print 'Hello World!'
Hello World!
1+4
5
%matplotlib inline
%pylab inline
from IPython.display import Image
import warnings
warnings.filterwarnings('ignore')
Populating the interactive namespace from numpy and matplotlib
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)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12'
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 0x7f505bf7d1d0>, 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_21')
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
(1940080, 'C[N+](C)(CCCCCC[N+]1(C)[C@H]2C[C@@H](OC(=O)[C@H](CO)c3ccccc3)C[C@@H]1[C@H]1O[C@@H]21)CCCN1C(=O)c2ccccc2C1=O', 'CHEMBL3558234', Decimal('619.79'), Decimal('0.55')) (1940079, 'CC(C)(CN1C(=O)c2cccc3cccc(c23)C1=O)C[N+](C)(C)CCCCCC[N+]1(C)[C@H]2C[C@@H](OC(=O)[C@H](CO)c3ccccc3)C[C@@H]1[C@H]1O[C@@H]21', 'CHEMBL3558233', Decimal('697.90'), Decimal('2.31')) (1521972, 'CO[C@H]1[C@H]([C@@]2(C)O[C@@H]2CC=C(C)C)[C@@](O)(CCl)CC[C@H]1OC(=O)CCC(=O)O', 'CHEMBL2332344', Decimal('418.91'), Decimal('2.06')) (1591552, 'CC(C)C[C@H](NC(=O)[C@@H]1O[C@@H]1C(=O)O)C(=O)N1CCC[C@H]1C(=O)OCc1ccccc1', 'CHEMBL3038001', Decimal('432.47'), Decimal('1.55')) (1797500, 'C[C@]12CC[C@H]3[C@@H](CC[C@@]45O[C@H]4C(O)=C(C#N)C[C@]35C)[C@H]1CC[C@H]2O', 'CHEMBL3348889', Decimal('329.43'), Decimal('2.43')) (1589413, 'CC(C)NC(=O)Nc1ccc(Oc2ccc(S(=O)(=O)CC3CS3)cc2)cc1', 'CHEMBL2442884', Decimal('406.52'), Decimal('3.22')) (1589421, 'CC(C)OC(=O)Oc1ccc(Oc2ccc(S(=O)(=O)CC3CS3)cc2)cc1', 'CHEMBL2442892', Decimal('408.49'), Decimal('4.51')) (1589416, 'CCCOC(=O)Nc1ccc(Oc2ccc(S(=O)(=O)CC3CS3)cc2)cc1', 'CHEMBL2442887', Decimal('407.50'), Decimal('4.01')) (1589415, 'CCOC(=O)Nc1ccc(Oc2ccc(S(=O)(=O)CC3CS3)cc2)cc1', 'CHEMBL2442886', Decimal('393.48'), Decimal('3.49')) (1589420, 'CCCOC(=O)Oc1ccc(Oc2ccc(S(=O)(=O)CC3CS3)cc2)cc1', 'CHEMBL2442891', Decimal('408.49'), Decimal('4.66')) (1589407, 'CCNC(=O)Oc1ccc(Oc2ccc(S(=O)(=O)CC3CS3)cc2)cc1', 'CHEMBL2442878', Decimal('393.48'), Decimal('3.49')) (1589410, 'CNC(=O)Nc1ccc(Oc2ccc(S(=O)(=O)CC3CS3)cc2)cc1', 'CHEMBL2442881', Decimal('378.47'), Decimal('2.49')) (1795751, 'COC(=O)[C@]1(C)CCC[C@@]2(C)[C@H]1CC[C@]13C=C(C(C)C)[C@H](C[C@H]21)[C@H]1C(=O)[C@@H]2O[C@@H]2C(=O)[C@H]13', 'CHEMBL3343596', Decimal('440.57'), Decimal('3.74')) (1794380, 'CC1=C2[C@@H](C[C@@H]3[C@]4(CC[C@@H]5C(C)(C)CC[C@H](O)[C@@]35C)O[C@H]24)OC1=O', 'CHEMBL3342239', Decimal('332.43'), Decimal('2.70')) (1820044, 'CC(=O)/C=C/C1C(C)(C)CCC2OC21C', 'CHEMBL3355911', Decimal('208.30'), Decimal('1.99')) (1850887, 'CC(=O)Nc1csc(-c2cnc(/C=C(\\C)C[C@H]3OC[C@H](C[C@H]4O[C@H]4[C@@H](C)[C@@H](C)O)[C@@H](O)[C@H]3O)o2)c1', 'CHEMBL3434643', Decimal('506.61'), Decimal('1.26')) (1548659, 'C[C@@]1(C(=O)O)CCC[C@@]2(C)C3=CC[C@H]4C[C@@]3(CC[C@H]12)C[C@]41CO1', 'CHEMBL2374208', Decimal('316.43'), Decimal('3.38')) (1512920, 'COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1OC)OCO3)C[C@H](C)[C@]1(CO1)[C@H]2OC(=O)c1ccccc1', 'CHEMBL2313859', Decimal('534.55'), Decimal('4.94')) (1512102, 'C=C(C)[C@H]1C[C@H](O)C(C)=CCC[C@@]2(C)O[C@@H]2CCC(COC(C)=O)=C[C@@H]1O', 'CHEMBL2313049', Decimal('378.50'), Decimal('3.07')) (1790955, 'CC1=CCC[C@@]2(C)O[C@@H]2[C@H]2OC(=O)/C(=C/c3ccccc3Br)[C@@H]2CC1', 'CHEMBL3334827', Decimal('403.31'), Decimal('5.11')) (1790958, 'C[C@@]12CCC=C(CO)CC[C@@H]3/C(=C\\c4ccccc4Br)C(=O)O[C@@H]3[C@@H]1O2', 'CHEMBL3334830', Decimal('419.31'), Decimal('4.02')) (1790961, 'C[C@@]12CCC=C(CO)CC[C@@H]3/C(=C\\c4cccs4)C(=O)O[C@@H]3[C@@H]1O2', 'CHEMBL3334833', Decimal('346.44'), Decimal('3.22')) (1788945, 'C[C@@]12CC[C@@H](O)[C@@](C)(CO)[C@H]1CC[C@@]1(CO1)[C@H]2C/C=C1/C(=O)OC[C@H]1OC(=O)CCl', 'CHEMBL3329954', Decimal('442.93'), Decimal('1.83')) (1610133, 'CC1=C[C@@H]2O[C@@H](O)[C@@]3(C)O[C@@]23CCC(C)=CCC[C@](C)(O)[C@H](O)CC1', 'CHEMBL3099355', Decimal('352.47'), Decimal('2.53')) (1618940, 'COc1ccc(-n2cc(CNC[C@@H]3C(=O)O[C@H]4[C@H]3CCC(C)=C3C[C@H]5O[C@@]5(C)[C@@H]34)nn2)cc1', 'CHEMBL3115956', Decimal('450.53'), Decimal('2.72')) (1618941, 'CC1=C2C[C@H]3O[C@@]3(C)[C@@H]2[C@H]2OC(=O)[C@@H](CNCc3cn(-c4ccccc4[N+](=O)[O-])nn3)[C@@H]2CC1', 'CHEMBL3115957', Decimal('465.50'), Decimal('2.63')) (1618950, 'CC1=C2C[C@H]3O[C@@]3(C)[C@@H]2[C@H]2OC(=O)[C@@H](CNCc3cn(-c4cc(Cl)c(Cl)cc4Cl)nn3)[C@@H]2CC1', 'CHEMBL3115966', Decimal('523.84'), Decimal('4.73')) (1618951, 'CC1=C2C[C@H]3O[C@@]3(C)[C@@H]2[C@H]2OC(=O)[C@@H](CNCc3cn(-c4ccccc4)nn3)[C@@H]2CC1', 'CHEMBL3115967', Decimal('420.50'), Decimal('2.73')) (1618954, 'CC1=C2C[C@H]3O[C@@]3(C)[C@@H]2[C@H]2OC(=O)[C@@H](CNCc3cn(-c4ccccc4Br)nn3)[C@@H]2CC1', 'CHEMBL3115970', Decimal('499.40'), Decimal('3.48')) (1618957, 'COc1cccc(-n2cc(CNC[C@@H]3C(=O)O[C@H]4[C@H]3CCC(C)=C3C[C@H]5O[C@@]5(C)[C@@H]34)nn2)c1', 'CHEMBL3115973', Decimal('450.53'), Decimal('2.72')) (1590037, 'CCCCCC1OC1C/C=C\\CCCCCCCC(=O)O', 'CHEMBL2447889', Decimal('296.44'), Decimal('5.42')) (1168216, 'C=C(CO)[C@@]12O[C@@H]1[C@@]1(C)C(=CC2=O)[C@H](OC(=O)C(O)(CO)CC(C)CC(C)C(C)O)CC[C@@H]1C', 'CHEMBL1813185', Decimal('480.59'), Decimal('2.20')) (1699307, 'COc1cc(C(=O)O[C@H]2CC(C)=CCC[C@]3(C)O[C@@H]3C(O)C2C(C)C)cc(OC)c1OC', 'CHEMBL3210016', Decimal('448.55'), Decimal('4.15')) (1819357, 'CC1=C[C@@H]2[C@H](CC[C@]3(CO3)[C@H](OC(=O)Cc3ccccc3)[C@H]3[C@@H](OC(=O)Cc4ccccc4)[C@@H](C)C[C@]3(O)C1=O)C2(C)C', 'CHEMBL3355231', Decimal('586.71'), Decimal('5.50')) (1828705, 'O=C(OC[C@H]1O[C@@H](O[C@@H]2OC=C[C@@H]3[C@H]2[C@@]2(COC(=O)c4ccccc4)O[C@H]2[C@@H]3OC(=O)c2ccccc2)[C@H](O)[C@@H](OC(=O)c2ccccc2)[C@@H]1OC(=O)c1ccccc1)c1ccccc1', 'CHEMBL3394884', Decimal('882.86'), Decimal('6.64')) (1594544, 'C[N+]1(C)[C@H]2C[C@H](OC(=O)C(C(=O)OC3CCCCC3)c3ccccc3)C[C@@H]1[C@H]1O[C@@H]21', 'CHEMBL3084653', Decimal('414.51'), Decimal('1.79')) (1595090, 'C[N+]1(C)[C@H]2C[C@H](OC3c4ccccc4CSc4ccccc43)C[C@@H]1[C@H]1O[C@@H]21', 'CHEMBL3085199', Decimal('380.52'), Decimal('1.92')) (1594991, 'O=C(O[C@@H]1C[C@@H]2N[C@H](C1)[C@@H]1O[C@H]21)[C@H](CO)c1ccccc1', 'CHEMBL3085100', Decimal('289.33'), Decimal('0.29')) (1616391, 'C1=C2CCN3Cc4cc5c(cc4[C@H]([C@H](OC[C@@H]4CO4)[C@H]1OC[C@@H]1CO1)[C@@H]23)OCO5', 'CHEMBL3113433', Decimal('399.44'), Decimal('0.96')) (1844845, 'C/C(=C/C[C@]12OC(C)(C)[C@@H]3C[C@H](C1=O)C1OC14C(=O)c1c(O)cccc1O[C@@]342)C(=O)O', 'CHEMBL3427452', Decimal('426.42'), Decimal('1.66')) (1925376, 'CC(C)CC(NC(=O)C(CCc1ccccc1)NC(=O)CN1CCOCC1)C(=O)NC(Cc1ccccc1)C(=O)NC(CC(C)C)C(=O)C1(C)CO1', 'CHEMBL3542249', Decimal('719.91'), Decimal('3.80')) (1925131, 'C[C@]12CC[C@@H](O)C[C@H]1CC[C@@H]1[C@@H]2CC[C@]2(C)[C@@H](c3ccc(=O)oc3)[C@@H](O)[C@H]3O[C@]132', 'CHEMBL3527424', Decimal('400.51'), Decimal('2.21')) (1925299, 'CO[C@H]1[C@H]([C@@]2(C)O[C@@H]2CC=C(C)C)[C@]2(CC[C@H]1OC(=O)N[C@@H](C(N)=O)C(C)(C)O)CO2', 'CHEMBL3527591', Decimal('440.53'), Decimal('0.80')) (1841756, 'CC1=C(CO)C(=O)O[C@@H]([C@@H](C)[C@H]2C(=O)C[C@H]3[C@@H]4C[C@H]5O[C@]56CC=CC(=O)[C@]6(C)[C@H]4CC[C@@]32C)C1', 'CHEMBL3422314', Decimal('468.58'), Decimal('3.01')) (1840991, 'O=c1c2ccccc2oc2cc(OCC3CS3)cc(OCC3CS3)c12', 'CHEMBL3417778', Decimal('372.46'), Decimal('3.85')) (1243626, 'CC1CN1P1(=O)OCC(C)([N+](=O)[O-])CO1', 'CHEMBL1903055', Decimal('236.16'), Decimal('-0.25')) (1296095, 'COC(=O)C1(COCc2ccccc2)CCCC2OC21', 'CHEMBL1974804', Decimal('276.33'), Decimal('2.16')) (1296481, 'CCN(CC)C(=O)CCN1CC1', 'CHEMBL1975190', Decimal('170.25'), Decimal('0.35')) (1296551, 'CC(=O)OC1C[C@@H](C)C2(CC(c3ccoc3)OC2=O)C2CCC(O)C3(CO3)C12CO', 'CHEMBL1975260', Decimal('420.45'), Decimal('0.57')) (1486389, 'CC(=O)N1CC[C@@]23c4ccccc4N[C@@H]4N(C)c5cccc6c5[C@@]42CCN([C@@H]6[C@H]2OC2(C)C)[C@@H]13', 'CHEMBL2269100', Decimal('456.58'), Decimal('2.88')) (1284986, 'O=C(CCc1ccccc1)c1cc(F)ccc1OCC1CO1', 'CHEMBL1963275', Decimal('300.32'), Decimal('3.63')) (1286002, 'CC1OC(O[C@H]2C3C=CO[C@@H](OC4OC(CO)C(O)C(O)C4O)C3[C@@]3(COC(=O)/C=C/c4ccccc4)O[C@@H]23)C(O)C(O)C1O', 'CHEMBL1964711', Decimal('638.61'), Decimal('-1.93')) (1283089, 'CC(=O)[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', 'CHEMBL1957557', Decimal('332.48'), Decimal('2.47')) (1303337, 'C/C=C(/C)C(=O)O[C@H]1[C@H]2[C@@H]([C@@H](OC(C)=O)[C@H](C)C(=O)[C@@]34C[C@@H](C)C(=O)[C@]3(C=C(C)[C@H]1OC(C)=O)O4)C2(C)C', 'CHEMBL1982046', Decimal('530.61'), Decimal('3.32')) (1303518, 'COC12OC3(C4OC41)C(C(=O)O[C@H]3CO[Si](C)(C)C(C)(C)C)C2C(=O)Oc1ccccc1', 'CHEMBL1982227', Decimal('462.56'), None) (1286420, 'C=C1C(=O)OC2C=C(C)C3OC3C=C(C(=O)OC)C(OC(C)=O)C(OC(=O)C(C)(O)C(C)OC(C)=O)C12', 'CHEMBL1965129', Decimal('522.50'), Decimal('0.91')) (1294515, 'C=C1C(=O)O[C@@H]2[C@@H]3O[C@]3(C)C[C@@H]3C=C(C[C@H](OC(=O)C=C(C)C)[C@@H]12)C(=O)O3', 'CHEMBL1973224', Decimal('374.38'), Decimal('2.12')) (1287694, 'CCC1OC(=O)CC(O)C(C)C(OC2OC(C)CC(N(C)C)C2O)C(CC=O)CC(C)C(=O)C=CC2(C)OC2C1C', 'CHEMBL1966403', Decimal('581.74'), Decimal('2.34')) (1324918, 'CC1=C[C@H]2O[C@@H]3C[C@H]4OC(=O)C=CC=CC(C(C)O)OCC(O)C(C)CC(=O)OC[C@@]2(C[C@@H]1O)[C@]4(C)[C@@]31CO1', 'CHEMBL2003627', Decimal('548.62'), Decimal('0.62')) (1338748, 'C=C(C)[C@@]12O[C@@]3(c4ccccc4)O[C@@H]1[C@@H]1[C@@H]4O[C@]4(CO)[C@@H](O)[C@]4(O)C(=O)C(C)=C[C@H]4[C@@]1(O3)[C@H](C)[C@H]2OC(=O)/C=C/c1ccccc1', 'CHEMBL2023370', Decimal('628.67'), Decimal('3.48')) (1547730, 'C[C@@H]1C[C@]2(OC[C@]3(C)O[C@@H]32)O[C@H]2C[C@@]3(C)[C@@H]4CC[C@H]5C(C)(C)C(O[C@@H]6OC[C@@H](O)[C@H](O)[C@H]6O)CC[C@@]56C[C@@]46CC[C@]3(C)[C@H]21', 'CHEMBL2373279', Decimal('602.80'), Decimal('2.88')) (1299787, 'O=C1c2ccccc2OCC12OC21C=CC(Cl)=CC1', 'CHEMBL1978496', Decimal('274.70'), Decimal('2.35')) (1300804, 'O=C(O[C@@H]1[C@@H]2O[C@]2(CO)[C@H]2[C@H](OC3OC(CO)C(O)C(O)C3O)OC=C[C@@H]12)c1ccc(O)c(O)c1', 'CHEMBL1979513', Decimal('498.43'), Decimal('-2.02')) (1300984, 'CC1(C)CCC[C@@]2(C)C1CC[C@@]1(CO1)[C@@H]2/C=C\\C(C=O)CC=O', 'CHEMBL1979693', Decimal('318.45'), Decimal('2.94')) (1290593, 'Cc1ccc2c3c1[C@@H]1O[C@@H]1c1cccc(c1-3)[C@@H]1O[C@H]21', 'CHEMBL1969302', Decimal('248.28'), Decimal('2.70')) (1376887, 'Clc1ccc([C@]2(Cn3cncn3)O[C@H]2c2ccc(Cl)cc2Cl)cc1', 'CHEMBL2104617', Decimal('380.66'), Decimal('4.56')) (1385023, 'C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC[C@@H]2[C@@H]1CN1', 'CHEMBL2112772', Decimal('315.49'), Decimal('3.42')) (1385033, 'C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)C1=CC[C@@H]2[C@@H]1CN1', 'CHEMBL2112782', Decimal('313.48'), Decimal('3.17')) (1378261, 'O=c1n(CC2CO2)c(=O)n(CC2CO2)n1CC1CO1', 'CHEMBL2105991', Decimal('269.25'), Decimal('-1.29')) (1304213, 'Cc1ccc(S(=O)(=O)N2CC2CCCCC=O)cc1', 'CHEMBL1982922', Decimal('281.37'), Decimal('2.27')) (1383913, 'CC(C)CNC(=O)[C@H](CC(C)C)NC(=O)[C@@H]1O[C@@H]1C(=O)O', 'CHEMBL2111662', Decimal('300.35'), Decimal('0.65')) (1301882, 'C[C@@H]1CCC[C@]2(C)O[C@H]2CC[C@@](C)(O)[C@@H]2CC3=C(CO)C(=O)O[C@H]3[C@H]1O2', 'CHEMBL1980591', Decimal('366.45'), Decimal('1.71')) (1367965, 'CC1(C)CN1P(=O)(Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O)n1)N1CC1(C)C', 'CHEMBL2092776', Decimal('429.41'), Decimal('-2.30')) (1347014, 'C=C(C)[C@@]12OC3(c4ccccc4)O[C@@H]1[C@@H]1[C@@H]4O[C@]4(C)[C@@H](O)[C@@H]4C(=O)C(C)=C[C@@H]4[C@@]1(O3)[C@H](C)[C@@H]2OC(=O)c1ccccc1', 'CHEMBL2037469', Decimal('570.63'), Decimal('4.63')) (1486682, 'C/C=C(\\C)C(=O)O[C@H]1C[C@@H](OC(C)=O)[C@@]2(C(=O)OC)CO[C@H]3[C@@H](O)[C@@](C)([C@]45O[C@@]4(C)[C@H]4C[C@@H]5O[C@@H]5OCC[C@@]54O)[C@@H]4[C@@](OC)(C(=O)OC)OC[C@@]14[C@@H]32', 'CHEMBL2269390', Decimal('736.76'), Decimal('-1.10')) (1490004, 'C=C1Cc2c(Cl)cc3[nH]c4c5c3c2[C@H]2[C@@H]1C[C@@H]2C(C)(C)O[C@H]5[C@@H]1CC[C@@]2(O)[C@@]35O[C@@H]3[C@@H](O)[C@@H](C(=C)C)O[C@H]5CC[C@]2(C)[C@@]41C', 'CHEMBL2272678', Decimal('618.20'), Decimal('5.65')) (1548540, 'C=C(C)[C@H]1O[C@H]2CC[C@]3(C)[C@@]4(C)c5[nH]c6cc(Cl)c7c8c6c5[C@@H](OC(C)(C)[C@H]5C[C@H](C(=C)C7)[C@]85O)[C@@H]4CC[C@@]3(O)[C@]23O[C@@H]3[C@H]1O', 'CHEMBL2374089', Decimal('634.20'), Decimal('4.64')) (1302591, 'O=C1CN2C(Cl)(Cl)C2(c2ccccc2)c2cc(Cl)ccc2N1CC(F)(F)F', 'CHEMBL1981300', Decimal('435.65'), Decimal('5.25')) (1385010, 'CC(=O)[C@@]12O[C@@H]1C[C@H]1[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@@]12C', 'CHEMBL2112759', Decimal('328.45'), Decimal('2.92')) (1385139, 'C[C@]12CC[C@H](O)C[C@@H]1CC[C@@H]1[C@@H]2CC[C@@]2(C)[C@H]1C[C@H]1O[C@]12c1cccnc1', 'CHEMBL2112888', Decimal('367.52'), Decimal('3.58')) (1304487, 'CC(=O)O[C@H]1C[C@@H](OC(C)=O)[C@@](C)(O)[C@@H]2[C@@H](OC(C)=O)[C@@]3(O)[C@H](C=C(CCl)[C@H]4O[C@H]4[C@@H](OC(C)=O)[C@@]12C)OC(=O)[C@@H]3C', 'CHEMBL1983196', Decimal('617.04'), Decimal('-0.25')) (1140747, 'C[C@@H]1O[C@@H](C=C=CBr)C[C@H]2O[C@@H](C[C@H]2Cl)[C@@H](Br)C[C@H]2O[C@H]12', 'CHEMBL1765721', Decimal('442.57'), Decimal('2.54')) (1363863, 'CO[C@@]12[C@H](COC(N)=O)C3=C(C(=O)C(Br)=C(N)C3=O)N1C[C@@H]1N[C@@H]12', 'CHEMBL2079632', Decimal('399.20'), Decimal('-1.54')) (1593438, 'CO[C@@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(NCCc4ccccn4)C3=O)N1C[C@@H]1N[C@@H]12', 'CHEMBL3040627', Decimal('439.46'), Decimal('-0.22')) (1301081, 'C=C1C(=O)OC2(C)CCC1CC1OC1(C)CCC=C(C)CCC2O', 'CHEMBL1979790', Decimal('334.45'), Decimal('3.65')) (1359336, 'CC(=O)CC1CC2C(O1)[C@H]1O[C@]13[C@@H]1CC[C@@H]4C[C@@H](O)CC[C@]4(C)[C@H]1CC[C@]23C', 'CHEMBL2069022', Decimal('388.54'), Decimal('2.58')) (1378488, 'C[C@]1(O)CC[C@H]2[C@@H]3CC[C@@]45O[C@]4(C)C(O)=C(C#N)C[C@]5(C)[C@H]3CC[C@@]21C', 'CHEMBL2106218', Decimal('357.49'), Decimal('2.84')) (1384770, 'C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC1O[C@]12c1c[nH]cn1', 'CHEMBL2112519', Decimal('354.49'), Decimal('2.79')) (1298648, 'CC#CC#C/C=C1/O[C@]2(CCC(OC(=O)CC(C)C)CO2)[C@@H]2O[C@H]12', 'CHEMBL1977357', Decimal('330.37'), Decimal('3.13')) (1301139, 'CC(=O)c1ccc2c3c1[C@H]1O[C@H]1c1cccc(c1-3)[C@@H]1O[C@H]21', 'CHEMBL1979848', Decimal('276.29'), Decimal('1.96')) (1287453, 'C=C1C(=O)O[C@@H]2C=C(C)C=C[C@@H]3O[C@@]3(C)C[C@@H](O)C12', 'CHEMBL1966162', Decimal('262.30'), Decimal('1.12')) (1286741, 'C=C1C(=O)O[C@@H]2[C@H]1C[C@H]1O[C@]1(C)CC[C@@H]1O[C@@]1(C)CCC[C@@H](C)[C@@H]2O', 'CHEMBL1965450', Decimal('350.45'), Decimal('2.60')) (1303225, 'CC(=O)OCC1=C(C)CC(C(C)C2CCC3C4CC5OC56C(OC(C)=O)C=CC(=O)C6(C)C4CCC23C)OC1=O', 'CHEMBL1981934', Decimal('554.67'), Decimal('4.15')) (1295673, 'C=C1C(=O)OC2CCCCC3OC3C12', 'CHEMBL1974382', Decimal('194.23'), Decimal('1.54')) (1296635, 'COc1cc(O)c2c(c1)C(O)C(O)CC1OC1C(=O)C=CCC(C)OC2=O', 'CHEMBL1975344', Decimal('378.37'), Decimal('0.90')) (1302979, 'C=C1C(=O)OC2C=C(C)C(OC(C)=O)CC=C(C)C(OC(=O)C3(C)OC3C)C(O)C12', 'CHEMBL1981688', Decimal('420.45'), Decimal('1.99')) (1300314, 'C=C(C(=O)OC)[C@H]1CCC(C)=CCCC(C)=CCC[C@@]2(C)O[C@@H]2C1', 'CHEMBL1979023', Decimal('332.48'), Decimal('5.29')) (1332359, 'O=C(CCCCCc1ccc(-c2ccccc2)cc1)OCC1CO1', 'CHEMBL2011311', Decimal('324.41'), Decimal('4.78')) (1303342, 'CC(C)C1CN1CC(O)Cn1ccnc1[N+](=O)[O-]', 'CHEMBL1982051', Decimal('254.29'), Decimal('1.03')) (1298487, 'CC1OC(O[C@H]2C3C=CO[C@@H](OC4OC(CO)C(O)C(O)C4O)C3[C@@]3(COC(=O)/C=C/c4ccc(O)cc4)O[C@@H]23)C(O)C(O)C1O', 'CHEMBL1977196', Decimal('654.61'), Decimal('-2.17'))
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)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12', 1.0) (1351310, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCCC4)ccc3OCC)nc12', 0.88135593220339) (1351311, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCC4)ccc3OCC)nc12', 0.88135593220339) (80636, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCNCC4)ccc3OCC)nc12', 0.866666666666667) (80694, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCO)CC4)ccc3OCC)nc12', 0.838709677419355) (488008, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(c5ccccc5)CC4)ccc3OCC)nc12', 0.825396825396825) (512303, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCC(C(N)=O)CC4)ccc3OCC)nc12', 0.8125) (410662, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCC(=O)O)CC4)ccc3OCC)nc12', 0.8125) (488151, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C5CCCCC5)CC4)ccc3OCC)nc12', 0.8) (1334756, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(C)nn(C)c2c(=O)[nH]1', 0.8) (488072, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(c5ccc(F)cc5)CC4)ccc3OCC)nc12', 0.8) (410656, 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'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(F)c(OC)cc(O)c2c(=O)[nH]1', 0.597222222222222) (1441767, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(C(C)C)c(C)c(=O)[nH]1', 0.594202898550725) (1441763, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(C(C)C)c(I)c(=O)[nH]1', 0.594202898550725) (1441762, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(C(C)C)c(Br)c(=O)[nH]1', 0.594202898550725) (1441473, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(NC(C)=O)cc(=O)[nH]1', 0.594202898550725) (140805, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(=O)n(C)c(=O)n(CC(C)(C)C)c2[nH]1', 0.591549295774648) (1441773, 'CCCCCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(C(C)C)c(Br)c(=O)[nH]1', 0.591549295774648) (140087, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(=O)n(C)c(=O)n(CC(C)C)c2[nH]1', 0.591549295774648) (410684, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCO)CC4)cc4c3OCC4)nc12', 0.589041095890411) (560347, 'C=Cc1c(OC)cc(O)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12', 0.589041095890411) (1821316, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nnc2nn(C)c(C)c2n1', 0.588235294117647) (1441476, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(C(C)C)cc(=O)[nH]1', 0.588235294117647) (1441479, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(C(F)(F)F)cc(=O)[nH]1', 0.588235294117647) (555093, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2cc(OC)cc(O)c2c(=O)[nH]1', 0.585714285714286) (1441772, 'CCCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(C(C)C)c(Br)c(=O)[nH]1', 0.585714285714286) (1575540, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(C(F)(F)F)c(Br)c(=O)[nH]1', 0.585714285714286) (139960, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(=O)n(C)c(=O)n(CC3CCCCC3)c2[nH]1', 0.583333333333333) (140260, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(=O)n(C)c(=O)n(CC(C)CC)c2[nH]1', 0.583333333333333) (140807, 'C=CCCn1c(=O)n(C)c(=O)c2nc(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)[nH]c21', 0.583333333333333) (80559, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccccc3OCC3CC3)nc12', 0.582089552238806) (1441477, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(CC(C)C)cc(=O)[nH]1', 0.579710144927536) (1334762, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cccnc3OCC)nc12', 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)n2c(O)nc(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12', 0.571428571428571) (410702, 'CCCOc1ccc(NC(=O)C(C)C)cc1-c1nc2c(CCC)nn(C)c2c(=O)[nH]1', 0.569444444444444) (80558, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccccc3NS(C)(=O)=O)nc12', 0.569230769230769) (140519, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(=O)n(C)c(=O)n(CC(C)C)c2[nH]1', 0.567567567567568) (410687, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCO)CC4)cc4c3OCO4)nc12', 0.567567567567568) (410689, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCO)CC4)cc4c3OCCO4)nc12', 0.567567567567568) (1821317, 'CCOc1ccc(S(=O)(=O)N2CCN(S(=O)(=O)c3ccc(OCC)c(-c4nnc5c(n4)c(C)nn5C)c3)CC2)cc1-c1nnc2c(n1)c(C)nn2C', 0.567164179104478) (410686, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCO)CC4)cc4c3OCCC4)nc12', 0.565789473684211) (304580, 'CCCn1cnc2c(O)nc(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc21', 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(=O)n(C)c(=O)n(Cc3ccc(OC)cc3)c2[nH]1', 0.56) (102837, 'CCCOc1ccc(S(=O)(=O)N2CCN(CP(=O)(O)O)CC2)cc1-c1nc(O)c2c(n1)c(CCC)nn2C', 0.545454545454545) (1821318, 'CCOc1ccc(S(=O)(=O)N2CCCN(S(=O)(=O)c3ccc(OCC)c(-c4nnc5c(n4)c(C)nn5C)c3)CC2)cc1-c1nnc2c(n1)c(C)nn2C', 0.542857142857143) (325914, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(O)c2nc3c(C)cccn3c2n1', 0.540540540540541) (512228, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccccc3O)nc12', 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-c1nc(O)c2c(n1)c(CCC)nn2C', 0.538461538461538) (1334759, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cccnc3OC)nc12', 0.537313432835821) (1008491, 'CCCc1nn(C)c2c(O)nc(-c3cc(S(N)(=O)=O)ccc3OCC)nc12', 0.536231884057971) (1746346, 'CCOc1ccc(S(=O)(=O)N2CCNCC2)cc1-c1nnc2c(n1)c(C)nn2C', 0.535211267605634) (326033, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(O)c2nc3cc(C)ccn3c2n1', 0.533333333333333) (1334767, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cccnc3O)nc12', 0.53030303030303) (1746349, 'CCOc1ccc(S(=O)(=O)N2CCCC2)cc1-c1nnc2c(n1)c(C)nn2C', 0.528571428571429) (1469709, 'CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1-c1nc2ncccc2c(=O)[nH]1', 0.527777777777778) (325968, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(O)c2nc3ccc(Br)cn3c2n1', 0.526315789473684) (1334776, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccsc3)nc12', 0.523809523809524) (1334773, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cn(C)cn3)nc12', 0.523809523809524) (80670, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccccc3[N+](=O)[O-])nc12', 0.522388059701492) (1334761, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cccnc3OC(C)C)nc12', 0.521739130434783) (1746348, 'CCOc1ccc(S(=O)(=O)N2CCCCC2)cc1-c1nnc2c(n1)c(C)nn2C', 0.52112676056338) (971340, 'CCCc1nn(C)c2c(O)nc(-c3cc(S(=O)(=O)NC)ccc3OCC)nc12', 0.52112676056338) (1469710, 'CCOc1ccc(S(=O)(=O)N2CCN(c3ccccc3)CC2)cc1-c1nc2ncccc2c(=O)[nH]1', 0.520547945205479) (800246, 'CCCc1nn(C)c2c(O)nc(-c3cc(S(=O)(=O)N(CCO)CCO)ccc3OCC)nc12', 0.520547945205479) (140606, 'CC(C)COc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc2c(=O)n(C)c(=O)n(CC(C)C)c2[nH]1', 0.52) (326091, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(O)c2nc3ccc(C)cn3c2n1', 0.52) (1353820, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccc(C)cc3)nc12', 0.516129032258065) (512227, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccccc3)nc12', 0.516129032258065) (1334771, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cn(C)nc3C)nc12', 0.515625) (1353819, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccc(OC)cc3)nc12', 0.515625) (1212525, 'CCCc1nn(C)c2c(O)nc(-c3cc(S(=O)(=O)NCCO)ccc3OCC)nc12', 0.513513513513513) (1269220, 'CCCn1nc2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)cnc3OCCOC)nc2c1CC', 0.513513513513513) (140345, 'CCOc1ccc(S(=O)(=O)N2CCN(CC)CC2)cc1-c1nc2c(=O)n(C)c(=O)n(CC(C)C)c2[nH]1', 0.513157894736842) (1334775, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccnn3C)nc12', 0.507936507936508) (1353817, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccc(Br)cc3)nc12', 0.507936507936508) (1746347, 'CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1-c1nnc2c(n1)c(C)nn2C', 0.506849315068493) (1746350, 'CCOc1ccc(S(=O)(=O)N2CCCNCC2)cc1-c1nnc2c(n1)c(C)nn2C', 0.506666666666667) (28710, 'CCCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(O)c2cc3[nH]cnc3cc2n1', 0.506666666666667) (421326, 'CCCc1nc(C)c2c(=O)nc(-c3cc(S(=O)(=O)N4CCN(CC)CC4)ccc3OCC)[nH]n12', 0.506666666666667) (140382, 'CCOc1ccc(S(=O)(=O)N2CCN(CCN(C)C)CC2)cc1-c1nc2c(=O)n(C)c(=O)n(CC(C)C)c2[nH]1', 0.506329113924051) (1353818, 'CCCc1nn(C)c2c(=O)[nH]c(-c3cccc(Cl)c3)nc12', 0.5) (140451, 'CCOc1ccc(S(=O)(=O)N2CCN(CCO)CC2)cc1-c1nc2c(=O)n(C)c(=O)n(CC(C)C)c2[nH]1', 0.5) (1353816, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccc(Cl)cc3)nc12', 0.5) (1334770, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccc(=O)[nH]n3)nc12', 0.5) (326382, 'CCOc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1-c1nc(O)c2nc3cccc(CC)n3c2n1', 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)c2c(=O)[nH]c(-c3cccc(Br)c3)nc12', 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) (1334766, 'CCCc1nn(C)c2c(=O)[nH]c(-c3ccc(O)cc3)nc12', 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
data = pd.read_sql(sql2, conn)
data.shape
(217, 3)
data.head()
molregno | smiles | similarity | |
---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12 | 1.000000 |
1 | 1351310 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCCC4)ccc3OCC)nc12 | 0.881356 |
2 | 1351311 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCC4)ccc3OCC)nc12 | 0.881356 |
3 | 80636 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCNCC4)ccc3OCC)nc12 | 0.866667 |
4 | 80694 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCO)CC4)ccc3OCC)nc12 | 0.838710 |
nn = data[data['similarity'] >= 0.8]
nn.shape
(12, 3)
nn.head()
molregno | smiles | similarity | |
---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12 | 1.000000 |
1 | 1351310 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCCC4)ccc3OCC)nc12 | 0.881356 |
2 | 1351311 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCC4)ccc3OCC)nc12 | 0.881356 |
3 | 80636 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCNCC4)ccc3OCC)nc12 | 0.866667 |
4 | 80694 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCO)CC4)ccc3OCC)nc12 | 0.838710 |
PandasTools.AddMoleculeColumnToFrame(data,smilesCol='smiles',molCol='mol',includeFingerprints=True)
data.head()
molregno | smiles | similarity | mol | |
---|---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12 | 1.000000 | |
1 | 1351310 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCCC4)ccc3OCC)nc12 | 0.881356 | |
2 | 1351311 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCC4)ccc3OCC)nc12 | 0.881356 | |
3 | 80636 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCNCC4)ccc3OCC)nc12 | 0.866667 | |
4 | 80694 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCO)CC4)ccc3OCC)nc12 | 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)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12 | 1.000000 | 1.6109 | 474.587 | |
1 | 1351310 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCCC4)ccc3OCC)nc12 | 0.881356 | 3.2395 | 473.599 | |
2 | 1351311 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCC4)ccc3OCC)nc12 | 0.881356 | 2.8494 | 459.572 | |
3 | 80636 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCNCC4)ccc3OCC)nc12 | 0.866667 | 1.2687 | 460.560 | |
4 | 80694 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCO)CC4)ccc3OCC)nc12 | 0.838710 | 0.9734 | 504.613 |
data.sort(columns=['similarity']).head()
molregno | smiles | similarity | mol | logp | mw | |
---|---|---|---|---|---|---|
216 | 453288 | CCCc1c2nc(-c3cc(S(=O)(=O)N4CCN(CC)CC4)cnc3OCCOC)[nH]c(=O)c2nn1C | 0.5 | 1.0225 | 519.628 | |
207 | 1353818 | CCCc1nn(C)c2c(=O)[nH]c(-c3cccc(Cl)c3)nc12 | 0.5 | 2.9295 | 302.765 | |
208 | 140451 | CCOc1ccc(S(=O)(=O)N2CCN(CCO)CC2)cc1-c1nc2c(=O)n(C)c(=O)n(CC(C)C)c2[nH]1 | 0.5 | 0.4436 | 534.639 | |
209 | 1353816 | CCCc1nn(C)c2c(=O)[nH]c(-c3ccc(Cl)cc3)nc12 | 0.5 | 2.9295 | 302.765 | |
210 | 1334770 | CCCc1nn(C)c2c(=O)[nH]c(-c3ccc(=O)[nH]n3)nc12 | 0.5 | 0.3594 | 286.295 |
data[['mw', 'logp']].describe()
mw | logp | |
---|---|---|
count | 217.000000 | 217.000000 |
mean | 487.381023 | 2.263238 |
std | 91.319758 | 0.965502 |
min | 268.320000 | -0.048300 |
25% | 448.589000 | 1.548900 |
50% | 491.614000 | 2.286600 |
75% | 533.448000 | 2.894700 |
max | 866.980000 | 4.731700 |
rcParams['figure.figsize'] = 12,12
data['logp'].hist()
<matplotlib.axes._subplots.AxesSubplot at 0x7f5051e60d10>
scatter(data['mw'],data['logp'])
<matplotlib.collections.PathCollection at 0x7f5050f37f90>
data[data['mw']>800][['molregno','mol','mw','logp']]
molregno | mol | mw | logp | |
---|---|---|---|---|
74 | 487046 | 852.997 | 2.6245 | |
105 | 487045 | 866.980 | 2.7168 |
qsmi = 'c1nn(C)c2c1nc[nH]c2=O'
qmol = Chem.MolFromSmiles(qsmi)
qmol
subset = data[data['mol'] >= qmol]
subset.shape
(103, 6)
subset.head()
molregno | smiles | similarity | mol | logp | mw | |
---|---|---|---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12 | 1.000000 | 1.6109 | 474.587 | |
1 | 1351310 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCCC4)ccc3OCC)nc12 | 0.881356 | 3.2395 | 473.599 | |
2 | 1351311 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCC4)ccc3OCC)nc12 | 0.881356 | 2.8494 | 459.572 | |
3 | 80636 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCNCC4)ccc3OCC)nc12 | 0.866667 | 1.2687 | 460.560 | |
4 | 80694 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(CCO)CC4)ccc3OCC)nc12 | 0.838710 | 0.9734 | 504.613 |
data.groupby(data['mol'] >= qmol).describe().unstack()
molregno | similarity | logp | mw | |||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 114.0 | 886740.473684 | 597207.645589 | 28710.0 | 310086.75 | 565658.0 | 1441764.75 | 1831663.0 | 114.0 | 0.594148 | 0.053740 | 0.5 | 0.560411 | 0.598611 | 0.625946 | 0.734375 | 114.0 | 2.025773 | 0.780307 | -0.0483 | 1.4712 | 2.07581 | 2.5482 | 4.4372 | 114.0 | 493.521193 | 58.942393 | 391.453 | 456.1290 | 489.106 | 518.6400 | 762.879 |
True | 103.0 | 851594.970874 | 562828.499705 | 80558.0 | 410705.00 | 488147.0 | 1351307.50 | 1831961.0 | 103.0 | 0.672338 | 0.107084 | 0.5 | 0.577465 | 0.691176 | 0.740659 | 1.000000 | 103.0 | 2.526063 | 1.080157 | 0.3034 | 1.6615 | 2.59310 | 3.3193 | 4.7317 | 103.0 | 480.585107 | 117.141116 | 268.320 | 415.5065 | 502.641 | 552.6255 | 866.980 |
data['containsQ'] = data['mol'] >= qmol
data.head(2)
molregno | smiles | similarity | mol | logp | mw | containsQ | |
---|---|---|---|---|---|---|---|
0 | 410802 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12 | 1.000000 | 1.6109 | 474.587 | True | |
1 | 1351310 | CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCCCCC4)ccc3OCC)nc12 | 0.881356 | 3.2395 | 473.599 | True |
data.boxplot('similarity',by='containsQ')
<matplotlib.axes._subplots.AxesSubplot at 0x7f5050f47e10>
conn.close()