#1423 Common atoms loaded as aliphatic in SMARTS mode (#1424)

epam · Dec 21, 2023 · abfdcdb · abfdcdb
1 parent cc68258
commit abfdcdb
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diff --git a/api/c/tests/unit/tests/formats.cpp b/api/c/tests/unit/tests/formats.cpp
@@ -60,7 +60,7 @@ TEST_F(IndigoApiFormatsTest, molecule)
         EXPECT_EQ(7, indigoCountBonds(obj));
 
         // 3
-        const string expectedSmarts = "[C]1-[C]=[C]-[C]=[C]-[C]=1-[*]";
+        const string expectedSmarts = "C1-C=C-C=C-C=1-[*]";
         obj = indigoLoadStructureFromString(mStr.c_str(), "smarts");
         EXPECT_STREQ(expectedSmarts.c_str(), indigoSmarts(obj));
         EXPECT_EQ(7, indigoCountAtoms(obj));
@@ -83,7 +83,7 @@ TEST_F(IndigoApiFormatsTest, reaction)
 {
     const string react = "C1=C(*)C=CC=C1>>C1=CC=CC(*)=C1";
     const string expected = "C1C=CC=CC=1*>>C1C=C(*)C=CC=1";
-    const string expected_smarts = "[C]1-[C]=[C]-[C]=[C]-[C]=1-[*]>>[C]1-[C]=[C](-[*])-[C]=[C]-[C]=1";
+    const string expected_smarts = "C1-C=C-C=C-C=1-[*]>>C1-C=C(-[*])-C=C-C=1";
 
     try
     {

diff --git a/api/tests/integration/ref/arom/basic.py.out b/api/tests/integration/ref/arom/basic.py.out
diff --git a/api/tests/integration/ref/arom/elements.py.out b/api/tests/integration/ref/arom/elements.py.out
@@ -1,10 +1,10 @@
 005.sdf
 0
 [B-]1[N+]2=CC=CN2[B-]N2C=CC=[N+]21
-[b-]1[n+]2ccc[n]2[b-][n]2ccc[n+]21
+[B-]1:[n+]2ccc[n]2:[B-]:[n]2ccc[n+]2:1
 1
 BrC1=CN2[B-]N3C=C(Br)C=[N+]3[B-][N+]2=C1
-Brc1c[n+]2[b-][n+]3cc(Br)c[n]3[b-][n]2c1
+Brc1c[n+]2:[B-]:[n+]3cc(Br)c[n]3:[B-]:[n]2c1
 2
 F[B-](F)(F)F.[B-]1[N+]2=CC=CC=C2C2=CC=CC=[N+]21
 F[B-](F)(F)F.[B-]1[n+]2ccccc2-c2cccc[n+]21
@@ -13,82 +13,82 @@ F[B-](F)(F)F.[B-]1[n+]2ccccc2-c2cccc[n+]21
 [B-]1[n+]2ccccc2-c2cccc[n+]21
 4
 CC1C=C(C)N2[B-]N3C(C)=CC(C)=[N+]3[B-][N+]2=1
-Cc1cc(C)[n]2[b-][n]3c(C)cc(C)[n+]3[b-][n+]21
+Cc1cc(C)[n]2:[B-]:[n]3c(C)cc(C)[n+]3:[B-]:[n+]21
 5
 B1=NN=CC2SC=CC=21
-[b]1[n][n]cc2[s]ccc21
+[B]1:[n][n]cc2[s]ccc2:1
 6
 COC1=CC=CC=C1OC1C(NS(=O)(=O)NC2C=CC=CC=2)=NC(=NC=1CCOC1N=CC(Br)=CN=1)C1=BC=CC=N1
-COc1ccccc1Oc1c(NS(=O)(=O)Nc2ccccc2)[n]c([n]c1CCOc1[n]cc(Br)c[n]1)-c1[b]ccc[n]1
+COc1ccccc1Oc1c(NS(=O)(=O)Nc2ccccc2)[n]c([n]c1CCOc1[n]cc(Br)c[n]1)-c1:[B]:ccc[n]1
 7
 COC1=CC=CC=C1OC1=C(CCO)N=C(N=C1NS(=O)(=O)NC1C=CC=CC=1)C1=BC=CC=N1
-COc1ccccc1Oc1c(CCO)[n]c([n]c1NS(=O)(=O)Nc1ccccc1)-c1[b]ccc[n]1
+COc1ccccc1Oc1c(CCO)[n]c([n]c1NS(=O)(=O)Nc1ccccc1)-c1:[B]:ccc[n]1
 8
 B1=NN=CC2=CC=CC=C21
-[b]1[n][n]cc2ccccc21
+[B]1:[n][n]cc2ccccc2:1
 9
 CCN(CC)CC.B1C=CC=CC=1
-CCN(CC)CC.[b]1ccccc1
+CCN(CC)CC.[B]1:ccccc:1
 10
 B1C=CC=CC=1
-[b]1ccccc1
+[B]1:ccccc:1
 11
 CP(C)C.B1C=CC=CC=1
-CP(C)C.[b]1ccccc1
+CP(C)C.[B]1:ccccc:1
 12
 B1C=C(C(=C(N=1)C1C=CC=CC=1)C1C=CC=CC=1)C1C=CC=CC=1
-[b]1cc(c(c([n]1)-c1ccccc1)-c1ccccc1)-c1ccccc1
+[B]1:cc(c(c([n]:1)-c1ccccc1)-c1ccccc1)-c1ccccc1
 13
 CCCCCCC1=BC=CC=C1
-CCCCCCc1[b]cccc1
+CCCCCCc1:[B]:cccc1
 14
 B1C=CC=N[NH+]=1
-[b]1ccc[n][nH+]1
+[B]1:ccc[n][nH+]:1
 15
 B1=CC=CN=N1
-[b]1ccc[n][n]1
+[B]1:ccc[n][n]:1
 16
 B1=NC=CO1
-[b]1[n]cco1
+[B]1:[n]cco:1
 17
 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
+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
+Cc1:[B]:c(Cc2:[B]:c(C)c(C)c(C)c2C)c(C)c(C)c1C
 19
 CC1C(CC2=C(C)C(C)=C(C)B=C2C)=C(C)B=C(C)C=1C
-Cc1[b]c(C)c(C)c(C)c1Cc1c(C)c(C)c(C)[b]c1C
+Cc1:[B]:c(C)c(C)c(C)c1Cc1c(C)c(C)c(C):[B]:c1C
 20
 CC1B=C(C)C(C)=C(CC2=C(C)C(C)=BC(C)=C2C)C=1C
-Cc1[b]c(C)c(C)c(Cc2c(C)c(C)[b]c(C)c2C)c1C
+Cc1:[B]:c(C)c(C)c(Cc2c(C)c(C):[B]:c(C)c2C)c1C
 21
 CC1C(CC2=C(C)C(C)=C(C)B=C2C)=C(C)C(C)=BC=1C
-Cc1[b]c(C)c(C)c(C)c1Cc1c(C)c(C)[b]c(C)c1C
+Cc1:[B]:c(C)c(C)c(C)c1Cc1c(C)c(C):[B]:c(C)c1C
 22
 CC1B=C(C)C(C)=C(CC2B=C(C)C(C)=C(C)C=2C)C=1C
-Cc1[b]c(Cc2c(C)c(C)[b]c(C)c2C)c(C)c(C)c1C
+Cc1:[B]:c(Cc2c(C)c(C):[B]:c(C)c2C)c(C)c(C)c1C
 23
 B1=CC=CC2=CC=CC=C21
-[b]1cccc2ccccc21
+[B]1:cccc2ccccc2:1
 24
 CC1C(C)=BC=CC=1C
-Cc1c(C)[b]ccc1C
+Cc1c(C):[B]:ccc1C
 25
 CCCCCC1C(=BC=CC=1CCCCC)CCCCC
-CCCCCc1c([b]ccc1CCCCC)CCCCC
+CCCCCc1c(:[B]:ccc1CCCCC)CCCCC
 26
 CCNC1=C(N)B=BB=C1N(CC)CC
-CCNc1c(N)[b][b][b]c1N(CC)CC
+CCNc1c(N):[B]:[B]:[B]:c1N(CC)CC
 27
 ClC1C(Cl)=BC=CC=1Cl
-Clc1c(Cl)[b]ccc1Cl
+Clc1c(Cl):[B]:ccc1Cl
 28
 CC(C)C1C(=BC=CC=1C(C)C)C(C)C
-CC(C)c1c([b]ccc1C(C)C)C(C)C
+CC(C)c1c(:[B]:ccc1C(C)C)C(C)C
 29
 CC(C)(C)C1C(=BC=CC=1C(C)(C)C)C(C)(C)C
-CC(C)(C)c1c([b]ccc1C(C)(C)C)C(C)(C)C
+CC(C)(C)c1c(:[B]:ccc1C(C)(C)C)C(C)(C)C
 006.sdf
 0
 [O-][N+](=O)C1C=C(C=CC=1Cl)[N+]([O-])=O

diff --git a/api/tests/integration/ref/basic/load.py.out b/api/tests/integration/ref/basic/load.py.out
@@ -45,7 +45,7 @@ scanner: appendLine(): end of stream
 ** 11 **
 molecule auto loader: SMILES loader: invalid character within atom description: '"'
 ** 12 **
-molecule auto loader: SMILES loader: unrecognized lowercase symbol: e
+molecule auto loader: SMILES loader: unrecognized lowercase symbol: b
 ** 13 **
 C1C=CC=CC=1
 ** 14 **

diff --git a/api/tests/integration/ref/basic/load_structure.py.out b/api/tests/integration/ref/basic/load_structure.py.out
@@ -26,7 +26,7 @@ C1C=CC=CC=1*>>C1C=C(*)C=CC=1
 C1C=CC=CC=1* |$;;;;;;A$|
 
 (** #8 **): Smarts, (smarts parameter):
-[O;H]-[c]1-,:[c]-,:[c]-,:[c]-,:[c]-,:[c]-,:1
+[O;H]-c1ccccc1
 
 (** #9 **): Smarts, (query parameter):
 [OH]C1:C:C:C:C:C:1

diff --git a/api/tests/integration/ref/bingo/molecules.py.out b/api/tests/integration/ref/bingo/molecules.py.out
@@ -24777,7 +24777,7 @@ Finished indexing 2026 structures. 304 wrong structures excluded
 	8 CN(C)[N] |^3:3| CN(C)[N] |^3:3|
 	1249 CN(C)[N] |^4:3| CN(C)[N] |^4:3|
 ** searchExact(N1(N=CC2=CC=CC=C2B1O)S(=O)(=O)C1SN=CC=1, '') **
-	9 [n]1(S(c2cc[n][s]2)(=O)=O)[b](O)c2c(cccc2)c[n]1 [n]1(S(c2cc[n][s]2)(=O)=O)[b](O)c2c(cccc2)c[n]1
+	9 [n]1(S(c2cc[n][s]2)(=O)=O):[B](O):c2c(cccc2)c[n]1 [n]1(S(c2cc[n][s]2)(=O)=O):[B](O):c2c(cccc2)c[n]1
 ** searchExact([C@]([H])(C)(I)F |&1:0,r|, '') **
 	10 [C@](F)(I)(C)[H] |&1:0,r| [C@](F)(I)(C)[H] |&1:0,r|
 	243 [C@@H](F)(I)C [C@@H](F)(I)C
@@ -24820,7 +24820,7 @@ Finished indexing 2026 structures. 304 wrong structures excluded
 	22 C[C+](C)O[C-](C)C C[C+](C)O[C-](C)C
 	893 CC(C)=[O+][C-](C)C CC(C)=[O+][C-](C)C
 ** searchExact(B1(OC)OB(OC)OB(OC)O1, '') **
-	23 [b]1(o[b](OC)o[b](OC)o1)OC [b]1(o[b](OC)o[b](OC)o1)OC
+	23 [B]1(:o:[B](OC):o:[B](OC):o:1)OC [B]1(:o:[B](OC):o:[B](OC):o:1)OC
 ** searchExact(N/C(/N)=N/N=C(\C)/C=N/NC(=N)N, '') **
 	24 N/C(=N/N=C(/C=N/NC(N)=N)\C)/N N/C(=N/N=C(/C=N/NC(N)=N)\C)/N
 	347 N=C(/N=N/C(=C/N/N=C(/N)\N)/C)N N=C(/N=N/C(=C/N/N=C(/N)\N)/C)N

diff --git a/api/tests/integration/ref/formats/custom_query.py.out b/api/tests/integration/ref/formats/custom_query.py.out
@@ -1,5 +1,5 @@
 **** #1310 error at opening SMARTS with comma ****
-[#6]1-[#6]=[#6]-[#6]=[#6]-[b;r;3;s&2,X3]=1 OK. Expected string found.
+[#6]1-[#6]=[#6]-[#6]=[#6]-[B;r;3;s&2,X3]=1 OK. Expected string found.
 **** #1331 wrong smarts for ring bond count as drawn ****
 ket_with_rb_as_drawn.ket OK. Smarts equals expected string '[#6](-[#6])(-[#6;x0])-[#6]'
 **** #1337 wrong smarts for ring bond count as drawn ****

diff --git a/api/tests/integration/ref/formats/reaction_to_smarts.py.out b/api/tests/integration/ref/formats/reaction_to_smarts.py.out
@@ -1 +1 @@
-[#6]=[#6]-[#35].[#7](-[#1])-[#6]>[#17]>[#6]=[#6]-[#7]-[#6]
+[#6]=[#6]-Br.[#7](-[H])-[#6]>Cl>[#6]=[#6]-[#7]-[#6]
diff --git a/api/tests/integration/ref/formats/serialize_check.py.out b/api/tests/integration/ref/formats/serialize_check.py.out
@@ -74,9 +74,9 @@ Item
   sssr:41
   stereocenters:7
   superatoms:0
-C1(C)[C@H](C(PC2CC3C45C67C(CC8CCC9C%10C8C86C6%10C%10%11C%12(C%13%14C%15%16C%13C(CC%13%17C%18(C%19C%20%21C%22(CC%20CC%18)C%18%20C%23(C%24%25C8(C86C%14%10C6C%15(C%18%24C86)C%20%21C%16%13%19)C4%25C3%23)C%22)CC%17)CC%12)CC%11C9)CCC2C75)[C@@](O)(C)N)[14N]([15NH][14CH](C)[C@H]([CH])[C@H]([CH2])/C(/[13CH])=C(\[CH2+])/[CH2-])[C@H](O)[C@H](C(CC)C(C)C(/C(/C([PH2+2])[P-2])=C\C)C)C1C/C=C%91/[11CH]%92[10CH3].C*(*)C.[*:2]%92[15CH]%92%93.[*:1]%92.[*:5]%93.C(C(=[C@@]=C(O)C)C=[C@@]=CC)=[C@]=CC.C(S)(C)=[C@]=C(C)O.C(S)(C)=[C@@]=C(CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(N)C(C)C(c1c[n]ccc1)C(C)C(N)CN)O.c12ccccc1cc1c([n+](C)c[n]1C)c2.[o+]1(C)cccc1.c1c[bH]occ1.C1=CC=CC=CC=CC=CC=CC=CCC1.S1C#CCNC1C#CC.[W+5].[W-5].C(S)(C)=C=C(C)O.[Ag].[3HH].[Ar].[Xe].[Mn].[Zn].[Cu].B.[Kr].[Pd].[Rn].[Pt].[Cd].[HH].[LiH].[NaH].[KH].[RbH].[CsH].[Sc].[Y].[La].[Ce].[Tb].[Th].[Bk].[2HH].[Be].[Mg].[Ca].[Sr].[Ba].[Ti].[Zr].[Hf].[Pr].[Dy].[Pa].[Cf].[He].[Ne].[AlH3].[GaH3].[InH3].[TlH].[V].[Nb].[Ta].[Nd].[Ho].[U].[Es].[FrH].C.[SiH4].[GeH4].[SnH2].[PbH2].[Cr].[Mo].[W].[Pm].[Er].[Np].[Fm].[Ra].N.P.[AsH3].[SbH3].[BiH3].[Fe].[Tc].[Re].[Sm].[Tm].[Pu].[Md].[Ac].O.S.[SeH2].[TeH2].[PoH2].[Ni].[Ru].[Os].[Eu].[Yb].[Am].[No].[Rf].F.Cl.Br.I.[AtH].[Co].[Rh].[Ir].[Gd].[Lu].[Cm].[Lr].[Hg].[Au].[*:1]%91 |c:317,321,325,t:315,319,323,a:2,72,&1:62,o1:70,o2:79,81,w:95,r,^3:71,^1:73,^4:75,$;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;SDF;SDF;;_R2;;_R1;_R5;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;_AP1$,ha:2,3,65,66,67,76,77,80,83,95,96,hb:1,97,98,101,112,113,114,126,294,316,SgD:83,73,74,78,84,77:comment:Selection::: :,Sg:n:110,109,111:n:ht,Sg:n:104,103:n:hh,Sg:n:183:n:eu,Sg:gen:174,175:,Sg:n:326,325,324,327:Z:eu,Sg:n:337:Z:eu|
+C1(C)[C@H](C(PC2CC3C45C67C(CC8CCC9C%10C8C86C6%10C%10%11C%12(C%13%14C%15%16C%13C(CC%13%17C%18(C%19C%20%21C%22(CC%20CC%18)C%18%20C%23(C%24%25C8(C86C%14%10C6C%15(C%18%24C86)C%20%21C%16%13%19)C4%25C3%23)C%22)CC%17)CC%12)CC%11C9)CCC2C75)[C@@](O)(C)N)[14N]([15NH][14CH](C)[C@H]([CH])[C@H]([CH2])/C(/[13CH])=C(\[CH2+])/[CH2-])[C@H](O)[C@H](C(CC)C(C)C(/C(/C([PH2+2])[P-2])=C\C)C)C1C/C=C%91/[11CH]%92[10CH3].C*(*)C.[*:2]%92[15CH]%92%93.[*:1]%92.[*:5]%93.C(C(=[C@@]=C(O)C)C=[C@@]=CC)=[C@]=CC.C(S)(C)=[C@]=C(C)O.C(S)(C)=[C@@]=C(CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(N)C(C)C(c1c[n]ccc1)C(C)C(N)CN)O.c12ccccc1cc1c([n+](C)c[n]1C)c2.[o+]1(C)cccc1.c1c:[BH]:occ1.C1=CC=CC=CC=CC=CC=CC=CCC1.S1C#CCNC1C#CC.[W+5].[W-5].C(S)(C)=C=C(C)O.[Ag].[3HH].[Ar].[Xe].[Mn].[Zn].[Cu].B.[Kr].[Pd].[Rn].[Pt].[Cd].[HH].[LiH].[NaH].[KH].[RbH].[CsH].[Sc].[Y].[La].[Ce].[Tb].[Th].[Bk].[2HH].[Be].[Mg].[Ca].[Sr].[Ba].[Ti].[Zr].[Hf].[Pr].[Dy].[Pa].[Cf].[He].[Ne].[AlH3].[GaH3].[InH3].[TlH].[V].[Nb].[Ta].[Nd].[Ho].[U].[Es].[FrH].C.[SiH4].[GeH4].[SnH2].[PbH2].[Cr].[Mo].[W].[Pm].[Er].[Np].[Fm].[Ra].N.P.[AsH3].[SbH3].[BiH3].[Fe].[Tc].[Re].[Sm].[Tm].[Pu].[Md].[Ac].O.S.[SeH2].[TeH2].[PoH2].[Ni].[Ru].[Os].[Eu].[Yb].[Am].[No].[Rf].F.Cl.Br.I.[AtH].[Co].[Rh].[Ir].[Gd].[Lu].[Cm].[Lr].[Hg].[Au].[*:1]%91 |c:317,321,325,t:315,319,323,a:2,72,&1:62,o1:70,o2:79,81,w:95,r,^3:71,^1:73,^4:75,$;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;SDF;SDF;;_R2;;_R1;_R5;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;_AP1$,ha:2,3,65,66,67,76,77,80,83,95,96,hb:1,97,98,101,112,113,114,126,294,316,SgD:83,73,74,78,84,77:comment:Selection::: :,Sg:n:110,109,111:n:ht,Sg:n:104,103:n:hh,Sg:n:183:n:eu,Sg:gen:174,175:,Sg:n:326,325,324,327:Z:eu,Sg:n:337:Z:eu|
 
-C1(C(C/C=C%91/[11CH]%92[10CH3])[C@@H](C(C(C(C)/C(=C\C)/C([P-2])[PH2+2])C)CC)[C@@H](O)[14N]([15NH][14CH]([C@@H]([C@@H](/C(=C(/[CH2-])\[CH2+])/[13CH])[CH2])[CH])C)[C@H]1C([C@](N)(C)O)PC1C2C3C45C67C(C89CC%10%11C%128C8%13C%14%15C%16C%108C(CCC8%16CCC8%14CC8CCC%10%14CC%16CC%17C%18C%19%20C%21%22C%23C%24C%13(C%12%23C96C%217C6%19C43C(CC2)CC(C%186)CC%17)C2%15C8C%102C%22%24C%20%14%16)C%11)C5C1)C.C*(C)*.[*:2]%92[15CH]%92%93.[*:1]%92.[*:5]%93.C(=[C@]=CC)C(C=[C@@]=CC)=[C@]=C(C)O.C(=[C@]=C(O)C)(C)S.C(=[C@@]=C(O)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(C(C(C(C(CN)N)C)c1ccc[n]c1)C)N)(C)S.c12cc3[n+](c[n](C)c3cc1cccc2)C.[o+]1(cccc1)C.c1cco[bH]c1.C1CCC=CC=CC=CC=CC=CC=CC=1.S1C(C#CC)NCC#C1.[W+5].[W-5].C(=C=C(O)C)(C)S.[Ag].[3HH].[Ar].[Xe].[Mn].[Zn].[Cu].B.[Kr].[Pd].[Rn].[Pt].[Cd].[HH].[LiH].[NaH].[KH].[RbH].[CsH].[Sc].[Y].[La].[Ce].[Tb].[Th].[Bk].[2HH].[Be].[Mg].[Ca].[Sr].[Ba].[Ti].[Zr].[Hf].[Pr].[Dy].[Pa].[Cf].[He].[Ne].[AlH3].[GaH3].[InH3].[TlH].[V].[Nb].[Ta].[Nd].[Ho].[U].[Es].[FrH].C.[SiH4].[GeH4].[SnH2].[PbH2].[Cr].[Mo].[W].[Pm].[Er].[Np].[Fm].[Ra].N.P.[AsH3].[SbH3].[BiH3].[Fe].[Tc].[Re].[Sm].[Tm].[Pu].[Md].[Ac].O.S.[SeH2].[TeH2].[PoH2].[Ni].[Ru].[Os].[Eu].[Yb].[Am].[No].[Rf].F.Cl.Br.I.[AtH].[Co].[Rh].[Ir].[Gd].[Lu].[Cm].[Lr].[Hg].[Au].[*:1]%91 |c:316,320,324,t:318,322,326,w:1,o1:7,21,o2:26,a:27,36,&1:38,r,^4:32,^1:33,^3:34,$;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;SDF;;SDF;_R2;;_R1;_R5;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;_AP1$,ha:1,2,19,22,23,24,29,31,36,37,39,hb:6,7,18,20,23,25,35,36,300,325,SgD:83,73,74,78,84,77:comment:Selection::: :,Sg:n:110,109,111:n:ht,Sg:n:104,103:n:hh,Sg:n:183:n:eu,Sg:gen:174,175:,Sg:n:326,325,324,327:Z:eu,Sg:n:337:Z:eu|
+C1(C(C/C=C%91/[11CH]%92[10CH3])[C@@H](C(C(C(C)/C(=C\C)/C([P-2])[PH2+2])C)CC)[C@@H](O)[14N]([15NH][14CH]([C@@H]([C@@H](/C(=C(/[CH2-])\[CH2+])/[13CH])[CH2])[CH])C)[C@H]1C([C@](N)(C)O)PC1C2C3C45C67C(C89CC%10%11C%128C8%13C%14%15C%16C%108C(CCC8%16CCC8%14CC8CCC%10%14CC%16CC%17C%18C%19%20C%21%22C%23C%24C%13(C%12%23C96C%217C6%19C43C(CC2)CC(C%186)CC%17)C2%15C8C%102C%22%24C%20%14%16)C%11)C5C1)C.C*(C)*.[*:2]%92[15CH]%92%93.[*:1]%92.[*:5]%93.C(=[C@]=CC)C(C=[C@@]=CC)=[C@]=C(C)O.C(=[C@]=C(O)C)(C)S.C(=[C@@]=C(O)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(C(C(C(C(CN)N)C)c1ccc[n]c1)C)N)(C)S.c12cc3[n+](c[n](C)c3cc1cccc2)C.[o+]1(cccc1)C.C1CCo:[BH]:c1.C1CCC=CC=CC=CC=CC=CC=CC=1.S1C(C#CC)NCC#C1.[W+5].[W-5].C(=C=C(O)C)(C)S.[Ag].[3HH].[Ar].[Xe].[Mn].[Zn].[Cu].B.[Kr].[Pd].[Rn].[Pt].[Cd].[HH].[LiH].[NaH].[KH].[RbH].[CsH].[Sc].[Y].[La].[Ce].[Tb].[Th].[Bk].[2HH].[Be].[Mg].[Ca].[Sr].[Ba].[Ti].[Zr].[Hf].[Pr].[Dy].[Pa].[Cf].[He].[Ne].[AlH3].[GaH3].[InH3].[TlH].[V].[Nb].[Ta].[Nd].[Ho].[U].[Es].[FrH].C.[SiH4].[GeH4].[SnH2].[PbH2].[Cr].[Mo].[W].[Pm].[Er].[Np].[Fm].[Ra].N.P.[AsH3].[SbH3].[BiH3].[Fe].[Tc].[Re].[Sm].[Tm].[Pu].[Md].[Ac].O.S.[SeH2].[TeH2].[PoH2].[Ni].[Ru].[Os].[Eu].[Yb].[Am].[No].[Rf].F.Cl.Br.I.[AtH].[Co].[Rh].[Ir].[Gd].[Lu].[Cm].[Lr].[Hg].[Au].[*:1]%91 |c:316,320,324,t:318,322,326,w:1,o1:7,21,o2:26,a:27,36,&1:38,r,^4:32,^1:33,^3:34,$;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;SDF;;SDF;_R2;;_R1;_R5;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;_AP1$,ha:1,2,19,22,23,24,29,31,36,37,39,hb:6,7,18,20,23,25,35,36,300,325,SgD:83,73,74,78,84,77:comment:Selection::: :,Sg:n:110,109,111:n:ht,Sg:n:104,103:n:hh,Sg:n:183:n:eu,Sg:gen:174,175:,Sg:n:326,325,324,327:Z:eu,Sg:n:337:Z:eu|
 
 * checkEqualProperties *
 allenecenters: 5 5 
@@ -104,7 +104,7 @@ components: 119 119
 data Sgroups: 1 1 
 generic Sgroups: 1 1 
 heavy atoms: 419 419 
-hydrogens: 500 500 
+hydrogens: 503 503 
 multiple groups: 0 0 
 pseudoatoms: 2 2 
 repeating units: 5 5 

diff --git a/api/tests/integration/ref/formats/smarts.py.out b/api/tests/integration/ref/formats/smarts.py.out
@@ -5,11 +5,11 @@ CC[C+5]CCCCC
 [#6]-[#6]-[#6;+5]-[#6]-[#6]-[#6]-[#6]-[#6]
 CC[C+5]CCCCC
 **** Load and Save as Query with not list ****
-[#6]-[#6]-[!#5!#6!#7]-[#6]-[#6]-[#6]-[#6]-[#6]-[#6]
+[#6]-[#6]-[!B!#6!#7]-[#6]-[#6]-[#6]-[#6]-[#6]-[#6]
 **** Load and Save as Query with component-level grouping ****
 ([#8].[#6]) is ok. smarts_in==smarts_out
 ([#8].[#6]).([#8].[#6]) is ok. smarts_in==smarts_out
-[!C;!b] is ok. smarts_in==smarts_out
+[!C;!B] is ok. smarts_in==smarts_out
 [*] is ok. smarts_in==smarts_out
 [*;R1] is ok. smarts_in==smarts_out
 [*;R3] is ok. smarts_in==smarts_out
@@ -22,22 +22,22 @@ CC[C+5]CCCCC
 [v3] is ok. smarts_in==smarts_out
 [+0] is ok. smarts_in==smarts_out
 [#6]@[#6] is ok. smarts_in==smarts_out
-[#9]/[#6] is ok. smarts_in==smarts_out
-[#9]/[#6]=[C]/[#17] is ok. smarts_in==smarts_out
+F/[#6] is ok. smarts_in==smarts_out
+F/[#6]=C/Cl is ok. smarts_in==smarts_out
 [O;H] is ok. smarts_in==smarts_out
 [!O;H] is ok. smarts_in==smarts_out
 ([#6]1-[#6]-[#6]-1.[#6]) is ok. smarts_in==smarts_out
-[#9]/[#6]=[#6]/[#6]=[#6]/[#6] is ok. smarts_in==smarts_out
-[#9]\[#6]=[#6]\[#6]=[#6]\[#6] is ok. smarts_in==smarts_out
-[#9]/[#6]=[#6]/[#6]=[#6]/[#6] is ok. smarts_in==smarts_out
-[#9]/[#6]=[#6]/[#6]=[#6]/[#6] is ok. json_in==json_out
-[#9]/[#6]=[#6]/[#6]=[#6]/[#6] is ok. expected string found in json
-[#9]\[#6]=[#6]/[#6]=[#6]\[#6] is ok. smarts_in==smarts_out
-[#9]\[#6]=[#6]/[#6]=[#6]\[#6] is ok. json_in==json_out
-[#9]\[#6]=[#6]/[#6]=[#6]\[#6] is ok. expected string found in json
-[#9]\?[#6]=[#6]/?[#6]=[#6]\?[#6] is ok. smarts_in==smarts_out
-[#9]\?[#6]=[#6]/?[#6]=[#6]\?[#6] is ok. json_in==json_out
-[#9]\?[#6]=[#6]/?[#6]=[#6]\?[#6] is ok. expected string found in json
+F/[#6]=[#6]/[#6]=[#6]/[#6] is ok. smarts_in==smarts_out
+F\[#6]=[#6]\[#6]=[#6]\[#6] is ok. smarts_in==smarts_out
+F/[#6]=[#6]/[#6]=[#6]/[#6] is ok. smarts_in==smarts_out
+F/[#6]=[#6]/[#6]=[#6]/[#6] is ok. json_in==json_out
+F/[#6]=[#6]/[#6]=[#6]/[#6] is ok. expected string found in json
+F\[#6]=[#6]/[#6]=[#6]\[#6] is ok. smarts_in==smarts_out
+F\[#6]=[#6]/[#6]=[#6]\[#6] is ok. json_in==json_out
+F\[#6]=[#6]/[#6]=[#6]\[#6] is ok. expected string found in json
+F\?[#6]=[#6]/?[#6]=[#6]\?[#6] is ok. smarts_in==smarts_out
+F\?[#6]=[#6]/?[#6]=[#6]\?[#6] is ok. json_in==json_out
+F\?[#6]=[#6]/?[#6]=[#6]\?[#6] is ok. expected string found in json
 [C;@OH2] is ok. smarts_in==smarts_out
 [C;@OH2] is ok. json_in==json_out
 [C;@OH2] is ok. expected string found in json
@@ -63,17 +63,21 @@ smarts loaded OK
 [!#6!#7!#8] is ok. expected string found in json
 #1355 Error appeared at save query molecule with RSite as smarts
 Ok expected smarts generated
-[!#40!#79!#30]-[#6]-[#6] is ok. smarts_in==smarts_out
+[!Zr!Au!Zn]-[#6]-[#6] is ok. smarts_in==smarts_out
+[!Zr!Au!Zn]-[#6]-[#6] is ok. json_in==json_out
+[!Zr!Au!Zn]-[#6]-[#6] is ok. expected string found in json
 [!#40!#79!#30]-[#6]-[#6] is ok. json_in==json_out
 [!#40!#79!#30]-[#6]-[#6] is ok. expected string found in json
-[#40,#79,#30]-[#6]-[#6] is ok. smarts_in==smarts_out
-[#40,#79,#30]-[#6]-[#6] is ok. json_in==json_out
-[#40,#79,#30]-[#6]-[#6] is ok. expected string found in json
-[#6,#7;a]:[o] is ok. smarts_in==smarts_out
-[#6,#7;a]:[o] is ok. json_in==json_out
-[#6,#7;a]:[o] is ok. expected string found in json
-[c,n,o]:[o] is ok. json_in==json_out
-[c,n,o]:[o] is ok. expected string found in json
+[Zr,Au,Zn]-[#6]-[#6] is ok. smarts_in==smarts_out
+[Zr,Au,Zn]-[#6]-[#6] is ok. json_in==json_out
+[Zr,Au,Zn]-[#6]-[#6] is ok. expected string found in json
+[#40#79#30]-[#6]-[#6] is ok. json_in==json_out
+[#40#79#30]-[#6]-[#6] is ok. expected string found in json
+[#6,#7;a]:o is ok. smarts_in==smarts_out
+[#6,#7;a]:o is ok. json_in==json_out
+[#6,#7;a]:o is ok. expected string found in json
+[c,n,o]:o is ok. json_in==json_out
+[c,n,o]:o is ok. expected string found in json
 [c,C,c] is ok. smarts_in==smarts_out
 [c,C,c] is ok. json_in==json_out
 [c,C,c] is ok. expected string found in json

diff --git a/api/tests/integration/ref/inchi/compare.py.out b/api/tests/integration/ref/inchi/compare.py.out
@@ -40565,10 +40565,10 @@ Warning: CSmiles are different:
   InChI key: HCFSGRMEEXUOSS-SAEZQQPQSA-N
 4365:
   Smiles1: ClN1B(C2C=CC=CC=2)N(Cl)B(C2C=CC=CC=2)N(Cl)B1C1C=CC=CC=1
-  CSmiles1: Cl[n]1[b](-c2ccccc2)[n](Cl)[b](-c2ccccc2)[n](Cl)[b]1-c1ccccc1
+  CSmiles1: Cl[n]1:[B](-c2ccccc2):[n](Cl):[B](-c2ccccc2):[n](Cl):[B]:1-c1ccccc1
   InChI1: InChI=1S/C18H15B3Cl3N3/c22-25-19(16-10-4-1-5-11-16)26(23)21(18-14-8-3-9-15-18)27(24)20(25)17-12-6-2-7-13-17/h1-15H
   Smiles2: C1C=CC(B2N(Cl)B(N(Cl)B(N2Cl)C2C=CC=CC=2)C2C=CC=CC=2)=CC=1
-  CSmiles2: Cl[n]1[b](-c2ccccc2)[n](Cl)[b](-c2ccccc2)[n](Cl)[b]1-c1ccccc1
+  CSmiles2: Cl[n]1:[B](-c2ccccc2):[n](Cl):[B](-c2ccccc2):[n](Cl):[B]:1-c1ccccc1
   InChI2: InChI=1S/C18H15B3Cl3N3/c22-25-19(16-10-4-1-5-11-16)26(23)21(18-14-8-3-9-15-18)27(24)20(25)17-12-6-2-7-13-17/h1-15H
   InChI key: NVBQPAAXHSMATH-UHFFFAOYSA-N
 4366:

diff --git a/api/tests/integration/tests/arom/basic.py b/api/tests/integration/tests/arom/basic.py
@@ -48,8 +48,8 @@ def processMolecule(m):
 mols = [
     "[si]1(c(OC)c(c(C)cc1)c2ccccc2)OC",  # Cactvs: [si]
     "c1ccc2[as]c3ccccc3[siH]c2c1",
-    "c1ccc2[te]c3ccccc3[bH]c2c1",  # RDKit: [te]
-    "C[b]1o[b](C)o[b](C)o1",
+    "c1ccc2[te]c3ccccc3[BH]c2c1",  # RDKit: [te]
+    "C[B]1o[B](C)o[B](C)o1",
 ]
 for smiles in mols:
     print("***\n%s: " % (smiles))
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		[#6]=[#6]-[#35].[#7](-[#1])-[#6]>[#17]>[#6]=[#6]-[#7]-[#6]
		[#6]=[#6]-Br.[#7](-[H])-[#6]>Cl>[#6]=[#6]-[#7]-[#6]