print 'Hello World!'
Hello World!
1+4
5
from rdkit.Chem import AllChem as Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Descriptors
from rdkit import DataStructs
smi = 'CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4' #sildenafil
m = Chem.MolFromSmiles(smi)
m
Descriptors.MolWt(m)
474.5870000000004
Descriptors.TPSA(m)
113.41999999999999
Descriptors.RingCount(m)
4
Chem.MolToSmiles(m, True)
'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(C)CC3)ccc1OCC)[nH]c2=O'
Chem.MolToInchi(m)
'InChI=1S/C22H30N6O4S/c1-5-7-17-19-20(27(4)25-17)22(29)24-21(23-19)16-14-15(8-9-18(16)32-6-2)33(30,31)28-12-10-26(3)11-13-28/h8-9,14H,5-7,10-13H2,1-4H3,(H,23,24,29)'
print Chem.MolToMolBlock(m)
RDKit 33 36 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 1 0 6 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 12 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 1 0 22 23 1 0 17 24 1 0 24 25 2 0 24 26 2 0 24 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 14 4 1 0 14 8 2 0 20 15 1 0 33 27 1 0 M END
# Let's add 2D coordinates...
Chem.Compute2DCoords(m)
0
# The mol block has been updated
print Chem.MolToMolBlock(m)
RDKit 2D 33 36 0 0 0 0 0 0 0 0999 V2000 -8.2094 2.2189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5208 0.8863 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0224 0.8163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3338 -0.5163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0072 -1.8566 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.9405 -2.9112 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.1666 -4.3941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6079 -2.2226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2044 -2.7522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9613 -4.2323 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0441 -1.8015 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.2872 -0.3214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6907 0.2082 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.8510 -0.7424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1269 0.6292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2765 0.0997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4368 1.0503 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1937 2.5305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7903 3.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3700 2.1094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7734 2.6390 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0166 4.1191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4200 4.6487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8402 0.5208 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 3.3107 -0.8826 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3698 1.9242 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2436 -0.0088 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.4867 -1.4889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8902 -2.0185 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0505 -1.0679 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 9.4539 -1.5974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8074 0.4123 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4039 0.9418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 1 0 6 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 12 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 1 0 22 23 1 0 17 24 1 0 24 25 2 0 24 26 2 0 24 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 14 4 1 0 14 8 2 0 20 15 1 0 33 27 1 0 M END
fp = Chem.GetMorganFingerprintAsBitVect(m,2,nBits=2048)
fp.ToBitString()
'00000000000000100000000000000000000000000000000000000000000000000000000001000000100000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010000000000000000000000000000010000000000000000000000000000001000000000000000000000000010000000000000000000100001000000000000000000000000000000101000010000000010000000000010000000000000000001000000000000000000000000000100000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010000000000000000000000000000000000000010000000000000000000010000000000000000000000000000000000000000000000000000000000000000100000000000000000000010000000000000000000000100000000000000000001000000000000000000000000000000000010000001000000000000000000000010000000000000100000100000000000000000000000000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000000000000000100000000100000000000000000000000000000000000000000100000000000000000000000000010000000000000000000000000000000000000000000000000001000000000000000000000000000000000000000000000001000000001000000000000000000000000000000100000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010100001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000000000000000000010000000000010000000000000000000000010001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000100000000000000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000000000000101001000000000000000100001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000000000001000100000000000000000001000000000000000000000000000000000000000000000000000010000010000000000000100000000000000000000000000000000000000000000000000000000000000000000000000000'
fp.GetNumOnBits()
61
fp.GetNumBits()
2048
smi2 = 'CCCc1nc(C)c2C(=O)N=C(Nn12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(CC)CC4' #vardenafil
m2 = Chem.MolFromSmiles(smi2)
fp2 = Chem.GetMorganFingerprintAsBitVect(m2, 2, nBits=2048)
m2
m
DataStructs.TanimotoSimilarity(fp,fp2)
0.5
from rdkit.Chem.Draw import SimilarityMaps
SimilarityMaps.GetSimilarityMapForFingerprint(m2, m, SimilarityMaps.GetMorganFingerprint)
(<matplotlib.figure.Figure at 0x7f88641b3050>, 0.14414414414414412)
sma = 'C1C[!#1!#6]1' #oxirane or aziridine
from IPython.display import Image
from urllib import quote_plus
Image(url='http://www.smartsview.de/smartsview/auto/png/1/dynamic/{0}'.format(quote_plus(sma)))
import psycopg2
conn = psycopg2.connect(port=5432, user='chembl', dbname='chembl_19')
cur = conn.cursor()
sql1 = """
SELECT mr.*, md.chembl_id, cp.full_mwt, cp.alogp
from mols_rdkit mr, molecule_dictionary md, compound_properties cp
where
mr.m @> 'C1C[!#1!#6]1'::qmol
and
mr.molregno = md.molregno
and
md.molregno = cp.molregno
limit 100
"""
cur.execute(sql1)
for c in cur: print c
(504141, 'CC(=O)O[C@H]1C[C@@H]2O[C@]2(C)[C@@H]2[C@@H](O)[C@]34O[C@]3(C)C(=O)O[C@H]4C=C(C)CC[C@@H](OC(C)=O)[C@@]12C', 'CHEMBL465387', Decimal('464.51'), Decimal('0.65')) (511156, 'CC[C@@]12CC(C(=O)OC)=C3Nc4cc(OC)c(O)cc4[C@@]34CCN(C(=O)[C@@H]3O[C@@H]31)[C@H]42', 'CHEMBL525919', Decimal('412.44'), Decimal('1.06')) (1558653, 'C=C(C)[C@]12C[C@@H](C)[C@]34O[C@@]5(CCCCCCC[C@@H](C)[C@@H]6[C@@H]3[C@@](O)(C(=O)[C@H]6C)[C@H](O)[C@@]3(CO)O[C@H]3[C@H]4[C@H]1O5)O2', 'CHEMBL2376812', Decimal('532.67'), Decimal('3.60')) (507693, 'O=C1c2c(O)ccc3c2[C@@]2(Oc4cccc5c4[C@](O3)(O2)[C@H](O)C[C@@H]5O)[C@@H]2O[C@H]12', 'CHEMBL488950', Decimal('382.32'), Decimal('1.01')) (507695, 'O=C1CC[C@]23Oc4ccc(O)c5c4[C@](Oc4cccc1c42)(O3)[C@@H]1O[C@@H]1[C@@H]5O', 'CHEMBL485874', Decimal('366.32'), Decimal('1.66')) (507740, 'CO[C@@H]1CC(=O)c2cccc3c2[C@@]12Oc1ccc(O)c4c1[C@](O3)(O2)[C@@H]1O[C@@H]1[C@@H]4O', 'CHEMBL487724', Decimal('396.35'), Decimal('1.50')) (1558663, 'C=C(C)[C@]12C[C@@H](C)[C@@]34OC(c5ccccc5)(OC1[C@@H]3[C@@H]1O[C@]1(COC(=O)c1ccccc1)[C@@H](O)[C@@]1(O)[C@H]4C[C@H](C)[C@@H]1O)O2', 'CHEMBL2376822', Decimal('590.66'), Decimal('3.77')) (1573582, 'CC[C@H]1C[C@@H]2CN3CCc4c5ccc(OC)c([C@H]6C[C@@H]7[C@]8(O[C@@H]8C)[C@@H]8OC[C@]7(C(=O)OC)[C@H](Cc7c9ccccc9[nH]c76)N8C)c5[nH]c4[C@](C(=O)OC)(C2)[C@H]13', 'CHEMBL2409162', Decimal('748.91'), Decimal('6.27')) (664813, 'Cn1cc(NC(=O)c2cc(NC(=O)c3cc(NC(=O)c4cc(NC(=O)C5CO5)cn4C)cn3C)cn2C)cc1C(=O)NCCC(=N)N', 'CHEMBL1190863', Decimal('645.67'), Decimal('-0.28')) (686885, 'CC(=O)OCC1=CO[C@@H](OC(C)=O)[C@H]2[C@@H]1C[C@H](OC(=O)CC(C)C)[C@]21CO1', 'CHEMBL1215026', Decimal('382.40'), Decimal('0.93')) (686886, 'CC(=O)OCC1=CO[C@@H](OC(=O)CC(C)C)[C@H]2[C@@H]1C[C@H](OC(C)=O)[C@]21CO1', 'CHEMBL1215027', Decimal('382.40'), Decimal('0.93')) (698093, 'c1ccc([C@@H]2CO2)cc1', 'CHEMBL1235743', Decimal('120.15'), Decimal('1.48')) (1523873, 'CN(C)CCn1nc2c3c1ccc(NCCCCN1CC1)c3C(=O)c1ccncc1-2', 'CHEMBL2334226', Decimal('404.51'), Decimal('2.60')) (628080, 'C=C(C)[C@@H]1CC(=O)C[C@H]2O[C@](C)(CC2=O)C[C@H]2OC(=O)[C@@]3(O[C@H]23)[C@@H](O)C1', 'CHEMBL1094859', Decimal('364.39'), Decimal('0.16')) (643623, 'O=C(O)[C@H]1O[C@@H]1c1ccc(F)cc1', 'CHEMBL1162084', Decimal('182.15'), Decimal('1.30')) (643624, 'O=C(O)[C@H]1O[C@@H]1c1ccccc1', 'CHEMBL1162085', Decimal('164.16'), Decimal('1.10')) (1573320, 'NS(=O)(=O)c1ccc(-n2cc(CNC(=O)[C@H](Cc3cscn3)NC(=O)[C@H]3O[C@@H]3C(=O)O)nn2)cc1', 'CHEMBL2408902', Decimal('521.53'), Decimal('-1.36')) (1573342, 'CC(C)C[C@H](NC(=O)[C@H]1O[C@@H]1C(=O)O)C(=O)Nc1c(F)cccc1F', 'CHEMBL2408924', Decimal('356.32'), Decimal('1.44')) (593645, 'COc1cc(C(=O)[C@H]2O[C@@H]2c2cc(OC)c(OC)c(OC)c2)cc(OC)c1OC', 'CHEMBL596033', Decimal('404.41'), Decimal('2.77')) (593623, 'COc1cc(C(=O)[C@H]2O[C@@H]2c2ccc(C)cc2)cc(OC)c1OC', 'CHEMBL594612', Decimal('328.36'), Decimal('3.31')) (593568, 'Cc1ccc(C(=O)[C@H]2O[C@@H]2c2ccc(C)cc2)cc1', 'CHEMBL593208', Decimal('252.31'), Decimal('3.84')) (1573333, 'O=C(O)[C@@H]1O[C@H]1C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)Nc1nc2ccc(F)cc2s1', 'CHEMBL2408915', Decimal('419.39'), Decimal('0.22')) (1576269, 'N#Cc1c(Cl)nc(SCC2CO2)nc1-c1ccccc1', 'CHEMBL2415028', Decimal('303.77'), Decimal('3.53')) (501263, 'CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3C[C@@H]4O[C@@]45C[C@@H](O)CC[C@]5(C)[C@H]3CC[C@]12C', 'CHEMBL497438', Decimal('402.65'), Decimal('6.22')) (501490, 'CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3[C@@H]4O[C@@]45C[C@@H](O)CC[C@]5(C)[C@H]3CC[C@]12C', 'CHEMBL496408', Decimal('388.63'), Decimal('5.83')) (504154, 'CC(=O)O[C@H]1CC=C(C)[C@@H]2[C@@H](OC(C)=O)[C@]34O[C@]3(C)C(=O)O[C@H]4C=C(C)CC[C@@H](OC(C)=O)[C@@]12C', 'CHEMBL463137', Decimal('490.54'), Decimal('2.38')) (501187, 'CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3[C@@H](O)[C@@H]4O[C@@]45C[C@@H](O)CC[C@]5(C)[C@H]3CC[C@]12C', 'CHEMBL497835', Decimal('418.65'), Decimal('5.32')) (501265, 'CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3[C@@H](O)[C@H]4O[C@]45C[C@@H](O)CC[C@]5(C)[C@H]3CC[C@]12C', 'CHEMBL497816', Decimal('418.65'), Decimal('5.32')) (501428, 'CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3C[C@H]4O[C@]45[C@@H](O)[C@@H](O)CC[C@]5(C)[C@H]3CC[C@]12C', 'CHEMBL496805', Decimal('418.65'), Decimal('5.65')) (501492, 'CC(=O)O[C@H]1[C@@H](O)CC[C@]2(C)[C@H]3CC[C@]4(C)[C@@H]([C@H](C)CCCC(C)C)CC[C@H]4[C@@H]3C[C@H]3O[C@@]312', 'CHEMBL501171', Decimal('460.69'), Decimal('6.03')) (506514, 'CC(C)(O)[C@@H]1[C@H]2OC(=O)[C@@H]1[C@]1(O)C[C@H]3O[C@]34C(=O)O[C@H]2[C@@]41C', 'CHEMBL478523', Decimal('310.30'), Decimal('-1.33')) (504155, 'CC(=O)O[C@H]1C[C@@H]2O[C@]2(C)[C@@H]2[C@@H](OC(C)=O)[C@]34O[C@]3(C)C(=O)O[C@H]4C=C(C)CC[C@@H](OC(C)=O)[C@@]12C', 'CHEMBL456944', Decimal('506.54'), Decimal('1.02')) (507225, 'CC1(C)CC2=C(O1)C1(CO1)c1ccccc1C2=O', 'CHEMBL508314', Decimal('242.27'), Decimal('1.75')) (555538, 'COc1c2ccc(=O)oc2c(C(C)(C)C2CO2)c2c1C1OC1C(C)(C)O2', 'CHEMBL560276', Decimal('358.39'), Decimal('2.51')) (1522289, 'C[C@@H]1C(=O)O[C@@H]2C[C@@]3(C)CCC[C@H](C)[C@@]34O[C@H]4[C@@H]21', 'CHEMBL2332658', Decimal('250.33'), Decimal('2.34')) (700632, 'COC(=O)/C(C)=C\\C[C@@]12OC(C)(C)[C@H]3C[C@@H](C=C4C(=O)c5c(O)c6c(c(CC7OC7(C)C)c5O[C@]431)O[C@]1(C)CCC(=C(C)C)C6C1)C2=O', 'CHEMBL1241413', Decimal('658.78'), Decimal('5.61')) (710317, 'CC(C)[C@]12O[C@H]1C=C1[C@]3(O[C@H]3C[C@@H]3C4=C(CC[C@]13C)C(=O)OC4)[C@@H]2O', 'CHEMBL1271068', Decimal('344.40'), Decimal('1.63')) (587281, 'CC1=CC(=O)OC[C@]23CCC(C)=C[C@H]2O[C@@H]2C[C@@H](OC(=O)C=CC=CC(=O)OCC1)[C@@]3(C)[C@]21CO1', 'CHEMBL576350', Decimal('484.54'), Decimal('2.98')) (1487228, 'C[C@]12C=CC(=O)C(C)(C)C1C(O)(C(=O)O)[C@@]1(C)C[C@@]34O[C@@H]3C[C@@H](c3ccoc3)C4C[C@H]21', 'CHEMBL2269930', Decimal('426.50'), Decimal('2.36')) (1563065, 'CO[C@H]1O[C@@H]([C@@H]2OC2(C)C)C[C@H]1[C@@H]1CC=C2[C@@]1(C)CC[C@@H]1[C@@]3(C)C=CC(=O)C(C)(C)[C@@H]3C[C@@H](O)[C@@]21C', 'CHEMBL2386300', Decimal('498.69'), Decimal('4.18')) (1486978, 'CC[C@@](C)(OC(C)=O)C(=O)O[C@H]1[C@H](O)C[C@@H]2[C@@](C)([C@@H]3C[C@H]4C=CO[C@H]4O3)C(C)=C[C@H](OC(C)=O)[C@@]2(COC(C)=O)[C@@]12CO2', 'CHEMBL2269683', Decimal('606.66'), Decimal('1.06')) (1523988, 'CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1ccc(OCC2CO2)c(C)c1', 'CHEMBL2334340', Decimal('438.60'), Decimal('6.96')) (700047, 'CC1=CCC(C)(C)C=C[C@H](O)[C@@]2(C)O[C@H]2CC1', 'CHEMBL1240835', Decimal('236.35'), Decimal('2.97')) (1560200, 'C=C1C(=O)O[C@@H]2C=C(C)CC[C@H]3O[C@]3(COC(C)=O)C[C@@H](OC(=O)C3(C)OC3C)[C@@H]12', 'CHEMBL2380317', Decimal('420.45'), Decimal('1.68')) (671160, 'CCNC[C@@H]1C(=O)O[C@@H]2[C@@H]3O[C@]3(C)CCC=C(C)CC[C@@H]12', 'CHEMBL1197210', Decimal('293.40'), Decimal('2.31')) (671111, 'CC1=CCC[C@@]2(C)O[C@H]2[C@H]2OC(=O)[C@@H](CN3CCC(C)CC3)[C@@H]2CC1', 'CHEMBL1197161', Decimal('347.49'), Decimal('3.66')) (701512, 'CCNC(=O)O[C@H]1CC[C@H](C)[C@@H](/C(C)=C/C=C/[C@@H](C)C[C@H]2O[C@@H]2[C@H](C)[C@@H](O)CC)OC(=O)C[C@H](O)CC[C@@]1(C)O', 'CHEMBL1242284', Decimal('567.75'), Decimal('4.47')) (693999, 'CO[C@H]1[C@H](OC(C)=O)CC(=O)O[C@H](C)C[C@@H]2O[C@H]2C=CC(=O)[C@H](C)C[C@H](CC=O)[C@@H]1O[C@@H]1O[C@H](C)[C@@H](O[C@H]2C[C@@](C)(O)[C@@H](OC(=O)CC(C)C)[C@H](C)O2)[C@H](N(C)C)[C@H]1O', 'CHEMBL1231649', Decimal('841.98'), Decimal('2.22')) (691245, 'CC1(C)[C@H]2C=C(C=O)CC[C@H]3O[C@]3(C)CC[C@H]21', 'CHEMBL1224785', Decimal('234.33'), Decimal('2.63')) (567142, 'CCCCCCS(=O)(=O)c1cc(Cl)c(C(=O)CCN2CC2C)c(Cl)c1', 'CHEMBL563943', Decimal('406.37'), Decimal('5.12')) (1564400, 'O=S(=O)(c1cc(Cl)cc(Cl)c1)C1CO1', 'CHEMBL2385106', Decimal('253.10'), Decimal('2.57')) (1577777, 'CNC[C@@H]1C(=O)O[C@H]2[C@H]1CCC(C)=C1C[C@H]3O[C@@]3(C)[C@@H]12', 'CHEMBL2419001', Decimal('277.36'), Decimal('1.18')) (1563057, 'C=C1[C@@H]2[C@@H](O[C@H]3CC(=O)C(C)(C)[C@H](CC(=O)OC)[C@@]23C)[C@H](OC(C)=O)[C@@]2(C)[C@H](c3ccoc3)C[C@H]3O[C@]132', 'CHEMBL2386292', Decimal('512.59'), Decimal('2.28')) (675258, 'C[N+]1(C)C2CC(OC(=O)C(O)(c3cccs3)c3cccs3)CC1[C@@H]1O[C@H]12', 'CHEMBL1201307', Decimal('392.51'), Decimal('0.90')) (446686, 'C/C(=C\\c1csc(CO)n1)[C@@H]1C[C@@H]2O[C@@H]2CCC[C@H](C)[C@H](O)[C@@H](C)C(=O)C(C)(C)[C@@H](O)CC(=O)O1', 'CHEMBL470478', Decimal('509.66'), Decimal('2.90')) (446687, 'C/C(=C\\c1csc(CO)n1)[C@@H]1C[C@@H]2O[C@]2(C)CCC[C@H](C)[C@H](O)[C@@H](C)C(=O)C(C)(C)[C@@H](O)CC(=O)O1', 'CHEMBL513726', Decimal('523.68'), Decimal('3.11')) (1545943, 'Cc1c(OCCN2CC2)cc(C(=O)N[C@@H]2C(=O)N[C@H](C(C)C)C(=O)N3CCC[C@H]3C(=O)N(C)CC(=O)N(C)[C@@H](C(C)C)C(=O)O[C@@H]2C)c2nc3c(C(=O)N[C@@H]4C(=O)N[C@H](C(C)C)C(=O)N5CCC[C@H]5C(=O)N(C)CC(=O)N(C)[C@@H](C(C)C)C(=O)O[C@@H]4C)c(N)c(=O)c(C)c-3oc12', 'CHEMBL2371492', Decimal('1340.52'), None) (701554, 'C[C@H]1C(=O)C=CC(C)(C)C[C@@H]2O[C@]2(C)CC[C@H]1NCc1ccccc1', 'CHEMBL1242326', Decimal('341.49'), Decimal('3.88')) (701553, 'CCCCN[C@@H]1CC[C@@]2(C)O[C@H]2CC(C)(C)C=CC(=O)[C@@H]1C', 'CHEMBL1242325', Decimal('307.47'), Decimal('3.63')) (578137, 'CO[C@@H]1[C@H](OC(=O)N[C@H]2CN3CCC2CC3)CC[C@]2(CO2)[C@H]1[C@@]1(C)O[C@@H]1CC=C(C)C', 'CHEMBL578806', Decimal('434.57'), Decimal('2.31')) (578138, 'CO[C@@H]1[C@H](OC(=O)N[C@@H](C(=O)Nc2cccc(C(=O)O)c2)C(C)C)CC[C@]2(CO2)[C@H]1[C@@]1(C)O[C@@H]1CC=C(C)C', 'CHEMBL585936', Decimal('544.64'), Decimal('3.36')) (580238, 'CC[C@H](C)[C@H](NC(C)=O)C(=O)N[C@@H](CO)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CC(=O)C1(C)CO1)C(=O)O', 'CHEMBL570439', Decimal('656.73'), Decimal('-2.28')) (792884, 'COC(=O)[C@@H]1OC(=O)[C@H]2O[C@]23[C@]2(C)C(=O)C[C@@H]4[C@](C)(C=CC(=O)OC4(C)C)[C@H]2CC[C@@]13C', 'CHEMBL1369000', Decimal('446.49'), Decimal('1.84')) (1558650, 'C=C(C)[C@]12C[C@@H](C)[C@]34O[C@@]5(CCCCCCC[C@@H](C)[C@@H]6[C@@H]3[C@@](O)([C@@H](O)[C@H]6C)[C@H](O)[C@@]3(COC(=O)c6ccccc6)O[C@H]3[C@H]4[C@H]1O5)O2', 'CHEMBL2376809', Decimal('638.79'), Decimal('5.40')) (1293799, 'CCC12C[N+]3([O-])CC(CC(C(=O)OC)(c4cc5c(cc4OC)N(C)C4C56CCN5CC=CC(CC)(C56)C(OC(C)=O)C4(O)C(=O)OC)c4[nH]c5ccccc5c4CC3)C1O2', 'CHEMBL1972508', Decimal('824.96'), Decimal('3.89')) (1078424, 'CCCCC[C@@H]1OC=C2[C@@H]3OC(C)(C)[C@@H](O)C[C@@]34O[C@H]4C(=O)[C@@]23[C@@H]2O[C@@H](CCCCC)[C@@H](C4=C2[C@H]2OC(C)(C)[C@@H](O)C[C@@]25O[C@H]5C4=O)[C@@H]13', 'CHEMBL1689808', Decimal('668.81'), Decimal('2.29')) (503834, 'CC(C)=C1C(=O)C[C@]2(C)CC=C(C)CC[C@@H]3O[C@@]3(C)CC[C@@H]12', 'CHEMBL516013', Decimal('302.45'), Decimal('4.49')) (504227, 'COC(C)(C)C1=C[C@H]2O[C@]2(C)CCC=C(C)CC[C@H]2O[C@]2(C)CC1', 'CHEMBL516336', Decimal('334.49'), Decimal('3.96')) (668302, 'CC1=CCC[C@@]2(C)O[C@H]2[C@H]2OC(=O)[C@@H](CNCCN)[C@@H]2CC1', 'CHEMBL1194352', Decimal('308.42'), Decimal('1.13')) (668290, 'CC1=CCC[C@@]2(C)O[C@H]2[C@H]2OC(=O)[C@@H](CNNC(C)(C)C)[C@@H]2CC1', 'CHEMBL1194340', Decimal('336.47'), Decimal('2.33')) (622066, 'CC1=CC(=O)[C@H]2C(C)(C)CCC[C@]2(C)[C@H]1[C@@H]1O[C@@H]1c1ccoc1', 'CHEMBL1092575', Decimal('314.42'), Decimal('3.72')) (651597, 'NC(=O)c1cccc(C2CO2)c1', 'CHEMBL1171468', Decimal('163.17'), Decimal('0.48')) (671180, 'C=CCN(CC=C)C[C@@H]1C(=O)O[C@@H]2[C@@H]3O[C@]3(C)CCC=C(C)CC[C@@H]12', 'CHEMBL1197230', Decimal('345.48'), Decimal('3.73')) (900155, 'CC1C(=O)OC2C1CC[C@@]1(C)C=CC(=O)[C@@]3(C)O[C@]231', 'CHEMBL1476271', Decimal('262.30'), Decimal('1.60')) (1285594, 'Cc1ccc(OCC2CO2)c(Br)c1', 'CHEMBL1964303', Decimal('243.10'), Decimal('2.76')) (916793, 'O=C1c2ccccc2C(=O)C2OC12', 'CHEMBL1492909', Decimal('174.15'), Decimal('0.82')) (1067289, 'Nc1ncnc2c1ncn2CC1CN1Cc1ccccc1', 'CHEMBL1668522', Decimal('280.33'), Decimal('1.33')) (1303258, 'CC(CO)[C@H]1OC(=O)C=C2[C@@]13O[C@@H]3[C@H]1OC(=O)[C@@]3(C)[C@H]4O[C@H]4C[C@@]2(C)[C@@H]13', 'CHEMBL1981967', Decimal('362.37'), Decimal('0.17')) (1063560, 'CC(=O)O[C@H](C[C@@H](C)[C@H]1C(=O)[C@H](O)[C@@]2(C)[C@@H]3CC[C@@H]4[C@]5(C[C@@]35CC[C@]12C)CC[C@H](O)C4(C)C)[C@H]1OC1(C)C', 'CHEMBL1651286', Decimal('530.74'), Decimal('3.80')) (1604603, 'Cc1ccc(S(=O)(=O)N2CC2(C)CO[C@@H]2O[C@@H]3CO[C@H](c4ccccc4)O[C@@H]3[C@H](O)[C@H]2O)cc1', 'CHEMBL3087128', Decimal('491.55'), Decimal('1.62')) (1079618, 'Cc1ccc(NC(=O)N2CC2)cc1NC(=O)N1CC1', 'CHEMBL1698887', Decimal('260.29'), Decimal('0.60')) (1073725, 'C=C1C[C@@H]2CC[C@@]34C[C@H]5O[C@@H]6[C@@H](O[C@H]7CC[C@H](CC(=O)C[C@@H]8[C@@H](OC)[C@@H](C[C@@H](CN9C[C@@H]9C)OC)O[C@H]8C[C@H]8O[C@@H](CC[C@@H]1O2)C[C@@H](C)C8=C)O[C@@H]7[C@@H]6O3)[C@H]5O4', 'CHEMBL1683598', Decimal('783.99'), Decimal('2.54')) (1063555, 'CC(=O)O[C@@H]1C[C@@]23C[C@@]24CC[C@H](O[C@@H]2OC[C@@H](O)[C@H](O)[C@H]2O)C(C)(C)[C@@H]4CC[C@H]3[C@]2(C)C[C@@H]3O[C@]4(C[C@@H](C)[C@@H]3[C@@]12C)O[C@H](O)[C@@]1(C)O[C@@H]14', 'CHEMBL1651281', Decimal('676.83'), Decimal('1.81')) (1164261, 'C[C@H]1CC[C@@H]2[C@@H](OC(=O)[C@]23CN3c2ccccc2[N+](=O)[O-])[C@]2(C)C(=O)C=C[C@@]12O', 'CHEMBL1806585', Decimal('398.41'), Decimal('2.56')) (1217498, 'CC1(C)O[C@H]2O[C@H]([C@H](O)CO/N=C3\\[C@H]4O[C@H]4[C@@H](O)[C@H]4[C@@H]3CCn3c(=O)n(-c5ccccc5)c(=O)n34)[C@H](O)[C@H]2O1', 'CHEMBL1876927', Decimal('546.53'), Decimal('-1.24')) (1077476, 'C=C(C)[C@H]1CC(=O)[C@]2(C)CC=C(C)CC[C@@H]3O[C@@]3(C)CC[C@@H]12', 'CHEMBL1689080', Decimal('302.45'), Decimal('4.34')) (1564392, 'CCCC1OC1S(=O)(=O)c1ccccc1', 'CHEMBL2387614', Decimal('226.29'), Decimal('2.60')) (1548035, 'CCCNC(=O)OC[C@H]1O[C@@H](CCO/N=C2/[C@H]3O[C@@H]3[C@@H](O)[C@H]3[C@H]2CCn2c(=O)n(-c4ccccc4)c(=O)n23)C=C[C@@H]1Oc1ccc(OC)cc1', 'CHEMBL2373584', Decimal('691.73'), Decimal('2.81')) (1277391, 'CCCCCCCCCCCCC(=O)/C=C/CCCOC[C@H]1CO1', 'CHEMBL1946010', Decimal('338.52'), Decimal('6.04')) (1614132, 'CCCCN(C)C(=O)O[C@@H](C)/C=C\\C(=O)N[C@H]1CO[C@@H](C/C=C(C)/C=C/[C@@H]2C[C@]3(CO3)CC(C)(C)O2)OC1', 'CHEMBL3108937', Decimal('534.68'), Decimal('2.90')) (1614136, 'CC(/C=C/[C@@H]1C[C@]2(CO2)CC(C)(C)O1)=C\\C[C@H]1OC[C@@H](NC(=O)/C=C\\[C@H](C)OC(=O)N2CCCCC2)CO1', 'CHEMBL3108941', Decimal('532.67'), Decimal('2.48')) (1059753, 'O=C(/C=C/c1ccc(OCC2CS2)cc1)c1ccc(OCC2CS2)cc1', 'CHEMBL1644751', Decimal('384.51'), Decimal('4.59')) (1059755, 'COc1ccc(/C=C/C(=O)c2ccc(OCC3CS3)cc2OCC2CS2)cc1', 'CHEMBL1644753', Decimal('414.54'), Decimal('4.58')) (1063269, 'CC1(C)O[C@H]1COc1cc(=O)oc2cc3occc3cc12', 'CHEMBL1651087', Decimal('286.28'), Decimal('2.19')) (1572813, 'CC(=O)O[C@H]1[C@H]2O[C@H]2C[C@@H]2[C@@H](O)C(=O)[C@H]3[C@@H]4[C@@H](O)[C@@H]5[C@H]([C@H](C)C=C6OC(=O)[C@@](C)(O)[C@@]65C)[C@@]4(C)[C@@H](OC(C)=O)[C@@H](OC(C)=O)[C@@H]3[C@@]12C', 'CHEMBL2408400', Decimal('660.71'), Decimal('-0.52')) (1300641, 'CC(O)CCOP(=O)(N(CCCl)CCCl)N1CC1', 'CHEMBL1979350', Decimal('319.17'), Decimal('0.19')) (1573338, 'CC(C)C[C@H](NC(=O)[C@@H]1O[C@H]1C(=O)O)C(=O)Nc1nc(-c2ccc(F)cc2)cs1', 'CHEMBL2408920', Decimal('421.44'), Decimal('2.18')) (1579396, 'CC[C@H](O)[C@@H](C)[C@H]1O[C@@H]1C[C@H](C)/C=C/C=C(\\C)[C@H]1OC(=O)CCCCCCC=C[C@@H]1C', 'CHEMBL2420604', Decimal('432.64'), Decimal('6.40')) (998031, 'O=C(Cn1c2ccccc2n(CC2CS2)c1=O)N1CCCCC1', 'CHEMBL1574147', Decimal('331.43'), Decimal('1.75')) (1226861, 'O=C1C=CC(O)C2(CO)OC12', 'CHEMBL1886290', Decimal('156.14'), Decimal('-1.21'))
smi = 'CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4' #sildenafil
sql2 = """
select molregno,m as smiles,tanimoto_sml(morganbv_fp('CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4'::mol),mfp2) as similarity
from fps_rdkit join mols_rdkit using (molregno)
where morganbv_fp('CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4'::mol)%mfp2
order by morganbv_fp('CCCc1nn(C)c2C(=O)NC(=Nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4'::mol)<%>mfp2;
"""
cur.execute(sql2)
for c in cur: print c
(410802, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(C)CC3)ccc1OCC)[nH]c2=O', 1.0) (1351311, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCC3)ccc1OCC)[nH]c2=O', 0.88135593220339) (1351310, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCCC3)ccc1OCC)[nH]c2=O', 0.88135593220339) (80636, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCNCC3)ccc1OCC)[nH]c2=O', 0.866666666666667) (80694, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(CCO)CC3)ccc1OCC)[nH]c2=O', 0.838709677419355) (488008, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(c4ccccc4)CC3)ccc1OCC)[nH]c2=O', 0.825396825396825) (512303, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCC(C(N)=O)CC3)ccc1OCC)[nH]c2=O', 0.8125) (410662, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(CCC(=O)O)CC3)ccc1OCC)[nH]c2=O', 0.8125) (488151, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(C4CCCCC4)CC3)ccc1OCC)[nH]c2=O', 0.8) (410656, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCC(C(=O)O)CC3)ccc1OCC)[nH]c2=O', 0.8) (1334756, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(C)nn(C)c2c(=O)[nH]1', 0.8) (488072, 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'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(C(F)(F)F)c(Br)c(=O)[nH]1', 0.585714285714286) (140260, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c([nH]1)n(CC(C)CC)c(=O)n(C)c2=O', 0.583333333333333) (140807, 'C=CCCn1c2[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc2c(=O)n(C)c1=O', 0.583333333333333) (139960, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c([nH]1)n(CC1CCCCC1)c(=O)n(C)c2=O', 0.583333333333333) (80559, 'CCCc1nn(C)c2c1nc(-c1ccccc1OCC1CC1)[nH]c2=O', 0.582089552238806) (1441477, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(CC(C)C)cc(=O)[nH]1', 0.579710144927536) (1334762, 'CCCc1nn(C)c2c1nc(-c1cccnc1OCC)[nH]c2=O', 0.578125) (410698, 'CCCOc1ccc(NC(=O)CCC)cc1-c1nc2c(CCC)nn(C)c2c(=O)[nH]1', 0.577464788732394) (410696, 'CCCOc1ccc(NC(=O)CC)cc1-c1nc2c(CCC)nn(C)c2c(=O)[nH]1', 0.577464788732394) (1441478, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(-c2ccccc2)cc(=O)[nH]1', 0.571428571428571) (304703, 'CCCc1nc(C)n2c1nc(-c1cc(S(=O)(=O)N3CCN(C)CC3)ccc1OCC)nc2O', 0.571428571428571) (410702, 'CCCOc1ccc(NC(=O)C(C)C)cc1-c1nc2c(CCC)nn(C)c2c(=O)[nH]1', 0.569444444444444) (80558, 'CCCc1nn(C)c2c1nc(-c1ccccc1NS(C)(=O)=O)[nH]c2=O', 0.569230769230769) (140519, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c([nH]1)n(CC(C)C)c(=O)n(C)c2=O', 0.567567567567568) (410689, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(CCO)CC3)cc3c1OCCO3)[nH]c2=O', 0.567567567567568) (410687, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(CCO)CC3)cc3c1OCO3)[nH]c2=O', 0.567567567567568) (410686, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(CCO)CC3)cc3c1OCCC3)[nH]c2=O', 0.565789473684211) (304580, 'CCCn1cnc2c1nc(-c1cc(S(=O)(=O)N3CCN(C)CC3)ccc1OCC)nc2O', 0.563380281690141) (304707, 'CCCc1nc(CC)c2c(O)nc(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nn12', 0.561643835616438) (140816, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c([nH]1)n(Cc1ccc(OC)cc1)c(=O)n(C)c2=O', 0.56) (102837, 'CCCOc1ccc(S(=O)(=O)N2CCN(CP(=O)(O)O)CC2)cc1-c1nc2c(CCC)nn(C)c2c(O)n1', 0.545454545454545) (325914, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(nc3c(C)cccn32)c(O)n1', 0.540540540540541) (512228, 'CCCc1nn(C)c2c1nc(-c1ccccc1O)[nH]c2=O', 0.53968253968254) (410708, 'CCCOc1ccc(NC(=O)C2CCCCC2)cc1-c1nc2c(CCC)nn(C)c2c(=O)[nH]1', 0.539473684210526) (102529, 'CCCOc1ccc(S(=O)(=O)N2CCN(CP(=O)(OCC)OCC)CC2)cc1-c1nc2c(CCC)nn(C)c2c(O)n1', 0.538461538461538) (1334759, 'CCCc1nn(C)c2c1nc(-c1cccnc1OC)[nH]c2=O', 0.537313432835821) (1008491, 'CCCc1nn(C)c2c1nc(-c1cc(S(N)(=O)=O)ccc1OCC)nc2O', 0.536231884057971) (326033, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(nc3cc(C)ccn32)c(O)n1', 0.533333333333333) (1334767, 'CCCc1nn(C)c2c1nc(-c1cccnc1O)[nH]c2=O', 0.53030303030303) (1469709, 'CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1-c1nc2ncccc2c(=O)[nH]1', 0.527777777777778) (325968, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(nc3ccc(Br)cn32)c(O)n1', 0.526315789473684) (1334776, 'CCCc1nn(C)c2c1nc(-c1ccsc1)[nH]c2=O', 0.523809523809524) (1334773, 'CCCc1nn(C)c2c1nc(-c1cn(C)cn1)[nH]c2=O', 0.523809523809524) (80670, 'CCCc1nn(C)c2c1nc(-c1ccccc1[N+](=O)[O-])[nH]c2=O', 0.522388059701492) (1334761, 'CCCc1nn(C)c2c1nc(-c1cccnc1OC(C)C)[nH]c2=O', 0.521739130434783) (971340, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)NC)ccc1OCC)nc2O', 0.52112676056338) (800246, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N(CCO)CCO)ccc1OCC)nc2O', 0.520547945205479) (1469710, 'CCOc1ccc(S(=O)(=O)N2CCN(c3ccccc3)CC2)cc1-c1nc2ncccc2c(=O)[nH]1', 0.520547945205479) (140606, 'CC(C)COc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c([nH]1)n(CC(C)C)c(=O)n(C)c2=O', 0.52) (1227092, 'CCCc1nn(C)c2c1nc(-c1cc([S+](=O)([O-])N3CCN(C)CC3)ccc1OCC)nc2O', 0.52) (326091, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(nc3ccc(C)cn32)c(O)n1', 0.52) (1353820, 'CCCc1nn(C)c2c1nc(-c1ccc(C)cc1)[nH]c2=O', 0.516129032258065) (512227, 'CCCc1nn(C)c2c1nc(-c1ccccc1)[nH]c2=O', 0.516129032258065) (1334771, 'CCCc1nn(C)c2c1nc(-c1cn(C)nc1C)[nH]c2=O', 0.515625) (1353819, 'CCCc1nn(C)c2c1nc(-c1ccc(OC)cc1)[nH]c2=O', 0.515625) (1212525, 'CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)NCCO)ccc1OCC)nc2O', 0.513513513513513) (1269220, 'CCCn1nc2c(nc(-c3cc(S(=O)(=O)N4CCN(C)CC4)cnc3OCCOC)[nH]c2=O)c1CC', 0.513513513513513) (140345, 'CCOc1ccc(S(=O)(=O)N2CCN(CC)CC2)cc1-c1nc2c([nH]1)n(CC(C)C)c(=O)n(C)c2=O', 0.513157894736842) (1353817, 'CCCc1nn(C)c2c1nc(-c1ccc(Br)cc1)[nH]c2=O', 0.507936507936508) (1334775, 'CCCc1nn(C)c2c1nc(-c1ccnn1C)[nH]c2=O', 0.507936507936508) (421326, 'CCCc1nc(C)c2c(=O)nc(-c3cc(S(=O)(=O)N4CCN(CC)CC4)ccc3OCC)[nH]n12', 0.506666666666667) (28710, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(O)c2cc3[nH]cnc3cc2n1', 0.506666666666667) (140382, 'CCOc1ccc(S(=O)(=O)N2CCN(CCN(C)C)CC2)cc1-c1nc2c([nH]1)n(CC(C)C)c(=O)n(C)c2=O', 0.506329113924051) (1334770, 'CCCc1nn(C)c2c1nc(-c1ccc(=O)[nH]n1)[nH]c2=O', 0.5) (511950, 'CCCCN1C(=O)C2=C(N=C(c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)NC2)C1=O', 0.5) (1353821, 'CCCc1nn(C)c2c1nc(-c1cccc(Br)c1)[nH]c2=O', 0.5) (326382, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(nc3cccc(CC)n32)c(O)n1', 0.5) (1353818, 'CCCc1nn(C)c2c1nc(-c1cccc(Cl)c1)[nH]c2=O', 0.5) (1353816, 'CCCc1nn(C)c2c1nc(-c1ccc(Cl)cc1)[nH]c2=O', 0.5) (140451, 'CCOc1ccc(S(=O)(=O)N2CCN(CCO)CC2)cc1-c1nc2c([nH]1)n(CC(C)C)c(=O)n(C)c2=O', 0.5) (1334766, 'CCCc1nn(C)c2c1nc(-c1ccc(O)cc1)[nH]c2=O', 0.5) (1351307, 'CCOc1ccc(S(=O)(=O)Nc2ccc(O)c(C(=O)O)c2)cc1-c1nc2c(C(C)(C)C)nn(C)c2c(=O)[nH]1', 0.5) (453288, 'CCCc1c2nc(-c3cc(S(=O)(=O)N4CCN(CC)CC4)cnc3OCCOC)[nH]c(=O)c2nn1C', 0.5)
from rdkit.Chem import PandasTools
import pandas as pd
height has been deprecated.
data = pd.read_sql(sql2, conn)
data.shape
(194, 3)
data.head()
molregno | smiles | similarity | |
---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(C)CC3)ccc1OCC)[nH]c2=O | 1.000000 |
1 | 1351311 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCC3)ccc1OCC)[nH]c2=O | 0.881356 |
2 | 1351310 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCCC3)ccc1OCC)[nH]c2=O | 0.881356 |
3 | 80636 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCNCC3)ccc1OCC)[nH]c2=O | 0.866667 |
4 | 80694 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(CCO)CC3)ccc1OCC)[nH]c2=O | 0.838710 |
nn = data[data['similarity'] >= 0.8]
nn.shape
(12, 3)
nn.head()
molregno | smiles | similarity | |
---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(C)CC3)ccc1OCC)[nH]c2=O | 1.000000 |
1 | 1351311 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCC3)ccc1OCC)[nH]c2=O | 0.881356 |
2 | 1351310 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCCC3)ccc1OCC)[nH]c2=O | 0.881356 |
3 | 80636 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCNCC3)ccc1OCC)[nH]c2=O | 0.866667 |
4 | 80694 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(CCO)CC3)ccc1OCC)[nH]c2=O | 0.838710 |
PandasTools.AddMoleculeColumnToFrame(data,smilesCol='smiles',molCol='mol',includeFingerprints=True)
data.head()
molregno | smiles | similarity | mol | |
---|---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(C)CC3)ccc1OCC)[nH]c2=O | 1.000000 | |
1 | 1351311 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCC3)ccc1OCC)[nH]c2=O | 0.881356 | |
2 | 1351310 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCCC3)ccc1OCC)[nH]c2=O | 0.881356 | |
3 | 80636 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCNCC3)ccc1OCC)[nH]c2=O | 0.866667 | |
4 | 80694 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(CCO)CC3)ccc1OCC)[nH]c2=O | 0.838710 |
data['logp'] = data['mol'].map(Descriptors.MolLogP)
data['mw'] = data['mol'].map(Descriptors.MolWt)
data.head()
molregno | smiles | similarity | mol | logp | mw | |
---|---|---|---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(C)CC3)ccc1OCC)[nH]c2=O | 1.000000 | 1.6109 | 474.587 | |
1 | 1351311 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCC3)ccc1OCC)[nH]c2=O | 0.881356 | 2.8494 | 459.572 | |
2 | 1351310 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCCC3)ccc1OCC)[nH]c2=O | 0.881356 | 3.2395 | 473.599 | |
3 | 80636 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCNCC3)ccc1OCC)[nH]c2=O | 0.866667 | 1.2687 | 460.560 | |
4 | 80694 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(CCO)CC3)ccc1OCC)[nH]c2=O | 0.838710 | 0.9734 | 504.613 |
data.sort(columns=['similarity']).head()
molregno | smiles | similarity | mol | logp | mw | |
---|---|---|---|---|---|---|
193 | 453288 | CCCc1c2nc(-c3cc(S(=O)(=O)N4CCN(CC)CC4)cnc3OCCOC)[nH]c(=O)c2nn1C | 0.5 | 1.0225 | 519.628 | |
184 | 1334770 | CCCc1nn(C)c2c1nc(-c1ccc(=O)[nH]n1)[nH]c2=O | 0.5 | 0.3594 | 286.295 | |
185 | 511950 | CCCCN1C(=O)C2=C(N=C(c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)NC2)C1=O | 0.5 | 0.7942 | 489.598 | |
186 | 1353821 | CCCc1nn(C)c2c1nc(-c1cccc(Br)c1)[nH]c2=O | 0.5 | 3.0386 | 347.216 | |
187 | 326382 | CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(nc3cccc(CC)n32)c(O)n1 | 0.5 | 2.5473 | 496.593 |
data[['mw', 'logp']].describe()
mw | logp | |
---|---|---|
count | 194.000000 | 194.000000 |
mean | 486.932845 | 2.290035 |
std | 91.490079 | 0.970899 |
min | 268.320000 | -0.048300 |
25% | 448.825000 | 1.579575 |
50% | 498.012000 | 2.293320 |
75% | 537.399000 | 2.924625 |
max | 866.980000 | 4.731700 |
rcParams['figure.figsize'] = 12,12
data['logp'].hist()
<matplotlib.axes.AxesSubplot at 0x7f883e6e4d50>
scatter(data['mw'],data['logp'])
<matplotlib.collections.PathCollection at 0x7f883e395950>
data[data['mw']>800][['molregno','mol','mw','logp']]
molregno | mol | mw | logp | |
---|---|---|---|---|
62 | 487046 | 852.997 | 2.6245 | |
92 | 487045 | 866.980 | 2.7168 |
qsmi = 'c1nn(C)c2c1nc[nH]c2=O'
qmol = Chem.MolFromSmiles(qsmi)
qmol
subset = data[data['mol'] >= qmol]
subset.shape
(90, 6)
subset.head()
molregno | smiles | similarity | mol | logp | mw | |
---|---|---|---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(C)CC3)ccc1OCC)[nH]c2=O | 1.000000 | 1.6109 | 474.587 | |
1 | 1351311 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCC3)ccc1OCC)[nH]c2=O | 0.881356 | 2.8494 | 459.572 | |
2 | 1351310 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCCC3)ccc1OCC)[nH]c2=O | 0.881356 | 3.2395 | 473.599 | |
3 | 80636 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCNCC3)ccc1OCC)[nH]c2=O | 0.866667 | 1.2687 | 460.560 | |
4 | 80694 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(CCO)CC3)ccc1OCC)[nH]c2=O | 0.838710 | 0.9734 | 504.613 |
data.groupby(data['mol'] >= qmol).describe().unstack()
logp | molregno | mw | similarity | |||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
count | mean | std | min | 25% | 50% | 75% | max | count | mean | std | min | 25% | 50% | 75% | max | count | mean | std | min | 25% | 50% | 75% | max | count | mean | std | min | 25% | 50% | 75% | max | |
mol | ||||||||||||||||||||||||||||||||
False | 104 | 2.074994 | 0.778351 | -0.0483 | 1.549950 | 2.10405 | 2.586725 | 4.4372 | 104 | 795393.692308 | 546222.400768 | 28710 | 304713.75 | 562140.5 | 1441476.25 | 1575540 | 104 | 493.938654 | 45.641263 | 391.453 | 462.61600 | 491.0795 | 518.88700 | 624.701 | 104 | 0.595978 | 0.052087 | 0.5 | 0.566521 | 0.600000 | 0.626866 | 0.734375 |
True | 90 | 2.538528 | 1.107499 | 0.3034 | 1.620075 | 2.65905 | 3.322050 | 4.7317 | 90 | 709987.411111 | 449869.213609 | 80558 | 410694.50 | 488009.5 | 1334760.50 | 1376119 | 90 | 478.837244 | 124.968717 | 268.320 | 386.95875 | 504.5910 | 558.42875 | 866.980 | 90 | 0.670030 | 0.113819 | 0.5 | 0.567983 | 0.691176 | 0.753623 | 1.000000 |
data['containsQ'] = data['mol'] >= qmol
data.head(2)
molregno | smiles | similarity | mol | logp | mw | containsQ | |
---|---|---|---|---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCN(C)CC3)ccc1OCC)[nH]c2=O | 1.000000 | 1.6109 | 474.587 | True | |
1 | 1351311 | CCCc1nn(C)c2c1nc(-c1cc(S(=O)(=O)N3CCCCC3)ccc1OCC)[nH]c2=O | 0.881356 | 2.8494 | 459.572 | True |
data.boxplot('similarity',by='containsQ')
<matplotlib.axes.AxesSubplot at 0x7f883e07f1d0>
conn.close()