molecule encoder/decoder in deepchem #rdkit #deepchem

Posted byiwatobipenPosted inprogrammingTags:, , ,

Today I updated deepchem in my mac.
It was easy to install new version of deepchem on Mac.

iwatobipen$ git clone https://github.com/deepchem/deepchem.git
iwatobipen$ cd deepchem
iwatobipen$ bash scripts/install_deepchem_conda.sh

That’s all. ;-)

New version of deepchem is implemented MoleculeVAE. MoeculeVAE generates new molecules by using pre defined model.
Deepchem can use pre defined model that was trained with Zinc Dataset.
OK let’s run the code.
I tested moleculeVAE by reference to following web page.
https://www.deepchem.io/_modules/deepchem/models/autoencoder_models/test_tensorflowEncoders.html

Deepchem provides lots of useful function for data preparation.
For example, convert smiles to one hot vector and vise versa.
I used cdk2.sdf for structure generation.

from __future__ import print_function
import os
from rdkit import Chem, RDConfig
from rdkit.Chem import Draw
import deepchem as dc
from deepchem.models.autoencoder_models.autoencoder import TensorflowMoleculeEncoder, TensorflowMoleculeDecoder
from deepchem.feat.one_hot import zinc_charset
from deepchem.data import DiskDataset

datadir = os.path.join( RDConfig.RDDocsDir, 'Book/data/cdk2.sdf' )

mols = [ mol for mol in Chem.SDMolSupplier( datadir ) ]
smiles = [ Chem.MolToSmiles( mol ) for mol in mols ]
print( len( smiles ))

tf_encoder = TensorflowMoleculeEncoder.zinc_encoder()
tf_decoder = TensorflowMoleculeDecoder.zinc_decoder()

featurizer = dc.feat.one_hot.OneHotFeaturizer( zinc_charset, 120 )

# default setting ; encode smiles to one_hot vector and padding to 120 character.
features = featurizer( mols )
print( features.shape )

dataset = DiskDataset.from_numpy( features, features )
prediction = tf_encoder.predict_on_batch( dataset.X )
one_hot_dec = tf_decoder.predict_on_batch( prediction )
decoded_smiles = featurizer.untransform( one_hot_dec )

for smiles in decoded_smiles:
    print( smiles[0] )
    print( Chem.MolFromSmiles( smiles[0] ))
mols = [ Chem.MolFromSmiles( smi[0] ) for smi in decoded_smiles ]
im = Draw.MolsToGridImage( mols )
im.save( 'res.png' )

And results was …. ;-(

iwatobipen$ python molVAE.py
/Users/iwatobipen/.pyenv/versions/anaconda3-2.4.0/lib/python3.5/site-packages/sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
Using TensorFlow backend.
47
2017-10-10 22:25:23.051035: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use SSE4.2 instructions, but these are available on your machine and could speed up CPU computations.
2017-10-10 22:25:23.051056: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use AVX instructions, but these are available on your machine and could speed up CPU computations.
2017-10-10 22:25:23.051060: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use AVX2 instructions, but these are available on your machine and could speed up CPU computations.
2017-10-10 22:25:23.051064: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use FMA instructions, but these are available on your machine and could speed up CPU computations.
(47, 120, 35)
TIMING: dataset construction took 0.059 s
Loading dataset from disk.
CCCCNC(=O)CCn1c(=O)ncc[n1)ccn2
[22:25:29] SMILES Parse Error: syntax error for input: 'CCCCNC(=O)CCn1c(=O)ncc[n1)ccn2'
None
CC(C))CCN1CCCC1)c2nc[nH+]nn2
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(C))CCN1CCCC1)c2nc[nH+]nn2'
None
CC(C)(C)C(CCC(=O)NCCc1cc[nH+]cn1
[22:25:29] SMILES Parse Error: extra open parentheses for input: 'CC(C)(C)C(CCC(=O)NCCc1cc[nH+]cn1'
None
CC(C)(C)N1CCCCC1)c2nc[nH+]nn2
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(C)(C)N1CCCCC1)c2nc[nH+]nn2'
None
CC(C)CCNCCCC)CN=C)c1cc[nH+]cn1
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(C)CCNCCCC)CN=C)c1cc[nH+]cn1'
None
Cc1ccnnc1SCc2ccccc2Crc2NCCC))F)C
[22:25:29] SMILES Parse Error: syntax error for input: 'Cc1ccnnc1SCc2ccccc2Crc2NCCC))F)C'
None
CC((C)))C(=O)NCc1ccccc1)c(/c(=C)C(C(=])C
[22:25:29] SMILES Parse Error: syntax error for input: 'CC((C)))C(=O)NCc1ccccc1)c(/c(=C)C(C(=])C'
None
Cc1ccnn1CCC(=O)N((C)(C)Ccc2[n(ccn2)CCC)(C)C
[22:25:29] SMILES Parse Error: syntax error for input: 'Cc1ccnn1CCC(=O)N((C)(C)Ccc2[n(ccn2)CCC)(C)C'
None
CC(CC)(C)CC(C)(C)CCNCCC(CCC)N
<rdkit.Chem.rdchem.Mol object at 0x10079c210>
COc1ccc2c(c1)CC)Cc2cc((cn=O)C(=O)N3
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'COc1ccc2c(c1)CC)Cc2cc((cn=O)C(=O)N3'
None
Cc1ncsc(=O)n1C)CC(=O)Nc2ccss[N/C(=O)[C)[O-])C
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Cc1ncsc(=O)n1C)CC(=O)Nc2ccss[N/C(=O)[C)[O-])C'
None
Cc1c(c(=O)n2c(n1)C(=O)CC(C)C)C)C
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Cc1c(c(=O)n2c(n1)C(=O)CC(C)C)C)C'
None
CN(C))(O)CNN(Cc1cccn1+c2cc[nH]c2c2N
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CN(C))(O)CNN(Cc1cccn1+c2cc[nH]c2c2N'
None
CC11ccc2n1c(ccnH=)Nc3cc((c(c3=O)C)NCC2OO
[22:25:29] SMILES Parse Error: syntax error for input: 'CC11ccc2n1c(ccnH=)Nc3cc((c(c3=O)C)NCC2OO'
None
CCNH+]1CCc2cnc2c1c(n(c3=))c4cc(cc(cc3C)C))CC1=O
[22:25:29] SMILES Parse Error: syntax error for input: 'CCNH+]1CCc2cnc2c1c(n(c3=))c4cc(cc(cc3C)C))CC1=O'
None
CC(=O)Nc1cc(ccc1OC)CCc2c3c([nH+nn2)cccco3
[22:25:29] SMILES Parse Error: syntax error for input: 'CC(=O)Nc1cc(ccc1OC)CCc2c3c([nH+nn2)cccco3'
None
COc1ccc2c(n1)C)C)ccnc3ccccc3)NCC=)))C(=O)CC
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'COc1ccc2c(n1)C)C)ccnc3ccccc3)NCC=)))C(=O)CC'
None
CCS(=O)(=O)c1ccc(c(c1)C)2CC=c3cc(ccc3)NC(C)C)C(=O)N2
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CCS(=O)(=O)c1ccc(c(c1)C)2CC=c3cc(ccc3)NC(C)C)C(=O)N2'
None
CC(=O)Nc1cccccc1OC)CCc2c3c([nH+]n23cccccc4
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(=O)Nc1cccccc1OC)CCc2c3c([nH+]n23cccccc4'
None
Cc1cccc2c11[nH]nc(c2))CCC(=O)N(C3)CCc3ccc(H+]c)C
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Cc1cccc2c11[nH]nc(c2))CCC(=O)N(C3)CCc3ccc(H+]c)C'
None
Cc1cc(cc211[nH]cc(c2)CCCC(=O)CC(=O)NC3CCCn4ccc(=O)n4C
[22:25:29] SMILES Parse Error: extra open parentheses for input: 'Cc1cc(cc211[nH]cc(c2)CCCC(=O)CC(=O)NC3CCCn4ccc(=O)n4C'
None
Ccc1ccc2ccnn))n3c2ccc1)c4ccccc4F)
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Ccc1ccc2ccnn))n3c2ccc1)c4ccccc4F)'
None
Cc1nc(c2c(nn))n3c2ccc3)S4ccs2)C(C)(C[NH+]CCC))C)))n
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Cc1nc(c2c(nn))n3c2ccc3)S4ccs2)C(C)(C[NH+]CCC))C)))n'
None
CC(CCc1ccncc1)Cc2cccc3c2NN3CCNCC3=O
[22:25:29] SMILES Parse Error: unclosed ring for input: 'CC(CCc1ccncc1)Cc2cccc3c2NN3CCNCC3=O'
None
CC(=O)(=OOc1ccn1C(=C)C(=O)N)2cc(=O)(c2=O)())
[22:25:29] SMILES Parse Error: syntax error for input: 'CC(=O)(=OOc1ccn1C(=C)C(=O)N)2cc(=O)(c2=O)())'
None
CNS(=O)(=O)c(ccn1C((C)C(=O)Nc2ccc(cc2Cl)F
[22:25:29] SMILES Parse Error: syntax error for input: 'CNS(=O)(=O)c(ccn1C((C)C(=O)Nc2ccc(cc2Cl)F'
None
CCCC)CCC(=O)(=O)c1cO)1C(CC)C(=O)Nc2ccccc2F)/s1
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CCCC)CCC(=O)(=O)c1cO)1C(CC)C(=O)Nc2ccccc2F)/s1'
None
CC((Cc1c(=O)nnc(=O)C(=O)CC(C)))c2ccccc2C2=O
[22:25:29] SMILES Parse Error: syntax error for input: 'CC((Cc1c(=O)nnc(=O)C(=O)CC(C)))c2ccccc2C2=O'
None
c1cs=c1C(=O)N(C2(CCCC2))c3c[nH]c(=O)])
[22:25:29] SMILES Parse Error: syntax error for input: 'c1cs=c1C(=O)N(C2(CCCC2))c3c[nH]c(=O)])'
None
CS(=O)(=O)c1cc(1CCc=O)NCC2CCC(CC2)c3c[nH+]c(=+)n3
[22:25:29] SMILES Parse Error: syntax error for input: 'CS(=O)(=O)c1cc(1CCc=O)NCC2CCC(CC2)c3c[nH+]c(=+)n3'
None
CN(Cc1ccccc1)c2nc(nnn+]c2c(c2SCc4ccccc4
[22:25:29] SMILES Parse Error: syntax error for input: 'CN(Cc1ccccc1)c2nc(nnn+]c2c(c2SCc4ccccc4'
None
CS(=O)(=O)c1cc==O)2c(n3c2cccc1SCC(=O)NO)))c(cc)/(([O)on
[22:25:29] SMILES Parse Error: syntax error for input: 'CS(=O)(=O)c1cc==O)2c(n3c2cccc1SCC(=O)NO)))c(cc)/(([O)on'
None
CN(C)C(=O)CC(C(=O)[O-])C(=O)CSc1ccc[nH+]c1=N
[22:25:29] Can't kekulize mol.  Unkekulized atoms: 14 15 16 17 18

None
Cc1c=O(c=n1Cc2cccn2)c3c(n2)CC((((=C)C)])CC-/)
[22:25:29] SMILES Parse Error: syntax error for input: 'Cc1c=O(c=n1Cc2cccn2)c3c(n2)CC((((=C)C)])CC-/)'
None
CC(C)(CC))C(=O)NCc1cccnc1Cl)CCc(=O)(=))CC///n2
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(C)(CC))C(=O)NCc1cccnc1Cl)CCc(=O)(=))CC///n2'
None
CC(C)(CCN)C(=O)CSc1cc(=O)c(=CC))]))))))))S2/c2)=O)C))/s)
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(C)(CCN)C(=O)CSc1cc(=O)c(=CC))]))))))))S2/c2)=O)C))/s)'
None
CCN1CC11C(C2)C(=O)N2C2N(C2S((=O)NC3CC2)C(=O)OCC
[22:25:29] SMILES Parse Error: syntax error for input: 'CCN1CC11C(C2)C(=O)N2C2N(C2S((=O)NC3CC2)C(=O)OCC'
None
CCN=N)c1cc=1Cc==)(=O)C)(C))C)CC2CCCCCC2)))())
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CCN=N)c1cc=1Cc==)(=O)C)(C))C)CC2CCCCCC2)))())'
None
CC(CCc2ccccc2)C[=O)c3c(=O)n(c)+n3)c3nc(nc))c1
[22:25:29] SMILES Parse Error: syntax error for input: 'CC(CCc2ccccc2)C[=O)c3c(=O)n(c)+n3)c3nc(nc))c1'
None
CCS(=O)(=O)CS(=O)NC1CC)C(=O)Nc1ccc2c1cccc1F))n1
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CCS(=O)(=O)CS(=O)NC1CC)C(=O)Nc1ccc2c1cccc1F))n1'
None
CC1CCc2c(s2c2nc(n(=O)n)NC(=O)c3cccc(c3)SS(=O)=OO)C1
[22:25:29] SMILES Parse Error: unclosed ring for input: 'CC1CCc2c(s2c2nc(n(=O)n)NC(=O)c3cccc(c3)SS(=O)=OO)C1'
None
C[NH+]1CCCC(=O)[O-])CCc1c(=O)oc2c2c2cccc2C(s=])CCCC2=O
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'C[NH+]1CCCC(=O)[O-])CCc1c(=O)oc2c2c2cccc2C(s=])CCCC2=O'
None
Cc1cn(c(=O)c1C)CC(=O)Nc2ccss[N]S(=O)N)C(O)C)3(CCCC(C)\C)//)))C
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Cc1cn(c(=O)c1C)CC(=O)Nc2ccss[N]S(=O)N)C(O)C)3(CCCC(C)\C)//)))C'
None
C[NH]11CCCC(=O)[O-])NC(=O)CN1C)c2ccn12)C((O)/O))C)CCCC)2)C1
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'C[NH]11CCCC(=O)[O-])NC(=O)CN1C)c2ccn12)C((O)/O))C)CCCC)2)C1'
None
CCN1CC11(CCN)n(c(=NCc2ccccc2))4ccn23C4CCCC4=O2CCC
[22:25:29] SMILES Parse Error: unclosed ring for input: 'CCN1CC11(CCN)n(c(=NCc2ccccc2))4ccn23C4CCCC4=O2CCC'
None
CC(C=()Scc1n[nH]c2c(n1)CCCC(=O)CC(=O)N3CC[NH+](CC3)CCc4cccon)))
[22:25:29] SMILES Parse Error: syntax error for input: 'CC(C=()Scc1n[nH]c2c(n1)CCCC(=O)CC(=O)N3CC[NH+](CC3)CCc4cccon)))'
None
CC1CCc2c(c3cccccn2)C[H+]ccc(1O((((=+]3)Cc4ccss4Cl)1
[22:25:29] SMILES Parse Error: syntax error for input: 'CC1CCc2c(c3cccccn2)C[H+]ccc(1O((((=+]3)Cc4ccss4Cl)1'
None
[22:25:29] SMILES Parse Error: syntax error for input: 'CCCCNC(=O)CCn1c(=O)ncc[n1)ccn2'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(C))CCN1CCCC1)c2nc[nH+]nn2'
[22:25:29] SMILES Parse Error: extra open parentheses for input: 'CC(C)(C)C(CCC(=O)NCCc1cc[nH+]cn1'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(C)(C)N1CCCCC1)c2nc[nH+]nn2'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(C)CCNCCCC)CN=C)c1cc[nH+]cn1'
[22:25:29] SMILES Parse Error: syntax error for input: 'Cc1ccnnc1SCc2ccccc2Crc2NCCC))F)C'
[22:25:29] SMILES Parse Error: syntax error for input: 'CC((C)))C(=O)NCc1ccccc1)c(/c(=C)C(C(=])C'
[22:25:29] SMILES Parse Error: syntax error for input: 'Cc1ccnn1CCC(=O)N((C)(C)Ccc2[n(ccn2)CCC)(C)C'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'COc1ccc2c(c1)CC)Cc2cc((cn=O)C(=O)N3'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Cc1ncsc(=O)n1C)CC(=O)Nc2ccss[N/C(=O)[C)[O-])C'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Cc1c(c(=O)n2c(n1)C(=O)CC(C)C)C)C'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CN(C))(O)CNN(Cc1cccn1+c2cc[nH]c2c2N'
[22:25:29] SMILES Parse Error: syntax error for input: 'CC11ccc2n1c(ccnH=)Nc3cc((c(c3=O)C)NCC2OO'
[22:25:29] SMILES Parse Error: syntax error for input: 'CCNH+]1CCc2cnc2c1c(n(c3=))c4cc(cc(cc3C)C))CC1=O'
[22:25:29] SMILES Parse Error: syntax error for input: 'CC(=O)Nc1cc(ccc1OC)CCc2c3c([nH+nn2)cccco3'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'COc1ccc2c(n1)C)C)ccnc3ccccc3)NCC=)))C(=O)CC'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CCS(=O)(=O)c1ccc(c(c1)C)2CC=c3cc(ccc3)NC(C)C)C(=O)N2'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(=O)Nc1cccccc1OC)CCc2c3c([nH+]n23cccccc4'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Cc1cccc2c11[nH]nc(c2))CCC(=O)N(C3)CCc3ccc(H+]c)C'
[22:25:29] SMILES Parse Error: extra open parentheses for input: 'Cc1cc(cc211[nH]cc(c2)CCCC(=O)CC(=O)NC3CCCn4ccc(=O)n4C'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Ccc1ccc2ccnn))n3c2ccc1)c4ccccc4F)'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Cc1nc(c2c(nn))n3c2ccc3)S4ccs2)C(C)(C[NH+]CCC))C)))n'
[22:25:29] SMILES Parse Error: unclosed ring for input: 'CC(CCc1ccncc1)Cc2cccc3c2NN3CCNCC3=O'
[22:25:29] SMILES Parse Error: syntax error for input: 'CC(=O)(=OOc1ccn1C(=C)C(=O)N)2cc(=O)(c2=O)())'
[22:25:29] SMILES Parse Error: syntax error for input: 'CNS(=O)(=O)c(ccn1C((C)C(=O)Nc2ccc(cc2Cl)F'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CCCC)CCC(=O)(=O)c1cO)1C(CC)C(=O)Nc2ccccc2F)/s1'
[22:25:29] SMILES Parse Error: syntax error for input: 'CC((Cc1c(=O)nnc(=O)C(=O)CC(C)))c2ccccc2C2=O'
[22:25:29] SMILES Parse Error: syntax error for input: 'c1cs=c1C(=O)N(C2(CCCC2))c3c[nH]c(=O)])'
[22:25:29] SMILES Parse Error: syntax error for input: 'CS(=O)(=O)c1cc(1CCc=O)NCC2CCC(CC2)c3c[nH+]c(=+)n3'
[22:25:29] SMILES Parse Error: syntax error for input: 'CN(Cc1ccccc1)c2nc(nnn+]c2c(c2SCc4ccccc4'
[22:25:29] SMILES Parse Error: syntax error for input: 'CS(=O)(=O)c1cc==O)2c(n3c2cccc1SCC(=O)NO)))c(cc)/(([O)on'
[22:25:29] Can't kekulize mol.  Unkekulized atoms: 14 15 16 17 18

[22:25:29] SMILES Parse Error: syntax error for input: 'Cc1c=O(c=n1Cc2cccn2)c3c(n2)CC((((=C)C)])CC-/)'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(C)(CC))C(=O)NCc1cccnc1Cl)CCc(=O)(=))CC///n2'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CC(C)(CCN)C(=O)CSc1cc(=O)c(=CC))]))))))))S2/c2)=O)C))/s)'
[22:25:29] SMILES Parse Error: syntax error for input: 'CCN1CC11C(C2)C(=O)N2C2N(C2S((=O)NC3CC2)C(=O)OCC'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CCN=N)c1cc=1Cc==)(=O)C)(C))C)CC2CCCCCC2)))())'
[22:25:29] SMILES Parse Error: syntax error for input: 'CC(CCc2ccccc2)C[=O)c3c(=O)n(c)+n3)c3nc(nc))c1'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'CCS(=O)(=O)CS(=O)NC1CC)C(=O)Nc1ccc2c1cccc1F))n1'
[22:25:29] SMILES Parse Error: unclosed ring for input: 'CC1CCc2c(s2c2nc(n(=O)n)NC(=O)c3cccc(c3)SS(=O)=OO)C1'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'C[NH+]1CCCC(=O)[O-])CCc1c(=O)oc2c2c2cccc2C(s=])CCCC2=O'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'Cc1cn(c(=O)c1C)CC(=O)Nc2ccss[N]S(=O)N)C(O)C)3(CCCC(C)\C)//)))C'
[22:25:29] SMILES Parse Error: extra close parentheses for input: 'C[NH]11CCCC(=O)[O-])NC(=O)CN1C)c2ccn12)C((O)/O))C)CCCC)2)C1'
[22:25:29] SMILES Parse Error: unclosed ring for input: 'CCN1CC11(CCN)n(c(=NCc2ccccc2))4ccn23C4CCCC4=O2CCC'
[22:25:29] SMILES Parse Error: syntax error for input: 'CC(C=()Scc1n[nH]c2c(n1)CCCC(=O)CC(=O)N3CC[NH+](CC3)CCc4cccon)))'
[22:25:29] SMILES Parse Error: syntax error for input: 'CC1CCc2c(c3cccccn2)C[H+]ccc(1O((((=+]3)Cc4ccss4Cl)1'
Exception ignored in: <bound method BaseSession.__del__ of <tensorflow.python.client.session.Session object at 0x12a606128>>
Traceback (most recent call last):
  File "/Users/iwatobipen/.pyenv/versions/anaconda3-2.4.0/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 701, in __del__
TypeError: 'NoneType' object is not callable

Hmm…. I could not get suitable structure from Molecule autoencoder.
It has difficulty for molecule generator because structure of input data based on SMILES strings.  Now ratio of invalid smiles were high. But I think DeepChem and rdkit show nice combination for chemoinformatics.

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Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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