Ricardo Avila ravila4

## CypherBox.py
#!/usr/bin/env python3

# Qt GUI application for encoding text in a Caesar cypher
# Form implementation generated from reading ui file 'cypherbox.ui'
#
# Created: Sun Aug  9 13:02:22 2015
#      by: PyQt5 UI code generator 5.2.1


from PyQt5 import QtCore, QtGui, QtWidgets

## receptor_to_pdbqt.py
#!/usr/bin/env python3

# Ricardo Avila
# Script for converting receptors to pdbqt using ODDT

import sys
import oddt
from oddt.docking.AutodockVina import write_vina_pdbqt

if len(sys.argv) != 4:

## deepchem_PDBbind_featurizer.py
# Ricardo Avila
# Script to use grid featurizer on the PDBbind dataset

import glob
import csv
import deepchem as dc
from deepchem.feat.rdkit_grid_featurizer import RdkitGridFeaturizer

receptors = glob.glob("./refined-set/*/*protein.pdb")
ligands = glob.glob("./refined-set/*/*ligand.sdf")

## DeepChem_featurizer.ipynb

      
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                ravila4
                / DeepChem_featurizer.ipynb
            
            
              Created
              March 1, 2018 16:43
            
              
                Featurizer experiments using deepchem
              
          
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## OXR_docking_analysis.ipynb

      
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                / OXR_docking_analysis.ipynb
            
            
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              March 17, 2018 04:46
            
              
                Docking analysis of orexin receptor antagonists
              
          
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## k-means.ipynb

      
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                ravila4
                / k-means.ipynb
            
            
              Created
              April 8, 2018 02:29
            
              
                Snippet to calculate k-means
              
          
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## PCA.ipynb

      
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                ravila4
                / PCA.ipynb
            
            
              Created
              April 8, 2018 19:32
            
              
                PCA analysis on Swiss Bank Notes
              
          
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## mol2vec_amino_acids.ipynb

      
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                ravila4
                / mol2vec_amino_acids.ipynb
            
            
              Created
              April 17, 2018 20:44
            
              
                Mol2vec example
              
          
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## getting_chembl_ligs.ipynb

      
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                / getting_chembl_ligs.ipynb
            
            
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              April 20, 2018 21:37
            
              
                Fetching ligand activities from ChEMBL
              
          
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## vec_analysis.ipynb

      
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                ravila4
                / vec_analysis.ipynb
            
            
              Created
              April 22, 2018 13:55
            
              
                Multi dimensional scaling of prot2vec embedding features on a collection of receptors
              
          
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	#!/usr/bin/env python3

	# Qt GUI application for encoding text in a Caesar cypher
	# Form implementation generated from reading ui file 'cypherbox.ui'
	#
	# Created: Sun Aug 9 13:02:22 2015
	# by: PyQt5 UI code generator 5.2.1


	from PyQt5 import QtCore, QtGui, QtWidgets
	#!/usr/bin/env python3

	# Ricardo Avila
	# Script for converting receptors to pdbqt using ODDT

	import sys
	import oddt
	from oddt.docking.AutodockVina import write_vina_pdbqt

	if len(sys.argv) != 4:
	# Ricardo Avila
	# Script to use grid featurizer on the PDBbind dataset

	import glob
	import csv
	import deepchem as dc
	from deepchem.feat.rdkit_grid_featurizer import RdkitGridFeaturizer

	receptors = glob.glob("./refined-set//protein.pdb")
	ligands = glob.glob("./refined-set//ligand.sdf")