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Remove ext part from canonical smiles #1211

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merged 6 commits into from
Aug 4, 2023
Merged

Remove ext part from canonical smiles #1211

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19b275e
#1199 CanonicalSmiles saver contains extended part
AliaksandrDziarkach Aug 2, 2023
9ed5086
Fix python file formating
AliaksandrDziarkach Aug 2, 2023
958a3b4
Fix indigo-api-unit-test
AliaksandrDziarkach Aug 2, 2023
dc9d229
Fix indigo-core-unit-tests
AliaksandrDziarkach Aug 2, 2023
561741f
Fix integration tests deco_iter and exact/reload
AliaksandrDziarkach Aug 3, 2023
f636bb3
Fix python file formating
AliaksandrDziarkach Aug 3, 2023
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2 changes: 1 addition & 1 deletion api/c/tests/unit/tests/formats.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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));

Expand Down
56 changes: 28 additions & 28 deletions api/tests/integration/ref/arom/elements.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down
10 changes: 5 additions & 5 deletions api/tests/integration/ref/basic/attachment_points.py.out
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Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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 |$;_AP1$|
Expand Down Expand Up @@ -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 |$;_AP1;_AP2$|
Expand Down Expand Up @@ -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 |$;_AP1;_AP2$|
Expand Down
10 changes: 5 additions & 5 deletions api/tests/integration/ref/basic/basic.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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 ********
Expand Down Expand Up @@ -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 *****
Expand Down
10 changes: 5 additions & 5 deletions api/tests/integration/ref/basic/basic_load.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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 ********
Expand Down
16 changes: 8 additions & 8 deletions api/tests/integration/ref/basic/chiral_test.py.out
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Original file line number Diff line number Diff line change
@@ -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
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8 changes: 4 additions & 4 deletions api/tests/integration/ref/basic/reaction_instrumentation.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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: *
8 changes: 4 additions & 4 deletions api/tests/integration/ref/basic/stereocenters.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
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4 changes: 2 additions & 2 deletions api/tests/integration/ref/basic/zbo_load.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -82,7 +82,7 @@ M V30 END BOND
M V30 END CTAB
M END

[*-][Fe+2][*-].c1cccc1.c1cccc1 |$*;;*;;;;;;;;;;$|
[*-][Fe+2][*-].c1cccc1.c1cccc1

-INDIGO-01000000002D

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