add columns

model/framework/code/main.py

@@ -24,7 +24,7 @@
 for smiles in smiles_list:
     outputs += [sampler.sample(smiles)]
 
-header = ["sim-{0}".format(i) for i in range(100)]
+header = ["smiles_{0}".format(str(i).zfill(2)) for i in range(100)]
 blank = [None] * len(header)
 R = []
 for o in outputs:

model/framework/columns/run_columns.csv

@@ -0,0 +1,101 @@
+name,type,direction,description
+smiles_00,string,,Similar compound index 0 queried using SmallWorld on the Wuxi chemical space
+smiles_01,string,,Similar compound index 1 queried using SmallWorld on the Wuxi chemical space
+smiles_02,string,,Similar compound index 2 queried using SmallWorld on the Wuxi chemical space
+smiles_03,string,,Similar compound index 3 queried using SmallWorld on the Wuxi chemical space
+smiles_04,string,,Similar compound index 4 queried using SmallWorld on the Wuxi chemical space
+smiles_05,string,,Similar compound index 5 queried using SmallWorld on the Wuxi chemical space
+smiles_06,string,,Similar compound index 6 queried using SmallWorld on the Wuxi chemical space
+smiles_07,string,,Similar compound index 7 queried using SmallWorld on the Wuxi chemical space
+smiles_08,string,,Similar compound index 8 queried using SmallWorld on the Wuxi chemical space
+smiles_09,string,,Similar compound index 9 queried using SmallWorld on the Wuxi chemical space
+smiles_10,string,,Similar compound index 10 queried using SmallWorld on the Wuxi chemical space
+smiles_11,string,,Similar compound index 11 queried using SmallWorld on the Wuxi chemical space
+smiles_12,string,,Similar compound index 12 queried using SmallWorld on the Wuxi chemical space
+smiles_13,string,,Similar compound index 13 queried using SmallWorld on the Wuxi chemical space
+smiles_14,string,,Similar compound index 14 queried using SmallWorld on the Wuxi chemical space
+smiles_15,string,,Similar compound index 15 queried using SmallWorld on the Wuxi chemical space
+smiles_16,string,,Similar compound index 16 queried using SmallWorld on the Wuxi chemical space
+smiles_17,string,,Similar compound index 17 queried using SmallWorld on the Wuxi chemical space
+smiles_18,string,,Similar compound index 18 queried using SmallWorld on the Wuxi chemical space
+smiles_19,string,,Similar compound index 19 queried using SmallWorld on the Wuxi chemical space
+smiles_20,string,,Similar compound index 20 queried using SmallWorld on the Wuxi chemical space
+smiles_21,string,,Similar compound index 21 queried using SmallWorld on the Wuxi chemical space
+smiles_22,string,,Similar compound index 22 queried using SmallWorld on the Wuxi chemical space
+smiles_23,string,,Similar compound index 23 queried using SmallWorld on the Wuxi chemical space
+smiles_24,string,,Similar compound index 24 queried using SmallWorld on the Wuxi chemical space
+smiles_25,string,,Similar compound index 25 queried using SmallWorld on the Wuxi chemical space
+smiles_26,string,,Similar compound index 26 queried using SmallWorld on the Wuxi chemical space
+smiles_27,string,,Similar compound index 27 queried using SmallWorld on the Wuxi chemical space
+smiles_28,string,,Similar compound index 28 queried using SmallWorld on the Wuxi chemical space
+smiles_29,string,,Similar compound index 29 queried using SmallWorld on the Wuxi chemical space
+smiles_30,string,,Similar compound index 30 queried using SmallWorld on the Wuxi chemical space
+smiles_31,string,,Similar compound index 31 queried using SmallWorld on the Wuxi chemical space
+smiles_32,string,,Similar compound index 32 queried using SmallWorld on the Wuxi chemical space
+smiles_33,string,,Similar compound index 33 queried using SmallWorld on the Wuxi chemical space
+smiles_34,string,,Similar compound index 34 queried using SmallWorld on the Wuxi chemical space
+smiles_35,string,,Similar compound index 35 queried using SmallWorld on the Wuxi chemical space
+smiles_36,string,,Similar compound index 36 queried using SmallWorld on the Wuxi chemical space
+smiles_37,string,,Similar compound index 37 queried using SmallWorld on the Wuxi chemical space
+smiles_38,string,,Similar compound index 38 queried using SmallWorld on the Wuxi chemical space
+smiles_39,string,,Similar compound index 39 queried using SmallWorld on the Wuxi chemical space
+smiles_40,string,,Similar compound index 40 queried using SmallWorld on the Wuxi chemical space
+smiles_41,string,,Similar compound index 41 queried using SmallWorld on the Wuxi chemical space
+smiles_42,string,,Similar compound index 42 queried using SmallWorld on the Wuxi chemical space
+smiles_43,string,,Similar compound index 43 queried using SmallWorld on the Wuxi chemical space
+smiles_44,string,,Similar compound index 44 queried using SmallWorld on the Wuxi chemical space
+smiles_45,string,,Similar compound index 45 queried using SmallWorld on the Wuxi chemical space
+smiles_46,string,,Similar compound index 46 queried using SmallWorld on the Wuxi chemical space
+smiles_47,string,,Similar compound index 47 queried using SmallWorld on the Wuxi chemical space
+smiles_48,string,,Similar compound index 48 queried using SmallWorld on the Wuxi chemical space
+smiles_49,string,,Similar compound index 49 queried using SmallWorld on the Wuxi chemical space
+smiles_50,string,,Similar compound index 50 queried using SmallWorld on the Wuxi chemical space
+smiles_51,string,,Similar compound index 51 queried using SmallWorld on the Wuxi chemical space
+smiles_52,string,,Similar compound index 52 queried using SmallWorld on the Wuxi chemical space
+smiles_53,string,,Similar compound index 53 queried using SmallWorld on the Wuxi chemical space
+smiles_54,string,,Similar compound index 54 queried using SmallWorld on the Wuxi chemical space
+smiles_55,string,,Similar compound index 55 queried using SmallWorld on the Wuxi chemical space
+smiles_56,string,,Similar compound index 56 queried using SmallWorld on the Wuxi chemical space
+smiles_57,string,,Similar compound index 57 queried using SmallWorld on the Wuxi chemical space
+smiles_58,string,,Similar compound index 58 queried using SmallWorld on the Wuxi chemical space
+smiles_59,string,,Similar compound index 59 queried using SmallWorld on the Wuxi chemical space
+smiles_60,string,,Similar compound index 60 queried using SmallWorld on the Wuxi chemical space
+smiles_61,string,,Similar compound index 61 queried using SmallWorld on the Wuxi chemical space
+smiles_62,string,,Similar compound index 62 queried using SmallWorld on the Wuxi chemical space
+smiles_63,string,,Similar compound index 63 queried using SmallWorld on the Wuxi chemical space
+smiles_64,string,,Similar compound index 64 queried using SmallWorld on the Wuxi chemical space
+smiles_65,string,,Similar compound index 65 queried using SmallWorld on the Wuxi chemical space
+smiles_66,string,,Similar compound index 66 queried using SmallWorld on the Wuxi chemical space
+smiles_67,string,,Similar compound index 67 queried using SmallWorld on the Wuxi chemical space
+smiles_68,string,,Similar compound index 68 queried using SmallWorld on the Wuxi chemical space
+smiles_69,string,,Similar compound index 69 queried using SmallWorld on the Wuxi chemical space
+smiles_70,string,,Similar compound index 70 queried using SmallWorld on the Wuxi chemical space
+smiles_71,string,,Similar compound index 71 queried using SmallWorld on the Wuxi chemical space
+smiles_72,string,,Similar compound index 72 queried using SmallWorld on the Wuxi chemical space
+smiles_73,string,,Similar compound index 73 queried using SmallWorld on the Wuxi chemical space
+smiles_74,string,,Similar compound index 74 queried using SmallWorld on the Wuxi chemical space
+smiles_75,string,,Similar compound index 75 queried using SmallWorld on the Wuxi chemical space
+smiles_76,string,,Similar compound index 76 queried using SmallWorld on the Wuxi chemical space
+smiles_77,string,,Similar compound index 77 queried using SmallWorld on the Wuxi chemical space
+smiles_78,string,,Similar compound index 78 queried using SmallWorld on the Wuxi chemical space
+smiles_79,string,,Similar compound index 79 queried using SmallWorld on the Wuxi chemical space
+smiles_80,string,,Similar compound index 80 queried using SmallWorld on the Wuxi chemical space
+smiles_81,string,,Similar compound index 81 queried using SmallWorld on the Wuxi chemical space
+smiles_82,string,,Similar compound index 82 queried using SmallWorld on the Wuxi chemical space
+smiles_83,string,,Similar compound index 83 queried using SmallWorld on the Wuxi chemical space
+smiles_84,string,,Similar compound index 84 queried using SmallWorld on the Wuxi chemical space
+smiles_85,string,,Similar compound index 85 queried using SmallWorld on the Wuxi chemical space
+smiles_86,string,,Similar compound index 86 queried using SmallWorld on the Wuxi chemical space
+smiles_87,string,,Similar compound index 87 queried using SmallWorld on the Wuxi chemical space
+smiles_88,string,,Similar compound index 88 queried using SmallWorld on the Wuxi chemical space
+smiles_89,string,,Similar compound index 89 queried using SmallWorld on the Wuxi chemical space
+smiles_90,string,,Similar compound index 90 queried using SmallWorld on the Wuxi chemical space
+smiles_91,string,,Similar compound index 91 queried using SmallWorld on the Wuxi chemical space
+smiles_92,string,,Similar compound index 92 queried using SmallWorld on the Wuxi chemical space
+smiles_93,string,,Similar compound index 93 queried using SmallWorld on the Wuxi chemical space
+smiles_94,string,,Similar compound index 94 queried using SmallWorld on the Wuxi chemical space
+smiles_95,string,,Similar compound index 95 queried using SmallWorld on the Wuxi chemical space
+smiles_96,string,,Similar compound index 96 queried using SmallWorld on the Wuxi chemical space
+smiles_97,string,,Similar compound index 97 queried using SmallWorld on the Wuxi chemical space
+smiles_98,string,,Similar compound index 98 queried using SmallWorld on the Wuxi chemical space
+smiles_99,string,,Similar compound index 99 queried using SmallWorld on the Wuxi chemical space

model/framework/examples/input.csv

@@ -0,0 +1,4 @@
+smiles
+OS(=O)(=O)ON1[C@H]2CN([C@@H](CC2)C(=O)NC2CCNCC2)C1=O
+[H][C@@]12CCC(=C)[C@@]1(C)CC[C@@]([H])([C@H]2CN)[C@@]1(C)CC[C@H](O)C[C@@H]1CO
+N[C@@H]1CCN(O)C1=O

model/framework/examples/output.csv

@@ -0,0 +1,4 @@
+smiles_00,smiles_01,smiles_02,smiles_03,smiles_04,smiles_05,smiles_06,smiles_07,smiles_08,smiles_09,smiles_10,smiles_11,smiles_12,smiles_13,smiles_14,smiles_15,smiles_16,smiles_17,smiles_18,smiles_19,smiles_20,smiles_21,smiles_22,smiles_23,smiles_24,smiles_25,smiles_26,smiles_27,smiles_28,smiles_29,smiles_30,smiles_31,smiles_32,smiles_33,smiles_34,smiles_35,smiles_36,smiles_37,smiles_38,smiles_39,smiles_40,smiles_41,smiles_42,smiles_43,smiles_44,smiles_45,smiles_46,smiles_47,smiles_48,smiles_49,smiles_50,smiles_51,smiles_52,smiles_53,smiles_54,smiles_55,smiles_56,smiles_57,smiles_58,smiles_59,smiles_60,smiles_61,smiles_62,smiles_63,smiles_64,smiles_65,smiles_66,smiles_67,smiles_68,smiles_69,smiles_70,smiles_71,smiles_72,smiles_73,smiles_74,smiles_75,smiles_76,smiles_77,smiles_78,smiles_79,smiles_80,smiles_81,smiles_82,smiles_83,smiles_84,smiles_85,smiles_86,smiles_87,smiles_88,smiles_89,smiles_90,smiles_91,smiles_92,smiles_93,smiles_94,smiles_95,smiles_96,smiles_97,smiles_98,smiles_99
+CS(=O)(=O)CCC(=O)N1CC[C@@H](O)C[C@H]1C(=O)NC1CCCCC1,CS(=O)(=O)NCC(=O)N1CC[C@@H](O)C[C@H]1C(=O)NC1CCCCC1,CS(=O)(=O)CC(=O)N1CCCCC1C(=O)NC1CCCCC1,CS(=O)(=O)CCC(=O)N1CCCCC1C(=O)N[C@H]1CCC[C@@H](O)C1,CN1CCC(NC(=O)C2CCCCN2C(=O)CCS(C)(=O)=O)CC1,CS(=O)(=O)NCC(=O)N1CCCCC1C(=O)N[C@H]1CCC[C@@H](O)C1,CN1CCC(NC(=O)C2CCCCN2C(=O)CNS(C)(=O)=O)CC1,CS(=O)(=O)NCC(=O)N1[C@@H]2C[C@H]2C[C@H]1C(=O)NC1CCCCC1,CS(=O)(=O)CCC(=O)N1[C@@H](C(=O)NC2CCCCC2)C[C@H]2C[C@@H]21,CS(=O)(=O)CCC(=O)N1[C@@H](C(=O)NC2CCCCC2)C[C@@H]2C[C@@H]21,CS(=O)(=O)CCC(=O)N1CCCCC1C(=O)NC1CCCCC1,CS(=O)(=O)NCC(=O)N1CCCCC1C(=O)NC1CCCCC1,CS(=O)(=O)NCC(=O)N1[C@@H](C(=O)NC2CCCCC2)C[C@H]2C[C@@H]21,CS(=O)(=O)CCC(=O)N1[C@H](C(=O)NC2CCCCC2)C[C@H]2C[C@@H]21,CS(=O)(=O)NCC(=O)N1[C@H](C(=O)NC2CCCCC2)C[C@H]2C[C@@H]21,CS(=O)(=O)CCC(=O)N1[C@@H]2C[C@H]2C[C@H]1C(=O)NC1CCCCC1,CS(=O)(=O)NCC(=O)N1[C@@H](C(=O)NC2CCCCC2)C[C@@H]2C[C@@H]21,CS(=O)(=O)CC(=O)N1CCOCC1C(=O)NC1CCCCC1,CS(=O)(=O)CC(=O)N1CCOC[C@H]1C(=O)NC1CCCCC1,CS(=O)(=O)CC(=O)N1CCSCC1C(=O)NC1CCCCC1,CN1CCC(NC(=O)[C@@H]2COCCN2C(=O)CNS(C)(=O)=O)CC1,CS(=O)(=O)CCC(=O)N1CCSCC1C(=O)N[C@H]1CCC[C@@H](O)C1,CS(=O)(=O)CCC(=O)N1CCOCC1C(=O)N[C@H]1CCC[C@@H](O)C1,CN1CCC(NC(=O)C2COCCN2C(=O)CNS(C)(=O)=O)CC1,CS(=O)(=O)NCC(=O)N1CCOCC1C(=O)N[C@H]1CCC[C@@H](O)C1,CN1CCC[C@H](NC(=O)C2CCCCN2C(=O)CCS(C)(=O)=O)C1,CS(=O)(=O)NCC(=O)N1CCOC[C@H]1C(=O)N[C@H]1CCC[C@@H](O)C1,CN1CCC(NC(=O)C2CSCCN2C(=O)CCS(C)(=O)=O)CC1,CS(=O)(=O)CCC(=O)N1CCOC[C@H]1C(=O)N[C@H]1CCC[C@@H](O)C1,CS(=O)(=O)NCC(=O)N1CCSCC1C(=O)N[C@H]1CCC[C@@H](O)C1,CN1CCC(NC(=O)C2CSCCN2C(=O)CNS(C)(=O)=O)CC1,CN1CCC(NC(=O)C2COCCN2C(=O)CCS(C)(=O)=O)CC1,CN1CCC(NC(=O)[C@@H]2COCCN2C(=O)CCS(C)(=O)=O)CC1,CN1CCC[C@H](NC(=O)C2CCCCN2C(=O)CNS(C)(=O)=O)C1,CS(=O)(=O)CCC(=O)N1CCOC[C@H]1C(=O)NC1CCCCC1,CS(=O)(=O)CCC(=O)N1CCOCC1C(=O)NC1CCCCC1,CS(=O)(=O)NCC(=O)N1CCOCC1C(=O)NC1CCCCC1,CS(=O)(=O)CCC(=O)N1CCSCC1C(=O)NC1CCCCC1,CS(=O)(=O)NCC(=O)N1CCOC[C@H]1C(=O)N1C2CCC1CC2,CS(=O)(=O)NCC(=O)N1CCOCC1C(=O)N1C2CCC1CC2,CS(=O)(=O)NCC(=O)N1CCSCC1C(=O)N1C2CCC1CC2,CS(=O)(=O)NCC(=O)N1CCOC[C@H]1C(=O)NC1CCCCC1,CS(=O)(=O)NCC(=O)N1CCCCC1C(=O)N1C2CCC1CC2,CS(=O)(=O)NCC(=O)N1CCSCC1C(=O)NC1CCCCC1,CS(=O)(=O)CC(=O)N1CCCCC1C(=O)NC1CCCOC1,CS(=O)(=O)CCC(=O)N1CCCCC1C(=O)N1C2CCC1CC2,CS(=O)(=O)CCC(=O)N1CCCCC1C(=O)NC1CCCOC1,CS(=O)(=O)CCC(=O)N1CCOC[C@H]1C(=O)N1C2CCC1CC2,CS(=O)(=O)CCC(=O)N1CCSCC1C(=O)N1C2CCC1CC2,CS(=O)(=O)CCC(=O)N1CCOCC1C(=O)N1C2CCC1CC2,CS(=O)(=O)NCC(=O)N1CCCCC1C(=O)NC1CCCOC1,O=C(O)C#CC(=O)N1CCCCC1C(=O)NC1CCCCC1,CC(=O)OCC(=O)N1CCCCC1C(=O)NC1CCCCC1,CS(=O)(=O)NCC(=O)N1[C@H](C(=O)NC2CCCOC2)C[C@H]2C[C@@H]21,CS(=O)(=O)NCC(=O)N1[C@@H](C(=O)NC2CCCOC2)C[C@@H]2C[C@@H]21,CS(=O)(=O)NCC(=O)N1[C@@H]2C[C@H]2C[C@H]1C(=O)NC1CCCOC1,CS(=O)(=O)CCC(=O)N1[C@@H](C(=O)NC2CCCOC2)C[C@@H]2C[C@@H]21,CS(=O)(=O)NCC(=O)N1[C@@H](C(=O)NC2CCCOC2)C[C@H]2C[C@@H]21,CS(=O)(=O)CCC(=O)N1[C@@H](C(=O)NC2CCCOC2)C[C@H]2C[C@@H]21,CS(=O)(=O)CCC(=O)N1[C@H](C(=O)NC2CCCOC2)C[C@H]2C[C@@H]21,CS(=O)(=O)CCC(=O)N1[C@@H]2C[C@H]2C[C@H]1C(=O)NC1CCCOC1,CN1CCC(NC(=O)C2CCCCN2C(=O)COC(C)(C)C)CC1,CC(=O)OCC(=O)N1CCOC[C@H]1C(=O)NC1CCCCC1,CC(=O)OCC(=O)N1CCSCC1C(=O)NC1CCCCC1,CC(=O)SCC(=O)N1CCCCC1C(=O)NC1CCCCC1,CC(=O)OCC(=O)N1CCOCC1C(=O)NC1CCCCC1,O=C(O)C#CC(=O)N1CCSCC1C(=O)NC1CCCCC1,O=C(O)C#CC(=O)N1CCOC[C@H]1C(=O)NC1CCCCC1,NC(=O)CCC(=O)N1CCCCC1C(=O)NC1CCCCC1,CC(=O)NCC(=O)N1CCCCC1C(=O)NC1CCCCC1,O=C(O)C#CC(=O)N1CCOCC1C(=O)NC1CCCCC1,NC(=O)NCC(=O)N1CCCCC1C(=O)NC1CCCCC1,CC(=O)CCC(=O)N1CCCCC1C(=O)NC1CCCCC1,CC(C)OCC(=O)N1CCCCC1C(=O)NC1CCCCC1,O=C(O)C#CC(=O)N1CCCCC1C(=O)NC1CCCOC1,CC(=O)OCC(=O)N1CCCCC1C(=O)NC1CCCOC1,CS(=O)(=O)NCC(=O)N1CCCCC1C(=O)N1C2COCC1C2,CS(=O)(=O)CCC(=O)N1CCCCC1C(=O)N1C2COCC1C2,CC1(NC(=O)C2CCCCN2C(=O)CCS(C)(=O)=O)CCCCC1,CC1(NC(=O)C2CCCCN2C(=O)CNS(C)(=O)=O)CCCCC1,CCC[C@@H](CO)NC(=O)C1CCCCN1C(=O)CNS(C)(=O)=O,CCC[C@@H](CO)NC(=O)C1CCCCN1C(=O)CCS(C)(=O)=O,CCOCCCNC(=O)C1CCCCN1C(=O)CNS(C)(=O)=O,CS(=O)(=O)CCC(=O)N1CCCCC1C(=O)NCCCCCO,CS(=O)(=O)NCC(=O)N1CCCCC1C(=O)NCCCCCO,CCOCCCNC(=O)C1CCCCN1C(=O)CCS(C)(=O)=O,CCCCCCNC(=O)C1CCCCN1C(=O)CCS(C)(=O)=O,CCCCCCNC(=O)C1CCCCN1C(=O)CNS(C)(=O)=O,CCOCCCNC(=O)[C@@H]1COCCN1C(=O)CCS(C)(=O)=O,CCOCCCNC(=O)C1CSCCN1C(=O)CCS(C)(=O)=O,CCOCCCNC(=O)C1CSCCN1C(=O)CNS(C)(=O)=O,CCOCCCNC(=O)C1COCCN1C(=O)CCS(C)(=O)=O,CCOCCCNC(=O)[C@@H]1COCCN1C(=O)CNS(C)(=O)=O,CCOCCCNC(=O)C1COCCN1C(=O)CNS(C)(=O)=O,CCCCCCNC(=O)C1COCCN1C(=O)CNS(C)(=O)=O,CCCCCCNC(=O)[C@@H]1COCCN1C(=O)CNS(C)(=O)=O,CCCCCCNC(=O)C1CSCCN1C(=O)CCS(C)(=O)=O,CCCCCCNC(=O)C1COCCN1C(=O)CCS(C)(=O)=O,CCCCCCNC(=O)[C@@H]1COCCN1C(=O)CCS(C)(=O)=O,CCCCCCNC(=O)C1CSCCN1C(=O)CNS(C)(=O)=O
+CCCCC(C)CCC(=O)N1CCN(C(=O)CC)CC1C#N,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+CCCC(N)=O,CCNC(C)=O,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,