Ricardo Avila ravila4

Passionate about bioinformatics, data science, and open source.

ravila4 / CypherBox.py

Last active August 29, 2015 14:27

A small Qt application that handles coding / decoding text in a Caesar cypher

	#!/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

ravila4 / receptor_to_pdbqt.py

Created February 12, 2018 02:34

Script for converting receptors to pdbqt using ODDT

	#!/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:

ravila4 / deepchem_PDBbind_featurizer.py

Created February 27, 2018 00:19

Test script to to generate features on the PDBbind dataset, using DeepChem

	# 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")

ravila4 / DeepChem_featurizer.ipynb

Created March 1, 2018 16:43

Featurizer experiments using deepchem

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