Some more cleanups and deletions

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

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:

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.

deepchem.featurizers package

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

Submodules

----------

deepchem.featurizers.basic module

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

.. automodule:: deepchem.featurizers.basic

    :members:

    :undoc-members:

    :show-inheritance:

deepchem.featurizers.coulomb_matrices module

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

.. automodule:: deepchem.featurizers.coulomb_matrices

    :members:

    :undoc-members:

    :show-inheritance:

deepchem.featurizers.featurize module

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

.. automodule:: deepchem.featurizers.featurize

    :members:

    :undoc-members:

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deepchem.featurizers.fingeprints module

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

.. automodule:: deepchem.featurizers.fingerprints

    :members:

    :undoc-members:

    :show-inheritance:

deepchem.featurizers.nnscore module

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

.. automodule:: deepchem.featurizers.nnscore

    :members:

    :undoc-members:

    :show-inheritance:

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:

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: