Updated Badges and docs

* Added badges and CNAME file
* Updated badges
* Updated CM doc slightly

Author: andersx

README.md

@@ -1,5 +1,5 @@
 # QML: A Python Toolkit for Quantum Machine Learning
-[![Build Status](https://travis-ci.org/qmlcode/qml.svg?branch=master)](https://travis-ci.org/qmlcode/qml)
+[![Build Status](https://travis-ci.org/qmlcode/qml.svg?branch=master)](https://travis-ci.org/qmlcode/qml) [![doi](https://badge.fury.io/py/qml.svg)](https://badge.fury.io/py/qml) [![doi](https://zenodo.org/badge/89045103.svg)](https://zenodo.org/badge/latestdoi/89045103)
 
 QML is a Python2/3-compatible toolkit for representation learning of properties of molecules and solids. 
 

docs/Makefile

@@ -19,3 +19,4 @@ help:
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 	touch build/html/.nojekyll
+	echo "www.qmlcode.org" > build/html/CNAME

docs/source/examples.rst

@@ -1,4 +1,4 @@
-xamples
+Examples
 --------
 
 Generating representations using the ``Compound`` class

docs/source/index.rst

@@ -3,7 +3,7 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-|Build Status| |Beta|
+|Build Status| |pypi| |doi| |Beta|
 
 QML: A Python Toolkit for Quantum Machine Learning
 ==================================================
@@ -79,6 +79,12 @@ QML is freely available under the terms of the MIT license.
 .. |Build Status| image:: https://travis-ci.org/qmlcode/qml.svg?branch=master
    :target: https://travis-ci.org/qmlcode/qml
 
+.. |doi| image:: https://zenodo.org/badge/89045103.svg
+   :target: https://zenodo.org/badge/latestdoi/89045103
+
 .. |Beta| image:: http://i.imgur.com/5fMAeek.jpg
    :width: 90 px
    :target: https://github.com/qmlcode/qml
+
+.. |Pypi| image:: https://badge.fury.io/py/qml.svg
+    :target: https://badge.fury.io/py/qml

qml/representations.py

@@ -40,6 +40,7 @@
 
 def generate_coulomb_matrix(nuclear_charges, coordinates, size = 23, sorting = "row-norm"):
     """ Creates a Coulomb Matrix representation of a molecule.
+        Sorting of the elements can either be done by ``sorting="row-norm"`` or ``sorting="unsorted"``.
         A matrix :math:`M` is constructed with elements
 
         .. math::
@@ -52,12 +53,16 @@ def generate_coulomb_matrix(nuclear_charges, coordinates, size = 23, sorting = "
 
         where :math:`i` and :math:`j` are atom indices, :math:`Z` is nuclear charge and
         :math:`\\bf R` is the coordinate in euclidean space.
-        if ``sorting = 'row-norm'``, the atom indices are reordered such that
+        If ``sorting = 'row-norm'``, the atom indices are reordered such that
 
             :math:`\\sum_j M_{1j}^2 \\geq \\sum_j M_{2j}^2 \\geq ... \\geq \\sum_j M_{nj}^2`
 
         The upper triangular of M, including the diagonal, is concatenated to a 1D
         vector representation.
+
+        If ``sorting = 'unsorted``, the elements are sorted in the same order as the input coordinates
+        and nuclear charges.
+
         The representation is calculated using an OpenMP parallel Fortran routine.
 
         :param nuclear_charges: Nuclear charges of the atoms in the molecule