Merge branch 'master' of https://github.com/pandegroup/deep-learning

deep_chem

deepchem

=============

Deep Learning Toolchain for Cheminformatics and Protein Analysis

* [sklearn](https://github.com/scikit-learn/scikit-learn.git)

* [numpy](https://store.continuum.io/cshop/anaconda/)

* [keras](keras.io)

* [vs_utils] (https://github.com/pandegroup/vs-utils.git)

* [vs-utils] (https://github.com/pandegroup/vs-utils.git)

Linux (64-bit) Installation 

------------------

Deep_chem currently requires Python 2.7

```deepchem``` currently requires Python 2.7

###Anaconda 2.7

Download the **64-bit Python 2.7** version of Anaconda for linux [here](https://www.continuum.io/downloads#_unix).

python setup.py develop

```

###deep_chem

###deepchem

Clone the deep_chem git repository

```bash

git clone https://github.com/pandegroup/deep-learning.git

git clone https://github.com/pandegroup/deepchem.git

```

Cd into the deep-learning directory and execute 

Cd into the deepchem directory and execute 

```bash

python setup.py develop

```

# -*- coding: utf-8 -*-

#

# deepchem documentation build configuration file, created by

# sphinx-quickstart on Tue Jan 19 17:37:50 2016.

#

# This file is execfile()d with the current directory set to its

# containing dir.

#

# Note that not all possible configuration values are present in this

# autogenerated file.

#

# All configuration values have a default; values that are commented out

# serve to show the default.

import sys

import os

import shlex

# If extensions (or modules to document with autodoc) are in another directory,

# add these directories to sys.path here. If the directory is relative to the

# documentation root, use os.path.abspath to make it absolute, like shown here.

#sys.path.insert(0, os.path.abspath('.'))

sys.path.insert(0, os.path.abspath("../../deepchem"))

# -- General configuration ------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.

#needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be

# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom

# ones.

extensions = [

    'sphinx.ext.autodoc',

    'sphinx.ext.autosummary',

    'sphinx.ext.doctest',

    'sphinx.ext.intersphinx',

    'sphinx.ext.coverage',

    'sphinx.ext.mathjax',

    'sphinx.ext.ifconfig',

    'numpydoc',

    'sphinx.ext.viewcode',

]

autosummary_generate = True

autodoc_default_flags = ['members', 'inherited-members']

numpydoc_class_members_toctree = False

# Add any paths that contain templates here, relative to this directory.

templates_path = ['_templates']

# The suffix(es) of source filenames.

# You can specify multiple suffix as a list of string:

# source_suffix = ['.rst', '.md']

source_suffix = '.rst'

# The encoding of source files.

#source_encoding = 'utf-8-sig'

# The master toctree document.

master_doc = 'index'

# General information about the project.

project = u'deepchem'

copyright = u'2016, Stanford University and the Authors'

# The version info for the project you're documenting, acts as replacement for

# |version| and |release|, also used in various other places throughout the

# built documents.

#

# The short X.Y version.

version = '0.1'

# The full version, including alpha/beta/rc tags.

release = '0.1'

# The language for content autogenerated by Sphinx. Refer to documentation

# for a list of supported languages.

#

# This is also used if you do content translation via gettext catalogs.

# Usually you set "language" from the command line for these cases.

language = None

# There are two options for replacing |today|: either, you set today to some

# non-false value, then it is used:

#today = ''

# Else, today_fmt is used as the format for a strftime call.

#today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and

# directories to ignore when looking for source files.

exclude_patterns = []

# The reST default role (used for this markup: `text`) to use for all

# documents.

#default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.

#add_function_parentheses = True

# If true, the current module name will be prepended to all description

# unit titles (such as .. function::).

#add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the

# output. They are ignored by default.

#show_authors = False

# The name of the Pygments (syntax highlighting) style to use.

pygments_style = 'sphinx'

# A list of ignored prefixes for module index sorting.

#modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.

#keep_warnings = False

# If true, `todo` and `todoList` produce output, else they produce nothing.

todo_include_todos = False

# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for

# a list of builtin themes.

html_theme = 'sphinx_rtd_theme'

# Theme options are theme-specific and customize the look and feel of a theme

# further.  For a list of options available for each theme, see the

# documentation.

#html_theme_options = {}

# Add any paths that contain custom themes here, relative to this directory.

#html_theme_path = []

# The name for this set of Sphinx documents.  If None, it defaults to

# "<project> v<release> documentation".

#html_title = None

# A shorter title for the navigation bar.  Default is the same as html_title.

#html_short_title = None

# The name of an image file (relative to this directory) to place at the top

# of the sidebar.

#html_logo = None

# The name of an image file (within the static path) to use as favicon of the

# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

# pixels large.

#html_favicon = None

# Add any paths that contain custom static files (such as style sheets) here,

# relative to this directory. They are copied after the builtin static files,

# so a file named "default.css" will overwrite the builtin "default.css".

html_static_path = ['_static']

# Add any extra paths that contain custom files (such as robots.txt or

# .htaccess) here, relative to this directory. These files are copied

# directly to the root of the documentation.

#html_extra_path = []

# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,

# using the given strftime format.

#html_last_updated_fmt = '%b %d, %Y'

# If true, SmartyPants will be used to convert quotes and dashes to

# typographically correct entities.

#html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.

#html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to

# template names.

#html_additional_pages = {}

# If false, no module index is generated.

#html_domain_indices = True

# If false, no index is generated.

#html_use_index = True

# If true, the index is split into individual pages for each letter.

#html_split_index = False

# If true, links to the reST sources are added to the pages.

#html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.

#html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.

#html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will

# contain a <link> tag referring to it.  The value of this option must be the

# base URL from which the finished HTML is served.

#html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").

#html_file_suffix = None

# Language to be used for generating the HTML full-text search index.

# Sphinx supports the following languages:

#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'

#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'

#html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.

# Now only 'ja' uses this config value

#html_search_options = {'type': 'default'}

# The name of a javascript file (relative to the configuration directory) that

# implements a search results scorer. If empty, the default will be used.

#html_search_scorer = 'scorer.js'

# Output file base name for HTML help builder.

htmlhelp_basename = 'deepchemdoc'

# -- Options for LaTeX output ---------------------------------------------

latex_elements = {

# The paper size ('letterpaper' or 'a4paper').

#'papersize': 'letterpaper',

# The font size ('10pt', '11pt' or '12pt').

#'pointsize': '10pt',

# Additional stuff for the LaTeX preamble.

#'preamble': '',

# Latex figure (float) alignment

#'figure_align': 'htbp',

}

# Grouping the document tree into LaTeX files. List of tuples

# (source start file, target name, title,

#  author, documentclass [howto, manual, or own class]).

latex_documents = [

  (master_doc, 'deepchem.tex', u'deepchem Documentation',

   u'Bharath Ramsundar, Evan Feinberg', 'manual'),

]

# The name of an image file (relative to this directory) to place at the top of

# the title page.

#latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,

# not chapters.

#latex_use_parts = False

# If true, show page references after internal links.

#latex_show_pagerefs = False

# If true, show URL addresses after external links.

#latex_show_urls = False

# Documents to append as an appendix to all manuals.

#latex_appendices = []

# If false, no module index is generated.

#latex_domain_indices = True

# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples

# (source start file, name, description, authors, manual section).

man_pages = [

    (master_doc, 'deepchem', u'deepchem Documentation',

     ["Stanford University"], 1)

]

# If true, show URL addresses after external links.

#man_show_urls = False

# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples

# (source start file, target name, title, author,

#  dir menu entry, description, category)

texinfo_documents = [

  (master_doc, 'deepchem', u'deepchem Documentation',

   'Stanford University', 'deepchem', 'Deep-learning models for drug discovery.',

   'Scientific'),

]

# Documents to append as an appendix to all manuals.

#texinfo_appendices = []

# If false, no module index is generated.

#texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.

#texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.

#texinfo_no_detailmenu = False

# Example configuration for intersphinx: refer to the Python standard library.

intersphinx_mapping = {'https://docs.python.org/': None}

deepchem.models package

=======================

Submodules

----------

deepchem.models module

---------------------------

.. automodule:: deepchem.models.__init__

    :members:

    :undoc-members:

    :show-inheritance:

deepchem.models.deep module

---------------------------

.. automodule:: deepchem.models.deep

    :members:

    :undoc-members:

    :show-inheritance:

deepchem.models.deep3d module

-----------------------------

.. automodule:: deepchem.models.deep3d

    :members:

    :undoc-members:

    :show-inheritance:

deepchem.models.standard module

-------------------------------

.. automodule:: deepchem.models.standard

    :members:

    :undoc-members:

    :show-inheritance:

Module contents

---------------

.. automodule:: deepchem.models

    :members:

    :undoc-members:

    :show-inheritance:

.. _modules:

Modules

=======

Subpackages

-----------

.. toctree::

    deepchem.models

    deepchem.scripts

    deepchem.utils

Module contents

---------------

.. automodule:: deepchem

    :members:

    :undoc-members:

    :show-inheritance:

deepchem.scripts package

========================

Submodules

----------

deepchem.scripts.modeler module

-------------------------------

.. automodule:: deepchem.scripts.modeler

    :members:

    :undoc-members:

    :show-inheritance:

Module contents

---------------

.. automodule:: deepchem.scripts

    :members:

    :undoc-members:

    :show-inheritance: