Remove ext part from canonical smiles (#1211)

epam · Aug 4, 2023 · bd166af · bd166af
1 parent 2da94fa
commit bd166af
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diff --git a/api/c/tests/unit/tests/formats.cpp b/api/c/tests/unit/tests/formats.cpp
@@ -55,7 +55,7 @@ TEST_F(IndigoApiFormatsTest, molecule)
         // 2
         obj = indigoLoadStructureFromString(mStr.c_str(), "");
         EXPECT_STREQ(expected.c_str(), indigoSmiles(obj));
-        EXPECT_STREQ("*C1C=CC=CC=1 |$A;;;;;;$|", indigoCanonicalSmiles(obj));
+        EXPECT_STREQ("*C1C=CC=CC=1", indigoCanonicalSmiles(obj));
         EXPECT_EQ(7, indigoCountAtoms(obj));
         EXPECT_EQ(7, indigoCountBonds(obj));
 

diff --git a/api/tests/integration/ref/arom/elements.py.out b/api/tests/integration/ref/arom/elements.py.out
@@ -51,8 +51,8 @@ B1=CC=CN=N1
 B1=NC=CO1
 [b]1[n]cco1
 17
-CC1[B]C(C)(C)C(C)=C(C)C=1CC1=BC(C)=C(C)C(C)=C1C |^1:2|
-CC1[B]C(C)(C)C(C)=C(C)C=1Cc1[b]c(C)c(C)c(C)c1C |^1:2|
+CC1[B]C(C)(C)C(C)=C(C)C=1CC1=BC(C)=C(C)C(C)=C1C
+CC1[B]C(C)(C)C(C)=C(C)C=1Cc1[b]c(C)c(C)c(C)c1C
 18
 CC1=BC(CC2B=C(C)C(C)=C(C)C=2C)=C(C)C(C)=C1C
 Cc1[b]c(Cc2[b]c(C)c(C)c(C)c2C)c(C)c(C)c1C
@@ -403,14 +403,14 @@ CCc1c(CC)c:[Si](CC):c([Si])c1CC
 CC1C=C[Si](O)=C(C)C=1C
 Cc1cc:[Si](O):c(C)c1C
 13
-C1=NC=[Si]C2=CC=CC=C21 |^1:3|
-c1[n]c:[Si]:c2ccccc21 |^1:3|
+C1=NC=[Si]C2=CC=CC=C21
+c1[n]c:[Si]:c2ccccc21
 14
 CC1C=C[Si](OCC)=C(OCC)C=1OCC
 Cc1cc:[Si](OCC):c(OCC)c1OCC
 15
-CC(C)(CC(C)(CN1C=[Si]C=[Si]1)C1C=CC(F)=CC=1)C1C=CC(F)=CC=1 |^1:9,11|
-CC(C)(CC(C)(C[n]1c:[Si]:c:[Si]:1)c1ccc(F)cc1)c1ccc(F)cc1 |^1:9,11|
+CC(C)(CC(C)(CN1C=[Si]C=[Si]1)C1C=CC(F)=CC=1)C1C=CC(F)=CC=1
+CC(C)(CC(C)(C[n]1c:[Si]:c:[Si]:1)c1ccc(F)cc1)c1ccc(F)cc1
 16
 CC1C=C[Si](Cl)=C(C)C=1C
 Cc1cc:[Si](Cl):c(C)c1C
@@ -424,8 +424,8 @@ C[Si]1:ccccc:1Cl
 CC1=C2C(OC=C1C)=[Si](CC)C(CC)=C2C
 Cc1c2c(occ1C):[Si](CC):c(CC)c2C
 20
-CC1=[Si]ON=C1C(=O)NC1C=CC(=CC=1)C(F)(F)F |^1:2|
-Cc1:[Si]:o[n]c1C(=O)Nc1ccc(cc1)C(F)(F)F |^1:2|
+CC1=[Si]ON=C1C(=O)NC1C=CC(=CC=1)C(F)(F)F
+Cc1:[Si]:o[n]c1C(=O)Nc1ccc(cc1)C(F)(F)F
 21
 CCCNC1C=C[Si](Cl)=C(Cl)C=1Cl
 CCCNc1cc:[Si](Cl):c(Cl)c1Cl
@@ -436,14 +436,14 @@ C[Si]1:[n]c(C)cc:[Si]:1-c1cccc2ccc3cc4ccccc4cc3c21
 CCOC1C(OCC)=[Si](C=CC=1C1C=CC=CC=1)OCC
 CCOc1c(OCC)c(cc:[Si]:1OCC)-c1ccccc1
 24
-C1C=CC=C2N[Si]=NC2=1 |^1:6|
-c1cccc2[nH]:[Si]:[n]c21 |^1:6|
+C1C=CC=C2N[Si]=NC2=1
+c1cccc2[nH]:[Si]:[n]c21
 25
-[Cl-].C1=C[Si]=[NH+]C2=CC=CC=C21 |^1:3|
-[Cl-].c1cccc2[nH+]:[Si]:ccc21 |^1:7|
+[Cl-].C1=C[Si]=[NH+]C2=CC=CC=C21
+[Cl-].c1cccc2[nH+]:[Si]:ccc21
 26
-C1=C[Si]=NC2=CC=CC=C21 |^1:2|
-c1cccc2[n]:[Si]:ccc21 |^1:6|
+C1=C[Si]=NC2=CC=CC=C21
+c1cccc2[n]:[Si]:ccc21
 27
 CC1=C2C(OC=C1C)=[Si](C)C(C)=C2C
 Cc1c(C)c2c(occ(C)c2C):[Si]:1C
@@ -673,11 +673,11 @@ Cc1c[asH]cc1C
 CC(C)(C)N1P2N3N(C)P(N([As]3Cl)C(C)(C)C)N(N2C)[As]1Cl
 CC(C)(C)[n]1[p]2[n]3[n](C)[p]([n]([as]3Cl)C(C)(C)C)[n]([n]2C)[as]1Cl
 12
-CC1=C[As]C=C1C |^1:3|
-CC1=C[As]C=C1C |^1:3|
+CC1=C[As]C=C1C
+CC1=C[As]C=C1C
 13
-C1=CC=C[As]1 |^1:4|
-C1=CC=C[As]1 |^1:4|
+C1=CC=C[As]1
+C1=CC=C[As]1
 14
 C[As]1C2=CC=CC=C2C=C1[Si](C)(C)C
 C[as]1c2ccccc2cc1[Si](C)(C)C
@@ -697,8 +697,8 @@ CC(C)(C)c1cc(cc2c1o[as](O[as]1oc3c(cc(cc3c3cc(cc(c3o1)C(C)(C)C)C(C)(C)C)C(C)(C)C
 C1=CC=[As]C2=CC=CC=C21
 c1cccc2[as]cccc21
 20
-[Sm].[Sm].CC1=C[AsH]C=C1C.CC1=C[As]C=C1C.CC1[C-](C)C(C)=C(C)C=1C.CC1[C-](C)C(C)=C(C)C=1C.CC1[C-](C)C(C)=C(C)C=1C.C[C-]1[C-](C)[C-](C)[C-](C)[C-]1C |^1:12|
-[Sm].[Sm].CC1=C[As]C=C1C.Cc1c[asH]cc1C.Cc1[c-](C)c(C)c(C)c1C.Cc1[c-](C)c(C)c(C)c1C.Cc1[c-](C)c(C)c(C)c1C.C[c-]1[c-](C)[c-](C)[c-](C)[c-]1C |^1:5|
+[Sm].[Sm].CC1=C[AsH]C=C1C.CC1=C[As]C=C1C.CC1[C-](C)C(C)=C(C)C=1C.CC1[C-](C)C(C)=C(C)C=1C.CC1[C-](C)C(C)=C(C)C=1C.C[C-]1[C-](C)[C-](C)[C-](C)[C-]1C
+[Sm].[Sm].CC1=C[As]C=C1C.Cc1c[asH]cc1C.Cc1[c-](C)c(C)c(C)c1C.Cc1[c-](C)c(C)c(C)c1C.Cc1[c-](C)c(C)c(C)c1C.C[c-]1[c-](C)[c-](C)[c-](C)[c-]1C
 21
 CC1=C(C)C(C)=C(C)[As]1C1C=CC=CC=1
 Cc1c(C)c(C)c(C)[as]1-c1ccccc1
@@ -712,17 +712,17 @@ Cl[as]1[n]c(c([n]1)-c1c[s]cc1)-c1c[s]cc1
 C1=CC=[As]N1
 c1cc[as][nH]1
 25
-C1=C[As]C2=CC=CC=C21 |^1:2|
-c1cccc2[As]C=Cc21 |^1:5|
+C1=C[As]C2=CC=CC=C21
+c1cccc2[As]C=Cc21
 26
-[Cl-].[Cl-].[Cl-].[Zr].[Zr].[Zr].CC1=[As][As]C(C)=C1C.CC1=[As][As]C(C)=C1C.CC1=[As][As]C(C)=C1C |^1:9,17,25|
-[Cl-].[Cl-].[Cl-].[Zr].[Zr].[Zr].CC1=[As][As]C(C)=C1C.CC1=[As][As]C(C)=C1C.CC1=[As][As]C(C)=C1C |^1:9,17,25|
+[Cl-].[Cl-].[Cl-].[Zr].[Zr].[Zr].CC1=[As][As]C(C)=C1C.CC1=[As][As]C(C)=C1C.CC1=[As][As]C(C)=C1C
+[Cl-].[Cl-].[Cl-].[Zr].[Zr].[Zr].CC1=[As][As]C(C)=C1C.CC1=[As][As]C(C)=C1C.CC1=[As][As]C(C)=C1C
 27
-CC1C(C)=[As][As]C=1C |^1:5|
-CC1C(C)=[As][As]C=1C |^1:5|
+CC1C(C)=[As][As]C=1C
+CC1C(C)=[As][As]C=1C
 28
-C1=CC=[As][As]1 |^1:4|
-C1=CC=[As][As]1 |^1:4|
+C1=CC=[As][As]1
+C1=CC=[As][As]1
 29
 C1=CC=[As]P1
 c1cc[as][pH]1

diff --git a/api/tests/integration/ref/basic/attachment_points.py.out b/api/tests/integration/ref/basic/attachment_points.py.out
@@ -1,10 +1,10 @@
 scaffold: CC1C(O)=CC(C(C)C=1)C
 full scaffold: C%91C1C(O%92)=C%93C(C(C%94%95)C%96=1)C%97%98.[*:1]%94%97.[*:2]%95.[*:3]%98.[*:4]%93.[*:5]%91%92.[*:6]%96 |$;;;;;;;;;;_R1;_R2;_R3;_R4;_R5;_R6$|
 Molecule: CC1C(O)=CC2C(CC3C(C2)CCCC3)C=1 |ha:0,1,2,3,4,5,6,7,10,15,hb:0,1,2,3,4,5,6,10,16,17|
-  decomposed molecule: CC1=CC(C%91)C(C%92)C=C1O.[*:1]%91%92 |$;;;;;;;;;;_R1$,RG:_R1={C1CCCC%91C%921.[*:2]%91.[*:1]%92 |$;;;;;;_AP2;_AP1$|}|
+  decomposed molecule: CC1C(O)=CC(C(C%91)C=1)C%92.[*:1]%91%92 |$;;;;;;;;;;_R1$,RG:_R1={C1%91C%92CCCC1.[*:1]%91.[*:2]%92 |$;;;;;;_AP1;_AP2$|}|
   mapped scaffold: CC1=CC(C)C(C)C=C1O
     RGROUP #1
-      fragment #0: C1CCCC%91C%921.[*:2]%91.[*:1]%92 |$;;;;;;_AP2;_AP1$|
+      fragment #0: C1%91C%92CCCC1.[*:1]%91.[*:2]%92 |$;;;;;;_AP1;_AP2$|
          Number of attachment points: 2
            Index: 0. Order 1
            Index: 5. Order 2
@@ -37,7 +37,7 @@ IC1CCCCC1I
 M  END
 
 Molecule: CC1C(O)=C(C)C(CF)C(CO)C=1 |ha:0,1,2,3,4,6,7,9,10,12,hb:0,1,2,3,5,6,8,9,11,12|
-  decomposed molecule: CC1=CC(C%91)C(C%92)C%93=C1O.[*:4]%93.[*:3]%92.[*:2]%91 |$;;;;;;;;;;_R4;_R3;_R2$,RG:_R2={O%91.[*:1]%91 |$;_AP1$|},_R3={F%91.[*:1]%91 |$;_AP1$|},_R4={C%91.[*:1]%91 |$;_AP1$|}|
+  decomposed molecule: CC1C(O)=C%91C(C%92)C(C%93)C=1.[*:2]%93.[*:3]%92.[*:4]%91 |$;;;;;;;;;;_R2;_R3;_R4$,RG:_R2={O%91.[*:1]%91 |$;_AP1$|},_R3={F%91.[*:1]%91 |$;_AP1$|},_R4={C%91.[*:1]%91 |$;_AP1$|}|
   mapped scaffold: CC1=CC(C)C(C)C=C1O
     RGROUP #2
       fragment #0: O%91.[*:1]%91 |$;_AP1$|
@@ -94,7 +94,7 @@ CI
 M  END
 
 Molecule: CC1C(O)=C(C)C2C(COC2)C=1 |ha:0,1,2,3,4,6,7,8,10,11,hb:0,1,2,3,5,6,7,10,11,12|
-  decomposed molecule: CC1=CC(C%91)C(C%92)C%93=C1O.[*:4]%93.[*:1]%92%91 |$;;;;;;;;;;_R4;_R1$,RG:_R1={O%91%92.[*:1]%91.[*:2]%92 |$;_AP1;_AP2$|},_R4={C%91.[*:1]%91 |$;_AP1$|}|
+  decomposed molecule: CC1C(O)=C%91C(C(C%92)C=1)C%93.[*:1]%92%93.[*:4]%91 |$;;;;;;;;;;_R1;_R4$,RG:_R1={O%91%92.[*:1]%91.[*:2]%92 |$;_AP1;_AP2$|},_R4={C%91.[*:1]%91 |$;_AP1$|}|
   mapped scaffold: CC1=CC(C)C(C)C=C1O
     RGROUP #1
       fragment #0: O%91%92.[*:1]%91.[*:2]%92 |$;_AP1;_AP2$|
@@ -137,7 +137,7 @@ CI
 M  END
 
 Molecule: CC1C2C(COC2)C(O)=C2C=1OCC2 |ha:1,2,3,4,6,7,9,10,11,13,hb:1,2,3,6,7,9,10,11,12,15|
-  decomposed molecule: [*:6]C1C(C%91)C(C%92)C%93=C(C%94)C=1O%95.[*:4]%93.[*:5]%95%94.[*:1]%91%92 |$_R6;;;;;;;;;;;_R4;_R5;_R1$,RG:_R1={O%91%92.[*:1]%91.[*:2]%92 |$;_AP1;_AP2$|},_R4={O%91.[*:1]%91 |$;_AP1$|},_R5={C%91%92.[*:1]%91.[*:2]%92 |$;_AP1;_AP2$|},_R6={C%91.[*:1]%91 |$;_AP1$|}|
+  decomposed molecule: C1%91C(C(C%92)C%93=C(C=1O%94)C%95)C%96.[*:5]%94%95.[*:4]%93.[*:1]%92%96.[*:6]%91 |$;;;;;;;;;;_R5;_R4;_R1;_R6$,RG:_R1={O%91%92.[*:1]%91.[*:2]%92 |$;_AP1;_AP2$|},_R4={O%91.[*:1]%91 |$;_AP1$|},_R5={C%91%92.[*:1]%91.[*:2]%92 |$;_AP1;_AP2$|},_R6={C%91.[*:1]%91 |$;_AP1$|}|
   mapped scaffold: CC1=CC(C)C(C)C=C1O
     RGROUP #1
       fragment #0: O%91%92.[*:1]%91.[*:2]%92 |$;_AP1;_AP2$|

diff --git a/api/tests/integration/ref/basic/basic.py.out b/api/tests/integration/ref/basic/basic.py.out
@@ -33,9 +33,9 @@ element: bad valence on N having 4 drawn bonds, charge 0, and 0 radical electron
 CC[C@H](/C=C\C)N
 C/C=C\[C@H](N)CC
 ***(*=**)* |$*;*;*;*;*;*;*$|
+***(*)*=**
 ***(*)*=** |$*;*;*;*;*;*;*$|
-***(*)*=** |$*;*;*;*;*;*;*$|
-***(*)*=** |$*;*;*;*;*;*;*$|
+***(*)*=**
 ****** Anormal properties ********
 0 8
 0 2
@@ -52,7 +52,7 @@ C/C=C\[C@H](N)CC
 0 2
 -10 1
 ****** Unmarked stereobonds ********
-C1C2CCC3CCC4C5CCCCC5CCC4[C@@]321 |&1:17,r|
+C1C2CCC3CCC4C5CCCCC5CCC4[C@@]321
 C1C2CCC3CCC4C5CCCCC5CCC4C321
 C1C2CCC3CCC4C5CCCCC5CCC4C321
 ****** Chemical formula ********
@@ -216,14 +216,14 @@ CC(=O)[C@H]1C[C@H](O)[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3C(=O)C[C@@]21C
 CC(=O)[C@H]1C[C@H](O)[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3C(=O)C[C@@]21C
 ****** SMILES cis-trans check *****
 IC1=C(C([H])=C([H])C([H])=C([H])C([H])=C([H])C2C=CC=CC(/C(=N/[H])/N([H])[H])=C([H])C=21)[H] |c:16,18,29,t:1,4,8,12,26|
-[H]/N=C(\N)/C1=CC2C(I)=CC=CC=CC=CC=2C=CC=C1 |c:8,10,12,14,18,20,t:4,16|
+[H]/N=C(\N)/C1=CC2C(I)=CC=CC=CC=CC=2C=CC=C1
 ****** Empty SDF saver *****
 0
 0
 ****** Normalize and serialize *****
 [O-]/[N+](=C\C1C=CC=CC=1)/C1C=CC=CC=1
 O=N(=CC1C=CC=CC=1)C1C=CC=CC=1
-CC=CC1C=CC=CC=1/[N+](/[O-])=C/C1=CC(/C=C/C)=CC=C1 |t:1|
+CC=CC1C=CC=CC=1/[N+](/[O-])=C/C1=CC(/C=C/C)=CC=C1
 C/C=C/C1C=CC=CC=1N(=O)=CC1=CC(/C=C/C)=CC=C1
 ***** Serialization of aromatic hydrogens *****
 ***** Reset options check *****

diff --git a/api/tests/integration/ref/basic/basic_load.py.out b/api/tests/integration/ref/basic/basic_load.py.out
@@ -348,7 +348,7 @@ M  END
 
 H2
 ****** S-group's SCL (CLASS) support ********
-NC(=O)C[C@@H](C=O)NC(=O)[C@H](CC(N)=O)NN[C@@H](CC(N)=O)C(=O)N[C@@H](CC(N)=O)C=O |&1:4,10,17,25,r|
+NC(=O)C[C@@H](C=O)NC(=O)[C@H](CC(N)=O)NN[C@@H](CC(N)=O)C(=O)N[C@@H](CC(N)=O)C=O
 
   -INDIGO-01000000002D
 
@@ -440,7 +440,7 @@ M  SCL   4 AA
 M  SAP   4  2  11  24 Al  31   0 Br
 M  END
 
-NC(=O)C[C@@H](C=O)NC(=O)[C@H](CC(N)=O)NN[C@@H](CC(N)=O)C(=O)N[C@@H](CC(N)=O)C=O |&1:4,10,17,25,r|
+NC(=O)C[C@@H](C=O)NC(=O)[C@H](CC(N)=O)NN[C@@H](CC(N)=O)C(=O)N[C@@H](CC(N)=O)C=O
 
   -INDIGO-01000000002D
 
@@ -531,7 +531,7 @@ M  V30 END CTAB
 M  END
 
 ****** S-group's SPL (PARENT) support ********
-CC(C)C[C@@H](C=O)NC(=O)[C@H](CS)NC(=O)[C@H](CS)NC(=O)[C@H](C)N |Sg:gen:0,3,4,5,6,7,20,21,22,23,24,1,2,8,9,10,11,12,13,14,15,16,17,18,19:,SgD:5:[DUP]:\10::: :|
+CC(C)C[C@@H](C=O)NC(=O)[C@H](CS)NC(=O)[C@H](CS)NC(=O)[C@H](C)N
 
   -INDIGO-01000000002D
 
@@ -614,7 +614,7 @@ M  SDD   5    -4.5860    5.0322    DAU   ALL  1       1
 M  SED   5 \10
 M  END
 
-CC(C)C[C@@H](C=O)NC(=O)[C@H](CS)NC(=O)[C@H](CS)NC(=O)[C@H](C)N |Sg:gen:0,3,4,5,6,7,20,21,22,23,24,1,2,8,9,10,11,12,13,14,15,16,17,18,19:,SgD:5:[DUP]:\10::: :|
+CC(C)C[C@@H](C=O)NC(=O)[C@H](CS)NC(=O)[C@H](CS)NC(=O)[C@H](C)N
 
   -INDIGO-01000000002D
 
@@ -1746,7 +1746,7 @@ Alias
 M  END
 
 ****** Alias handling (SMILES) ********
-CC |$;Alias$|
+CC
 ****** Test load from gzip buffer ********
 C1C=CC=CC=1
 ****** Load V3000 with DISP keyword ********

diff --git a/api/tests/integration/ref/basic/chiral_test.py.out b/api/tests/integration/ref/basic/chiral_test.py.out
@@ -1,17 +1,17 @@
 Chiral flag and canonical smiles:
-OC(=O)[C@@H](CC1C=CC=CC=1)NI |&1:3,r|. Chiral: False
-OC(=O)[C@@H](CC1C=CC=CC=1)NI |&1:3,r|. Chiral: False
+OC(=O)[C@@H](CC1C=CC=CC=1)NI. Chiral: False
+OC(=O)[C@@H](CC1C=CC=CC=1)NI. Chiral: False
 OC(=O)C(CC1C=CC=CC=1)NI. Chiral: False
 OC(=O)C(CC1C=CC=CC=1)NI. Chiral: False
 OC(=O)[C@H](CC1C=CC=CC=1)NI. Chiral: True
 OC(=O)[C@@H](CC1C=CC=CC=1)NI. Chiral: True
 OC(=O)[C@@H](CC1C=CC=CC=1)NI. Chiral: True
-OC(=O)[C@@H](CC1C=CC=CC=1)NI |o1:3,r|. Chiral: False
-OC(=O)[C@@H](CC1C=CC=CC=1)NI |&1:3,r|. Chiral: False
-OC(=O)C(CC1C=CC=CC=1)NI |w:3,r|. Chiral: False
-C[C@@H](C(NI)C(O)=O)C1C=CC=CC=1 |&1:1,w:2,r|. Chiral: False
-C[C@@H](C(NI)C(O)=O)C1C=CC=CC=1 |&1:1,w:2,r|. Chiral: False
-C[C@@H]([C@@H](NI)C(O)=O)C1C=CC=CC=1 |&1:1,o1:2,r|. Chiral: False
+OC(=O)[C@@H](CC1C=CC=CC=1)NI. Chiral: False
+OC(=O)[C@@H](CC1C=CC=CC=1)NI. Chiral: False
+OC(=O)C(CC1C=CC=CC=1)NI. Chiral: False
+C[C@@H](C(NI)C(O)=O)C1C=CC=CC=1. Chiral: False
+C[C@@H](C(NI)C(O)=O)C1C=CC=CC=1. Chiral: False
+C[C@@H]([C@@H](NI)C(O)=O)C1C=CC=CC=1. Chiral: False
 CC(C(NI)C(O)=O)C1C=CC=CC=1. Chiral: False
 Change stereocenters
 OC(=O)[C@H](CC1C=CC=CC=1)NI. Chiral: True

diff --git a/api/tests/integration/ref/basic/reaction_instrumentation.py.out b/api/tests/integration/ref/basic/reaction_instrumentation.py.out
@@ -86,12 +86,12 @@ MOLECULE: CN
 MOLECULE: CC
 MOLECULE: Oc1ccccc1
 MOLECULE: c1cccc[n]1
-MOLECULE: * |$2.  acid$|
+MOLECULE: *
 REACTANT: [PH5]
 REACTANT: CN
 REACTANT: Oc1ccccc1
 CATALYST: CC
-CATALYST: * |$2.  acid$|
+CATALYST: *
 PRODUCT:  c1cccc[n]1
 
 REMOVING
@@ -102,8 +102,8 @@ REMOVING
 MOLECULE: CN
 MOLECULE: CC
 MOLECULE: Oc1ccccc1
-MOLECULE: * |$2.  acid$|
+MOLECULE: *
 REACTANT: CN
 REACTANT: Oc1ccccc1
 CATALYST: CC
-CATALYST: * |$2.  acid$|
+CATALYST: *
diff --git a/api/tests/integration/ref/basic/stereocenters.py.out b/api/tests/integration/ref/basic/stereocenters.py.out
@@ -5421,23 +5421,23 @@ Initial:
   6: 0
   8: 0
   10: 0
-C[C@@H]1[C@H](C)[C@@H](C)[C@H](C)[C@@H](C)[C@@H]1C |o1:1,2,4,6,8,10,r|
+C[C@@H]1[C@H](C)[C@@H](C)[C@H](C)[C@@H](C)[C@@H]1C
 After changes:
   1: 0
   2: 1
   4: 2
   6: 3
   8: 4
   10: 5
-C[C@@H]1[C@@H](C)[C@@H](C)[C@@H](C)[C@@H](C)[C@@H]1C |o1:1,o2:2,o3:4,o4:6,o5:8,o6:10,r|
+C[C@@H]1[C@@H](C)[C@@H](C)[C@@H](C)[C@@H](C)[C@@H]1C
 Set all to one group:
   1: 2
   2: 2
   4: 2
   6: 2
   8: 2
   10: 2
-C[C@@H]1[C@H](C)[C@@H](C)[C@H](C)[C@@H](C)[C@@H]1C |o1:1,2,4,6,8,10,r|
+C[C@@H]1[C@H](C)[C@@H](C)[C@H](C)[C@@H](C)[C@@H]1C
 ****** Mark stereobonds ********
 
   -INDIGO-01000000002D
@@ -5516,7 +5516,7 @@ C[C@H]1C[C@H](C)[C@H](C)C[C@H]1C
   Cano:   C[C@@H]1C[C@@H](C)[C@@H](C)C[C@@H]1C
   Smiles: C[C@@H]1[C@H](C)C[C@@H](C)[C@@H](C)C1
   Validating...
-  Cano:   C[C@@H]1C[C@@H](C)[C@@H](C)C[C@@H]1C |&1:1,3,5,8,r|
+  Cano:   C[C@@H]1C[C@@H](C)[C@@H](C)C[C@@H]1C
   Smiles: C[C@@H]1[C@H](C)C[C@@H](C)[C@@H](C)C1 |&1:1,2,5,7,r|
 CCCCCCCC[C@H](C)C
   Cano:   CCCCCCCCC(C)C

diff --git a/api/tests/integration/ref/basic/zbo_load.py.out b/api/tests/integration/ref/basic/zbo_load.py.out
@@ -43,7 +43,7 @@ M  V30 END BOND
 M  V30 END CTAB
 M  END
 
-[*-][Fe+2][*-].[CH]1[CH][CH][CH][CH]1.[CH]1[CH][CH][CH][CH]1 |^1:3,4,5,6,7,8,9,10,11,12,$*;;*;;;;;;;;;;$|
+[*-][Fe+2][*-].[CH]1[CH][CH][CH][CH]1.[CH]1[CH][CH][CH][CH]1
 
   -INDIGO-01000000002D
 
@@ -82,7 +82,7 @@ M  V30 END BOND
 M  V30 END CTAB
 M  END
 
-[*-][Fe+2][*-].c1cccc1.c1cccc1 |$*;;*;;;;;;;;;;$|
+[*-][Fe+2][*-].c1cccc1.c1cccc1
 
   -INDIGO-01000000002D