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
from IPython.display import display,Image
In [2]:
ibu=Chem.MolFromSmiles('CC(C)CC1=CC=C(C=C1)C(C)C(=O)O')
AllChem.Compute2DCoords(ibu)
display(ibu)
Теперь добавим к нашему ибупрофену азид для клик-химии.
In [3]:
ibu=Chem.MolFromSmiles('N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C')
AllChem.Compute2DCoords(ibu)
display(ibu)
In [4]:
import rdkit.Chem.Lipinski as Lipinksi
print(Lipinksi.NumHDonors(ibu))
print(Lipinksi.NumHAcceptors(ibu)) #Тут не буду вставлять текст, из названия функции всё ясно.
print(str(Lipinksi.rdMolDescriptors.CalcExactMolWt(ibu))+' мол. масса')
print(str(Lipinksi.rdMolDescriptors.CalcCrippenDescriptors(ibu)[0])+' оценка logp')
2 3 273.147726848 мол. масса 2.3938000000000006 оценка logp
In [5]:
import pubchempy as pcp
In [6]:
compounds = []
per_page = 10**5
for smiles in ["N=N=N", "NN#N",]:
for i in range(200):
try:
a = pcp.get_properties(
properties="CanonicalSMILES",
identifier=smiles, namespace="smiles",
searchtype="substructure",
RingsNotEmbedded=True,
listkey_count=per_page, listkey_start=i*per_page
)
except:
break
print("Retrieved page {} of {} search".format(i+1, smiles))
compounds.extend(a)
Retrieved page 1 of N=N=N search Retrieved page 2 of N=N=N search Retrieved page 3 of N=N=N search Retrieved page 1 of NN#N search
In [7]:
len(compounds)
Out[7]:
294447
In [8]:
with open('2515324818764782706.txt', 'w', encoding='utf-8') as file:
for elem in compounds:
file.write(elem['ConnectivitySMILES'] + '\n')
In [9]:
smiles=[]
In [10]:
strings=np.genfromtxt('2515324818764782706.txt',dtype=str)
for line in strings:
if 5<len(line) < 30 and not '.' in line: #добавил дополнительное условие поскольку в списке были структуры формата 'CC.' и.др.
smiles.append(line)
In [11]:
len(smiles)
Out[11]:
27424
In [12]:
from rdkit.Chem import Descriptors
In [13]:
def lipinski(mol):
"""Возвращает True, если молекула соответствует правилу Липински, иначе False."""
if mol is None:
return False
mw = Chem.Descriptors.MolWt(mol)
logp = Chem.Descriptors.MolLogP(mol)
hbd = Chem.Lipinski.NumHDonors(mol)
hba = Chem.Lipinski.NumHAcceptors(mol)
return (mw <= 500 and logp <= 5 and hbd <= 5 and hba <= 10)
In [14]:
filt=[]
for smi in smiles:
if "N=[N+]=[N-]" in smi[:1500]:
newsmi=smi.replace('N=[N+]=[N-]','N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C')
else:
continue
try:
newmol=Chem.MolFromSmiles(newsmi)
if lipinski(newmol):
filt.append(newmol)
except:
pass
[23:10:52] Explicit valence for atom # 2 Cl, 3, is greater than permitted [23:10:52] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:52] Explicit valence for atom # 2 Cl, 3, is greater than permitted [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CCOC(=O)C(CCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CC(CC(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(=O)OC' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CC(CC(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CC(C(N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)OC(C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CC(CC(CCOCCOCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CC(CCCC1(CC1)CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CCOC(=O)C(CCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CCOC(=O)C(CCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CC(CCC(=O)OCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CC(CCC(=S)OCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CN1C2=C(C(=C1CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:52] SMILES Parse Error: extra open parentheses for input: 'CC1(COC(CC1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC1=CC(=CC(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC1=C(C=CC(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC1=C(C=CC(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'C1CC(CCC1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)N(CCOCCC' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)([N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)([N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)([N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC1C(OC(C(C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C[N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C[N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C[N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C[N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C[N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C[N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C[N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C[N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(CC' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'C1=C(C=C(C(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] Explicit valence for atom # 3 Cl, 3, is greater than permitted [23:10:53] Explicit valence for atom # 1 Cl, 3, is greater than permitted [23:10:53] Explicit valence for atom # 1 Cl, 5, is greater than permitted [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)([N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)([N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)([N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)([N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)([N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)([N+]' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'C1CN(CCC1(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(CCC(=O)OCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(CC' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(CC' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(CC' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(CC' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(CC' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(CC' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'C(=C1C(=C(C(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'C(=C1C(=C(C(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(CCC(=O)NCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'CC(CCC(=O)OCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:53] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C(=C1)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:54] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:54] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:54] SMILES Parse Error: extra open parentheses for input: 'C1=C(C=NC(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:54] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:54] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:54] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:54] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:54] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)CC' [23:10:54] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=NC(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(CC' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:55] Explicit valence for atom # 1 Cl, 3, is greater than permitted [23:10:55] SMILES Parse Error: extra open parentheses for input: 'C1=C(N(C(=N1)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'C[C](CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(=O)N(CC' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)N(C' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'C1=CC2=C(C=C1N(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'CC(C)CC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)N(CC' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'CCC(C)C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)N(CC' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'CC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'CC(C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)N(CC' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'CC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)N(CC' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=CC=C1C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'CC(C)C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)N(CC' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'CC(C)(CC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'CC(CCC(=O)NCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:55] SMILES Parse Error: extra open parentheses for input: 'CC(CCC(=O)NCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:56] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:56] SMILES Parse Error: extra open parentheses for input: 'C1=C(C(=C(N1)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:56] Explicit valence for atom # 4 Cl, 3, is greater than permitted [23:10:57] SMILES Parse Error: extra open parentheses for input: 'CC1C(OC(C1(C)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'CC1=C(C=CC(=C1CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'CC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(COC(=O)CCCC' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'C1=C(C=NC(=C1CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'CC1C=C(C=CC1OCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'CC1=CC(=C(C(=N1)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=CC=C1C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=CC=C1C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'C(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)CC(C(=O)OCC' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'CCOC(=O)C(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'CCOC(=O)C(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(CC' [23:10:57] SMILES Parse Error: extra open parentheses for input: 'C=C(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C1(CCCC1CC' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'C1CCC(C(C1)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)N(C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'CC(CCC(=O)OCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'CC1=C(C(C(C(C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'C1=CC(C(C(C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'CC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'C1CC(C(CC1CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'C1=C(N(C(=N1)CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'CC(CCC(=O)OCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'CCC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C(=CC' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'CC(CCCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'CC(CCCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'CC1=C(C=CC(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'C1CC(CCC1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(CC' [23:10:58] SMILES Parse Error: extra open parentheses for input: 'CC(CCC(=O)OCCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:59] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:59] SMILES Parse Error: extra open parentheses for input: 'CC=CC(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:59] SMILES Parse Error: extra open parentheses for input: 'CCC=CC(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:59] SMILES Parse Error: extra open parentheses for input: 'CCC=CC(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:59] SMILES Parse Error: extra open parentheses for input: 'C1CC(OC1(CO)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:10:59] SMILES Parse Error: extra open parentheses for input: 'C(CNC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:59] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=CC=C1NC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:59] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=CC=C1NC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:59] SMILES Parse Error: extra open parentheses for input: 'C(CNC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:10:59] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=CC=C1NC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:11:00] SMILES Parse Error: extra open parentheses for input: 'C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)CN(CC' [23:11:00] Explicit valence for atom # 26 Cl, 3, is greater than permitted [23:11:01] SMILES Parse Error: extra open parentheses for input: 'CC1=CC(=C(C(=C1)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:11:01] SMILES Parse Error: extra open parentheses for input: 'COC(=O)C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)N(CC' [23:11:01] SMILES Parse Error: extra open parentheses for input: 'C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(CC(CC' [23:11:01] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:11:01] SMILES Parse Error: extra open parentheses for input: 'CC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)CN1CCC(CC1)(C' [23:11:01] SMILES Parse Error: extra open parentheses for input: 'C1=C(N=C(C(=N1)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:11:01] SMILES Parse Error: extra open parentheses for input: 'CC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)CN1CCC(CC1)(C' [23:11:01] SMILES Parse Error: extra open parentheses for input: 'C1=CC(=C(C=C1CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:11:01] SMILES Parse Error: extra open parentheses for input: 'C1=C(C=C(C(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'C1=C(OC(=C1)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C=C(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'CC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'CCC=CCCC(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'CC=CCC(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'CC(=CCC(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'CC=CCC(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'C=CCC(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'CCC(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'CCC(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'C[Si](C)(C)OC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'CC(CC(C(=O)OC)N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'CCC=CCCC(CCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'CC(=CCC(CCCN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'COCC(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)(C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)COC(=C[N+]' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'C1=C(C=NC(=C1N1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)C' [23:11:02] SMILES Parse Error: extra open parentheses for input: 'C(CN1N=NC(=C1)C(C(O)=O)(C)C1=CC=C(C=C1)CC(C)C)COC(=C[N+]'
In [16]:
from IPython.display import SVG
display(Draw.MolsToGridImage(filt[:8], useSVG=True, molsPerRow=3, subImgSize=(200, 200)))
In [19]:
from rdkit.Chem.Draw import SimilarityMaps
paint = Draw.MolDraw2DCairo(600, 600)
fingerprint = SimilarityMaps.GetMorganFingerprint(filt[3], fpType='bv')
fingerprint, maxweight = SimilarityMaps.GetSimilarityMapForFingerprint(ibu, filt[3], SimilarityMaps.GetMorganFingerprint, draw2d=paint)
paint.FinishDrawing()
Image(paint.GetDrawingText())
Out[19]:
In [20]:
m3d=Chem.AddHs(filt[3])
Chem.AllChem.EmbedMolecule(m3d)
AllChem.MMFFOptimizeMolecule(m3d,maxIters=500,nonBondedThresh=200)
m3d
Out[20]:
In [22]:
import nglview as nv
view = nv.show_rdkit(m3d)
view
NGLWidget()
In [ ]: