Data collector

config/langfuse_config.json

@@ -0,0 +1,28 @@
+{
+  "sessions": {
+    "default": {
+      "generation_name": "retrosynthesis",
+      "project": "DeepRetro",
+      "version": "0.0.1",
+      "trace_name": "retrosynthesis_pipeline",
+      "trace_user_id": "system",
+      "session_id": "default"
+    },
+    "metadata": {
+      "generation_name": "metadata_prediction",
+      "project": "DeepRetro",
+      "version": "0.0.1",
+      "trace_name": "metadata_pipeline",
+      "trace_user_id": "system",
+      "session_id": "metadata_agent"
+    },
+    "retrosynthesis": {
+      "generation_name": "retrosynthesis",
+      "project": "DeepRetro",
+      "version": "0.0.1",
+      "trace_name": "retrosynthesis_pipeline",
+      "trace_user_id": "system",
+      "session_id": "retrosynthesis_pipeline"
+    }
+  }
+} 

data/targets.smi

@@ -0,0 +1,190 @@
+Cn1nccc1[C@]1(O)CCCC[C@H]1O
+CC1=NC2(N=C1N)c1cc(-c3cc(Cl)cc(C#N)c3)ccc1CCC21CC1
+CCC/C=C/[C@H]1CC[C@H](C(CO)CO)CC1
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCC(C)(C)O)c1
+C=CCC1C=C(C)CC(C)CC(OC)C2OC(O)(C(=O)C(=O)N3CCCCC3C(=O)OC(C(C)=CC3CCC(O)C(OC)C3)C(C)C=CC1O)C(C)CC2OC
+CC(=O)NC[C@H]1CC[C@@H](C(=O)Nc2cccc(OC(F)(F)F)c2)N1
+COC(=O)c1ccc2c(c1)C=CC(=C(Cl)Cl)CO2
+Cc1ccc(C(C)(C)C)cc1S[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O
+COC(=O)[C@@H]1CCCC2(CCCCC2)[C@H]1O
+CC(C)S(=O)(=O)N[C@H]1CCOC[C@H]1c1ccc(I)cc1
+CN1CC[C@@H](c2c(O)cc(O)c3c(=O)cc(-c4ccc(C(F)(F)F)cc4)oc23)[C@@H]1CO
+CC#CCn1c(Br)nc(C=O)c1C(=O)OC
+Cc1ccn2cc(CO)n(-c3ccccc3)c(=O)c12
+CC(C)(CO)n1c(CO)nc2cnc(Br)cc21
+C[C@H](c1ccccc1)N1C[C@]2(C(=O)OC(C)(C)C)C=CC[C@@H]2C1=S
+CCOC(=O)c1nc(N2CC[C@H](NC(=O)c3nc(C(F)(F)F)c(CC)[nH]3)[C@H](OC)C2)sc1C
+COC[C@H](C)COCc1ccc([C@@]2(O)CCNC[C@@H]2c2noc(-c3ccccc3CCNC(C)=O)c2Br)cc1
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCCCC#N)c1
+C[C@@H](O)c1nc2cnc3ccsc3c2n1[C@H]1CC[C@H](CO)CC1
+C#CC1(O)C(C)=CC2(CC1(C)C(F)(F)F)OC(C)C(C)O2
+CC(C)(C)OC(=O)N[C@@H]1c2cccnc2C(=O)CC[C@H]1c1cccc(F)c1F
+CS(=O)(=O)CCN1CCC(c2ccc3c(c2)-n2nc(-c4ncnn4CC(F)(F)F)cc2CCO3)CC1
+C[C@@H]1CCCN1CCc1nnc2cc(Br)ccc2c1O
+O=C(Cc1cccs1)NC1C(=O)N2C(C(=O)O)C(CBr)=CS[C@H]12
+CN1CCN(c2ccc3c(c2)[nH]c2c(C(N)=O)cc(-c4cnn(C)c4)nc23)CC1
+CC1(C)OCC(C)(C=O)N(Cc2ccccc2)C1=O
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OS(=O)(=O)C(F)(F)F)c1
+OC1CCCc2sc(-c3ccncc3)cc2C1c1ccc(Cl)cc1
+N[C@H]1CC[C@H]1c1ccc(Cl)cc1
+CN(C)CC(OCC1(c2ccc(F)cc2)CCN(C(=O)OC(C)(C)C)CC1)c1cc(Cl)cc2cn(COCC[Si](C)(C)C)nc12
+C=C(C[C@@H](Cc1ccc(-c2ccccc2)cc1)NC(=O)OC(C)(C)C)C(=O)O
+Nc1ccc(OC2(S(=O)(=O)c3ccccc3)CC2)nc1Cl
+C[C@]1(F)CC(F)(F)[C@@](C)(c2cc(N)ccc2F)N=C1N
+N[C@H]1CCOC[C@H]1c1ccc(I)cc1
+COc1ccc2c(Nc3c(Cl)cncc3Cl)cc(=O)[nH]c2c1OCCCCCCN1CCCNCC1
+COc1cc2ncc3c(N)nc(-c4cncc(OCCNCc5ccc(F)cc5)c4)cc3c2cc1OC
+CC(C)c1ccc2c(c1)OC1(O)c3ccccc3C(=O)C21NC(=O)c1cc(-c2ccccc2)n[nH]1
+N#Cc1cc(F)cc([C@H]2C[C@H](F)CN2c2ccn3ncc(C(N)=O)c3c2)c1
+NC(=O)c1cc(-c2ccc3c(cnn3CCN3CCOCC3)c2)nc2c1[nH]c1cc(N3CCOCC3)ccc12
+Cn1oc(=O)nc1/C(=N\OCc1cccc(N)n1)c1ccccc1
+CN1CCN(c2ccc3c(c2)[nH]c2c(C(N)=O)cc(-c4ccc(O)c(Cl)c4)nc23)CC1
+COC(=O)CCc1cc2cc(-c3noc(-c4ccc(OC(C)C)c(Cl)c4)n3)ccc2n1C
+CCOP(=O)(Cc1ccc(Nc2ncc(C(F)(F)F)c(Nc3ccc([C@H]4CC[C@H](N5CCN(C)CC5)CC4)c4c3C(=O)N(C)C4)n2)c(OC)c1)OCC
+COc1ccc(C[C@H](C[C@H](O[Si](C)(C)C(C)(C)C)[C@H](CC2CCCCC2)NC(=O)OC(C)(C)C)C(=O)O)c(OC)c1OC
+CC1(C)COCc2nc3cnc(Br)cc3n21
+CC(C)S(=O)(=O)N[C@H]1CCOC[C@H]1c1ccc(-c2ccc(C#N)s2)cc1
+C[C@H](c1ccccc1)N1C[C@]2(C(=O)OC(C)(C)C)C=CC[C@@H]2C1=O
+CCc1nc(C)c(C(=O)Nc2ccc(-c3ccc(C45CCC(CC(=O)OC)(CC4)OC5)cc3)cc2)o1
+COc1cc2c(Oc3cc(C)c(C)nc3-c3cccc(C)n3)ccnc2cc1OCCNCCO
+O=C(CO)N1CCC(c2ccc3c(c2)-n2nc(-c4ncnn4CC(F)(F)F)cc2CCO3)CC1
+CC(C)(C)OC(=O)NC1(C2CCc3cc(Sc4cccc(OCc5ccccc5)c4)ccc3C2)COC(C)(C)OC1
+CCC[C@@H](CCO)Nc1nc(N)nc(C)c1Cc1ccc(CN2CCC[C@@H]2C(=O)O)cc1OC
+COc1cc(-c2cccc(C(F)(F)F)c2)c(F)cc1-c1nncc2cc(S(=O)(=O)Nc3ccon3)ccc12
+CCC/C=C/[C@H]1CC[C@H](C(C(=O)O)C(=O)O)CC1
+CCOC(=O)[C@@H]1C[C@H]1COc1cc(CCCOC)cc(CN(C(=O)[C@H]2CNCC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)c1
+CCCCOC(=O)N1CCN(C(=O)[C@H](CCCO[Si](c2ccccc2)(c2ccccc2)C(C)(C)C)NC(=O)OC(C)(C)C)CC1
+CC1(C)OCC(C)(CO)N(Cc2ccccc2)C1=O
+CCc1[nH]c(C(=O)N[C@H]2CCN(c3cccc(C(=O)O)c3)C[C@H]2OC)nc1C(F)(F)F
+CC(C)(C)OC(=O)N[C@@H]1c2cccnc2[C@H](N2C(=O)c3ccccc3C2=O)CC[C@H]1c1cccc(F)c1F
+CC(C)c1ccc(OC2CCC3(CC2)N[C@@H](C(=O)O)C(C)(C)S3)cc1
+CCOC(=O)CCc1cc2cc(-c3noc(-c4ccc(OC(C)C)c(Cl)c4)n3)ccc2[nH]1
+CN(C1CC1)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
+CC(=O)c1ccc2c(c1)C=CC(O)(CO)CO2
+C[C@H]1OC[C@@H]2CC[C@@H](c3nc(-c4ccc(C(=O)Nc5cc(C(F)(F)F)ccn5)cc4)c4c(N)nccn34)CN2C1=O
+C[C@@H](n1ncn(-c2ccc(Cl)cc2)c1=O)[C@@]1(c2ccc(F)cc2F)CO1
+CC(=O)NC[C@H]1CN(c2ccc3c(c2)CCCc2c(C(C)C)n[nH]c2-3)C(=O)O1
+COc1ccccc1C[C@H](C[C@H](O[Si](C)(C)C(C)(C)C)[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C)C(=O)O
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCCOC)c1
+CC(C)N1CCC(Oc2ccc3c(c2)cc2n3[C@H](C)CN(CCO)C2=O)CC1
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCC2(CC#N)CC2)c1
+CC(C)(C)OC(=O)N[C@@H]1c2cccnc2[C@H](N)CC[C@H]1c1cccc(F)c1F
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCC2(CC(=O)OC)CC2)c1
+CCCCCN1C(=O)C2(CNC(=O)c3cc4c(cc32)OCO4)c2ccccc21
+O=[N+]([O-])c1ccc(OC2(S(=O)(=O)c3ccccc3)CC2)nc1Cl
+C[Si](C)(C)CCOCn1cc(C2CCc3c(C(=O)O)nn(COCC[Si](C)(C)C)c3C2)cn1
+CC1=NC2(N=C1N)c1cc(-c3cc(F)cc(C#N)c3)ccc1CCC21CC1
+O=C(O)[C@H]1CCOC[C@H]1c1ccc(I)cc1
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OC[C@@H]2C[C@H]2C(=O)OCC(=O)N(C)C)c1
+C[C@H](C(=O)NCCF)N(C)C(=O)c1ccc2c(c1)c1c(n2C)CCC(C2CCOCC2)C1
+C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1CC(O)CC(C)(C)N1
+CCc1[nH]c(C(=O)N[C@H]2CCN(c3cccc(C(=O)OC(C)(C)C)c3)C[C@H]2OC)nc1C(F)(F)F
+CC[C@@H](OC(=O)c1ccccc1)[C@H]1CCCN(C(=O)OC(C)(C)C)C1
+CC(=O)OCc1nc2cnc(Br)cc2n1C(C)(C)COC(C)=O
+CC(=O)NC[C@H]1CC[C@@H](C(=O)Nc2cccc(OC(F)(F)F)c2)N1C(=O)OCc1ccccc1
+O=C1C=C(N2CCNCC2)C(C2CCCCC2)CC1
+FC(F)(F)Cn1ncnc1-c1cc2n(n1)-c1cc(C3CCNCC3)ccc1OCC2
+COC(=O)[C@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1c1ccc(OCCOc2c(Cl)cc(C)cc2Cl)cc1
+CCOC(=O)/C(N)=N/Nc1cc(Cl)ccc1[N+](=O)[O-]
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OC[C@@H]2C[C@H]2C(=O)Oc2ccc3c(c2)CCC3)c1
+ClCc1ccc2c(c1)Nc1nccnc1S2
+COC[C@H](C)COCc1ccc([C@@]2(O)CCN(C(=O)OC(C)(C)C)C[C@@H]2C=O)cc1
+CCOC(=O)c1cc2c(F)cccc2nc1[C@H](C)NC(=O)OC(C)(C)C
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCC2(CC(=O)O)CC2)c1
+CC(=O)N1c2ccc(N3CCNCC3)nc2[C@H](Nc2ccccc2)[C@@H](C)[C@@H]1C1CC1
+COCCCc1cc(CN(C(=O)[C@H]2CNCC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCCOC)c1
+O=S(=O)(C#Cc1ccc(Cl)cc1)N1CCNCC1
+COc1ccc2c(Nc3c(Cl)cncc3Cl)cc(=O)[nH]c2c1OCCCCCCN1CCCN(C)CC1
+Oc1ccc2c(c1)[C@H](c1ccc(OCCN3CCCC3)cc1)[C@H](c1ccccc1)CO2
+CCOC(=O)/C=C1\CC[C@@H](c2cccc(F)c2F)[C@H](NC(=O)OC(C)(C)C)c2cccnc21
+OC[C@H]1C[C@@H](c2cnn3c(N[C@H]4CCc5ccccc54)ncnc23)C[C@@H]1O
+CC(=O)OCC1=CS[C@@H]2C(NC(=O)Cc3cccs3)C(=O)N2C1C(=O)O
+O=C(OCc1ccccc1)N1CC[C@H]2CCCNC[C@H]21
+C/N=C(\C)C1=C(O)C=C2Oc3c(C(=O)NCc4c(C)ccc5ccccc45)c(OC)cc(O)c3[C@]2(C)C1=O
+C[C@@]1(O)[C@H](O)[C@@H](CO)O[C@H]1n1cc(-c2ccccc2)c2c(N)ncnc21
+CC(=O)Nc1nc2c(s1)-c1c(c(C3CC3)nn1C1CCNCC1)CC2
+CC(C)c1ccc2c(c1)OC1(O)c3ccccc3C(=O)C21NC(=O)C(=O)c1cccs1
+Cc1cc(C#N)cnc1C(=O)Nc1ccc(F)c([C@@]2(C)N=C(N)[C@@](C)(F)CC2(F)F)c1
+C[C@@]1(O)[C@H](O)[C@@H](CO)O[C@H]1n1ccc2c(N)nc(N)nc21
+CC(C)(C)OC(=O)[C@@]12C=CC[C@@H]1CN(C(=O)OCc1ccccc1)C2
+NC1=N[C@@]2(c3ccc(F)cc3F)CO[C@@H](c3nnco3)C[C@H]2CS1
+CNC(=O)c1ccc2ncc(C(=O)OCn3ccnc3)c(Nc3ccc(OC)cc3)c2c1
+COc1ccc2nccc(C(N)CC[C@@H]3CCN(CCSc4cccs4)C[C@@H]3C(=O)O)c2c1
+O=C(Nc1ccc(-c2cnc(C34CC5CC(CC(C(=O)O)(C5)C3)C4)s2)cc1)Nc1ccccc1F
+OC[C@H]1O[C@](O)(c2ccc(Cl)c(Cc3ccc(C#Cc4cnccn4)cc3)c2)[C@H](O)[C@@H](O)[C@@H]1O
+Nc1ncnc2c1c(-c1ccc3ccc(-c4ccccc4)nc3c1)cn2C1CCC1
+CCCC[C@@H](C(=O)N1CCC[C@H]1C(=O)O)[C@@H](F)C(=O)OC
+NC1=Nc2ccc(F)cc2C2CCCC12
+CC1(C)OCC(C)(CO[Si](C)(C)C(C)(C)C)N(Cc2ccccc2)C1=O
+CCc1[nH]c(C(=O)N[C@H]2CCN(c3nc(C(=O)O)c(C)s3)C[C@H]2OC)nc1C(F)(F)F
+Cn1oc(=O)nc1/C(=N\OCc1cccc(NC(=O)OCCc2ccccc2)n1)c1ccccc1
+CCCC[Sn](/C=C/C1(O)C(C)=CC2(CC1(C)C(F)(F)F)OC(C)C(C)O2)(CCCC)CCCC
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCc2ccc(-c3nnn[nH]3)cc2)c1
+C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1CC(=O)CC(C)(C)N1
+COC(=O)C(C)(C)CC(CCCCO)CCCc1cccnc1
+Oc1ccc2c3c(ccc2c1)Cc1ccccc1OC3c1ccc(OCCN2CCCCC2)cc1
+CC(C)(C)OC(=O)N1CC=C(c2ccc3c(c2)-n2nc(-c4ncnn4CC(F)(F)F)cc2CCO3)CC1
+COCCCc1cc(O)cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)c1
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCCC(C)(C)C(=O)O)c1
+CC(=O)Nc1cccc(N2CCN(CCc3nn(C)c(=O)n3CC3CCCCC3)CC2)c1
+COC(=O)c1ccc(-c2ccc(O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)c(Cl)c2)cc1
+CCC(C)(C)OC(=O)Nc1nc(C(O)C(=O)NC2C(=O)N3C(C(=O)O)=C(CSc4nnc(C)s4)CS[C@H]23)cs1
+C[C@@H](n1ccn(-c2ccc(Cl)cc2)c1=O)[C@@]1(c2ccc(F)cc2F)CO1
+COC(=O)CC12CCC(c3ccc(Br)cc3)(CC1)CO2
+CC(C)(C)OC(=O)NC1(c2nc(NCc3ccccn3)c3c(Cl)ccn3n2)CC1
+Cc1cc(Nc2nccc(C(F)(F)F)n2)cc(-c2cnc([C@@](C)(O)[C@H]3CC[C@H](C(=O)O)CC3)s2)c1
+CC(C)c1ccc(-n2nc(O)c3c(=O)c4ccc(Cl)cc4[nH]c3c2=O)cc1
+O=C(Nc1cccc(Cl)c1)N1CCc2[nH]nc(C(=O)N3CC(F)CO3)c2C1
+COc1ccc2nc(-c3ccc(OC)c(F)c3)nc(C(=O)NC(CO)Cc3c[nH]c4cccnc34)c2c1
+C[C@@H]1CNC(=O)c2cc3cc(OCCCN4CCCCC4)ccc3n21
+CC1(C)Oc2ccc(CC(=O)NC3CCCc4ccccc43)cc2C(N)C1O
+O=C(NC[C@@H]1CC[C@@H](COc2ccccc2)OC1)c1ccc(O)cc1
+COC(=O)c1ccc2c(c1)C=CC(=CCl)CO2
+COCCCCC1(CNC(=O)C2CCCNC2)c2ccccc2Oc2ccccc21
+Cn1nccc1[C@]12CCCC[C@H]1OC(=O)O2
+CC(C)(C)OC(=O)N[C@@H]1c2cccnc2[C@@H](O)CC[C@H]1c1cccc(F)c1F
+C=C(C[C@@H](Cc1ccc(-c2ccccc2)cc1)NC(=O)OC(C)(C)C)C(=O)OC
+CC(C)(C)OC(=O)NC1(c2nc(O)c3c(Cl)ccn3n2)CC1
+C=CC[C@@H]1C(=O)N([C@H](C)c2ccccc2)C[C@@]1(C=C)C(=O)OC(C)(C)C
+NC(=O)CN1CCC(c2ccc3c(c2)-n2nc(-c4ncnn4CC(F)(F)F)cc2CCO3)CC1
+CC(=O)Nc1nc2c(s1)-c1c(c(C3CC3)nn1C1CCN(C(=O)N3CCN(C(C)C)CC3)CC1)CC2
+CC(=O)N1c2ccc(N3CCNCC3)cc2[C@H](Nc2ccccc2)[C@@H](C)[C@@H]1C
+CC1=NC2(N=C1N)c1cc(-c3cc(F)cc(F)c3)ccc1CCC21CC1
+CCc1ccc(S(=O)(=O)NC2c3cc(CC(=O)NC4CCCc5ccccc54)ccc3OC(C)(C)C2O)cc1
+CCCCCCC(C)(C)c1ccc([C@H]2C[C@@H](O)CCN2C=O)c(OCc2ccccc2)c1
+COC[C@H](C)COCc1ccc([C@@]2(O)CCN(C(=O)OC(C)(C)C)C[C@@H]2C=NO)cc1
+Cc1cc(Nc2nccc(C(F)(F)F)n2)cc(-c2cnc([C@](C)(O)[C@H]3CC[C@H](C(=O)O)CC3)s2)c1
+C[C@@H](O)C[C@H]1OC[C@@H](C2CCCCC2)N(c2cc(C#CC(C)(C)C)sc2C(=O)O)C1=O
+C/C=C/c1c(N)nc(-c2ccc(Cl)c(OC)c2F)nc1C(=O)OC
+CC(C)(C)OC(=O)N[C@@H]1c2cccnc2[C@H](O)CC[C@H]1c1cccc(F)c1F
+COc1cc2c(=O)[nH]c(=O)n([C@@H]3O[C@H](CO)[C@H]4OC(C)(C)O[C@H]43)c2cc1OC
+CC1=NC2(N=C1N)c1cc(Br)ccc1CCC21CC1
+CC1=NC2(N=C1N)c1cc(-c3cncc(Cl)c3)ccc1CCC21CC1
+CC(=O)OC1CCC2C(CO)CCC12
+O[C@H]1C[C@H](c2cnn3c(N[C@H]4CCc5ccccc54)ncnc23)C=C1COCc1ccccc1
+Cc1nnc(SCC2=C(C(=O)O)N3C(=O)C(NC(=O)C(O)c4csc(N)n4)[C@H]3SC2)s1
+COC[C@H](C)COCc1ccc([C@@]2(O)CCN(C(=O)OC(C)(C)C)C[C@@H]2c2noc(-c3ccccc3CCNC(C)=O)c2Br)cc1
+C[Si](C)(C)CCOCn1c(O[C@@H]2CO[C@H]3[C@@H]2OC[C@H]3O)nc2cc(Cl)c(-c3ccc(-c4ccc(N=S(C)(=O)N5CCC5)cc4)cc3)nc21
+CCOC(=O)[C@H]1[C@H](c2ccc3c(c2)OC(F)(F)O3)C1(C)C
+CCCN(CCC)Cc1cc(CO)c(=O)n2c(-c3c(C)cc(C)cc3C)cccc12
+C[C@H](c1ccccc1)N1C[C@H]2CC=C[C@@]2(C(=O)OC(C)(C)C)C1
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OC[C@@H]2C[C@H]2C(=O)O)c1
+COc1cc2ncc3c(N)nc(-c4cncc(OCCN(Cc5ccc(F)cc5)C(=O)OC(C)(C)C)c4)cc3c2cc1OC
+O=C(Nc1ccc(-c2cnc(C34CC5CC(CC(C(=O)O)(C5)C3)C4)s2)cc1)Nc1cccc(C(F)(F)F)c1
+O=C(OCc1ccccc1)N1CC[C@H]2CCCN(CCc3ccccc3)C[C@H]21
+NS(=O)(=O)OC[C@H]1C[C@@H](c2cnn3c(N[C@H]4CCc5ccccc54)ncnc23)C[C@@H]1O
+C[Si](C)(C)CCOCn1c(O[C@@H]2CO[C@H]3[C@@H]2OC[C@H]3O)nc2cc(Cl)c(-c3ccc(-c4ccc(N=S(C)(=O)N5CCCC5)cc4)cc3)nc21
+OC[C@H]1O[C@@H](SC(c2ccccc2)(c2ccccc2)c2ccccc2)[C@H](O)[C@@H](O)[C@@H]1O
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCc2ccc(C#N)cc2)c1
+CCCc1c(Cc2ccc(-c3ccccc3C#N)cc2F)c(=O)n([C@H]2CC[C@H](OCC3(C(C)=O)CCC3)CC2)c2ncnn12
+CCOC(=O)[C@@H]1C[C@H]1COc1cc(CCCOC)cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)c1
+COC(=O)CC12CCC(c3ccc(-c4ccc(NC(=O)c5nc(C)oc5C(F)(F)F)cc4)cc3)(CC1)CO2
+O=S(=O)(c1cc(C(F)(F)F)ccc1Br)C1CCOC(c2ccc(Cl)cc2)C1
+COCC1=CS[C@@H]2C(NC(=O)Cc3cccs3)C(=O)N2C1C(=O)O
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OC[C@@H]2C[C@H]2CO)c1
+COCCCc1cc(CN(C(=O)[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCCC(C)(C)C(=O)OC)c1
+COC[C@H](C)COCc1ccc([C@@]2(O)CCN(C(=O)OC(C)(C)C)C[C@@H]2CO)cc1
+COCCCc1cc(CN(C(=O)[C@H]2CNCC[C@@H]2c2ccc(OCCOc3c(Cl)cc(C)cc3Cl)cc2)C2CC2)cc(OCC(C)(C)O)c1
+COC(=O)[C@@]12C[C@H]1C=CCCCCC[C@H](NC(=O)CC1CC1)C(=O)N1C[C@H](Oc3nc(-c4ccccn4)nc4ccsc34)C[C@H]1C(=O)N2
+CCN1CCN(CCCCCCOc2c(OC)ccc3c(Nc4c(Cl)cncc4Cl)cc(=O)[nH]c23)CC1
+OCCN1CCC(c2ccc3c(c2)-n2nc(-c4ncnn4CC(F)(F)F)cc2CCO3)CC1

scripts/clean_checker_data.py

@@ -0,0 +1,107 @@
+import json
+import csv
+from pathlib import Path
+
+INPUT_PATH = Path("data/checker_dataset_pistachio.jsonl")
+OUTPUT_PATH = Path("data/checker_dataset_clean.csv")
+
+def main():
+    rows = []
+
+    with INPUT_PATH.open("r", encoding="utf-8") as f:
+        for line in f:
+            line = line.strip()
+            if not line:
+                continue
+            rec = json.loads(line)
+
+            target = rec.get("target_smiles_canonical")
+            product = rec.get("product_smiles_canonical")
+            hall = rec.get("hallucination_raw", {}) or {}
+
+            hallucination_score = hall.get("score")
+            hallucination_severity = hall.get("severity")
+
+            # stability_raw is a dict: reactant_smiles -> stability_dict
+            stability_raw = rec.get("stability_raw", {}) or {}
+
+            # reactant_smiles_canonical is a list of all reactants for this reaction step
+            reactants_canonical = rec.get("reactant_smiles_canonical", [])
+
+            # Join all reactants together (using "." as separator, common in SMILES)
+            all_reactants = ".".join(reactants_canonical) if reactants_canonical else ""
+
+            # Aggregate stability data across all reactants
+            stability_scores = []
+            stability_assessments = []
+            all_stability_issues = []
+
+            for rcanon in reactants_canonical:
+                stab = stability_raw.get(rcanon, {})  # prefer canonical key if present
+                if not stab:
+                    # fallback: try by non-canonical reactant name if needed
+                    for key, val in stability_raw.items():
+                        if key == rcanon:
+                            stab = val
+                            break
+
+                score = stab.get("stability_score")
+                if score is not None:
+                    stability_scores.append(score)
+
+                assessment = stab.get("assessment")
+                if assessment:
+                    stability_assessments.append(assessment)
+
+                issues = stab.get("issues", []) or []
+                if issues:
+                    # Prefix issues with reactant SMILES for clarity
+                    for issue in issues:
+                        all_stability_issues.append(f"{rcanon}: {issue}")
+
+            # Calculate average stability score
+            avg_stability_score = sum(stability_scores) / len(stability_scores) if stability_scores else None
+
+            # Determine overall assessment (use worst case if mixed)
+            overall_assessment = None
+            if stability_assessments:
+                if "Potentially unstable" in stability_assessments:
+                    overall_assessment = "Potentially unstable"
+                elif "Moderately stable" in stability_assessments:
+                    overall_assessment = "Moderately stable"
+                else:
+                    overall_assessment = "Likely stable"
+
+            stability_issues = "; ".join(all_stability_issues) if all_stability_issues else ""
+
+            rows.append({
+                "target_smiles_canonical": target,
+                "product_smiles_canonical": product,
+                "reactant_smiles_canonical": all_reactants,
+                "stability_score": avg_stability_score,
+                "stability_assessment": overall_assessment,
+                "stability_issues": stability_issues,
+                "hallucination_score": hallucination_score,
+                "hallucination_severity": hallucination_severity,
+            })
+
+    OUTPUT_PATH.parent.mkdir(parents=True, exist_ok=True)
+    with OUTPUT_PATH.open("w", encoding="utf-8", newline="") as out_f:
+        writer = csv.DictWriter(
+            out_f,
+            fieldnames=[
+                "target_smiles_canonical",
+                "product_smiles_canonical",
+                "reactant_smiles_canonical",
+                "stability_score",
+                "stability_assessment",
+                "stability_issues",
+                "hallucination_score",
+                "hallucination_severity",
+            ],
+        )
+        writer.writeheader()
+        writer.writerows(rows)
+
+if __name__ == "__main__":
+    main()

src/api.py

@@ -224,7 +224,9 @@ def retrosynthesis_api():
             use_protecting_group_feature=use_protecting_group_feature)
         save_result(smiles, result)
     except Exception as e:
-        print(e)
+        print(f"ERROR in retrosynthesis:")
+        print(f"  EXCEPTION: {str(e)}")
+        print(f"  TRACEBACK: {traceback.format_exc()}")
         return jsonify(
             {"error":
              f"Error in retrosynthesis: {str(e)}. Please rerun."}), 500
@@ -345,7 +347,9 @@ def rerun_retrosynthesis():
         # Store the result in partial.json
         save_result(molecule, result)
     except Exception as e:
-        print(e)
+        print(f"ERROR in rerun_retrosynthesis:")
+        print(f"  EXCEPTION: {str(e)}")
+        print(f"  TRACEBACK: {traceback.format_exc()}")
         return jsonify(
             {"error":
              f"Error in retrosynthesis: {str(e)}. Please rerun."}), 500

src/metadata.py

@@ -25,14 +25,7 @@
 litellm.success_callback = ["langfuse"]
 litellm.drop_params = True
 
-metadata = {
-    "generation_name": "prod",  # set langfuse generation name
-    "project": "Retrosynthesis",  # set langfuse project name
-    "version": "0.0.3",  # set langfuse version
-    "trace_name": "prod",  # set langfuse Trace Name
-    "trace_user_id": "sv",  # set langfuse Trace User ID
-    "session_id": "metadata",  # set langfuse Session ID
-}
+from src.utils.langfuse_config import get_langfuse_metadata
 
 
 @cache_results
@@ -146,7 +139,7 @@ def reagent_llm_call(reactants: list[str],
                               temperature=temperature,
                               seed=42,
                               top_p=0.9,
-                              metadata=metadata)
+                              metadata=get_langfuse_metadata("metadata"))
         res_text = response.choices[0].message.content
     except Exception as e:
         logger.info(f"Error in calling {LLM}: {e}")
@@ -263,7 +256,7 @@ def conditions_llm_call(reactants: list[str],
                               temperature=temperature,
                               seed=42,
                               top_p=0.9,
-                              metadata=metadata)
+                              metadata=get_langfuse_metadata("metadata"))
         res_text = response.choices[0].message.content
     except Exception as e:
 
@@ -338,7 +331,7 @@ def literature_agent(reactants: list[str],
                               temperature=temperature,
                               seed=42,
                               top_p=0.9,
-                              metadata=metadata)
+                              metadata=get_langfuse_metadata("metadata"))
         res_text = response.choices[0].message.content
     except Exception as e:
         logger.info(f"Error in calling {LLM}: {e}")