In [1]:

    

import pandas as pd
from rdkit import Chem
from rdkit.Chem import Draw


    

In [20]:

    

from rdkit.Chem.Draw import IPythonConsole


    

In [2]:

    

target_list = ["CHEMBL203", "CHEMBL204", "CHEMBL235", "CHEMBL236", 
               "CHEMBL244", "CHEMBL260", "CHEMBL4805", "CHEMBL4822"]


    

In [3]:

    

ChemDiv_dir = "/raid/xiaotaw/ChemDiv/"
fn_list = ["DC01_350000.sdf", "DC02_350000.sdf", 
           "DC03_222773.sdf", "DC_saltdata_not-available_124145.sdf", 
           "IC_non-excl_82693.sdf", "NC_340320.sdf"]
#sup0 = Chem.SDMolSupplier(ChemDiv_dir + fn_list[0])
#ms0 = [x for x in sup0 if x is not None]


    

In [4]:

    

#sup1 = Chem.SDMolSupplier(ChemDiv_dir + fn_list[1])
#ms1 = [x for x in sup1 if x is not None]
#sup2 = Chem.SDMolSupplier(ChemDiv_dir + fn_list[2])
#ms2 = [x for x in sup2 if x is not None]


    

In [46]:

    

target = target_list[0]
target = "CHEMBL267"
pred_dir = "/home/scw4750/Documents/chembl/dnn_model/pred_files/%s/" % target
pred_fn = pred_dir + "vs_chemdiv_%s_128_0.800_4.000e-03_2247900.pred1000" % target
chemdiv_pred = pd.read_csv(pred_fn, sep="\t", index_col=0, names=["id", "pred"])
#chemdiv_pred
id_list = chemdiv_pred["id"].values
#id_list


    

In [47]:

    

m1000 = []
for fn in fn_list:
    print("start %s" % fn)
    sup = Chem.SDMolSupplier(ChemDiv_dir + fn)
    for m in sup:
        if (m is not None) and (m.GetProp("IDNUMBER") in id_list):
            m1000.append(m)
            #print(m.GetProp("IDNUMBER"))        
    print("finished %s" % fn)


    

    




start DC01_350000.sdf
finished DC01_350000.sdf
start DC02_350000.sdf
finished DC02_350000.sdf
start DC03_222773.sdf
finished DC03_222773.sdf
start DC_saltdata_not-available_124145.sdf
finished DC_saltdata_not-available_124145.sdf
start IC_non-excl_82693.sdf
finished IC_non-excl_82693.sdf
start NC_340320.sdf
finished NC_340320.sdf

In [48]:

    

def get_pred_value(id_):
  return chemdiv_pred["pred"][chemdiv_pred["id"] == id_].values[0]

m1000.sort(key=lambda x: get_pred_value(x.GetProp("IDNUMBER")), reverse=True)


    

In [49]:

    

writer = Chem.SDWriter(pred_fn.replace(".pred1000", "_top1000.sdf"))
for m in m1000:
    writer.write(m)


    

In [ ]:

    




    

In [58]:

    

m1000[6]


    

    
Out[58]:

In [ ]:

    




    

In [60]:

    

import glob
import pandas as pd


    

In [215]:

    

def get_ids(target="CHEMBL203", top=1000):
    fn = glob.glob("pred_files/%s/vs_chemdiv_*.pred1000" % target)[0]
    df = pd.read_csv(fn, sep="\t", header=None, names=["none", "id", target+"_pred"], index_col=0, usecols=[1, 2])
    df[target+"_index"] = range(1000)
    fn = glob.glob("pred_files/%s/vs_chemdiv_*top1000.sdf" % target)[0]
    suppl = Chem.SDMolSupplier(fn)
    for m in suppl:
        if m.HasProp("IDNUMBER"):
            df.loc[m.GetProp("IDNUMBER"), "mol"] = m
    return df.reset_index()


    

In [216]:

    

a = get_ids("CHEMBL203")
b = get_ids("CHEMBL267")
c = get_ids("CHEMBL279")


    

In [192]:

    

ac = a.merge(c, on="id")
ac


    

    
Out[192]:






  

    

      

      
id
      
CHEMBL203_pred
      
CHEMBL203_index
      
mol_x
      
CHEMBL279_pred
      
CHEMBL279_index
      
mol_y
    
  
  

    

      
0
      
3486-0358
      
0.431300
      
3
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a4e6e0>
      
0.105957
      
469
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a87280>
    
    

      
1
      
C066-4881
      
0.361765
      
10
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a4e9f0>
      
0.178109
      
188
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a96590>
    
    

      
2
      
G887-0362
      
0.299174
      
24
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e7050>
      
0.099344
      
514
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a8d670>
    
    

      
3
      
3486-0421
      
0.291748
      
32
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e73d0>
      
0.137190
      
298
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a97670>
    
    

      
4
      
G887-0379
      
0.262502
      
55
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e7de0>
      
0.064254
      
993
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a73b40>
    
    

      
5
      
K405-2625
      
0.219095
      
121
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b9b40>
      
0.065322
      
965
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a78ec0>
    
    

      
6
      
C431-0049
      
0.216677
      
127
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b9de0>
      
0.258393
      
103
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e1fa0>
    
    

      
7
      
3486-0393
      
0.186619
      
189
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189c3980>
      
0.077227
      
767
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18aa66e0>
    
    

      
8
      
G887-0295
      
0.163087
      
274
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189cef30>
      
0.095529
      
539
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a981a0>
    
    

      
9
      
S538-0617
      
0.148430
      
339
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189dec20>
      
0.069567
      
886
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a71bb0>
    
    

      
10
      
S538-0920
      
0.148085
      
340
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189dec90>
      
0.113681
      
416
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a7ead0>
    
    

      
11
      
3486-0368
      
0.142170
      
372
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e6ad0>
      
0.074472
      
808
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a91910>
    
    

      
12
      
F173-0035
      
0.135746
      
414
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189d8d70>
      
0.083552
      
672
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18aa0c90>
    
    

      
13
      
H024-0410F
      
0.132401
      
435
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189bf6e0>
      
0.613138
      
22
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189babb0>
    
    

      
14
      
F173-0138
      
0.119737
      
552
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189daad0>
      
0.091560
      
578
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a8e2f0>
    
    

      
15
      
G818-0014
      
0.119420
      
555
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189dac20>
      
0.092198
      
568
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a98e50>
    
    

      
16
      
K905-0243
      
0.109851
      
665
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e3d00>
      
0.145087
      
269
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a7b980>
    
    

      
17
      
3909-8852
      
0.098246
      
827
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e5520>
      
0.141275
      
283
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a7bfa0>
    
    

      
18
      
S538-0232
      
0.092921
      
903
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b56e0>
      
0.084122
      
666
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18aa09f0>
    
    

      
19
      
S538-0894
      
0.090845
      
947
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b7a60>
      
0.103688
      
484
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a87910>
    
    

      
20
      
G887-0084
      
0.090686
      
950
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b7bb0>
      
0.104437
      
476
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a87590>
    
    

      
21
      
3966-3055
      
0.089641
      
974
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b8670>
      
0.737682
      
15
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189ba8a0>
    
  

In [193]:

    

ac.loc[1]["mol_x"]


    

    
Out[193]:

In [195]:

    

ac.loc[3]["mol_x"]


    

    
Out[195]:

In [196]:

    

ac.loc[6]["mol_x"]


    

    
Out[196]:

In [197]:

    

ac.loc[13]["mol_x"]


    

    
Out[197]:

In [198]:

    

ac.loc[21]["mol_x"]


    

    
Out[198]:

In [ ]:

    




    

In [217]:

    

ab = a.merge(b, on="id")
ab


    

    
Out[217]:






  

    

      

      
id
      
CHEMBL203_pred
      
CHEMBL203_index
      
mol_x
      
CHEMBL267_pred
      
CHEMBL267_index
      
mol_y
    
  
  

    

      
0
      
3486-0358
      
0.431300
      
3
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188b7750>
      
0.248166
      
357
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189cec20>
    
    

      
1
      
F360-0628
      
0.297467
      
27
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188ce210>
      
0.133103
      
883
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189afc20>
    
    

      
2
      
C431-0073
      
0.292120
      
31
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188ce3d0>
      
0.135970
      
842
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b09f0>
    
    

      
3
      
3486-0421
      
0.291748
      
32
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188ce440>
      
0.326512
      
234
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189bf520>
    
    

      
4
      
E939-0300
      
0.251230
      
73
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188cf670>
      
0.209726
      
470
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e7830>
    
    

      
5
      
F360-0672
      
0.241129
      
87
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188cfc90>
      
0.131491
      
898
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189ad2f0>
    
    

      
6
      
E939-0340
      
0.210057
      
140
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188d2440>
      
0.212946
      
457
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e7e50>
    
    

      
7
      
C660-0700
      
0.204045
      
148
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188d27c0>
      
0.126321
      
943
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189df6e0>
    
    

      
8
      
F360-0648
      
0.197876
      
159
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188d2c90>
      
0.224320
      
424
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b9d70>
    
    

      
9
      
E939-0417
      
0.196403
      
162
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188d2de0>
      
0.215093
      
453
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b9050>
    
    

      
10
      
0132-0028
      
0.186825
      
187
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188d3910>
      
0.459259
      
136
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e5280>
    
    

      
11
      
3486-0393
      
0.186619
      
189
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188d39f0>
      
0.163605
      
660
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b1910>
    
    

      
12
      
F360-0650
      
0.183807
      
200
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188d3ec0>
      
0.201038
      
497
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a4eb40>
    
    

      
13
      
E939-0420
      
0.159231
      
287
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188d9590>
      
0.145288
      
771
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189d2a60>
    
    

      
14
      
F360-0180
      
0.151201
      
325
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188da670>
      
0.188800
      
535
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189a8d70>
    
    

      
15
      
3486-0416
      
0.145643
      
353
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188db2f0>
      
0.348714
      
215
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189bfde0>
    
    

      
16
      
C660-0701
      
0.136169
      
409
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188dcbb0>
      
0.206647
      
478
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e74b0>
    
    

      
17
      
E939-0299
      
0.129776
      
453
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188def30>
      
0.203393
      
490
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a4ee50>
    
    

      
18
      
4477-2385
      
0.125402
      
490
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188dffa0>
      
0.155166
      
707
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a30de0>
    
    

      
19
      
C660-0698
      
0.123688
      
509
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188e1830>
      
0.122531
      
985
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189d7980>
    
    

      
20
      
C431-0074
      
0.113880
      
607
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188e43d0>
      
0.126176
      
947
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189df8a0>
    
    

      
21
      
F360-0644
      
0.112637
      
626
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188e4c20>
      
0.170800
      
625
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb1898e8a0>
    
    

      
22
      
C660-0754
      
0.111857
      
638
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188e51a0>
      
0.167572
      
642
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb1898e130>
    
    

      
23
      
3966-3256
      
0.109594
      
669
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188e5f30>
      
0.174584
      
604
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b2c20>
    
    

      
24
      
F360-0224
      
0.108625
      
686
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188e86e0>
      
0.245948
      
368
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189ce750>
    
    

      
25
      
K405-1035
      
0.106780
      
715
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188e93d0>
      
0.275051
      
300
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e66e0>
    
    

      
26
      
C431-0079
      
0.099658
      
808
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb188ecd00>
      
0.245222
      
370
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189ce670>
    
    

      
27
      
F360-0189
      
0.097899
      
834
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189868a0>
      
0.553293
      
92
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b5670>
    
    

      
28
      
G803-0279
      
0.097481
      
841
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18986bb0>
      
0.130888
      
903
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189ad520>
    
    

      
29
      
F360-0220
      
0.095688
      
869
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb1898c830>
      
0.822092
      
10
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189b8c90>
    
    

      
30
      
3486-0417
      
0.090629
      
952
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb1899ed00>
      
0.202268
      
493
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a4ed00>
    
    

      
31
      
F360-0645
      
0.090010
      
964
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189a12f0>
      
0.204695
      
486
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189e70c0>
    
    

      
32
      
K405-1032
      
0.088660
      
990
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb189a1de0>
      
0.149765
      
745
      
<rdkit.Chem.rdchem.Mol object at 0x7ffb18a54ec0>
    
  

In [218]:

    

ab.loc[29]["mol_x"]


    

    
Out[218]:

In [219]:

    

ab.loc[27]["mol_x"]


    

    
Out[219]:

In [220]:

    

ab.loc[15]["mol_x"]


    

    
Out[220]:

In [221]:

    

ab.loc[10]["mol_x"]


    

    
Out[221]:

In [222]:

    

ab.loc[3]["mol_x"]


    

    
Out[222]:

In [223]:

    

ab.loc[0]["mol_x"]


    

    
Out[223]:

In [ ]: