<jupyter_start><jupyter_text>Scaffolds of Keck_RMI_cdd<jupyter_code>Target_name = 'Keck_RMI_cdd'
smiles_list = []
for i in range(k):
    smiles_list.extend(data_pd_list[i][data_pd_list[i][Target_name]==1]['SMILES'].tolist())

scaffold_set = set()
for smiles in smiles_list:
    mol = Chem.MolFromSmiles(smiles)
    core = MurckoScaffold.GetScaffoldForMol(mol)
    scaffold = Chem.MolToSmiles(core)
    scaffold_set.add(scaffold)
    print 'Original SMILES is \t{}'.format(smiles)
    print 'The Scaffold is \t{}'.format(scaffold)
    print

print '{} total smiles'.format(len(smiles_list))
print '{} different scaffolds'.format(len(scaffold_set))<jupyter_output>Original SMILES is 	c1cc(cc2c1CCCN2CCOC)N
The Scaffold is 	c1ccc2c(c1)CCCN2

Original SMILES is 	c1ccc2c(c1)nc(s2)c3c4c(sc3NC(=O)c5ccc(cc5)OCC)CN(CC4)C(C)C
The Scaffold is 	O=C(Nc1sc2c(c1-c1nc3ccccc3s1)CCNC2)c1ccccc1

Original SMILES is 	c1cc2c(cc1C(=O)OC)sc(n2)NC(=O)c3ccc(cc3)N(C)C
The Scaffold is 	O=C(Nc1nc2ccccc2s1)c1ccccc1

Original SMILES is 	c1cc(ccc1C(=O)N=c2n(c3ccc(cc3s2)OC)CC(=O)OC)F
The Scaffold is 	O=C(N=c1[nH]c2ccccc2s1)c1ccccc1

Original SMILES is 	c1cc2c(cc1CCNC(=O)OCC)CCCN2CCC
The Scaffold is 	c1ccc2c(c1)CCCN2

Original SMILES is 	c1cc(cc2c1CCCN2CCOC)NS(=O)(=O)c3ccc(cc3F)F
The Scaffold is 	O=S(=O)(Nc1ccc2c(c1)NCCC2)c1ccccc1

Original SMILES is 	c1cc(ccc1c2cc(nc3c2c(c(s3)C(=O)N4CCOCC4)N)c5ccc(cc5)Cl)OC
The Scaffold is 	O=C(c1cc2c(-c3ccccc3)cc(-c3ccccc3)nc2s1)N1CCOCC1

Original SMILES is 	c1ccc(cc1)c2nnc3n2nc(cc3)OCCNC(=O)COC
The Scaffold is 	c1ccc(-c2nnc3cccnn23)cc1

Original SMILES is 	c1ccc2c(c1)nc(s2)c3c4c(sc3NC(=O)c5ccnn5C)CN(CC4)C(C)C
The Scaffold is 	O=C(Nc1sc2c(c1-[...]<jupyter_text>Below is scaffold for each fold  Scaffold for fold 0<jupyter_code>i = 0

smiles_list = data_pd_list[i][data_pd_list[i][Target_name]==1]['SMILES'].tolist()
scaffold_set = set()
for smiles in smiles_list:
    mol = Chem.MolFromSmiles(smiles)
    core = MurckoScaffold.GetScaffoldForMol(mol)
    scaffold = Chem.MolToSmiles(core)
    scaffold_set.add(scaffold)
    print 'Original SMILES is \t{}'.format(smiles)
    print 'The Scaffold is \t{}'.format(scaffold)
    print

print '{} total smiles'.format(len(smiles_list))
print '{} different scaffolds'.format(len(scaffold_set))<jupyter_output>Original SMILES is 	c1cc(cc2c1CCCN2CCOC)N
The Scaffold is 	c1ccc2c(c1)CCCN2

Original SMILES is 	c1ccc2c(c1)nc(s2)c3c4c(sc3NC(=O)c5ccc(cc5)OCC)CN(CC4)C(C)C
The Scaffold is 	O=C(Nc1sc2c(c1-c1nc3ccccc3s1)CCNC2)c1ccccc1

Original SMILES is 	c1cc2c(cc1C(=O)OC)sc(n2)NC(=O)c3ccc(cc3)N(C)C
The Scaffold is 	O=C(Nc1nc2ccccc2s1)c1ccccc1

Original SMILES is 	c1cc(ccc1C(=O)N=c2n(c3ccc(cc3s2)OC)CC(=O)OC)F
The Scaffold is 	O=C(N=c1[nH]c2ccccc2s1)c1ccccc1

Original SMILES is 	c1cc2c(cc1CCNC(=O)OCC)CCCN2CCC
The Scaffold is 	c1ccc2c(c1)CCCN2

Original SMILES is 	c1cc(cc2c1CCCN2CCOC)NS(=O)(=O)c3ccc(cc3F)F
The Scaffold is 	O=S(=O)(Nc1ccc2c(c1)NCCC2)c1ccccc1

Original SMILES is 	c1cc(ccc1c2cc(nc3c2c(c(s3)C(=O)N4CCOCC4)N)c5ccc(cc5)Cl)OC
The Scaffold is 	O=C(c1cc2c(-c3ccccc3)cc(-c3ccccc3)nc2s1)N1CCOCC1

Original SMILES is 	c1ccc(cc1)c2nnc3n2nc(cc3)OCCNC(=O)COC
The Scaffold is 	c1ccc(-c2nnc3cccnn23)cc1

Original SMILES is 	c1ccc2c(c1)nc(s2)c3c4c(sc3NC(=O)c5ccnn5C)CN(CC4)C(C)C
The Scaffold is 	O=C(Nc1sc2c(c1-[...]<jupyter_text>Scaffold for fold 1<jupyter_code>i = 1

smiles_list = data_pd_list[i][data_pd_list[i][Target_name]==1]['SMILES'].tolist()
scaffold_set = set()
for smiles in smiles_list:
    mol = Chem.MolFromSmiles(smiles)
    core = MurckoScaffold.GetScaffoldForMol(mol)
    scaffold = Chem.MolToSmiles(core)
    scaffold_set.add(scaffold)
    print 'Original SMILES is \t{}'.format(smiles)
    print 'The Scaffold is \t{}'.format(scaffold)
    print

print '{} total smiles'.format(len(smiles_list))
print '{} different scaffolds'.format(len(scaffold_set))<jupyter_output>Original SMILES is 	c1cc(ccc1C(=O)Nc2nc3c(s2)CCCC3)OCCCC
The Scaffold is 	O=C(Nc1nc2c(s1)CCCC2)c1ccccc1

Original SMILES is 	c1ccc(c(c1)c2csc(n2)NC(=O)C(C)C)OC
The Scaffold is 	c1ccc(-c2cscn2)cc1

Original SMILES is 	c1ccc2c(c1)-c3c(sc(n3)NC(=O)c4nc5ccccc5s4)C2
The Scaffold is 	O=C(Nc1nc2c(s1)Cc1ccccc1-2)c1nc2ccccc2s1

Original SMILES is 	c1cc2c(cc1CCNC(=O)C(=O)NCCOC)CCCN2CC
The Scaffold is 	c1ccc2c(c1)CCCN2

Original SMILES is 	c1cc(cc(c1)S(=O)(=O)NCCc2ccc3c(c2)CCCN3CCC)F
The Scaffold is 	O=S(=O)(NCCc1ccc2c(c1)CCCN2)c1ccccc1

Original SMILES is 	c1cc(ccc1CSc2nc(cs2)CC(=O)Nc3nccs3)Br
The Scaffold is 	O=C(Cc1csc(SCc2ccccc2)n1)Nc1nccs1

Original SMILES is 	c1ccnc(c1)CNC(=O)Cc2csc(n2)SCc3ccc(cc3)Br
The Scaffold is 	O=C(Cc1csc(SCc2ccccc2)n1)NCc1ccccn1

Original SMILES is 	c1cc2cc(oc2c(c1)OC)C(=O)Nc3nnc(o3)c4ccc(cc4)SC
The Scaffold is 	O=C(Nc1nnc(-c2ccccc2)o1)c1cc2ccccc2o1

Original SMILES is 	c1ccc(cc1)c2csc3c2ncn(c3=O)Cc4cc(=O)n5ccccc5n4
The Scaffold is 	O=c1c2scc(-c3ccccc3)c2ncn1Cc1cc(=O[...]<jupyter_text>Scaffold for fold 2<jupyter_code>i = 2

smiles_list = data_pd_list[i][data_pd_list[i][Target_name]==1]['SMILES'].tolist()
scaffold_set = set()
for smiles in smiles_list:
    mol = Chem.MolFromSmiles(smiles)
    core = MurckoScaffold.GetScaffoldForMol(mol)
    scaffold = Chem.MolToSmiles(core)
    scaffold_set.add(scaffold)
    print 'Original SMILES is \t{}'.format(smiles)
    print 'The Scaffold is \t{}'.format(scaffold)
    print

print '{} total smiles'.format(len(smiles_list))
print '{} different scaffolds'.format(len(scaffold_set))<jupyter_output>Original SMILES is 	c1ccc2c(c1)nc(s2)c3c4c(sc3NC(=O)c5c(cccc5F)F)CN(CC4)C(C)C
The Scaffold is 	O=C(Nc1sc2c(c1-c1nc3ccccc3s1)CCNC2)c1ccccc1

Original SMILES is 	c1ccc2c(c1)nc(s2)c3c4c(sc3NC(=O)c5ccc(s5)Cl)CN(CC4)C(C)C
The Scaffold is 	O=C(Nc1sc2c(c1-c1nc3ccccc3s1)CCNC2)c1cccs1

Original SMILES is 	c1cc2c(c(c1)N)C(=O)N(C2=O)C
The Scaffold is 	O=C1NC(=O)c2ccccc21

Original SMILES is 	c1c2c3c(cc1N)CCCN3C(=O)CC2
The Scaffold is 	O=C1CCc2cccc3c2N1CCC3

Original SMILES is 	c1ccc(c(c1)C(=O)NCCc2ccc3c(c2)CCCN3CCC)OCC
The Scaffold is 	O=C(NCCc1ccc2c(c1)CCCN2)c1ccccc1

Original SMILES is 	c1cc2c(cc1CCNC(=O)Cc3ccc(cc3)F)CCCN2CCC
The Scaffold is 	O=C(Cc1ccccc1)NCCc1ccc2c(c1)CCCN2

Original SMILES is 	c1cc(cc2c1CCCN2CCOC)NS(=O)(=O)Cc3ccc(cc3)Cl
The Scaffold is 	O=S(=O)(Cc1ccccc1)Nc1ccc2c(c1)NCCC2

Original SMILES is 	c1cc(ccc1SCC(=O)Nc2c(c3c(s2)CN(CC3)C(=O)C)C(=O)N)Cl
The Scaffold is 	O=C(CSc1ccccc1)Nc1cc2c(s1)CNCC2

Original SMILES is 	c1cc(ccc1S(=O)(=O)CC(=O)Nc2c(c3c(s2)CN(CC3)C(=O)C)C(=O)N)Cl
The[...]<jupyter_text>Scaffold for fold 3<jupyter_code>i = 3

smiles_list = data_pd_list[i][data_pd_list[i][Target_name]==1]['SMILES'].tolist()
scaffold_set = set()
for smiles in smiles_list:
    mol = Chem.MolFromSmiles(smiles)
    core = MurckoScaffold.GetScaffoldForMol(mol)
    scaffold = Chem.MolToSmiles(core)
    scaffold_set.add(scaffold)
    print 'Original SMILES is \t{}'.format(smiles)
    print 'The Scaffold is \t{}'.format(scaffold)
    print

print '{} total smiles'.format(len(smiles_list))
print '{} different scaffolds'.format(len(scaffold_set))<jupyter_output>Original SMILES is 	c1cc(cc(c1)CS(=O)(=O)Nc2ccc3c(c2)N(CCC3)CCOC)C
The Scaffold is 	O=S(=O)(Cc1ccccc1)Nc1ccc2c(c1)NCCC2

Original SMILES is 	c1ccc(cc1)N(C)S(=O)(=O)c2ccc(cc2)C(=O)Nc3c(c4c(s3)CN(CC4)CCC)C(=O)NC
The Scaffold is 	O=C(Nc1cc2c(s1)CNCC2)c1ccc(S(=O)(=O)Nc2ccccc2)cc1

Original SMILES is 	c1(c(c([nH]c1C)C(=O)CN2CCCCCC2)C)C(=O)OC
The Scaffold is 	O=C(CN1CCCCCC1)c1ccc[nH]1

Original SMILES is 	c1ccc(c(c1)C(=O)NCCc2ccc3c(c2)CCCN3CC)C(F)(F)F
The Scaffold is 	O=C(NCCc1ccc2c(c1)CCCN2)c1ccccc1

Original SMILES is 	c1cc2c(cc1CCNC(=O)C(C)(C)C)CCCN2CCC
The Scaffold is 	c1ccc2c(c1)CCCN2

Original SMILES is 	c1ccc(cc1)CCNC(=O)c2c(c3c(cc(nc3s2)c4ccc(cc4)Cl)c5ccc(cc5)OC)N
The Scaffold is 	O=C(NCCc1ccccc1)c1cc2c(-c3ccccc3)cc(-c3ccccc3)nc2s1

Original SMILES is 	c1ccc(c(c1)C(=O)Nc2cc(ccc2OC)c3cn4c(n3)ccc(n4)OC)Cl
The Scaffold is 	O=C(Nc1cccc(-c2cn3ncccc3n2)c1)c1ccccc1

Original SMILES is 	c1cc(cc(c1OC)S(=O)(=O)N2CCN(CC2)c3ccc(nn3)c4ccncc4)Cl
The Scaffold is 	O=S(=O)(c1ccccc1)N1CCN(c2ccc(-c3ccn[...]<jupyter_text>Scaffold for fold 4<jupyter_code>i = 4

smiles_list = data_pd_list[i][data_pd_list[i][Target_name]==1]['SMILES'].tolist()
scaffold_set = set()
for smiles in smiles_list:
    mol = Chem.MolFromSmiles(smiles)
    core = MurckoScaffold.GetScaffoldForMol(mol)
    scaffold = Chem.MolToSmiles(core)
    scaffold_set.add(scaffold)
    print 'Original SMILES is \t{}'.format(smiles)
    print 'The Scaffold is \t{}'.format(scaffold)
    print

print '{} total smiles'.format(len(smiles_list))
print '{} different scaffolds'.format(len(scaffold_set))<jupyter_output>Original SMILES is 	c1ccnc(c1)CN2Cc3c(ccc4c3OC(=Cc5cccc(c5)F)C4=O)OC2
The Scaffold is 	O=C1C(=Cc2ccccc2)Oc2c1ccc1c2CN(Cc2ccccn2)CO1

Original SMILES is 	C(#N)c1ccc(cc1)C(=O)Nc2c(c3c(s2)CCCC3)C#N
The Scaffold is 	O=C(Nc1cc2c(s1)CCCC2)c1ccccc1

Original SMILES is 	c1cc2c(cc1CCNC(=O)COCC)CCCN2CCC
The Scaffold is 	c1ccc2c(c1)CCCN2

Original SMILES is 	c1cc(ccc1C(=O)NCCc2ccc3c(c2)CCCN3CC)OC(C)C
The Scaffold is 	O=C(NCCc1ccc2c(c1)CCCN2)c1ccccc1

Original SMILES is 	c1cc2c(cc1CCNS(=O)(=O)C)CCCN2CCC
The Scaffold is 	c1ccc2c(c1)CCCN2

Original SMILES is 	c1cscc1C(CNC(=O)c2cc(cc(c2)OC)OC)N3CCCC3
The Scaffold is 	O=C(NCC(c1ccsc1)N1CCCC1)c1ccccc1

Original SMILES is 	c1cc(c(cc1c2csc3c2ncn(c3=O)Cc4cc(=O)n5ccccc5n4)OC)OC
The Scaffold is 	O=c1c2scc(-c3ccccc3)c2ncn1Cc1cc(=O)n2ccccc2n1

Original SMILES is 	c1ccc(cc1)c2cc(c3c(c(sc3n2)C(=O)NCC4CCCO4)N)c5ccc(cc5)OC
The Scaffold is 	O=C(NCC1CCCO1)c1cc2c(-c3ccccc3)cc(-c3ccccc3)nc2s1

Original SMILES is 	c1cc(c(cc1C(=O)c2c(c3c(c4c(nc3s2)CC(CC4=O)(C)C)CC)N)Cl[...]
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