Merge pull request #242 from rbharath/docs

sudo: required

dist: trusty

install:

- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then

    wget https://repo.continuum.io/archive/Anaconda2-4.2.0-Linux-x86_64.sh -O anaconda.sh;

  else

    wget https://repo.continuum.io/archive/Anaconda3-4.2.0-Linux-x86_64.sh -O anaconda.sh;

  fi

- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then wget https://repo.continuum.io/archive/Anaconda2-4.2.0-Linux-x86_64.sh

  -O anaconda.sh; else wget https://repo.continuum.io/archive/Anaconda3-4.2.0-Linux-x86_64.sh

  -O anaconda.sh; fi

- bash anaconda.sh -b -p $HOME/anaconda

- export PATH="$HOME/anaconda/bin:$PATH"

- hash -r

script:

- nosetests -v deepchem --nologcapture

after_success:

- echo $TRAVIS_SECURE_ENV_VARS

- source devtools/travis-ci/after_sucess.sh

# AWS access_key and secret key secured through travis secure var api.

env:

  global:

  - secure: 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

  - secure: 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

DeepChem

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

Deep Learning Toolchain for Drug Discovery and Quantum Chemistry. DeepChem is a package by the [Pande group](https://pande.stanford.edu/) at Stanford. For more information, see the "About Us" section below.

DeepChem aims to provide a high quality open-source toolchain for

democratizing the use of deep-learning in drug discovery and quantum

chemistry. DeepChem

is a package developed by the [Pande group](https://pande.stanford.edu/) at

Stanford and originally created by [Bharath Ramsundar](http://rbharath.github.io/). 

Requirements

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

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

The first step to getting started is looking at the examples in the `examples/` directory. Try running some of these examples on your system and verify that the models train successfully. Afterwards, to apply `deepchem` to a new problem, try starting from one of the existing examples and modifying it step by step to work with your new use-case.

Input Formats

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

Accepted input formats for deepchem include csv, pkl.gz, and sdf files. For

example, with a csv input, in order to build models, we expect the

following columns to have entries for each row in the csv file.

1. A column containing SMILES strings [1].

2. A column containing an experimental measurement.

3. (Optional) A column containing a unique compound identifier.

Here's an example of a potential input file. 

+---------------+-------------------------------------------+----------------+ 

|Compound ID    | measured log solubility in mols per litre | smiles         | 

+===============+===========================================+================+ 

| benzothiazole | -1.5                                      | c2ccc1scnc1c2  | 

+---------------+-------------------------------------------+----------------+ 

Here the "smiles" column contains the SMILES string, the "measured log

solubility in mols per litre" contains the experimental measurement and

"Compound ID" contains the unique compound identifier.

[2] Anderson, Eric, Gilman D. Veith, and David Weininger. "SMILES, a line

notation and computerized interpreter for chemical structures." US

Environmental Protection Agency, Environmental Research Laboratory, 1987.

Data Featurization

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

Most machine learning algorithms require that input data form vectors.

However, input data for drug-discovery datasets routinely come in the

format of lists of molecules and associated experimental readouts. To

transform lists of molecules into vectors, we need to use the ``deechem``

featurization class ``DataFeaturizer``. Instances of this class must be

passed a ``Featurizer`` object. ``deepchem`` provides a number of

different subclasses of ``Featurizer`` for convenience:

DeepChem Publications

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

1. [Computational Modeling of β-secretase 1 (BACE-1) Inhibitors using

Ligand Based

Approaches](http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00290)

About Us

--------

DeepChem is a package by the [Pande group](https://pande.stanford.edu/) at Stanford. DeepChem was originally created by [Bharath Ramsundar](http://rbharath.github.io/), and has grown through the contributions of a number of undergraduate, graduate, and postdoctoral researchers working with the Pande lab.

# Create the docs and push them to S3

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

echo "About to install numpydoc, s3cmd"

pip install numpydoc s3cmd

pip install numpydoc s3cmd msmb_theme sphinx_rtd_theme

conda list -e

mkdir -p docs/_build

echo "About to build docs"

sphinx-build -b html docs docs/_build

sphinx-apidoc -f -o docs/source deepchem

sphinx-build -b html docs/source docs/_build

echo "About to push docs to s3"

python devtools/travis-ci/push-docs-to-s3.py

BUCKET_NAME = 'deepchem.io'

if not any(d.project_name == 's3cmd' for d in pip.get_installed_distributions()):

  raise ImportError('The s3cmd pacakge is required. try $ pip install s3cmd')

  raise ImportError('The s3cmd package is required. try $ pip install s3cmd')

print("os.environ.keys()")

print(os.environ.keys())

# The secret key is available as a secure environment variable

# on travis-ci to push the build documentation to Amazon S3.

deepchem.featurizers.basic

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

.. automodule:: deepchem.featurizers.basic

   .. rubric:: Classes

   .. autosummary::

      Featurizer

      MolecularWeight

      RDKitDescriptors

 No newline at end of file