In [1]:
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit import RDConfig
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
import numpy as np
import pubchempy
from rdkit.Chem import rdMolDescriptors
from IPython.display import display,Image
Нарисуем ибупрофен¶
In [2]:
IBU = 'CC(C)CC1=CC=C(C=C1)C(C)C(=O)O'
ibu = Chem.MolFromSmiles(IBU)
AllChem.Compute2DCoords(ibu)
display(ibu)
Заменим изопропил на этин он же ацителен¶
In [3]:
IBU_PRE_MOD = 'C#CCC1=CC=C(C=C1)C(C)C(=O)O'
ibu_mod = Chem.MolFromSmiles(IBU_PRE_MOD)
AllChem.Compute2DCoords(ibu_mod)
display(ibu_mod)
# apply CuAAC
IBU_MOD = 'N1C=C(N=N1)C1=CC=C(C=C1)C(C)C(=O)O'
ibu_mod = Chem.MolFromSmiles(IBU_MOD)
AllChem.Compute2DCoords(ibu_mod)
display(ibu_mod)
Поиск радикалов с азидом и замена в найденых радикалах азидной группы на модифцированный ибупрофен.¶
In [4]:
AZIDE_SMILES = '[N-]N=[N+]'
In [5]:
data_frame = pubchempy.get_properties('CanonicalSMILES', AZIDE_SMILES, 'smiles', searchtype='substructure', RingsNotEmbedded=True, as_dataframe=True )
In [6]:
print('Len: %s' % data_frame.shape[0])
Len: 18788
In [7]:
data = data_frame[data_frame.CanonicalSMILES.str.len()<30][data_frame.CanonicalSMILES.str.contains('\.')==False]
/home/shad/miniconda2/envs/hse/lib/python2.7/site-packages/ipykernel_launcher.py:1: UserWarning: Boolean Series key will be reindexed to match DataFrame index. """Entry point for launching an IPython kernel.
In [8]:
print('Len: %s' % data.shape[0])
Len: 4366
In [9]:
rep_data = data[data.CanonicalSMILES.str.contains(AZIDE_SMILES)].CanonicalSMILES.str.replace(AZIDE_SMILES,IBU_MOD)
In [10]:
print('Len: %s' % rep_data.shape[0])
Len: 965
Отбор тех молекул, которые удовлетворяют правилу пяти Lipinski¶
In [11]:
import rdkit.Chem.Lipinski as Lipinski
import warnings
warnings.filterwarnings('ignore')
In [12]:
def LipinksyRuleOf5(x):
try:
if np.sum(
[(Lipinski.NumHDonors(x) <= 5),
(Lipinski.NumHAcceptors(x) <= 10),
(rdMolDescriptors.CalcExactMolWt(x) <= 500),
(rdMolDescriptors.CalcCrippenDescriptors(x)[0] <=5 )])>=3:
return True
else:
return False
except:
return False
In [14]:
new_data = rep_data[rep_data.apply(lambda x: LipinksyRuleOf5(Chem.MolFromSmiles(x)))]
RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 14 N, 4, is greater than permitted RDKit ERROR: [00:35:03] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 I, 7, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 I, 7, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 I, 7, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 16 I, 7, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 13 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 12 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 15 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 19 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 19 Cl, 3, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 19 Br, 3, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 I, 7, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 I, 7, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 I, 7, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 I, 7, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 12 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 14 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 14 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 12 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 13 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 15 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 15 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 14 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 12 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 14 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 15 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 12 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 13 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 22 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 14 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 14 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 12 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 13 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 15 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 17 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 16 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 12 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:03] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:03] Explicit valence for atom # 13 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:04] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 14 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 13 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:04] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:04] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:04] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 14 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 9 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:04] RDKit ERROR: RDKit ERROR: **** RDKit ERROR: Pre-condition Violation RDKit ERROR: bond already exists RDKit ERROR: Violation occurred on line 350 in file /opt/conda/conda-bld/rdkit_1499481310819/work/Code/GraphMol/ROMol.cpp RDKit ERROR: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph).second) RDKit ERROR: **** RDKit ERROR: RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 11 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 22 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 10 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 3 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 7 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 8 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 2 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 4 N, 4, is greater than permitted RDKit ERROR: [00:35:04] Explicit valence for atom # 5 N, 4, is greater than permitted
In [15]:
print('Len: %s' % new_data.shape)
Len: 389
In [16]:
for smiles in new_data.values[:10]:
chem_mol = Chem.MolFromSmiles(smiles)
AllChem.Compute2DCoords(chem_mol)
display(chem_mol)
