Rdkit: sdf to SMILES

[BillLawrence111]

Description:
Substance_000000001_000025000.sdf.zip
I downloaded a sdf file from PubChem and I want to convert sdf to SMILES, but I have some problems. I am very anxious, I hope to get help.

• RDKit Version:2018.09.1
• Platform:macOS High Sierra 10.13.4
• python:Python 3.6.5 |Anaconda, Inc.
  
  result：[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 6187
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 6637
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 9297
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 9454
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 17 H, 2, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 15469
  [11:23:40] ERROR: Explicit valence for atom # 17 H, 2, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 21963
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 11 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 25430
  [11:23:40] ERROR: Explicit valence for atom # 11 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 17 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 25618
  [11:23:40] ERROR: Explicit valence for atom # 17 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 26802
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 26919
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 27044
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 27169
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 27288
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 27407
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 27526
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 27649
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 27779
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 9 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 27911
  [11:23:40] ERROR: Explicit valence for atom # 9 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 28040
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 29495
  [11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 29606
  [11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 29717
  [11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 29830
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 30121
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 30759
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 30871
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 31948
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 32135
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 32292
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 32461
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 32628
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 32789
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 32950
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 33262
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 4 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 33429
  [11:23:40] ERROR: Explicit valence for atom # 4 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 33632
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 33791
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 33926
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 34057
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 34228
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 34403
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 34568
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 34759
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 34878
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 35079
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 35262
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 35385
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 35496
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 35609
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 35808
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 36019
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 36128
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 36249
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 36390
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 36535
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 36688
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 36817
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 36960
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 37097
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 37222
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 37351
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 37464
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 24 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 37779
  [11:23:40] ERROR: Explicit valence for atom # 24 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 24 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 38096
  [11:23:40] ERROR: Explicit valence for atom # 24 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 24 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 38415
  [11:23:40] ERROR: Explicit valence for atom # 24 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 24 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 38734
  [11:23:40] ERROR: Explicit valence for atom # 24 N, 4, is greater than permitted
  [11:23:40] WARNING: not removing hydrogen atom without neighbors
  [11:23:40] WARNING: not removing hydrogen atom without neighbors
  [11:23:40] Explicit valence for atom # 14 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 41791
  [11:23:40] ERROR: Explicit valence for atom # 14 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 15 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 42743
  [11:23:40] ERROR: Explicit valence for atom # 15 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 14 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 42869
  [11:23:40] ERROR: Explicit valence for atom # 14 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 17 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 42995
  [11:23:40] ERROR: Explicit valence for atom # 17 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 17 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 43121
  [11:23:40] ERROR: Explicit valence for atom # 17 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 15 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 43245
  [11:23:40] ERROR: Explicit valence for atom # 15 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 21 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 44189
  [11:23:40] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 21 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 44343
  [11:23:40] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 14 In, 7, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 44500
  [11:23:40] ERROR: Explicit valence for atom # 14 In, 7, is greater than permitted
  [11:23:40] Explicit valence for atom # 40 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 44746
  [11:23:40] ERROR: Explicit valence for atom # 40 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 21 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 45185
  [11:23:40] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 26 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 45442
  [11:23:40] ERROR: Explicit valence for atom # 26 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 50 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 45829
  [11:23:40] ERROR: Explicit valence for atom # 50 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 40 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 46787
  [11:23:40] ERROR: Explicit valence for atom # 40 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 2 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 49982
  [11:23:40] ERROR: Explicit valence for atom # 2 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 2 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 50060
  [11:23:40] ERROR: Explicit valence for atom # 2 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 1 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 50141
  [11:23:40] ERROR: Explicit valence for atom # 1 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 50241
  [11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 17 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 50507
  [11:23:40] ERROR: Explicit valence for atom # 17 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 17 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 50792
  [11:23:40] ERROR: Explicit valence for atom # 17 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 11 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 51029
  [11:23:40] ERROR: Explicit valence for atom # 11 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 53031
  [11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 56027
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 1 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 56670
  [11:23:40] ERROR: Explicit valence for atom # 1 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 56757
  [11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 56837
  [11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 56928
  [11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 57087
  [11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 57313
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 57392
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 57471
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 57550
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 57671
  [11:23:40] ERROR: Explicit valence for atom # 6 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 57805
  [11:23:40] ERROR: Explicit valence for atom # 6 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 57947
  [11:23:40] ERROR: Explicit valence for atom # 6 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 58095
  [11:23:40] ERROR: Explicit valence for atom # 6 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 1 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 58175
  [11:23:40] ERROR: Explicit valence for atom # 1 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 58253
  [11:23:40] ERROR: Explicit valence for atom # 3 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 1 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 61791
  [11:23:40] ERROR: Explicit valence for atom # 1 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 64840
  [11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 67314
  [11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 68206
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 68294
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 68384
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 68470
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 68559
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 68650
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 68741
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 68831
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 68921
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 69006
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 69091
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 69176
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 69261
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 69365
  [11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 69658
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 69758
  [11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 4 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 70180
  [11:23:40] ERROR: Explicit valence for atom # 4 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 9 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 70290
  [11:23:40] ERROR: Explicit valence for atom # 9 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 10 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 70479
  [11:23:40] ERROR: Explicit valence for atom # 10 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 11 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 70674
  [11:23:40] ERROR: Explicit valence for atom # 11 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 75495
  [11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 75587
  [11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 75670
  [11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 75766
  [11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 75857
  [11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 75948
  [11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 76041
  [11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 76134
  [11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 76231
  [11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 76330
  [11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 76412
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 76494
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 1 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 76609
  [11:23:40] ERROR: Explicit valence for atom # 1 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 76721
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 77219
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 77298
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 77377
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 77456
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 79215
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] Explicit valence for atom # 13 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 83871
  [11:23:40] ERROR: Explicit valence for atom # 13 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 21 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 84056
  [11:23:40] ERROR: Explicit valence for atom # 21 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 17 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 84213
  [11:23:40] ERROR: Explicit valence for atom # 17 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 16 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 84366
  [11:23:40] ERROR: Explicit valence for atom # 16 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 16 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 84519
  [11:23:40] ERROR: Explicit valence for atom # 16 C, 5, is greater than permitted
  [11:23:40] Explicit valence for atom # 13 C, 5, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 84657
  [11:23:40] ERROR: Explicit valence for atom # 13 C, 5, is greater than permitted
  [11:23:40] WARNING: not removing hydrogen atom without neighbors
  [11:23:40] Explicit valence for atom # 3 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 90624
  [11:23:40] ERROR: Explicit valence for atom # 3 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 95534
  [11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 5 K, 2, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 95790
  [11:23:40] ERROR: Explicit valence for atom # 5 K, 2, is greater than permitted
  [11:23:40] Explicit valence for atom # 15 H, 2, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 98395
  [11:23:40] ERROR: Explicit valence for atom # 15 H, 2, is greater than permitted
  [11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 100309
  [11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:40] Explicit valence for atom # 0 In, 6, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 102244
  [11:23:40] ERROR: Explicit valence for atom # 0 In, 6, is greater than permitted
  [11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:40] ERROR: Could not sanitize molecule ending on line 103429
  [11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
  [11:23:41] WARNING: not removing hydrogen atom without neighbors
  [11:23:41] Explicit valence for atom # 2 O, 3, is greater than permitted
  [11:23:41] ERROR: Could not sanitize molecule ending on line 104584
  [11:23:41] ERROR: Explicit valence for atom # 2 O, 3, is greater than permitted
  [11:23:41] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:41] ERROR: Could not sanitize molecule ending on line 127594
  [11:23:41] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:41] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:41] ERROR: Could not sanitize molecule ending on line 127768
  [11:23:41] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:41] Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:41] ERROR: Could not sanitize molecule ending on line 127856
  [11:23:41] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
  [11:23:41] Explicit valence for atom # 2 N, 4, is greater than permitted
  [11:23:41] ERROR: Could not sanitize molecule ending on line 157013
  [11:23:41] ERROR: Explicit valence for atom # 2 N, 4, is greater than permitted
  [11:23:41] Warning: conflicting stereochemistry at atom 20 ignored.
  [11:23:41] Warning: conflicting stereochemistry at atom 20 ignored.
  [11:23:41] Explicit valence for atom # 0 Cl, 7, is greater than permitted
  [11:23:41] ERROR: Could not sanitize molecule ending on line 175069
  [11:23:41] ERROR: Explicit valence for atom # 0 Cl, 7, is greater than permitted
  [11:23:41] WARNING: not removing hydrogen atom without neighbors
  [11:23:41] WARNING: not removing hydrogen atom without neighbors
  [11:23:42] Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:42] ERROR: Could not sanitize molecule ending on line 490585
  [11:23:42] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
  [11:23:43] Warning: conflicting stereochemistry at atom 2 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 11 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 11 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 3 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 3 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 10 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 10 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 8 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 8 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 14 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 14 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 13 ignored.
  [11:23:44] Warning: conflicting stereochemistry at atom 13 ignored.
  Traceback (most recent call last):
  File "22.py", line 20, in
  converter(sys.argv[1])
  File "22.py", line 13, in converter
  smi = Chem.MolToSmiles(mol)
  Boost.Python.ArgumentError: Python argument types in
  rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
  did not match C++ signature:
  MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)
  

import sys
from rdkit import Chem

def converter(file_name):
    mols = [mol for mol in Chem.SDMolSupplier(file_name)]
    outname = file_name.split(".sdf")[0] + ".txt"
    out_file = open(outname, "w")
    for mol in mols:
        smi = Chem.MolToSmiles(mol)
        name = mol.GetProp("_Name")
        out_file.write("{}\t{}\n".format(smi, name))
    out_file.close()

if __name__ == "__main__":
    converter(sys.argv[1])

[shayakhmetov]

from rdkit.Chem.PandasTools import LoadSDF
df = LoadSDF(sdf_filename, smilesName='SMILES')

This will create a pandas DataFrame with 'SMILES' column

[sshojiro]

@BillLawrence111
If you handle thoudsands or millions of compounds at once, you shouldn't keep all mol objects on python array in terms of memory usage. SDMolSupplier is a generator, thus you may directly run iteration over the supplier like this:

import sys
from rdkit import Chem

def converter(file_name):
    sppl = Chem.SDMolSupplier(file_name)
    outname = file_name.replace(".sdf", ".txt")
    out_file = open(outname, "w")
    for mol in sppl:
        if mol is not None:# some compounds cannot be loaded.
            smi = Chem.MolToSmiles(mol)
            name = mol.GetProp("_Name")
            out_file.write(f"{smi}\t{name}\n")
    out_file.close()
if __name__ == "__main__":
    converter(sys.argv[1])

Besides, the error you encountered was caused by invalid forms of structure. You may correct compounds before using RDKit. Otherwise, you must ignore such compounds as the above code does.

[Frank-LIU-520]

So how can we know which molecules are indeed invalid and remove them from the dataset?