Bugfixes

- conda install h5py

- pip install keras

- export KERAS_BACKEND=tensorflow

- conda install seaborn

- conda install six

- conda install dill

- conda install runipy

- pip install runipy

- pip install nglview

- conda install -c omnia mdtraj

- python setup.py install

#- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then export TF_BINARY_URL=https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-0.12.0rc1-cp27-none-linux_x86_64.whl;

#  -O else export TF_BINARY_URL=https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-0.12.0rc1-cp35-cp35m-linux_x86_64.whl;

#  -O fi 

#- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then pip install --ignore-installed --upgrade $TF_BINARY_URL;

#  -O else pip3 install --ignore-installed --upgrade $TF_BINARY_URL;

#  -O fi

- conda install -c https://conda.anaconda.org/jjhelmus tensorflow=0.10.0rc0

script:

- nosetests -v deepchem --nologcapture

import numpy as np

import csv

import numbers

import dill

import tempfile

from rdkit import Chem

import time

    2) Complex featurization

      -) PDB files for interacting molecules.

    3) User specified featurizations.

  """

  time1 = time.time()

  df[featurizer.feature_fields] = df[featurizer.feature_fields].apply(pd.to_numeric)

import nglview

import tempfile

import os

import mdtraj as md

import numpy as np

import tempfile

from rdkit import Chem

from rdkit.Chem import Draw

from itertools import islice

from IPython.display import Image, HTML, display

def combine_mdtraj(protein, ligand):

  chain = protein.topology.add_chain()

  residue = protein.topology.add_residue("LIG", chain, resSeq=1)

  for atom in ligand.topology.atoms:

      protein.topology.add_atom(atom.name, atom.element, residue)

  protein.xyz = np.hstack([protein.xyz, ligand.xyz])

  protein.topology.create_standard_bonds()

  return protein

def visualize_complex(complex_mdtraj):

  ligand_atoms = [a.index for a in complex_mdtraj.topology.atoms if "LIG" in str(a.residue)]

  binding_pocket_atoms = md.compute_neighbors(complex_mdtraj, 0.5, ligand_atoms)[0]

  binding_pocket_residues = list(set([complex_mdtraj.topology.atom(a).residue.resSeq for a in binding_pocket_atoms]))

  binding_pocket_residues = [str(r) for r in binding_pocket_residues]

  binding_pocket_residues = " or ".join(binding_pocket_residues)

  traj = nglview.MDTrajTrajectory( complex_mdtraj ) # load file from RCSB PDB

  ngltraj = nglview.NGLWidget( traj )

  ngltraj.representations = [

  { "type": "cartoon", "params": {

  "sele": "protein", "color": "residueindex"

  } },

  { "type": "licorice", "params": {

  "sele": "(not hydrogen) and (%s)" %  binding_pocket_residues

  } },

  { "type": "ball+stick", "params": {

  "sele": "LIG"

  } }

  ]

  return ngltraj

def visualize_ligand(ligand_mdtraj):

  traj = nglview.MDTrajTrajectory( ligand_mdtraj ) # load file from RCSB PDB

  ngltraj = nglview.NGLWidget( traj )

  ngltraj.representations = [

    { "type": "ball+stick", "params": {"sele": "all" } } ]

  return ngltraj

def convert_lines_to_mdtraj(molecule_lines):

  tempdir = tempfile.mkdtemp()

  molecule_file = os.path.join(tempdir, "molecule.pdb")

  with open(molecule_file, "wb") as f:

    f.writelines(molecule_lines)

  molecule_mdtraj = md.load(molecule_file)

  return molecule_mdtraj

def display_images(filenames):

    """Helper to pretty-print images."""

    imagesList=''.join(

        ["<img style='width: 140px; margin: 0px; float: left; border: 1px solid black;' src='%s' />"

         % str(s) for s in sorted(filenames)])

    display(HTML(imagesList))

def mols_to_pngs(mols, basename="test"):

    """Helper to write RDKit mols to png files."""

    filenames = []

    for i, mol in enumerate(mols):

        filename = "%s%d.png" % (basename, i)

        Draw.MolToFile(mol, filename)

        filenames.append(filename)

    return filenames

# TODO(rbharath): Commenting out this file for now. Will be moved to a new repository.

#import nglview

#import tempfile

#import os

#import mdtraj as md

#import numpy as np

#import tempfile

#from rdkit import Chem

#from rdkit.Chem import Draw

#from itertools import islice

#from IPython.display import Image, HTML, display

#

#def combine_mdtraj(protein, ligand):

#  chain = protein.topology.add_chain()

#  residue = protein.topology.add_residue("LIG", chain, resSeq=1)

#  for atom in ligand.topology.atoms:

#      protein.topology.add_atom(atom.name, atom.element, residue)

#  protein.xyz = np.hstack([protein.xyz, ligand.xyz])

#  protein.topology.create_standard_bonds()

#  return protein

#

#def visualize_complex(complex_mdtraj):

#  ligand_atoms = [a.index for a in complex_mdtraj.topology.atoms if "LIG" in str(a.residue)]

#  binding_pocket_atoms = md.compute_neighbors(complex_mdtraj, 0.5, ligand_atoms)[0]

#  binding_pocket_residues = list(set([complex_mdtraj.topology.atom(a).residue.resSeq for a in binding_pocket_atoms]))

#  binding_pocket_residues = [str(r) for r in binding_pocket_residues]

#  binding_pocket_residues = " or ".join(binding_pocket_residues)

#

#  traj = nglview.MDTrajTrajectory( complex_mdtraj ) # load file from RCSB PDB

#  ngltraj = nglview.NGLWidget( traj )

#  ngltraj.representations = [

#  { "type": "cartoon", "params": {

#  "sele": "protein", "color": "residueindex"

#  } },

#  { "type": "licorice", "params": {

#  "sele": "(not hydrogen) and (%s)" %  binding_pocket_residues

#  } },

#  { "type": "ball+stick", "params": {

#  "sele": "LIG"

#  } }

#  ]

#  return ngltraj

#

#def visualize_ligand(ligand_mdtraj):

#  traj = nglview.MDTrajTrajectory( ligand_mdtraj ) # load file from RCSB PDB

#  ngltraj = nglview.NGLWidget( traj )

#  ngltraj.representations = [

#    { "type": "ball+stick", "params": {"sele": "all" } } ]

#  return ngltraj

#

#def convert_lines_to_mdtraj(molecule_lines):

#  tempdir = tempfile.mkdtemp()

#  molecule_file = os.path.join(tempdir, "molecule.pdb")

#  with open(molecule_file, "wb") as f:

#    f.writelines(molecule_lines)

#  molecule_mdtraj = md.load(molecule_file)

#  return molecule_mdtraj

#

#def display_images(filenames):

#    """Helper to pretty-print images."""

#    imagesList=''.join(

#        ["<img style='width: 140px; margin: 0px; float: left; border: 1px solid black;' src='%s' />"

#         % str(s) for s in sorted(filenames)])

#    display(HTML(imagesList))

#

#def mols_to_pngs(mols, basename="test"):

#    """Helper to write RDKit mols to png files."""

#    filenames = []

#    for i, mol in enumerate(mols):

#        filename = "%s%d.png" % (basename, i)

#        Draw.MolToFile(mol, filename)

#        filenames.append(filename)

#    return filenames

echo '$TRAVIS_PULL_REQUEST $TRAVIS_BRANCH'

echo $TRAVIS_PULL_REQUEST $TRAVIS_BRANCH

############################################################ DEBUG

## TODO(rbharath): UNCOMMENT BEFORE MERGE!

#if [[ "$TRAVIS_PULL_REQUEST" != "false" ]]; then

#    echo "This is a pull request. No deployment will be done."; exit 0

#fi

#

#if [[ "$TRAVIS_BRANCH" != "master" ]]; then

#    echo "No deployment on BRANCH='$TRAVIS_BRANCH'"; exit 0

#fi

############################################################ DEBUG

if [[ "$TRAVIS_PULL_REQUEST" != "false" ]]; then

    echo "This is a pull request. No deployment will be done."; exit 0

fi

if [[ "$TRAVIS_BRANCH" != "master" ]]; then

    echo "No deployment on BRANCH='$TRAVIS_BRANCH'"; exit 0

fi

# Create the docs and push them to S3

# -----------------------------------