Commit aaffb2be authored by miaecle's avatar miaecle
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Merge remote-tracking branch 'remotes/origin/master' into master2

parents 4bbcb551 a37c108a
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@@ -20,7 +20,8 @@ install:
- conda install -c omnia openbabel
- conda install joblib
- conda install h5py
- pip install keras
- pip install six
#- pip install keras
- export KERAS_BACKEND=tensorflow
- conda install -c omnia mdtraj
- pip install tensorflow
+11 −8
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@@ -17,6 +17,7 @@ Stanford and originally created by [Bharath Ramsundar](http://rbharath.github.io
* [Contributing to DeepChem](#contributing-to-deepchem)
    * [Code Style Guidelines](#code-style-guidelines)
    * [Documentation Style Guidelines](#documentation-style-guidelines)
    * [Gitter](#gitter)
* [DeepChem Publications](#deepchem-publications)
* [Examples](/examples)
* [About Us](#about-us)
@@ -29,7 +30,7 @@ Stanford and originally created by [Bharath Ramsundar](http://rbharath.github.io
* [joblib](https://pypi.python.org/pypi/joblib)
* [sklearn](https://github.com/scikit-learn/scikit-learn.git)
* [numpy](https://store.continuum.io/cshop/anaconda/)
* [keras](http://keras.io)
* [six](https://pypi.python.org/pypi/six)
* [mdtraj](http://mdtraj.org/)
* [tensorflow](https://www.tensorflow.org/)

@@ -56,11 +57,10 @@ Installation from source is the only currently supported format. ```deepchem```
   conda install joblib 
   ```

5. `keras`
5. `six`
   ```bash
   pip install keras
   pip install six
   ```
   `deepchem` only supports the `tensorflow` (default) backend for keras.
      
6. `mdtraj`
   ```bash
@@ -72,7 +72,7 @@ Installation from source is the only currently supported format. ```deepchem```
    contact your local sysadmin to work out a custom installation. If your
    version of Linux is recent, then the following command will work:
    ```
    conda install -c https://conda.anaconda.org/jjhelmus tensorflow
    pip install tensorflow-gpu
    ```

8. `deepchem`: Clone the `deepchem` github repo:
@@ -332,6 +332,9 @@ Aim for a score of at least 8/10 on contributed files.
### Documentation Style Guidelines
DeepChem uses [NumPy style documentation](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt). Please follow these conventions when documenting code, since we use [Sphinx+Napoleon](http://www.sphinx-doc.org/en/stable/ext/napoleon.html) to automatically generate docs on [deepchem.io](deepchem.io).

### Gitter
Join us on gitter at [https://gitter.im/deepchem/Lobby](https://gitter.im/deepchem/Lobby). Probably the easiest place to ask simple questions or float requests for new features.

## DeepChem Publications
1. [Computational Modeling of β-secretase 1 (BACE-1) Inhibitors using
Ligand Based
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@@ -162,8 +162,10 @@ class Dataset(object):
    """Get an object that iterates over the samples in the dataset.

    Example:

    >>> for x, y, w, id in dataset.itersamples():
    >>>   print(x, y, w, id)

    """
    raise NotImplementedError()

@@ -317,8 +319,10 @@ class NumpyDataset(Dataset):
    """Get an object that iterates over the samples in the dataset.

    Example:

    >>> for x, y, w, id in dataset.itersamples():
    >>>   print(x, y, w, id)

    """
    n_samples = self._X.shape[0]
    return ((self._X[i], self._y[i], self._w[i], self._ids[i])
@@ -580,6 +584,7 @@ class DiskDataset(Dataset):
    """Get an object that iterates over the samples in the dataset.

    Example:

    >>> for x, y, w, id in dataset.itersamples():
    >>>   print(x, y, w, id)
    """
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