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update code for drawing figures
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@Kartinaa
Kartinaa committed Dec 27, 2024
1 parent f85e234 commit cbcb83c
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Showing 24 changed files with 197,876 additions and 22,471 deletions.
8,395 changes: 6,760 additions & 1,635 deletions 3D_generative_SBDD/Ring_systems.ipynb
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9,802 changes: 7,693 additions & 2,109 deletions ChEMBL_clinical_smmolecules/Ring_systems.ipynb
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7,791 changes: 6,451 additions & 1,340 deletions Crossdock_datasets/Ring_systems.ipynb
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20 changes: 10 additions & 10 deletions Crossdock_datasets/crossdock_ligand_smi.smi
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Original file line number Diff line number Diff line change
Expand Up @@ -5128,7 +5128,7 @@ CN(C)c1nc2ccc1CCCCn1cc(c3ccccc31)C1=C(C(=O)NC1=O)c1cn(c3ccccc13)CCC2
CCN(CC)S(=O)(=O)c1ccc2c(c1)C(C1=C(NO)C3=CCC=CC3=N1)C(=O)N2
Clc1cc(C2=C3CC=CN=C3N=C2)cc(NC2CCCCC2)n1
COc1nc(-c2ccnc(NC(=O)C3CC3)c2)ncc1C(N)=O
NC1=CN2c3c(c4c(c5c6c(n(c35)[Ru@OH10]23(Cl)(CO)NCC2C=CC=CN23)=CC=CC6)C(=O)NC4=O)=C1
NC1=CN2c3c(c4c(c5c6c(n(c35)[Ru@OH12]23(Cl)(CO)NCC2C=CC=CN23)=CC=CC6)C(=O)NC4=O)=C1
COc1ccc(C2=NNC(=O)/C2=N/Nc2ccc(Cl)cc2)cc1OC
CN(C)CCNS(=O)(=O)c1ccc(-c2cnc(N)c(C(=O)Nc3cccnc3)n2)cc1
O=C(Nc1cc(-c2ccc3ccncc3c2)ccn1)C1CC1
Expand Down Expand Up @@ -6531,7 +6531,7 @@ NC1CCN(c2nc(Nc3cc(C4CC4)[nH]n3)c3sccc3n2)CC1
COCCNc1nc2ccc(C#CC3(O)CCCCC3)cc2n1-c1ccnc(N)n1
NC1CCN(c2nc(NC3=NN=C(C4CC4)C3)c3sccc3n2)CC1
O=C(C1=C2CC(c3cnn(C4CCNCC4)c3)=CN=C2N=C1)c1cc(CO)ccc1Cl
O=C1NC(=O)c2c1c1c3c4c2=C2C=C(O)C=CC2N4[Ru@OH22]2(Cl)(CO)(N4CC=CC=C4CN2c2ccccc2)N3C=C(F)C=1
O=C1NC(=O)c2c1c1c3c4c2=C2C=C(O)C=CC2N4[Ru@OH26]2(Cl)(CO)(N4CC=CC=C4CN2c2ccccc2)N3C=C(F)C=1
O=C1NC(=O)c2cc3c(cc21)C1C=CC=CN1[Ru]312(NCS)[S@H]3CC[S@H]1CC[S@@H]2CC3
O=C1NC(=O)c2c1c1c3c4c2=C2C=C(O)C=CC2N4[Ru@OH20](CO)(C2CC=CC2)N3C=CC=1
O=C(C[C@@H](Cc1ccc2ccccc2c1)n1cc(CNC(=O)c2ccc(F)cc2)nn1)NO
Expand Down Expand Up @@ -8155,7 +8155,7 @@ c1ccc(-c2ncc[nH]2)cc1
Clc1cc(Cl)cc(Cl)c1
CC(C)(C(=O)c1cccnc1)c1cccnc1
c1ccccc1
CC1=CCN2C(=C1)C1C=C(Cc3c(F)c(F)c(-c4c(F)c(F)c(N[C@H]5[C@@H]6C[C@H]7C[C@@H](C6)C[C@@H]5C7)c(F)c4F)c(F)c3F)C=CN1[Ru@OH8]213(N2CC=CC=C2C2C=CC=CN21)N1CC=CC=C1C1C=CC=CN13
CC1=CCN2C(=C1)C1C=C(Cc3c(F)c(F)c(-c4c(F)c(F)c(N[C@H]5[C@@H]6C[C@H]7C[C@@H](C6)C[C@@H]5C7)c(F)c4F)c(F)c3F)C=CN1[Ru@OH7]213(N2CC=CC=C2C2C=CC=CN21)N1CC=CC=C1C1C=CC=CN13
CN(C)c1cccc2c(S(=O)(=O)NCCCCCCCCNC(=O)[C@@]34C[C@@H]5C[C@@H](C[C@@](O)(C5)C3)C4)cccc12
CN(C)c1cccc2c(S(=O)(=O)NCCCCCCCCNC(=O)C[C@]34C[C@H]5C[C@H](C[C@H](C5)C3)C4)cccc12
NC(=O)CCCC(=O)NCCCCCCCCNC(=O)[C@]12C[C@H]3C[C@H](C[C@H](C3)C1)C2
Expand Down Expand Up @@ -8970,7 +8970,7 @@ C[C@](O)(CN(C1CC1)S(=O)(=O)c1ccc(O)cc1)c1ccccc1
O=C(c1ccc(OCCN2CCCCC2)cc1)c1c(-c2ccc(O)cc2)sc2cc(O)ccc12
CCCCC(=O)N[C@H]1C(=N)O[C@H](C=O)[C@@H](O)[C@@H]1O
CC(=O)N[C@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@H](C=O)[C@@H](O)[C@@H]1O
CCC1=Cc2c(C)c(CC)c3n2[Fe@SP3]24N1C=Cc1c(CCC(=O)O)c(C)c(n12)Cc1c(CC)c(C)c(n14)O3
CCC1=Cc2c(C)c(CC)c3n2[Fe@SP1]24N1C=Cc1c(CCC(=O)O)c(C)c(n12)Cc1c(CC)c(C)c(n14)O3
OC[C@H]1O[C@H](O[C@@H]2CNc3ccc(Br)c(Cl)c32)[C@@H](O)[C@@H](O)[C@@H]1O
O[C@H](C[C@H]1c2c(F)cccc2-c2cncn21)C1CCCCC1
O[C@H](C[C@H]1c2ccccc2-c2cncn21)C1CCCCC1
Expand Down Expand Up @@ -9291,14 +9291,14 @@ COC(=O)[C@H](C)NC(=O)[C@@H](CCCCN(O)C(C)=O)NC(=O)c1cccc(O)c1O
O=C(NCCN(CCNC(=O)c1cccc(=O)n1O)CCNC(=O)c1cccc(=O)n1O)c1cccc(O)c1O
O=C(NCCCN(CCCCN(CCCNC(=O)C1C=CCC(=O)N1O)C(=O)c1cccc(=O)n1O)C(=O)c1cccc(=O)n1O)c1cccc(=O)n1O
O=C1C=CCC(C(=O)N[C@@H](COC(=O)[C@H](CO)NC(=O)c2cccc(O)c2O)C(=O)OC[C@@H](NC(=O)c2cccc(O)c2O)C(=O)O)=C1O
C[C@H]1CC(=O)N[C@H]2CCCCN3O[Fe@OH15]456(Oc7ccccc7C7OC[C@@H](C(=O)N[C@@H](CCCCN(O4)C(/C=C\CCCC=C=CC(=O)O)O5)C(=O)O1)N76)OC23
O=C(O)C=C=CCCC/C=C\C1O[Fe@OH7]2345Oc6ccccc6C6OC[C@@H](C(=O)N[C@@H](CCCCN1O2)C(=O)OCCC(=O)N[C@H]1CCCCN(O3)C1O4)N65
C[C@H]1CC(=O)N[C@H]2CCCCN3O[Fe@OH29]456(O/C(=C\CCCCC=C=CC(=O)O)N(CCCC[C@H](NC(=O)[C@@H]7COC(c8ccccc8O4)N75)C(=O)O1)O6)OC23
C[C@H]1CC(=O)N[C@H]2CCCCN3O[Fe@OH27]456(Oc7ccccc7C7OC[C@@H](C(=O)N[C@@H](CCCCN(O4)C(/C=C\CCCC=C=CC(=O)O)O5)C(=O)O1)N76)OC23
O=C(O)C=C=CCCC/C=C\C1O[Fe@OH11]2345Oc6ccccc6C6OC[C@@H](C(=O)N[C@@H](CCCCN1O2)C(=O)OCCC(=O)N[C@H]1CCCCN(O3)C1O4)N65
C[C@H]1CC(=O)N[C@H]2CCCCN3O[Fe@OH7]456(O/C(=C\CCCCC=C=CC(=O)O)N(CCCC[C@H](NC(=O)[C@@H]7COC(c8ccccc8O4)N75)C(=O)O1)O6)OC23
O=C(NCCN(CCNC(=O)c1cccc(O)c1O)CCNC(=O)c1cccc(=O)n1O)c1cccc(O)c1O
CN1[C@@H]([C@H]2CS[C@H](c3ccccc3O)N2)SC[C@H]1C(=O)O
N[C@@H](CO)C(=O)OC[C@H](NC(=O)c1cccc(O)c1O)C(=O)O
O=C(NCCCN(CCCCN(CCCNC(=O)[C@@H]1C=CCC(=O)N1O)C(=O)c1cccc(=O)n1O)C(=O)c1cccc(=O)n1O)c1cccc(=O)n1O
O=C(O)C=C=CCCCC/C=C1\O[Fe@OH7]2345Oc6ccccc6C6OC[C@@H](C(=O)N[C@@H](CCCCN1O2)C(=O)OCCC(=O)N[C@H]1CCCCN(O3)C1O4)N65
O=C(O)C=C=CCCCC/C=C1\O[Fe@OH11]2345Oc6ccccc6C6OC[C@@H](C(=O)N[C@@H](CCCCN1O2)C(=O)OCCC(=O)N[C@H]1CCCCN(O3)C1O4)N65
CC(C)Cn1c(=O)n(C)c(=O)c2c(-c3cncn3C)n(Cc3cccc4ccccc34)nc21
CC(C)Cn1c(=O)n(C)c(=O)c2c(-c3ccncc3)n(Cc3cccc4ccccc34)nc21
c1ccn(-c2oc(C3CC3)nc2-c2nn[nH]n2)c1
Expand Down Expand Up @@ -10986,8 +10986,8 @@ C[C@@H](N[C@@H](CCCN=C(N)N)C(=O)O)C(=O)O
C[C@@H](N[C@@H](CC1=NC=NC1)C(=O)O)C(=O)O
CC1(C)CN2C(CS/C(=N/C3CCCCC3)NC3CCCCC3)=CSC2=N1
O=C(O)c1ccc2c(c1)N1Cc3ccccc3O[Fe@@]13Oc1ccccc1CN23
c1ccc2c(c1)CN1c3ccccc3N3Cc4ccccc4O[Fe@TB3]13O2
O=C(O)CCc1ccc2c(c1)N1Cc3ccccc3O[Fe@TB19]13Oc1ccccc1CN23
c1ccc2c(c1)CN1c3ccccc3N3Cc4ccccc4O[Fe@TB6]13O2
O=C(O)CCc1ccc2c(c1)N1Cc3ccccc3O[Fe@TB14]13Oc1ccccc1CN23
O=C(O)CCc1ccc2c(c1)O[Cr@SP2]1OC3C=CC=CC3=CN21
Cn1c2c(c3ccc(Cl)c(Cl)c31)CC=NC2=O
O=C(NO)[C@@H]1[C@H](c2ccccc2)[C@H]1c1ccc(-c2cnco2)cc1
Expand Down
7,536 changes: 6,375 additions & 1,161 deletions Decomopt/Ring_systems.ipynb
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