def testSubgraphIsomorphismManyLabels(self):
molecule = Molecule() # specific case (species)
molecule.fromAdjacencyList("""
1 *1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 C u0 p0 c0 {1,S} {3,S} {5,S} {6,S}
3 C u0 p0 c0 {1,S} {2,S} {7,S} {8,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {3,S}
8 H u0 p0 c0 {3,S}
""")
group = Group() # general case (functional group)
group.fromAdjacencyList("""
1 *1 C u1 p0 c0 {2,S}, {3,S}
2 R!H u0 p0 c0 {1,S}
3 R!H u0 p0 c0 {1,S}
""")
labeled1 = molecule.getLabeledAtoms()
labeled2 = group.getLabeledAtoms()
initialMap = {}
for label, atom1 in labeled1.iteritems():
initialMap[atom1] = labeled2[label]
self.assertTrue(molecule.isSubgraphIsomorphic(group, initialMap))
mapping = molecule.findSubgraphIsomorphisms(group, initialMap)
self.assertEqual(len(mapping), 2)
for map in mapping:
self.assertTrue(
len(map) == min(len(molecule.atoms), len(group.atoms)))
for key, value in map.iteritems():
self.assertTrue(key in molecule.atoms)
self.assertTrue(value in group.atoms)
def testSubgraphIsomorphismManyLabels(self):
molecule = Molecule() # specific case (species)
molecule.fromAdjacencyList("""
1 *1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 C u0 p0 c0 {1,S} {3,S} {5,S} {6,S}
3 C u0 p0 c0 {1,S} {2,S} {7,S} {8,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {3,S}
8 H u0 p0 c0 {3,S}
""")
group = Group() # general case (functional group)
group.fromAdjacencyList("""
1 *1 C u1 p0 c0 {2,S}, {3,S}
2 R!H u0 p0 c0 {1,S}
3 R!H u0 p0 c0 {1,S}
""")
labeled1 = molecule.getLabeledAtoms()
labeled2 = group.getLabeledAtoms()
initialMap = {}
for label,atom1 in labeled1.iteritems():
initialMap[atom1] = labeled2[label]
self.assertTrue(molecule.isSubgraphIsomorphic(group, initialMap))
mapping = molecule.findSubgraphIsomorphisms(group, initialMap)
self.assertEqual(len(mapping), 2)
for map in mapping:
self.assertTrue(len(map) == min(len(molecule.atoms), len(group.atoms)))
for key, value in map.iteritems():
self.assertTrue(key in molecule.atoms)
self.assertTrue(value in group.atoms)
def clean_detergent(self):
"""
Return molecular representation of input detergent structure """
try:
detergent = Molecule()
detergent.fromAdjacencyList(str(self.cleaned_data['detergent']))
except Exception, e:
import traceback
traceback.print_exc(e)
raise forms.ValidationError('Invalid SMILES entry.')
def clean_detergent(self):
"""
Return molecular representation of input detergent structure """
try:
detergent = Molecule()
detergent.fromAdjacencyList(str(self.cleaned_data['detergent']))
except Exception, e:
import traceback
traceback.print_exc(e)
raise forms.ValidationError('Invalid SMILES entry.')
def clean_reactant1(self):
"""
Custom validation for the reactant1 field to ensure that a valid
adjacency list has been provided.
"""
try:
molecule = Molecule()
molecule.fromAdjacencyList(str(self.cleaned_data['reactant1']))
except Exception, e:
import traceback
traceback.print_exc(e)
raise forms.ValidationError('Invalid adjacency list.')
def clean_reactant1(self):
"""
Custom validation for the reactant1 field to ensure that a valid
adjacency list has been provided.
"""
try:
molecule = Molecule()
molecule.fromAdjacencyList(str(self.cleaned_data['reactant1']))
except Exception, e:
import traceback
traceback.print_exc(e)
raise forms.ValidationError('Invalid adjacency list.')
def clean_adjlist(self):
"""
Custom validation for the adjlist field to ensure that a valid adjacency
list has been provided.
"""
try:
adjlist = str(self.cleaned_data['adjlist'])
if adjlist == '' : return ''
molecule = Molecule()
molecule.fromAdjacencyList(adjlist)
except Exception, e:
import traceback
traceback.print_exc(e)
raise forms.ValidationError('Invalid adjacency list.')
def clean_adjlist(self):
"""
Custom validation for the adjlist field to ensure that a valid adjacency
list has been provided.
"""
try:
adjlist = str(self.cleaned_data['adjlist'])
if adjlist == '' : return ''
molecule = Molecule()
molecule.fromAdjacencyList(adjlist)
except Exception, e:
import traceback
traceback.print_exc(e)
raise forms.ValidationError('Invalid adjacency list.')
def testSubgraphIsomorphismAgain(self):
molecule = Molecule()
molecule.fromAdjacencyList("""
1 * C u0 p0 c0 {2,D} {7,S} {8,S}
2 C u0 p0 c0 {1,D} {3,S} {9,S}
3 C u0 p0 c0 {2,S} {4,D} {10,S}
4 C u0 p0 c0 {3,D} {5,S} {11,S}
5 C u0 p0 c0 {4,S} {6,S} {12,S} {13,S}
6 C u0 p0 c0 {5,S} {14,S} {15,S} {16,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {1,S}
9 H u0 p0 c0 {2,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {4,S}
12 H u0 p0 c0 {5,S}
13 H u0 p0 c0 {5,S}
14 H u0 p0 c0 {6,S}
15 H u0 p0 c0 {6,S}
16 H u0 p0 c0 {6,S}
""")
group = Group()
group.fromAdjacencyList("""
1 * C u0 p0 c0 {2,D} {3,S} {4,S}
2 C u0 p0 c0 {1,D}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
""")
labeled1 = molecule.getLabeledAtoms().values()[0]
labeled2 = group.getLabeledAtoms().values()[0]
initialMap = {labeled1: labeled2}
self.assertTrue(molecule.isSubgraphIsomorphic(group, initialMap))
initialMap = {labeled1: labeled2}
mapping = molecule.findSubgraphIsomorphisms(group, initialMap)
self.assertTrue(
len(mapping) == 2,
"len(mapping) = %d, should be = 2" % (len(mapping)))
for map in mapping:
self.assertTrue(
len(map) == min(len(molecule.atoms), len(group.atoms)))
for key, value in map.iteritems():
self.assertTrue(key in molecule.atoms)
self.assertTrue(value in group.atoms)
def testSubgraphIsomorphismAgain(self):
molecule = Molecule()
molecule.fromAdjacencyList("""
1 * C u0 p0 c0 {2,D} {7,S} {8,S}
2 C u0 p0 c0 {1,D} {3,S} {9,S}
3 C u0 p0 c0 {2,S} {4,D} {10,S}
4 C u0 p0 c0 {3,D} {5,S} {11,S}
5 C u0 p0 c0 {4,S} {6,S} {12,S} {13,S}
6 C u0 p0 c0 {5,S} {14,S} {15,S} {16,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {1,S}
9 H u0 p0 c0 {2,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {4,S}
12 H u0 p0 c0 {5,S}
13 H u0 p0 c0 {5,S}
14 H u0 p0 c0 {6,S}
15 H u0 p0 c0 {6,S}
16 H u0 p0 c0 {6,S}
""")
group = Group()
group.fromAdjacencyList("""
1 * C u0 p0 c0 {2,D} {3,S} {4,S}
2 C u0 p0 c0 {1,D}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
""")
labeled1 = molecule.getLabeledAtoms().values()[0]
labeled2 = group.getLabeledAtoms().values()[0]
initialMap = {labeled1: labeled2}
self.assertTrue(molecule.isSubgraphIsomorphic(group, initialMap))
initialMap = {labeled1: labeled2}
mapping = molecule.findSubgraphIsomorphisms(group, initialMap)
self.assertTrue(len(mapping) == 2, "len(mapping) = %d, should be = 2" % (len(mapping)))
for map in mapping:
self.assertTrue(len(map) == min(len(molecule.atoms), len(group.atoms)))
for key, value in map.iteritems():
self.assertTrue(key in molecule.atoms)
self.assertTrue(value in group.atoms)
