molml 0.2.0

MolML

[](https://travis-ci.org/crcollins/molml) [](https://coveralls.io/github/crcollins/molml?branch=master)

A library to interface molecules and machine learning. The goal of this library is to be a simple way to convert molecules into a vector representation for later use with libraries such as [scikit-learn](http://scikit-learn.org/). This is done using a similar API scheme.

All of the coordinates are assumed to be in angstroms.

Example Usage

>>> from molml.features import CoulombMatrix
>>> feat = CoulombMatrix()
>>> H2 = (
...             ['H', 'H'],
...             [
...                     [0.0, 0.0, 0.0],
...                     [1.0, 0.0, 0.0],
...             ]
... )
>>> HCN = (
...             ['H', 'C', 'N'],
...             [
...                     [-1.0, 0.0, 0.0],
...                     [ 0.0, 0.0, 0.0],
...                     [ 1.0, 0.0, 0.0],
...             ]
... )
>>> feat.fit([H2, HCN])
CoulombMatrix(input_type='list', n_jobs=1)
>>> feat.transform([H2])
array([[ 0.5,  1. ,  0. ,  1. ,  0.5,  0. ,  0. ,  0. ,  0. ]])
>>> feat.transform([H2, HCN])
array([[  0.5      ,   1.       ,   0.       ,   1.       ,   0.5      ,
        0.       ,   0.       ,   0.       ,   0.       ],
        [  0.5      ,   6.       ,   3.5      ,   6.       ,  36.8581052,
        42.       ,   3.5      ,  42.       ,  53.3587074]])

Dependencies

MolML requires python 2.7, numpy, scipy, and pathos. The specific versions that have been tested are numpy 1.9.1, scipy 0.15.1, and pathos 0.2.0, but newer versions should work.

Install

Once the dependeicies are installed, the package can be installed with pip.

$ pip install molml

Or for the bleeding edge version, you can use

$ pip install git+git://github.com/crcollins/molml

Development

To install a development version, just clone the git repo.

$ git clone https://github.com/crcollins/molml

Pull requests and bug reports are welcomed!

Testing

To run the tests, make sure that nose is installed and then run:

$ nosetests

To include coverage information, make sure that coverage is installed and then run:

$ nosetests –with-coverage –cover-package=molml –cover-erase