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)
In [3]:
print smiles[1]
--------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-3-948c509209bf> in <module>() ----> 1 print smiles[1] NameError: name 'smiles' is not defined
In [4]:
ibu=Chem.MolFromSmiles('CC(C)CC1=CC=C(C=C1)C#C')
AllChem.Compute2DCoords(ibu)
display(ibu)
In [5]:
ibu=Chem.MolFromSmiles('C#CC1=CC=C(C=C1)C(C)C(=O)O')
AllChem.Compute2DCoords(ibu)
display(ibu)
In [6]:
ibu=Chem.MolFromSmiles('N(N=N1)C=C1C1=CC=C(C=C1)C(C)C(=O)O')
AllChem.Compute2DCoords(ibu)
display(ibu)
In [7]:
ibu=Chem.MolFromSmiles('CN(N=N1)C=C1C1=CC=C(C=C1)C(C)C(=O)O')
AllChem.Compute2DCoords(ibu)
display(ibu)
In [8]:
import rdkit.Chem.Lipinski as Lipinksy
print Lipinksy.NumHDonors(ibu)
print Lipinksy.NumHAcceptors(ibu)
print Lipinksy.rdMolDescriptors.CalcExactMolWt(ibu)
print Lipinksy.rdMolDescriptors.CalcCrippenDescriptors(ibu)[0]
1 4 231.100776656 1.6702
In [9]:
strings=np.genfromtxt('31387313851815764.txt.gz',dtype=np.str)
smiles = []
for line in strings:
if len(line[1]) < 30 and not '.' in line[1]:
smiles.append(line[1])
In [10]:
smiles
Out[10]:
['C1CCC(CC1)(CN=[N+]=[N-])C=N',
'C1CC(CCC1CC=N)CN=[N+]=[N-]',
'C1CC(CC(C1)C=N)CN=[N+]=[N-]',
'CC1CCCC(C1)CN=[N+]=[N-]',
'CC1=CC=CC=C1OCN=[N+]=[N-]',
'CCC(N=[N+]=[N-])(F)F',
'CC(=O)C(N=[N+]=[N-])(F)F',
'C',
'C',
'COC(=O)C(CCCCN=[N+]=[N-])Br',
'CCCSSCCN=[N+]=[N-]',
'CC(C)(C)NCC(CCN=[N+]=[N-])O',
'CC1C(CC(C(O1)O[C@H]2C',
'CC1C(CC(C(O1)O[C@H]2C',
'CC1C(CC(C(O1)O[C@H]2C',
'CC1C(CC(C(O1)O[C@H]2C',
'CC',
'CC1C(CC(C(O1)O[C@H]2C',
'CC',
'CC1C(C(C(C(O1)O[C@H]2C',
'CC1C(C(C(C(O1)O[C@H]2C',
'CC1C(C(C(C(O1)O[C@H]2C',
'CC',
'C(C(O)(F)F)N=[N+]=[N-]',
'C(CO)CS(=O)(=O)SN=[N+]=[N-]',
'CC(C(CNC(=O)NC(=O)C(=C)C',
'CCC1CCC2(N1CCC2)CN=[N+]=[N-]',
'C1CCN(C(C1)O)N=[N+]=[N-]',
'C1CCN(C(C1)N=[N+]=[N-])O',
'CC(=O)N1CCOC(C1)N=[N+]=[N-]',
'C',
'C1CSSC1CCCCCN=[N+]=[N-]',
'CC(C)(C)C(=O)CCCCN=[N+]=[N-]',
'CCC1=CC=CC=C1OCN=[N+]=[N-]',
'CCC(=O)CCCCN=[N+]=[N-]',
'COC(=O)C1=C(C(=S)NC(=C1)C',
'C1CCC2=C(C1)C(=C(C(=O)N2)C',
'C(C(=O)/C=C\\N)N=[N+]=[N-]',
'C1CC(CC=C1)OCN=[N+]=[N-]',
'C1NOC(=N1)CCN=[N+]=[N-]',
'C1CSC(=C1)CN=[N+]=[N-]',
'C(COC(=O)C(CO)CO)N=[N+]=[N-]',
'CC1CCC(C1)(CN=[N+]=[N-])O',
'CCC(N=[N+]=[N-])S(=O)(=O)N',
'CC1(N=N1)CCN=[N+]=[N-]',
'CCCCCCC(=O)NCCSSCCC(=O)NCC',
'C1C(C(OC1N2C=C(C(=O)NC2=O)C',
'C1CC(CCC1C(CN=[N+]=[N-])C=N)O',
'C1C[C@@H](CC(C1)N=[N+]=[N-])O',
'C1CCC([C@H](C1)O)N=[N+]=[N-]',
'CC1=CN=C(C=C1N=[N+]=[N-])Cl',
'C/C=C(/NCC',
'C(COCO)N=[N+]=[N-]',
'C1C(C(OC1N2C=C(C(=O)NC2=O)C',
'CN1C2=C(C=C(C=C2)C',
'CC1CC=CC(=C1)C(CO)N=[N+]=[N-]',
'CCCC',
'CCCCCCCCCCN1C2=C(C=C(C=C2)C',
'C1CC(C1CN=[N+]=[N-])O',
'C/C(=C/N=[N+]=[N-])/SC=C',
'CC(=C)S/C=C(/C)\\N=[N+]=[N-]',
'C/C(=C(\\C)/SC=C)/N=[N+]=[N-]',
'CC(=O)C1=CC=C(O1)N=[N+]=[N-]',
'C(C(C(C(C(C(C(C(C[N-][N+]',
'C',
'C1(=N[N+]',
'[C-]',
'[C-]',
'[C-]',
'CC1=CC=C(C=C1)S(=O)(=O)OCCCC',
'CS(CCOCCN=[N+]=[N-])(O)Cl',
'CS(CCOCCOCCN=[N+]=[N-])(O)Cl',
'C[N+](=C)N=[N+]=[N-]',
'[C-]',
'C',
'CC(C)(CC(C)(C)C(=O)OCC',
'[C-]',
'CCOC(=O)C1CCC(C1)CN=[N+]=[N-]',
'[C-]',
'CS(C)(CCOCCOCCN=[N+]=[N-])O',
'C',
'C1NC=CN1S(=O)(=O)N=[N+]=[N-]',
'[C-]',
'[C-]',
'CCC',
'CC(C)(C1=CC(=C(C=C1)F)[N+]',
'CS(C)(CCOCCN=[N+]=[N-])O',
'C(COCC=O)N=[N+]=[N-]',
'CC',
'C',
'C1=CC2=NC=CN2N=C1CN=[N+]=[N-]',
'[C-]',
'C=C1CCC(CC1)OCCN=[N+]=[N-]',
'C1=NC=NC(=N1)OC(C([N-][N+]',
'CC[N+](CC)(CC)CC',
'[C-]',
'[C-]',
'[C-]',
'CCC',
'CC',
'C1(=N[N+]',
'CC',
'C1(=C(C(=C(C(=NN=N)C1=N[N+]',
'C1=CN(C(=N1)N[N+]',
'C1=CN(C(=N[N+]',
'[C-]',
'C1=CC(=CN=C1)CCCN=[N+]=[N-]',
'CC(=O)OC1CCCCC=CC1N=[N+]=[N-]',
'COC(=O)C1CCCCC1CN=[N+]=[N-]',
'CS(=O)(=O)NC1CCCC1N=[N+]=[N-]',
'COC(=O)C1C(CCN1)N=[N+]=[N-]',
'CCCC(=O)OC1CCCC1N=[N+]=[N-]',
'C(C=CC(=O)O)N=[N+]=[N-]',
'CC(CNC)N=[N+]=[N-]',
'CC(=O)CCC(=O)C=CCN=[N+]=[N-]',
'CC(C(N=[N+]=[N-])O)O',
'C',
'C(CO)COCCOCCOCCOCCN=[N+]=[N-]',
'C1C=CC(CN1)N=[N+]=[N-]',
'C1C=C[C@H](CN1)N=[N+]=[N-]',
'CCCC(C)(CC)N=[N+]=[N-]',
'CCCCC(C)(CC)N=[N+]=[N-]',
'CCCCCCCCCC(C)(C)N=[N+]=[N-]',
'C',
'CC(=O)CCC(=O)ON=[N+]=[N-]',
'C',
'CC(NCC',
'C/C=C(/NCC',
'C1CN(CCC1C',
'CC(CN=[N+]=[N-])OOC(OC)Cl',
'CN1CCNC(C1)CN=[N+]=[N-]',
'CCOCCOCN=[N+]=[N-]',
'CC1C2CCC(C2)N1CCCN=[N+]=[N-]',
'CC(=O)CCC1(N=N1)CCN=[N+]=[N-]',
'C(COCN=[N+]=[N-])NN',
'CC(NNCN)N=[N+]=[N-]',
'C/C(=C\\C1=CC=C(C=C1)C',
'C1=CC=C(C=C1)/C=C(\\C',
'CN(C)C1=CC=C(C=C1)/C=C(\\C',
'[2H]OCC(=O)N=[N+]=[N-]',
'C/C=C(\\C=C)/N=[N+]=[N-]',
'CC(=O)C(CCCCOC)N=[N+]=[N-]',
'CC',
'C=CCN1CCN(C1)N=[N+]=[N-]',
'CC(=O)C(=C)NCCCCN=[N+]=[N-]',
'C1=CC(=CC',
'C',
'CC1=CC=C(C=C1)C(C(=O)NCC',
'CC(=O)N(CC',
'C1=CC(=CC=C1C',
'C1=CC(=CC=C1C',
'C1=CC(=CC=C1C',
'CS(=O)(=O)OCN=[N+]=[N-]',
'C1=CC=C(C=C1)C[C@@H](C(=O)OCC',
'C(/C=C/N=[N+]=[N-])P(=O)(O)O',
'C=CC(N=[N+]=[N-])P(=O)(O)O',
'C=CS(=O)(=O)CCOCCN=[N+]=[N-]',
'CCCCCCC(CCCCCC)CN=[N+]=[N-]',
'CCOCCOC(CN=[N+]=[N-])N',
'C',
'CCCNC(=O)CCCCN=[N+]=[N-]',
'CC',
'C',
'C=CCO[C@@H](CN=[N+]=[N-])CO',
'CC(=O)O[C@H](CN=[N+]=[N-])CO',
'CCC(C)C(=O)OCC(CN=[N+]=[N-])O',
'CC',
'CC',
'CCPN=[N+]=[N-]',
'CCCC(CCC)CN=[N+]=[N-]',
'CCOC(=O)/C(=C/C1=CC',
'CC(CC(CC(=O)O)CN)CN=[N+]=[N-]',
'COC1=C(C=CS1)N=[N+]=[N-]',
'C',
'C',
'C(C(C(C(=O)O)N=[N+]=[N-])O)O',
'C(CCN=[N+]=[N-])CC(=O)NCCN',
'C(CC(=O)ON)CN=[N+]=[N-]',
'CN(CN)N=[N+]=[N-]',
'CC(CCN1C=CN=C1C=O)N=[N+]=[N-]',
'CC1CCC(C(C1)C)CN=[N+]=[N-]',
'C(CCCC',
'CC(=O)[C@H](CN=[N+]=[N-])NC',
'CN[C@@H](CN=[N+]=[N-])C(=O)NC',
'CCC(N=[N+]=[N-])OCC1=CC=CC=C1',
'CCC(C)(C)C(C)(C)CN=[N+]=[N-]',
'C(C(=O)NS)N=[N+]=[N-]',
'C1=CC=C(C(=C1)CN=[N+]=[N-])SO',
'COC(=O)C',
'C1=CN=C(C=C1CN=[N+]=[N-])N=O',
'C1C=C(C=C(N1)N=O)CN=[N+]=[N-]',
'CCOC(=O)C',
'CC1C2C1C2(C)N=[N+]=[N-]',
'CCC(=CN=[N+]=[N-])C',
'CC1(CC(CCC1CN=[N+]=[N-])C=N)C',
'CN1CCN=C1OCN=[N+]=[N-]',
'CC(C)(C)NCCOCCOCCN=[N+]=[N-]',
'CCCCCC=C(CN=[N+]=[N-])C(=O)OC',
'CCCCC/C=C(/CN=[N+]=[N-])\\C',
'C1=CC=C(C(=C1)/C=C(\\CC',
'C1=CC=C(C(=C1)C=C(CC',
'C1=CC=C(C(=C1)/C=C(\\CC',
'C',
'C',
'C',
'CNCCCCCCCCCN=[N+]=[N-]',
'C(CCCCN)CCCCN=[N+]=[N-]',
'CCCCOCCC(C)(CN=[N+]=[N-])O',
'CCCCOCCC(C)(CO)N=[N+]=[N-]',
'CCCCOCC(C(C)(C)O)N=[N+]=[N-]',
'CCCCOCC(C(C)(C)N=[N+]=[N-])O',
'C/C(=N/N=C(N)N)/N=[N+]=[N-]',
'CC1COCC1N=[N+]=[N-]',
'CCC(C)(CC)N=[N+]=[N-]',
'C1=C(C(=O)NC1=O)N=[N+]=[N-]',
'CCCCC/C=C/CN=[N+]=[N-]',
'CCOC(=O)CC(=O)CCCN=[N+]=[N-]',
'C',
'C',
'C',
'C',
'C1=CC=C(C=C1)[C@H](C[C@@H](CC',
'CC(C)(C',
'C',
'C',
'C[Si](C)(C)C',
'C[Si](C)(C)C',
'C',
'C',
'CN(C)CCNCCN=[N+]=[N-]',
'CC(C)[Si](C',
'CC[Si](CC)(CC)C',
'CC[Si](CC)(CC)C',
'CC[Si](CC)(CC)C',
'CC(C)[Si](C',
'CCCCOC(=O)C(=C)N=[N+]=[N-]',
'C=COC1=CC=C(C=C1)N=[N+]=[N-]',
'C',
'C',
'C',
'C',
'CC(C1=CN=NN1C)N=[N+]=[N-]',
'CCC(C1=CC=CC=C1F)N=[N+]=[N-]',
'CC1=C(C=CC(=C1)N=[N+]=[N-])Cl',
'COC1=C(C=CC(=C1)N=[N+]=[N-])F',
'CSC1=CC=CC(=C1)N=[N+]=[N-]',
'CC1=C(C=CC(=C1)OC)N=[N+]=[N-]',
'C1CCC(C1)N2CC(C2)N=[N+]=[N-]',
'C1C(CN1CC(=O)N)N=[N+]=[N-]',
'CCC(C1=CC=CC=N1)N=[N+]=[N-]',
'COC1COCC1N=[N+]=[N-]',
'CCOC1CCCCC1N=[N+]=[N-]',
'C1CC1(C(F)F)N=[N+]=[N-]',
'C1CC1(C(F)(F)F)N=[N+]=[N-]',
'CC(CCN=[N+]=[N-])OC1CCCCO1',
'CC(C)(CCCCCO)N=[N+]=[N-]',
'CCCCC(CCCC(C)(C)N=[N+]=[N-])O',
'CC1(CCCCCC1)N=[N+]=[N-]',
'CC(=CCCC(C)(C)N=[N+]=[N-])C',
'CCCCCCCCC(C)(C)N=[N+]=[N-]',
'C/C=C\\C[C@@H](C)C',
'C/C=C\\CC(C)C',
'C1=CC(=CC=C1C',
'C(CSCCN=[N+]=[N-])N=[N+]=[N-]',
'C',
'CONCCCN=[N+]=[N-]',
'CC(C)(C)OC(=O)C(C',
'C[C@@H](CC',
'C1(=NN=C(N=N1)N=[N+]=[N-])N',
'C(CCO)CCS(=O)(=O)N=[N+]=[N-]',
'CN(CCN=[N+]=[N-])N[O-]',
'CN(CCN=[N+]=[N-])[NH2+][O-]',
'C1=CC=C(C=C1)C(C',
'C=CC(COC(=O)CCCCN=[N+]=[N-])F',
'C1=CC=C2C(=C1)C(=O)OI2C',
'C[SiH](C)CCCN=[N+]=[N-]',
'CCC(CCCCCBr)N=[N+]=[N-]',
'CCC(CC1=CC=CC=C1)N=[N+]=[N-]',
'CCCCCCCCC1(CCCC1)N=[N+]=[N-]',
'CCCCCCCCC1(CCCCC1)N=[N+]=[N-]',
'CCCCC(CC)(CCCC)N=[N+]=[N-]',
'CCCCCCCCCCC(C)(C)N=[N+]=[N-]',
'C',
'C1=CNC(=O)NC1N=[N+]=[N-]',
'C1=CN=CC=C1CCCCN=[N+]=[N-]',
'CCC(C)(C(=O)OC)N=[N+]=[N-]',
'CN1C(=C(C2=C(S1(=O)=O)SC=C2)C',
'CC1=CC=C(C=C1)S(=O)(=O)NCCN(C',
'COC(CN=[N+]=[N-])C1=CC=CC=C1',
'C1=CC=C(C=C1)C',
'CC(C1=CN=CC=C1)N=[N+]=[N-]',
'CC(C)(CCC=C)N=[N+]=[N-]',
'CC1(CC1)N=[N+]=[N-]',
'COC1=CC(=C(C=C1)N=[N+]=[N-])F',
'CC1=CN=CC(=N1)CCN=[N+]=[N-]',
'CC(CN=[N+]=[N-])C1=CC=CC=N1',
'C1C(C1(Cl)Cl)CCN=[N+]=[N-]',
'CC(C)(C)OC1CC(C1)N=[N+]=[N-]',
'CC1=C(C(=NN1)C)N=[N+]=[N-]',
'C[C@H](C1=CN=NN1C)N=[N+]=[N-]',
'C1CCC(C1)(CN=[N+]=[N-])C',
'C1CCC(CC1)(CN=[N+]=[N-])C',
'C(CN=[N+]=[N-])C(F)(F)Cl',
'CN1C=C(N=N1)CCN=[N+]=[N-]',
'C=CC1(CCCCC1N=[N+]=[N-])O',
'CC1=C(C=CC=C1Br)N=[N+]=[N-]',
'C1=C(C=C(C=C1F)Cl)N=[N+]=[N-]',
'CC1CCC(C(C1)N=[N+]=[N-])O',
'CC1(CCC(C1O)N=[N+]=[N-])C',
'C1CC(CC(C1)O)N=[N+]=[N-]',
'CC1C(SCCN1CCN=[N+]=[N-])C',
'C[C@H](C1=CC=CO1)N=[N+]=[N-]',
'CC[C@H](C1=CC=CS1)N=[N+]=[N-]',
'C[C@H](C1=CC=CS1)N=[N+]=[N-]',
'C[C@H](C1=CSC=C1)N=[N+]=[N-]',
'C[C@@H](C1=CC=CS1)N=[N+]=[N-]',
'C[C@@H](C1=CSC=C1)N=[N+]=[N-]',
'C[C@@H](C1=CC=CO1)N=[N+]=[N-]',
'C1CCC(CC1)C(CN=[N+]=[N-])O',
'CC(CN=[N+]=[N-])C(=O)NN',
'CCC(C(=O)NN)N=[N+]=[N-]',
'CC(CC(=O)NN)N=[N+]=[N-]',
'CC(C(=O)NN)N=[N+]=[N-]',
'CN1C(=CN=N1)N=[N+]=[N-]',
'CC1CCCCC1(C)N=[N+]=[N-]',
'C1C(CN1)CN=[N+]=[N-]',
'CCCCC',
'CC(CC1=CC=CC=C1N=[N+]=[N-])O',
'CC(CCCCCCN=[N+]=[N-])O',
'C',
'CN(CC=C)CN=[N+]=[N-]',
'CC(C)NC(=O)C(CCN=[N+]=[N-])NC',
'CC(CC(=O)CCCCN=[N+]=[N-])O',
'C(C(CI)I)NN=[N+]=[N-]',
'C(CNN=[N+]=[N-])C(CI)I',
'C=CCCNN=[N+]=[N-]',
'C(CCN=[N+]=[N-])CC(=O)NCCCl',
'C(CCN=[N+]=[N-])CC(=O)OBr',
'CNOCCOCCOCCN=[N+]=[N-]',
'CNOCCN=[N+]=[N-]',
'CC(C)(C',
'CCCC(C(N=[N+]=[N-])(F)F)(F)F',
'C1C2C1C(C(C2)N)N=[N+]=[N-]',
'C1C2CC2(CC1N)N=[N+]=[N-]',
'C1CC(C1)(N)N=[N+]=[N-]',
'C1C(CC1N=[N+]=[N-])N',
'C1CC(C1)(NC(=O)O)N=[N+]=[N-]',
'C1COC(=N1)C/C=C/N=[N+]=[N-]',
'C=CC(C1=NCCO1)N=[N+]=[N-]',
'C1=COC(=N1)CCCCN=[N+]=[N-]',
'C1COC(=N1)CCCCN=[N+]=[N-]',
'CC(OCCN=[N+]=[N-])OCCF',
'CC(OCCN=[N+]=[N-])OC(C)OCCF',
'CC(CC(CN=[N+]=[N-])O)O',
'CC(C)(C)N1CCCC(C1)N=[N+]=[N-]',
'CCOC1CCCC1N=[N+]=[N-]',
'CN1C(=CC(=N1)CN=[N+]=[N-])Cl',
'CCC1=CC(=NC=C1)CN=[N+]=[N-]',
'CC(C)OS(=O)(=O)CCCN=[N+]=[N-]',
'C(CS(=O)(=O)[O-])N=[N+]=[N-]',
'CCC1(CC(C1)N=[N+]=[N-])C',
'C1=CC(=C(N=C1)N=[N+]=[N-])C=O',
'CCOCC(=O)CN=[N+]=[N-]',
'C',
'CCCCCCC1(C2=C(C=CC(=C2)C',
'CCCCCCCC/C=C\\CCCCN=[N+]=[N-]',
'C(COP(=O)(O)ON=[N+]=[N-])N',
'C',
'C(COCCN=[N+]=[N-])C(=O)I',
'C(CCN=[N+]=[N-])CC(=O)I',
'C',
'CC1(CCC1)CN=[N+]=[N-]',
'C=CCC1=CC=C(C=C1)N=[N+]=[N-]',
'CC1=C(C(=CC=C1)CN=[N+]=[N-])O',
'CN1C[C@@H](C[C@H]1C',
'CC(C)N1C[C@@H](C[C@H]1C',
'COCC1=CC=CC(=N1)CN=[N+]=[N-]',
'CCOC(=O)CN(C(=O)N)N=[N+]=[N-]',
'C1C(=O)NC(=O)N1N=[N+]=[N-]',
'C(=N\\O)(\\N)/N=[N+]=[N-]',
'CC1(CCCCCCCCCCC1)N=[N+]=[N-]',
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'CNC(=O)[C@H](CN=[N+]=[N-])N',
'CC(=O)CC(=O)OCN=[N+]=[N-]',
'C1=C(OC(=C1)C=N)CN=[N+]=[N-]',
'C(C(COC=N)ON)N=[N+]=[N-]',
'C(CN=O)COCN=[N+]=[N-]',
'C[C@H](C(=C(C)C)F)N=[N+]=[N-]',
'CC(C)(CN=[N+]=[N-])C',
'CC(COC)OC(COCN=[N+]=[N-])C',
'CC(COC)OC(C)COCN=[N+]=[N-]',
'CC(COC)OC(CCCN=[N+]=[N-])COC',
'CCC(C)C(C)CN=[N+]=[N-]',
'COC1=CC(=C(C=C1)C(=O)OCC',
'COC1=CC(=C(C=C1)C(=O)OCC',
'CC(=O)NCC',
'CCOCC(=O)NCC',
'C(/C=C/NN)N=[N+]=[N-]',
'C=CC(NN)N=[N+]=[N-]',
'CC(=C(C',
'C(COCCOS(=O)O)N=[N+]=[N-]',
'C(COCCOS(=O)[O-])N=[N+]=[N-]',
'CCC1=CN=C(O1)CN=[N+]=[N-]',
'C=COC(=O)CN=[N+]=[N-]',
'C=NN/C=C\\N=[N+]=[N-]',
'C1=C(NC(=O)N=C1)N=[N+]=[N-]',
'C(CO)N(CCO)CN=[N+]=[N-]',
'C1=CN=CN=C1CN=[N+]=[N-]',
'CCOC(=O)C1=CN=C(N=C1NCCCCC',
'COCC1(COC1)CCN=[N+]=[N-]',
'CC1C(O1)(C)CN=[N+]=[N-]',
'C1CCC(C1)(N=[N+]=[N-])F',
'C(C(=C=NN)CN=[N+]=[N-])N',
'CNC(CN=[N+]=[N-])O',
'CC(C)CC(C)(C)N=[N+]=[N-]',
'CNC1=CC=CC=C1CN=[N+]=[N-]',
'C(C(N=[N+]=[N-])O)F',
'C1CN2C=CN=C2C1N=[N+]=[N-]',
'C1=CSC=C1CCCN=[N+]=[N-]',
'C1=CSC(=C1)CCCN=[N+]=[N-]',
'C1CC1C2COCC(O2)CN=[N+]=[N-]',
'CC1=CC(=NC=C1)CN=[N+]=[N-]',
'CCCCC(=O)NCCCCCN=[N+]=[N-]',
'CN(CCN=[N+]=[N-])Cl',
'COPN=[N+]=[N-]',
'C1=CC=C(C=C1)COC(=O)NC(CC',
'C1C(C(OC1N2C=C(C(=O)N2)C',
'C(COCCOCC(N)N=[N+]=[N-])O',
'CNC(=O)OCCOCCOCCN=[N+]=[N-]',
'COC1COC2C1OCC2N=[N+]=[N-]',
'C1=CC=C(C=C1)CN(C(CC',
'CC1=NNN=C1CN=[N+]=[N-]',
'C(CN=[N+]=[N-])NI',
'CCCOCCOCN=[N+]=[N-]',
'CCCCCCCOCN=[N+]=[N-]',
'CC(C)C1=C(SC=N1)CN=[N+]=[N-]',
'C1=NC(=C(S1)CN=[N+]=[N-])Cl',
'CC(C)C1=NC=C(S1)CN=[N+]=[N-]',
'CCC1=NC=C(S1)CN=[N+]=[N-]',
'CCC1=C(SC=N1)CN=[N+]=[N-]',
'C([C@@H](C(CO)O)O)N=[N+]=[N-]',
'C1=CC(=NC=C1CON)OCN=[N+]=[N-]',
'C1CN(CCC1N)S(=O)CN=[N+]=[N-]',
'C=CCC(=O)N=[N+]=[N-]',
'C1C(C1CO)CN=[N+]=[N-]',
'CCSSCN=[N+]=[N-]',
'CCCSCC(C)CSCCN=[N+]=[N-]',
'CCCC1=CC=C(C=C1)CCN=[N+]=[N-]',
'C1CNC[C@@]1(CN=[N+]=[N-])CO',
'COCOC[C@]1(CCNC1)CN=[N+]=[N-]',
'CC(C)(CC(=O)OC)N=[N+]=[N-]',
'CC1CC(CC1C=N)CN=[N+]=[N-]',
'CC(=O)OCCCCN=[N+]=[N-]',
'CC(CCCCC(=O)O)N=[N+]=[N-]',
'CC(CCCOC(=O)C)N=[N+]=[N-]',
'CC(CCCO)N=[N+]=[N-]',
'C(COCCOCC[18F])N=[N+]=[N-]',
'CC(C(=O)OCCCN=[N+]=[N-])S',
'CC1CCCC1(C)N=[N+]=[N-]',
'C(C(N)N=[N+]=[N-])N=[N+]=[N-]',
'C(C(COOO)O)N=[N+]=[N-]',
'C',
'C',
'CC(CCCN=[N+]=[N-])(C(=O)O)Br',
'C(CCN=[N+]=[N-])CC(C(=O)O)Br',
'CCC(CC(C(=O)O)Br)N=[N+]=[N-]',
'C',
'C',
'COC(=O)C1=CC(=C(C=C1)OCC',
'C',
'C',
'C',
'C',
'C',
'C',
'C',
'C(CN=[N+]=[N-])C(CCF)(CO)O',
'CCOC(CCF)CN=[N+]=[N-]',
'CP(CN=[N+]=[N-])C',
'CP(CN=[N+]=[N-])N=[N+]=[N-]',
'CCC(=O)C(C)(C)C(C)N=[N+]=[N-]',
'C(COCCOC(=O)NN)N=[N+]=[N-]',
'CCOP(=O)(C)CCN=[N+]=[N-]',
'CC(C)C(C(=O)O)NN=[N+]=[N-]',
'CCC1(OCC(CO1)(C(=O)NCC',
'C',
'CC(CCC1=NC2=C(C=C(C=C2C(=C1)C',
'CC(CCC1=NC2=CC(=C(C=C2C(=C1)C',
'C(CCN)CC(C(=O)O)N=[N+]=[N-]',
'CC1(CNC(=O)O1)CN=[N+]=[N-]',
'C1CC=CC(C1)CN=[N+]=[N-]',
'C1COC(CN1C(=O)O)CN=[N+]=[N-]',
'CC(C(CN=[N+]=[N-])O)NC(=O)O',
'CC1(CNC(O1)O)CN=[N+]=[N-]',
'CC1C(OC(=O)N1)CN=[N+]=[N-]',
'C1C(OC(=O)N1)CCN=[N+]=[N-]',
'CC(C1CNC(=O)O1)N=[N+]=[N-]',
'C1CC12C(OC(=O)N2)CN=[N+]=[N-]',
'CC(C)(C(N=[N+]=[N-])Cl)O',
'CC(CN=[N+]=[N-])(CCl)O',
'C/C(=C\\C=C/N=C)/N=[N+]=[N-]',
'CC(C(F)(F)F)(N=[N+]=[N-])OC',
'CCC(C)(N=[N+]=[N-])O',
'C(C(N=[N+]=[N-])(F)F)OC(=O)N',
'CCOC(=O)CC(N=[N+]=[N-])(F)F',
'C(C(=O)O)C(N=[N+]=[N-])(F)F',
'C(=O)(C(N=[N+]=[N-])(F)F)N',
'COC(=O)C1=CC=C(O1)N=[N+]=[N-]',
'CC(CCN)CN=[N+]=[N-]',
'CC(CN)C(C)CN=[N+]=[N-]',
'CNC1(SS1)N=[N+]=[N-]',
'C(C(=O)P)N=[N+]=[N-]',
'C1(SS1)(N)N=[N+]=[N-]',
'C',
'C([C@@H](CO)N=NN)N=[N+]=[N-]',
'C1CN(CCN1)CCOCCN=[N+]=[N-]',
'COC1=C(C=C2C(=C1)C(=C(C=N2)C',
'COC1=C(C=C2C(=C1)C(=C(C=N2)C',
'CC(C1=C(C=CC(=C1)Br)C',
'C1=C(C(=NC=C1Br)C',
'C(CCC(C(=O)O)N)CCN=[N+]=[N-]',
'C(CCCN=[N+]=[N-])CCC(C(=O)O)N',
'CC1(C(CN1)N=[N+]=[N-])C',
'C1CN(CCC1C',
'C(C(CO)OCN=[N+]=[N-])O',
'C(N=[N+]=[N-])OC(=O)NN',
'C(CON=N)N=[N+]=[N-]',
'CC1CCC(CN1)N=[N+]=[N-]',
'C1=CC(=C(N=C1)CN=[N+]=[N-])F',
'CC(C)(CCN=[N+]=[N-])C(=O)[O-]',
'CC(C)(CCN=[N+]=[N-])C(=O)O',
'CC(C(C)(C)C(=O)O)N=[N+]=[N-]',
'C1=C(C=NC=C1Cl)N=[N+]=[N-]',
'C1C2C(C2CN=[N+]=[N-])CN1',
'COCCCN1CC2C(C1)C2CN=[N+]=[N-]',
'CCC(C)(C)CC(C)N=[N+]=[N-]',
'CCC(C)(CC(C)(C)C)N=[N+]=[N-]',
'CC(C)CC(C)N=[N+]=[N-]',
'CCC(C)(C)CC(C)(C)N=[N+]=[N-]',
'CCC(C)(C)CC(C)(CC)N=[N+]=[N-]',
'C(C(=O)N=N)N=[N+]=[N-]',
'C1C(C(OC1N2C=C(C(=O)NC2=O)C',
'C1C2CC1(C2)N=[N+]=[N-]',
'C(COCCOCCOC(=O)Cl)N=[N+]=[N-]',
'CC(=C)C(=O)NCCCCN=[N+]=[N-]',
'CC1=CN=C(C=C1)CCCN=[N+]=[N-]',
'CN(C)CCN(CCN(C)C)N=[N+]=[N-]',
'CC(C)C[C@@H](C',
'COCCOCCOCN=[N+]=[N-]',
'COC1=NC(=NC(=C1C',
'C',
'C1=CC=C(C=C1)C',
'CNC1=NC(=NC(=C1C',
'CC1CCC2(N1CCC2)CN=[N+]=[N-]',
'C1CC2(CC(CN2C1)F)CN=[N+]=[N-]',
'C=C1CC2(CCCN2C1)CN=[N+]=[N-]',
'C1CCN2CCCC2(C1)CN=[N+]=[N-]',
'C1=CC(=C(C=C1CN=[N+]=[N-])O)O',
'CCCC(C(C)O)N=[N+]=[N-]',
'COCCON=[N+]=[N-]',
'C1CCCCC(CCC1)N=[N+]=[N-]',
'CC1=C(C2=C(N1C3=CC=C(C=C3)C',
'CC1=C(C2=C(N1C3=CC=C(C=C3)C',
'C1=CC(=C(C=C1N=[N+]=[N-])C',
'C1[C@H](C(CN1)N=[N+]=[N-])F',
'C1=CC=C2C(=C1)C(=C(C',
'C1=CC=C(C=C1)CC(C(=O)OCC',
'C1C(C(CN1)F)N=[N+]=[N-]',
'CC',
'CCC(C)(CC(CC(C)(C)C(=O)OCC',
'CC(=C)C(=O)NCCN=[N+]=[N-]',
'C1=CC(=O)C(C1=O)NCN=[N+]=[N-]',
'CC(CCC(C)CN=[N+]=[N-])CC',
'C=C(CN=[N+]=[N-])C(=O)Cl',
'C1CNC[C@H]1N=[N+]=[N-]',
'C1C(C1N=[N+]=[N-])C(=O)O',
'COC(=O)CCC(CN=[N+]=[N-])C=N',
'CN1CCCC(C1=O)(CC',
'COC1=CC(=C(C=C1)C(=O)OCC',
'COC1=CC(=C(C=C1)C(=O)OCC',
'C1CNC(CN1)C(=O)CN=[N+]=[N-]',
'CCCCCC[N+](C)(C)CCN=[N+]=[N-]',
'C[N+](C)(CCN=[N+]=[N-])C',
'CCCCCCCCCCCCNCCN=[N+]=[N-]',
'C=CN/C=C\\N=[N+]=[N-]',
'C(CNC(=O)CCS)CN=[N+]=[N-]',
'CCCC/C=C/C=C/CN=[N+]=[N-]',
'C(CCN=[N+]=[N-])CCS(=O)Cl',
'CC(=O)SCCCCCN=[N+]=[N-]',
'C1[C@@H]2C[C@@H]2N([C@@H]1C',
'C1[C@@H]2C[C@@H]2C([C@@H]1C',
'CCCCCCC/C=C/C=C/CN=[N+]=[N-]',
'CS(=O)(=O)OC1COCC1N=[N+]=[N-]',
'CC(CCOS(=O)(=O)C)N=[N+]=[N-]',
'CCCCC/C=C/C=C/CN=[N+]=[N-]',
'C[S@@](=O)CCOCCN=[N+]=[N-]',
'CS(=O)CCOCCN=[N+]=[N-]',
'C[C@@H](CN=[N+]=[N-])NC(=O)O',
'CC1CC([C@H](O1)CN=[N+]=[N-])O',
'C=CCCCCCCCCN=[N+]=[N-]',
'CCCC(C)(N=[N+]=[N-])I',
'CCCC(N=[N+]=[N-])I',
'C1CC(CC(C1N=[N+]=[N-])O)(F)F',
'CCC1CCC(CC1)CN=[N+]=[N-]',
'C(CCN=[N+]=[N-])CNO',
'CN(CCCO)CN=[N+]=[N-]',
'CN(CCCCN=[N+]=[N-])CCO',
'C(CCN=[N+]=[N-])CNC(CO)C(=O)O',
'C(CNCCO)CN=[N+]=[N-]',
'CCCNCCCN=[N+]=[N-]',
'CCCNCCN=[N+]=[N-]',
'CCCC[N+](C)(C)CN=[N+]=[N-]',
'CCC(C(=O)O)NCCCCN=[N+]=[N-]',
'C[N+](C)(CCO)CN=[N+]=[N-]',
'CCC[N+](C)(C)CCCN=[N+]=[N-]',
'C[N+](C)(CCN=[N+]=[N-])CCO',
'CCC[N+](C)(C)CCCCN=[N+]=[N-]',
'CCCNCCCCN=[N+]=[N-]',
'CC(C)(C',
'CC(C)SSC(CC[C@@H](C(=O)OCC',
'CC',
'CC(C)C(CCC',
'CC(C)C(CCC',
'CCC',
'C1CCNC(C1)CN=[N+]=[N-]',
'C',
'CC1=CN=C(C=C1)CN=[N+]=[N-]',
...]
Правила 5 Лепински следующие:
Not more than 5 hydrogen bond donors (nitrogen or oxygen atoms with one or more hydrogen atoms)
Not more than 10 hydrogen bond acceptors (nitrogen or oxygen atoms)
A molecular mass less than 500 daltons
An octanol-water partition coefficient log P not greater than 5
In [13]:
good_smiles=[]
min = Lipinksy.rdMolDescriptors.CalcCrippenDescriptors(ibu)[0]
min_index = 0
for smi in smiles[:50]:
if 'N=[N+]=[N-]' in smi:
newsmi=smi.replace('N=[N+]=[N-]','N1C=C(N=N1)C1=CC=C(C=C1)C(C)C(=O)O') #azid to ibuprophen
else:
continue
try:
newmol=Chem.MolFromSmiles(newsmi) #creating a molecute
if Lipinksy.NumHDonors(newmol) <= 5 and Lipinksy.NumHAcceptors(newmol) <= 10 and Lipinksy.rdMolDescriptors.CalcExactMolWt(newmol) <= 500 and Lipinksy.rdMolDescriptors.CalcCrippenDescriptors(newmol)[0] <= 5:
good_smiles.append(newmol)
AllChem.Compute2DCoords(newmol)
display(newmol)
except:
pass
In [ ]:
In [14]:
m3d=Chem.AddHs(good_smiles[1])
Chem.AllChem.EmbedMolecule(m3d)
AllChem.MMFFOptimizeMolecule(m3d,maxIters=500,nonBondedThresh=200)
Out[14]:
0
In [15]:
import nglview as nv
nv.show_rdkit(m3d)
