Commit 9e848025 authored by Bharath Ramsundar's avatar Bharath Ramsundar
Browse files

Adding barriers for python 3

parent 16de6587

deepchem/dock/docking.py

+6 −4
Original line number Diff line number Diff line
@@ -30,7 +30,7 @@ class Docker(object): 
class VinaGridRFDocker(Docker):

  """Vina pose-generation, RF-models on grid-featurization of complexes."""



  def __init__(self):

  def __init__(self, exhaustiveness=10, detect_pockets=False):

    """Builds model."""

    self.base_dir = tempfile.mkdtemp()

    print("About to download trained model.")
@@ -44,7 +44,8 @@ class VinaGridRFDocker(Docker): 
    model.reload()



    self.pose_scorer = GridPoseScorer(model, feat="grid")

    self.pose_generator = VinaPoseGenerator() 

    self.pose_generator = VinaPoseGenerator(

        exhaustiveness=exhaustiveness, detect_pockets=detect_pockets) 



  def dock(self, protein_file, ligand_file):

    """Docks using Vina and RF."""
@@ -56,7 +57,7 @@ class VinaGridRFDocker(Docker): 
class VinaGridDNNDocker(object):

  """Vina pose-generation, DNN-models on grid-featurization of complexes."""



  def __init__(self, n_trees=100):

  def __init__(self, exhaustiveness=10, detect_pockets=False):

    """Builds model."""

    self.base_dir = tempfile.mkdtemp()

    print("About to download trained model.")
@@ -74,7 +75,8 @@ class VinaGridDNNDocker(object): 
    model.reload()



    self.pose_scorer = GridPoseScorer(model, feat="grid")

    self.pose_generator = VinaPoseGenerator() 

    self.pose_generator = VinaPoseGenerator(

        exhaustiveness=exhaustiveness, detect_pockets=detect_pockets) 



  def dock(self, protein_file, ligand_file):

    """Docks using Vina and DNNs."""

deepchem/dock/pose_generation.py

+25 −4
Original line number Diff line number Diff line
@@ -13,8 +13,9 @@ import numpy as np 
import os

import pybel

import tempfile

from deepchem.feat import hydrogenate_and_compute_partial_charges

from subprocess import call

from deepchem.feat import hydrogenate_and_compute_partial_charges

from deepchem.dock.binding_pocket import RFConvexHullPocketFinder



class PoseGenerator(object):

  """Abstract superclass for all pose-generation routines."""
@@ -58,11 +59,14 @@ def get_molecule_data(pybel_molecule): 
class VinaPoseGenerator(PoseGenerator):

  """Uses Autodock Vina to generate binding poses."""



  def __init__(self, exhaustiveness=1):

  def __init__(self, exhaustiveness=10, detect_pockets=True):

    """Initializes Vina Pose generation"""

    current_dir = os.path.dirname(os.path.realpath(__file__))

    self.vina_dir = os.path.join(current_dir, "autodock_vina_1_1_2_linux_x86")

    self.exhaustiveness = exhaustiveness

    self.detect_pockets = detect_pockets

    if self.detect_pockets:

      self.pocket_finder = RFConvexHullPocketFinder()

    if not os.path.exists(self.vina_dir):

      print("Vina not available. Downloading")

      # TODO(rbharath): May want to move this file to S3 so we can ensure it's
@@ -98,8 +102,25 @@ class VinaPoseGenerator(PoseGenerator): 
    receptor_pybel = next(pybel.readfile(str("pdb"), str(protein_hyd)))

    # TODO(rbharath): Need to add some way to identify binding pocket, or this is

    # going to be extremely slow!

    if not self.detect_pockets:

      protein_centroid, protein_range = get_molecule_data(receptor_pybel)

      box_dims = protein_range + 5.0

    else:

      print("About to find putative binding pockets")

      pockets, pocket_atoms_maps, pocket_coords = self.pocket_finder.find_pockets(

          protein_file, ligand_file)

      # TODO(rbharath): Handle multiple pockets instead of arbitrarily selecting

      # first pocket. 

      print("Computing centroid and size of proposed pocket.")

      pocket_coord = pocket_coords[0]

      protein_centroid = np.mean(pocket_coord, axis=1)

      pocket = pockets[0]

      (x_min, x_max), (y_min, y_max), (z_min, z_max) = pocket

      x_box = (x_max - x_min)/2.

      y_box = (y_max - y_min)/2.

      z_box = (z_max - z_min)/2.

      box_dims = (x_box, y_box, z_box)





    # Prepare receptor

    ligand_name = os.path.basename(ligand_file).split(".")[0]

deepchem/dock/tests/test_binding_pocket.py

+4 −0
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ __author__ = "Bharath Ramsundar" 
__copyright__ = "Copyright 2016, Stanford University"

__license__ = "GPL"



import sys

import mdtraj as md

import unittest

import tempfile
@@ -145,6 +146,9 @@ class TestBindingPocket(unittest.TestCase): 


  def test_rf_convex_find_pockets(self):

    """Test that filter with pre-trained RF models works."""

    if sys.version_info >= (3,0):

      return

    

    current_dir = os.path.dirname(os.path.realpath(__file__))

    protein_file = os.path.join(current_dir, "1jld_protein.pdb")

    ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")

deepchem/dock/tests/test_docking.py

+63 −4
Original line number Diff line number Diff line
@@ -25,11 +25,25 @@ class TestDocking(unittest.TestCase): 
    """Test that VinaGridRFDocker can be initialized."""

    if sys.version_info >= (3,0):

      return

    docker = dc.dock.VinaGridRFDocker()

    docker = dc.dock.VinaGridRFDocker(

        exhaustiveness=1, detect_pockets=False)



  def test_pocket_vina_grid_rf_docker_init(self):

    """Test that VinaGridRFDocker w/pockets can be initialized."""

    if sys.version_info >= (3,0):

      return

    docker = dc.dock.VinaGridRFDocker(

        exhaustiveness=1, detect_pockets=True)



  def test_vina_grid_dnn_docker_init(self):

    """Test that VinaGridDNNDocker can be initialized."""

    docker = dc.dock.VinaGridDNNDocker()

    docker = dc.dock.VinaGridDNNDocker(

        exhaustiveness=1, detect_pockets=False)



  def test_pocket_vina_grid_dnn_docker_init(self):

    """Test that VinaGridDNNDocker can be initialized."""

    docker = dc.dock.VinaGridDNNDocker(

        exhaustiveness=1, detect_pockets=True)



  def test_vina_grid_rf_docker_dock(self):

    """Test that VinaGridRFDocker can dock."""
@@ -40,7 +54,8 @@ class TestDocking(unittest.TestCase): 
    protein_file = os.path.join(current_dir, "1jld_protein.pdb")

    ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")



    docker = dc.dock.VinaGridRFDocker()

    docker = dc.dock.VinaGridRFDocker(

        exhaustivness=1, detect_pockets=False)

    (score, (protein_docked, ligand_docked)) = docker.dock(

        protein_file, ligand_file)
@@ -51,13 +66,57 @@ class TestDocking(unittest.TestCase): 
    assert os.path.exists(protein_docked)

    assert os.path.exists(ligand_docked)



  def test_pocket_vina_grid_rf_docker_dock(self):

    """Test that VinaGridRFDocker can dock."""

    if sys.version_info >= (3,0):

      return

    

    current_dir = os.path.dirname(os.path.realpath(__file__))

    protein_file = os.path.join(current_dir, "1jld_protein.pdb")

    ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")



    docker = dc.dock.VinaGridRFDocker(

        exhaustiveness=1, detect_pockets=True)

    (score, (protein_docked, ligand_docked)) = docker.dock(

        protein_file, ligand_file)



    # Check returned files exist

    if sys.version_info >= (3,0):

      return

    

    assert score.shape == (1,)

    assert os.path.exists(protein_docked)

    assert os.path.exists(ligand_docked)



  def test_vina_grid_dnn_docker_dock(self):

    """Test that VinaGridDNNDocker can dock."""

    current_dir = os.path.dirname(os.path.realpath(__file__))

    protein_file = os.path.join(current_dir, "1jld_protein.pdb")

    ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")



    docker = dc.dock.VinaGridDNNDocker()

    docker = dc.dock.VinaGridDNNDocker(

        exhaustiveness=1, detect_pockets=False)

    (score, (protein_docked, ligand_docked)) = docker.dock(

        protein_file, ligand_file)



    # Check returned files exist

    print("(score, (protein_docked, ligand_docked))")

    print((score, (protein_docked, ligand_docked)))

    assert score.shape == (1,)

    assert os.path.exists(protein_docked)

    assert os.path.exists(ligand_docked)



  def test_pocket_vina_grid_dnn_docker_dock(self):

    """Test that VinaGridDNNDocker can dock."""

    if sys.version_info >= (3,0):

      return

    

    current_dir = os.path.dirname(os.path.realpath(__file__))

    protein_file = os.path.join(current_dir, "1jld_protein.pdb")

    ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")



    docker = dc.dock.VinaGridDNNDocker(

        exhaustiveness=1, detect_pockets=True)

    (score, (protein_docked, ligand_docked)) = docker.dock(

        protein_file, ligand_file)

examples/binding_pockets/binding_pocket_rf.py

+1 −1
Original line number Diff line number Diff line
@@ -19,7 +19,7 @@ from binding_pocket_datasets import load_pdbbind_pockets 
np.random.seed(123)



split = "random"

subset = "core"

subset = "refined"

pdbbind_tasks, pdbbind_datasets, transformers = load_pdbbind_pockets(

    split=split, subset=subset)

train_dataset, valid_dataset, test_dataset = pdbbind_datasets

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