This might be helpful - a rather dull python script for testing lots
of different orderings of reactants and templates.
On Wed, Aug 17, 2011 at 9:42 AM, Richard Cooper
<[email protected]> wrote:
> Dear Greg,
>
> Patch attached (to be applied in the GraphMol/ChemReactions folder).
>
#!/usr/bin/python
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors
from rdkit.Chem import Draw
print "Keep chirality if specified [C:17]>>[C:17]"
rxn = AllChem.ReactionFromSmarts( '[C:1]>>[C:1]')
rxn.Initialize()
ps =rxn.RunReactants((Chem.MolFromSmiles('F[C@H](Cl)(Br)'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
ps =rxn.RunReactants((Chem.MolFromSmiles('F[C@H](Br)(Cl)'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@@H](Cl)Br"
ps =rxn.RunReactants((Chem.MolFromSmiles('FC(Cl)Br'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: FC(Cl)Br"
print
print "Keep chirality if specified [C@:17]>>[C@:17]"
rxn = AllChem.ReactionFromSmarts( '[C@:1]>>[C@:1]')
rxn.Initialize()
ps =rxn.RunReactants((Chem.MolFromSmiles('F[C@H](Cl)(Br)'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
ps =rxn.RunReactants((Chem.MolFromSmiles('F[C@H](Br)(Cl)'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@@H](Cl)Br"
ps =rxn.RunReactants((Chem.MolFromSmiles('FC(Cl)Br'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: FC(Cl)Br"
print
print "Invert chirality if specified [C@@::17]>>[C@:17]"
rxn = AllChem.ReactionFromSmarts( '[C@@:1]>>[C@:1]')
rxn.Initialize()
ps =rxn.RunReactants((Chem.MolFromSmiles('F[C@H](Cl)(Br)'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@@H](Cl)Br"
ps =rxn.RunReactants((Chem.MolFromSmiles('F[C@H](Br)(Cl)'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
ps =rxn.RunReactants((Chem.MolFromSmiles('FC(Cl)Br'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: FC(Cl)Br"
print
print "Remove chirality if specified [C@::17]>>[C:17]"
rxn = AllChem.ReactionFromSmarts( '[C@:1]>>[C:1]')
rxn.Initialize()
ps =rxn.RunReactants((Chem.MolFromSmiles('F[C@H](Cl)(Br)'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: FC(Cl)Br"
ps =rxn.RunReactants((Chem.MolFromSmiles('F[C@H](Br)(Cl)'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: FC(Cl)Br"
ps =rxn.RunReactants((Chem.MolFromSmiles('FC(Cl)Br'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: FC(Cl)Br"
print
print "Add/replace chirality if specified [F:2][C:17]([Cl:3])[Br:4]>>[F:2][C@@:17]([Cl:3])[Br:4]"
rxn = AllChem.ReactionFromSmarts( '[F:2][C:1]([Cl:3])[Br:4]>>[F:2][C@@:1]([Cl:3])[Br:4]')
rxn.Initialize()
ps =rxn.RunReactants((Chem.MolFromSmiles('F[C@H](Cl)(Br)'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@@H](Cl)Br"
ps =rxn.RunReactants((Chem.MolFromSmiles('F[C@H](Br)(Cl)'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@@H](Cl)Br"
ps =rxn.RunReactants((Chem.MolFromSmiles('FC(Cl)Br'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@@H](Cl)Br"
print
# Cl Br
# \ /
# C.F
# |
# I
a1 = Chem.MolFromSmiles("FC(Cl)(Br)(I)")
odd1 = Chem.MolFromSmiles("C[C@@H](O)CCC(Cl)(Br)C/C=C\I")
r1 = Chem.MolFromSmiles("F[C@](Cl)(Br)(I)")
r2 = Chem.MolFromSmiles("F[C@](Br)(I)(Cl)")
r3 = Chem.MolFromSmiles("F[C@](I)(Cl)(Br)")
r4 = Chem.MolFromSmiles("Cl[C@](F)(I)(Br)")
r5 = Chem.MolFromSmiles("Cl[C@](Br)(F)(I)")
r6 = Chem.MolFromSmiles("Cl[C@](I)(Br)(F)")
r7 = Chem.MolFromSmiles("Br[C@](I)(F)(Cl)")
r8 = Chem.MolFromSmiles("Br[C@](F)(Cl)(I)")
r9 = Chem.MolFromSmiles("Br[C@](Cl)(I)(F)")
r10 = Chem.MolFromSmiles("I[C@](Br)(Cl)(F)")
r11 = Chem.MolFromSmiles("I[C@](F)(Br)(Cl)")
r12 = Chem.MolFromSmiles("I[C@](Cl)(F)(Br)")
r13 = Chem.MolFromSmiles("F[C@@](Br)(Cl)(I)")
r14 = Chem.MolFromSmiles("F[C@@](I)(Br)(Cl)")
r15 = Chem.MolFromSmiles("F[C@@](Cl)(I)(Br)")
r16 = Chem.MolFromSmiles("Cl[C@@](I)(F)(Br)")
r17 = Chem.MolFromSmiles("Cl[C@@](F)(Br)(I)")
r18 = Chem.MolFromSmiles("Cl[C@@](Br)(I)(F)")
r19 = Chem.MolFromSmiles("Br[C@@](F)(I)(Cl)")
r20 = Chem.MolFromSmiles("Br[C@@](Cl)(F)(I)")
r21 = Chem.MolFromSmiles("Br[C@@](I)(Cl)(F)")
r22 = Chem.MolFromSmiles("I[C@@](Cl)(Br)(F)")
r23 = Chem.MolFromSmiles("I[C@@](Br)(F)(Cl)")
r24 = Chem.MolFromSmiles("I[C@@](F)(Cl)(Br)")
l1 = Chem.MolFromSmiles("F[C@@](Cl)(Br)(I)")
l2 = Chem.MolFromSmiles("F[C@@](Br)(I)(Cl)")
l3 = Chem.MolFromSmiles("F[C@@](I)(Cl)(Br)")
l4 = Chem.MolFromSmiles("Cl[C@@](F)(I)(Br)")
l5 = Chem.MolFromSmiles("Cl[C@@](Br)(F)(I)")
l6 = Chem.MolFromSmiles("Cl[C@@](I)(Br)(F)")
l7 = Chem.MolFromSmiles("Br[C@@](I)(F)(Cl)")
l8 = Chem.MolFromSmiles("Br[C@@](F)(Cl)(I)")
l9 = Chem.MolFromSmiles("Br[C@@](Cl)(I)(F)")
l10 = Chem.MolFromSmiles("I[C@@](Br)(Cl)(F)")
l11 = Chem.MolFromSmiles("I[C@@](F)(Br)(Cl)")
l12 = Chem.MolFromSmiles("I[C@@](Cl)(F)(Br)")
l13 = Chem.MolFromSmiles("F[C@](Br)(Cl)(I)")
l14 = Chem.MolFromSmiles("F[C@](I)(Br)(Cl)")
l15 = Chem.MolFromSmiles("F[C@](Cl)(I)(Br)")
l16 = Chem.MolFromSmiles("Cl[C@](I)(F)(Br)")
l17 = Chem.MolFromSmiles("Cl[C@](F)(Br)(I)")
l18 = Chem.MolFromSmiles("Cl[C@](Br)(I)(F)")
l19 = Chem.MolFromSmiles("Br[C@](F)(I)(Cl)")
l20 = Chem.MolFromSmiles("Br[C@](Cl)(F)(I)")
l21 = Chem.MolFromSmiles("Br[C@](I)(Cl)(F)")
l22 = Chem.MolFromSmiles("I[C@](Cl)(Br)(F)")
l23 = Chem.MolFromSmiles("I[C@](Br)(F)(Cl)")
l24 = Chem.MolFromSmiles("I[C@](F)(Cl)(Br)")
g1 = Chem.MolFromSmiles('[C@H](Cl)(Br)I');
g2 = Chem.MolFromSmiles('[C@@H](Br)(Cl)I')
print "Greg 1: " + Chem.MolToSmiles(g1,True)
print "Greg 2: " + Chem.MolToSmiles(g2,True)
print "Greg's example: reactant changes"
rxn2 = AllChem.ReactionFromSmarts( '[Cl:2][C@H:1]([Br:3])[I:4]>>[Cl:2][C@@H:1]([Br:3])[F:4]')
rxn2.Initialize()
ps =rxn2.RunReactants((Chem.MolFromSmiles('[C@H](Cl)(Br)I'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
ps =rxn2.RunReactants((Chem.MolFromSmiles('[C@H](Br)(I)Cl'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
ps =rxn2.RunReactants((Chem.MolFromSmiles('[C@H](I)(Cl)Br'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
ps =rxn2.RunReactants((g1,))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
print
#Now provide the same input molecule with a different atom ordering:
ps =rxn2.RunReactants((Chem.MolFromSmiles('[C@@H](Br)(Cl)I'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
ps =rxn2.RunReactants((Chem.MolFromSmiles('[C@@H](I)(Br)Cl'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
ps =rxn2.RunReactants((Chem.MolFromSmiles('[C@@H](Cl)(I)Br'),))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
ps =rxn2.RunReactants((g2,))
print Chem.MolToSmiles(ps[0][0],True) + " expected: F[C@H](Cl)Br"
print
print "This should invert r1"
rxn2 = AllChem.ReactionFromSmarts("[I:5][C@@:1]([Br:4])([F:2])([Cl:3])>>[Br:4][C@:1]([I:5])([F:2])([Cl:3])")
# - r23 r7
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Invert: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
print "This should keep r1"
rxn2 = AllChem.ReactionFromSmarts("[I:5][C@:1]([F:2])([Br:4])([Cl:3])>>[Br:4][C@:1]([I:5])([F:2])([Cl:3])")
# r11 r7
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
print "This should keep r1"
rxn2 = AllChem.ReactionFromSmarts("[I:5][C@:1]([Br:4])([F:2])([Cl:3])>>[Br:4][C@:1]([I:5])([F:2])([Cl:3])")
# r23 r7
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
print "This should keep r1"
rxn2 = AllChem.ReactionFromSmarts("[Br:4][C@:1]([I:5])([F:2])([Cl:3])>>[I:5][C@:1]([Br:4])([F:2])([Cl:3])")
# r7 r23
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
print "This should invert r1"
rxn2 = AllChem.ReactionFromSmarts("[I:5][C@:1]([Br:4])([F:2])([Cl:3])>>[Br:4][C@@:1]([I:5])([F:2])([Cl:3])")
# r23inv r7inv
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Invert: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
#print Chem.MolToSmiles(r1, isomericSmiles=True)
#print Chem.MolToSmiles(r2, isomericSmiles=True)
#print Chem.MolToSmiles(r3, isomericSmiles=True)
#print Chem.MolToSmiles(r4, isomericSmiles=True)
#print Chem.MolToSmiles(r5, isomericSmiles=True)
#print Chem.MolToSmiles(r6, isomericSmiles=True)
#print Chem.MolToSmiles(r7, isomericSmiles=True)
#print Chem.MolToSmiles(r8, isomericSmiles=True)
#print Chem.MolToSmiles(r9, isomericSmiles=True)
#print Chem.MolToSmiles(r10, isomericSmiles=True)
#print Chem.MolToSmiles(r11, isomericSmiles=True)
#print Chem.MolToSmiles(r12, isomericSmiles=True)
#print Chem.MolToSmiles(r13, isomericSmiles=True)
#print Chem.MolToSmiles(r14, isomericSmiles=True)
#print Chem.MolToSmiles(r15, isomericSmiles=True)
#print Chem.MolToSmiles(r16, isomericSmiles=True)
#print Chem.MolToSmiles(r17, isomericSmiles=True)
#print Chem.MolToSmiles(r18, isomericSmiles=True)
#print Chem.MolToSmiles(r19, isomericSmiles=True)
#print Chem.MolToSmiles(r20, isomericSmiles=True)
#print Chem.MolToSmiles(r21, isomericSmiles=True)
#print Chem.MolToSmiles(r22, isomericSmiles=True)
#print Chem.MolToSmiles(r23, isomericSmiles=True)
#print Chem.MolToSmiles(r24, isomericSmiles=True)
rxn = AllChem.ReactionFromSmarts("[C@:1]>>[C@:1]")
rxn.Initialize()
print
print "Keep Products"
p1 = rxn.RunReactants((r1,))
print Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
p2 = rxn.RunReactants((r2,))
p3 = rxn.RunReactants((r3,))
p4 = rxn.RunReactants((r4,))
p5 = rxn.RunReactants((r5,))
p6 = rxn.RunReactants((r6,))
p7 = rxn.RunReactants((r7,))
p8 = rxn.RunReactants((r8,))
p9 = rxn.RunReactants((r9,))
p10 = rxn.RunReactants((r10,))
p11 = rxn.RunReactants((r11,))
p12 = rxn.RunReactants((r12,))
p13 = rxn.RunReactants((r13,))
p14 = rxn.RunReactants((r14,))
p15 = rxn.RunReactants((r15,))
p16 = rxn.RunReactants((r16,))
p17 = rxn.RunReactants((r17,))
p18 = rxn.RunReactants((r18,))
p19 = rxn.RunReactants((r19,))
p20 = rxn.RunReactants((r20,))
p21 = rxn.RunReactants((r21,))
p22 = rxn.RunReactants((r22,))
p23 = rxn.RunReactants((r23,))
p24 = rxn.RunReactants((r24,))
print Chem.MolToSmiles(p2[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p3[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p4[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p5[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p6[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p7[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p8[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p9[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p10[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p11[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p12[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p13[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p14[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p15[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p16[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p17[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p18[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p19[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p20[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p21[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p22[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p23[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p24[0][0], isomericSmiles=True)
rxn = AllChem.ReactionFromSmarts("[C@@:1]>>[C@:1]")
rxn.Initialize()
print
print "Invert Products"
p1 = rxn.RunReactants((r1,))
print Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
p2 = rxn.RunReactants((r2,))
p3 = rxn.RunReactants((r3,))
p4 = rxn.RunReactants((r4,))
p5 = rxn.RunReactants((r5,))
p6 = rxn.RunReactants((r6,))
p7 = rxn.RunReactants((r7,))
p8 = rxn.RunReactants((r8,))
p9 = rxn.RunReactants((r9,))
p10 = rxn.RunReactants((r10,))
p11 = rxn.RunReactants((r11,))
p12 = rxn.RunReactants((r12,))
p13 = rxn.RunReactants((r13,))
p14 = rxn.RunReactants((r14,))
p15 = rxn.RunReactants((r15,))
p16 = rxn.RunReactants((r16,))
p17 = rxn.RunReactants((r17,))
p18 = rxn.RunReactants((r18,))
p19 = rxn.RunReactants((r19,))
p20 = rxn.RunReactants((r20,))
p21 = rxn.RunReactants((r21,))
p22 = rxn.RunReactants((r22,))
p23 = rxn.RunReactants((r23,))
p24 = rxn.RunReactants((r24,))
print Chem.MolToSmiles(p2[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p3[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p4[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p5[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p6[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p7[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p8[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p9[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p10[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p11[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p12[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p13[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p14[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p15[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p16[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p17[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p18[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p19[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p20[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p21[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p22[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p23[0][0], isomericSmiles=True)
print Chem.MolToSmiles(p24[0][0], isomericSmiles=True)
print
print "Mixed reaction - the actual stereochemistry specified in the SMARTS is not relevant, only the relative stereochemistry."
rxn1 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[F:2][C@:1]([Cl:3])([Br:4])([I:5])")
rxn1.Initialize()
p1 = rxn1.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[F:2][C@@:1]([Br:4])([Cl:3])([I:5])")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Invert: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[F:2][C@@:1]([Cl:3])([I:5])([Br:4])")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Invert: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[I:5][C@@:1]([F:2])([Cl:3])([Br:4])")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Invert: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[F:2][C@@:1]([Cl:3])([Br:4])[I:5]")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Invert: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[F:2][C@@:1]([Cl:3])([Br:4])[I:5]")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Invert: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[F:2][C@@:1]([Br:4])([Cl:3])[I:5]")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Invert: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[Cl:3][C@:1]([Br:4])([F:2])([I:5])")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[Br:4][C@:1]([Cl:3])([I:5])([F:2])")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[Br:4][C@:1]([F:2])([Cl:3])([I:5])")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[F:2][C@:1]([Cl:3])([Br:4])[I:5]>>[Br:4][C@:1]([I:5])([F:2])([Cl:3])")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[I:5][C@:1]([F:2])([Br:4])([Cl:3])>>[Br:4][C@:1]([I:5])([F:2])([Cl:3])")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[I:5][C@:1]([Br:4])([F:2])([Cl:3])>>[Br:4][C@:1]([I:5])([F:2])([Cl:3])")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
rxn2 = AllChem.ReactionFromSmarts("[I:5][C@@:1]([Br:4])([F:2])([Cl:3])>>[Br:4][C@@:1]([I:5])([F:2])([Cl:3])")
rxn2.Initialize()
p1 = rxn2.RunReactants((r1,))
print "Keep: " + Chem.MolToSmiles(p1[0][0], isomericSmiles=True)
print "Richard's example: chiral in, chiral out - but only two bonds specified"
rxn2 = AllChem.ReactionFromSmarts( '[Cl:2][C@:1][Br:3]>>[Cl:2][C@:1][Br:3]')
rxn2.Initialize()
print Chem.MolToSmiles(rxn2.RunReactants((r1,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r2,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r3,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r4,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r5,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r6,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r7,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r8,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r9,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r10,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r11,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r12,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r13,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r14,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r15,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r16,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r17,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r18,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r19,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r20,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r21,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r22,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r23,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r24,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l1,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l2,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l3,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l4,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l5,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l6,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l7,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l8,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l9,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l10,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l11,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l12,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l13,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l14,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l15,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l16,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l17,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l18,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l19,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l20,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l21,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l22,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l23,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l24,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print "Richard's example: chiral in, chiral out - still only two bonds specified, but different template"
rxn2 = AllChem.ReactionFromSmarts( '[Cl:2][C@:1][Br:3]>>[Br:3][C@:1][Cl:2]')
rxn2.Initialize()
print Chem.MolToSmiles(rxn2.RunReactants((r1,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r2,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r3,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r4,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r5,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r6,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r7,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r8,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r9,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r10,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r11,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r12,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r13,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r14,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r15,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r16,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r17,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r18,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r19,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r20,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r21,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r22,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r23,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r24,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l1,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l2,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l3,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l4,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l5,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l6,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l7,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l8,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l9,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l10,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l11,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l12,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l13,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l14,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l15,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l16,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l17,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l18,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l19,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l20,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l21,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l22,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l23,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l24,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print "Richard's example: chiral in, chiral out - still only two bonds specified, but final template"
rxn2 = AllChem.ReactionFromSmarts( '[Cl:2][C@:1][Br:3]>>[C@:1]([Cl:2])[Br:3]')
rxn2.Initialize()
print Chem.MolToSmiles(rxn2.RunReactants((r1,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r2,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r3,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r4,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r5,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r6,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r7,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r8,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r9,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r10,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r11,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r12,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r13,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r14,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r15,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r16,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r17,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r18,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r19,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r20,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r21,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r22,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r23,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r24,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l1,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l2,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l3,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l4,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l5,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l6,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l7,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l8,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l9,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l10,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l11,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l12,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l13,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l14,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l15,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l16,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l17,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l18,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l19,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l20,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l21,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l22,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l23,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l24,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print "Richard's example: chiral in, chiral out - but only one bond specified"
rxn2 = AllChem.ReactionFromSmarts( '[Cl:2][C@:1]>>[Cl:2][C@:1]')
rxn2.Initialize()
print Chem.MolToSmiles(rxn2.RunReactants((r1,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r2,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r3,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r4,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r5,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r6,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r7,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r8,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r9,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r10,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r11,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r12,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r13,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r14,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r15,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r16,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r17,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r18,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r19,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r20,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r21,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r22,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r23,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r24,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l1,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l2,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l3,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l4,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l5,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l6,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l7,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l8,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l9,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l10,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l11,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l12,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l13,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l14,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l15,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l16,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l17,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l18,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l19,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l20,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l21,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l22,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l23,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l24,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((a1,))[0][0],True) + " expected: FC(Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((odd1,))[0][0],True) + " expected: C[C@@H](O)CCC(Cl)(Br)C/C=C\I"
print "Richard's example: chiral in, chiral out - but only one three bonds specified"
rxn2 = AllChem.ReactionFromSmarts( '[Cl:2][C@:1]([Br:3])[F:4]>>[Cl:2][C@:1]([Br:3])[F:4]')
rxn2.Initialize()
print Chem.MolToSmiles(rxn2.RunReactants((r1,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r2,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r3,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r4,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r5,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r6,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r7,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r8,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r9,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r10,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r11,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r12,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r13,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r14,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r15,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r16,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r17,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r18,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r19,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r20,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r21,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r22,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r23,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((r24,))[0][0],True) + " expected: F[C@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l1,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l2,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l3,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l4,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l5,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l6,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l7,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l8,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l9,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l10,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l11,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l12,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l13,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l14,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l15,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l16,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l17,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l18,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l19,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l20,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l21,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l22,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l23,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
print Chem.MolToSmiles(rxn2.RunReactants((l24,))[0][0],True) + " expected: F[C@@](Cl)(Br)I"
rxn = AllChem.ReactionFromSmarts( '[O:2][C@:1]>>[Cl:2][C@:1]') # replace OH with Cl. Keep chirality of C, if present.
rxn.Initialize()
print Chem.MolToSmiles(rxn.RunReactants((Chem.MolFromSmiles('C[C@](O)(Br)I'),))[0][0],True)
rxn = AllChem.ReactionFromSmarts( '[O:2][C@:1]>>[Cl:2][C@:1]') # replace OH with Cl. Keep chirality of C, if present.
rxn.Initialize()
print Chem.MolToSmiles(rxn.RunReactants((Chem.MolFromSmiles('CC(O)(Br)I'),))[0][0],True)
rxn = AllChem.ReactionFromSmarts( '[O:2][C:1]>>[Cl:2][C:1]') # replace OH with Cl. Should keep chirality of C, if present.
rxn.Initialize()
print Chem.MolToSmiles(rxn.RunReactants((Chem.MolFromSmiles('C[C@](O)(Br)I'),))[0][0],True)
#
# Cl\ /Br Cl\ /I
# C=C -> C=C
# F/ \I F/ \Br
#
#
rxn = AllChem.ReactionFromSmarts( '[C:1](\[Cl:3])(/[F:6])=[C:2](/[Br:4])(\[I:5])>>[C:1](\[Cl:3])(/[F:6])=[C:2](\[Br:4])(/[I:5])')
rxn.Initialize()
print Chem.MolToSmiles(rxn.RunReactants((Chem.MolFromSmiles('C(\Cl)(/F)=C(/Br)(\I)'),))[0][0],True)
print Chem.MolToSmiles( Chem.MolFromSmiles ( 'Cl\C=C/Br' ), True )
rt = Chem.MolFromSmiles ( 'Cl\C=C/Br' )
rt.UpdatePropertyCache()
Draw.MolToFile(rt, 'test.png')
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