ]
|
|
node [ id 2 label "C" ]
|
|
node [ id 3 label "H" ]
|
|
node [ id 4 label "C" ]
|
|
node [ id 5 label "H" ]
|
|
node [ id 6 label "C" ]
|
|
node [ id 7 label "H" ]
|
|
node [ id 8 label "C" ]
|
|
node [ id 9 label "H" ]
|
|
node [ id 10 label "C" ]
|
|
node [ id 11 label "H" ]
|
|
edge [ source 0 target 1 label "-" ]
|
|
edge [ source 0 target 2 label "=" ]
|
|
edge [ source 2 target 3 label "-" ]
|
|
edge [ source 2 target 4 label "-" ]
|
|
edge [ source 4 target 5 label "-" ]
|
|
edge [ source 4 target 6 label "=" ]
|
|
edge [ source 6 target 7 label "-" ]
|
|
edge [ source 6 target 8 label "-" ]
|
|
edge [ source 8 target 9 label "-" ]
|
|
edge [ source 8 target 10 label "=" ]
|
|
edge [ source 10 target 11 label "-" ]
|
|
edge [ source 10 target 0 label "-" ]
|
|
]"""
|
|
#, name="Benzene")
|
|
|
|
|
|
#pentadien = Graph.fromGMLString(
|
|
"""graph
|
|
[
|
|
node [ id 0 label "C" ]
|
|
node [ id 1 label "C" ]
|
|
node [ id 2 label "C" ]
|
|
node [ id 3 label "C" ]
|
|
node [ id 4 label "H" ]
|
|
node [ id 5 label "H" ]
|
|
node [ id 6 label "H" ]
|
|
node [ id 7 label "H" ]
|
|
node [ id 8 label "H" ]
|
|
node [ id 9 label "C" ]
|
|
node [ id 10 label "H" ]
|
|
node [ id 11 label "H" ]
|
|
node [ id 12 label "H" ]
|
|
edge [ source 0 target 1 label "=" ]
|
|
edge [ source 1 target 2 label "-" ]
|
|
edge [ source 2 target 3 label "=" ]
|
|
edge [ source 0 target 4 label "-" ]
|
|
edge [ source 0 target 5 label "-" ]
|
|
edge [ source 1 target 6 label "-" ]
|
|
edge [ source 2 target 7 label "-" ]
|
|
edge [ source 3 target 8 label "-" ]
|
|
edge [ source 3 target 9 label "-" ]
|
|
edge [ source 9 target 10 label "-" ]
|
|
edge [ source 9 target 11 label "-" ]
|
|
edge [ source 9 target 12 label "-" ]
|
|
]
|
|
"""
|
|
#, name="Pentadien")
|
|
|
|
restswap = Rule.fromGMLString(
|
|
"""rule [
|
|
left [
|
|
edge [ source 1 target 2 label "=" ]
|
|
edge [ source 3 target 4 label "=" ]
|
|
]
|
|
context [
|
|
node [ id 1 label "C" ]
|
|
node [ id 2 label "C"]
|
|
node [ id 3 label "C"]
|
|
node [ id 4 label "C"]
|
|
]
|
|
right [
|
|
edge [ source 1 target 3 label "=" ]
|
|
edge [ source 2 target 4 label "=" ]
|
|
]
|
|
]"""
|
|
)
|
|
|
|
dielsalder = Rule.fromGMLString(
|
|
"""rule [
|
|
left [
|
|
edge [ source 1 target 2 label "=" ]
|
|
edge [ source 2 target 3 label "-" ]
|
|
edge [ source 3 target 4 label "=" ]
|
|
edge [ source 5 target 6 label "=" ]
|
|
|
|
]
|
|
context [
|
|
node [ id 1 label "C" ]
|
|
node [ id 2 label "C"]
|
|
node [ id 3 label "C"]
|
|
node [ id 4 label "C"]
|
|
node [ id 5 label "C"]
|
|
node [ id 6 label "C"]
|
|
]
|
|
right [
|
|
edge [ source 1 target 2 label "-" ]
|
|
edge [ source 2 target 3 label "=" ]
|
|
edge [ source 3 target 4 label "-" ]
|
|
edge [ source 4 target 5 label "-" ]
|
|
edge [ source 5 target 6 label "-" ]
|
|
edge [ source 6 target 1 label "-" ]
|
|
]
|
|
]"""
|
|
)
|
|
|
|
def cyclesizes(g):
|
|
nxGraph = GraphObj(g).nx_graph
|
|
|
|
#Restriction to E/Z? Benzen can't be created or consumed by the reaction due to steric difficulties
|
|
|
|
#Chain restrictions: (No steric reason)
|
|
for nodestart in nxGraph.nodes:
|
|
for nodeend in nxGraph.nodes:
|
|
if nodeend != nodestart:
|
|
paths = sorted(list(nx.all_shortest_paths(nxGraph, nodestart, nodeend)))
|
|
for path in paths:
|
|
if len(path) > 10: #First node included in length
|
|
return True
|
|
|
|
#Cycle restrictions:
|
|
cycles = sorted(list(nx.chordless_cycles(nxGraph)))
|
|
cycle_lengths = [len(x) for x in cycles]
|
|
if cycles == []:
|
|
return False
|
|
#One Atom can't be in four different cycles
|
|
for vertice in nxGraph.nodes:
|
|
counter = 0
|
|
for cycle in cycles:
|
|
if vertice in cycle:
|
|
counter += 1
|
|
if counter >= 4:
|
|
return True
|
|
#One Cycle can't overlapp with another on over 2 Connection points
|
|
for cycle in cycles:
|
|
for cycleref in cycles:
|
|
if cycle != cycleref and len(list(set(cycle) & set(cycleref))) >= 3:
|
|
return True
|
|
#Only cordless cycles of length 5,6 and 7 are acceptable
|
|
if min(cycle_lengths) >= 6 and max(cycle_lengths) <=6:
|
|
return False
|
|
return True
|
|
|
|
#Disallows Allenes (Two Doublebonds on same carbon)
|
|
def doubledoublebond(g):
|
|
for vertice in g.vertices:
|
|
if (vertice.stringLabel == "C" and vertice.degree == 2): # and vertice.edges.label == ["=", "="]
|
|
for edge in vertice.incidentEdges:
|
|
print(type(edge.bondType))
|
|
bonds = [type(edge.bondType) for edge in vertice.incidentEdges]
|
|
if (bonds[0] == bonds[1] and len(bonds) == 2):
|
|
return True
|
|
return False
|
|
|
|
|
|
def restriction(dg):
|
|
for a in dg.right:
|
|
if a.vLabelCount("C") > 10:
|
|
return False
|
|
if doubledoublebond(a):
|
|
return False
|
|
if cyclesizes(a):
|
|
return False
|
|
return True
|
|
|
|
flowPrinter = FlowPrinter()
|
|
flowPrinter.printUnfiltered = False
|
|
|
|
postSection("Loaded Graphs")
|
|
for a in inputGraphs:
|
|
a.print()
|
|
postSection("Loaded Rules")
|
|
for a in inputRules:
|
|
a.print()
|
|
|
|
ethylen = Graph.fromSMILES('C=C')
|
|
goal = Graph.fromSMILES('C1C=CC=CC=1')
|
|
dg = DG(graphDatabase=inputGraphs)
|
|
dg.build().execute(
|
|
addSubset(inputGraphs)
|
|
>> rightPredicate[
|
|
restriction
|
|
](
|
|
repeat(revive(inputRules)) #Revive not necessary
|
|
)
|
|
)
|
|
|
|
|
|
print([str(a.graph.name) for a in dg.vertices])
|
|
print([str(a.graph.smiles) for a in dg.vertices])
|
|
dg.print()
|
|
postSection("Product Graphs")
|
|
for a in dg.vertices:
|
|
a.graph.print()
|
|
flow = Flow(dg)
|
|
flow.addSource(butadien)
|
|
|
|
flow.addSink(ethylen)
|
|
flow.addSink(goal)
|
|
flow.addConstraint(inFlow[butadien] >= 2)
|
|
#flow.addConstraint(outFlow[ethylen] == 1)
|
|
flow.addConstraint(outFlow[goal] == 1)
|
|
flow.findSolutions(maxNumSolutions=3)
|
|
flow.solutions.list()
|
|
flow.solutions.print(flowPrinter)
|
|
|
|
|
|
sys.exit(0)
|
|
|
|
rc = rcEvaluator(inputRules)
|
|
for dRef in dg.derivations:
|
|
der = dRef.derivation
|
|
educt = rcId(der.left[0])
|
|
for i in range(1, len(der.left)):
|
|
educt = educt *rcParallel* rcId(der.left[i])
|
|
product = rcId(der.right[0])
|
|
for i in range(1, len(der.right)):
|
|
product = product *rcParallel* rcId(der.right[i])
|
|
rcExp = educt *rcSuper(allowPartial=False)* der.rule *rcSuper(allowPartial=False)* product
|
|
res = rc.eval(rcExp)
|
|
dRef.print()
|
|
for a in res:
|
|
a.print()
|
|
a.printGML() |