dwhswenson · dwhswenson · Aug 5, 2019 · Jun 3, 2019 · Jun 5, 2019 · Aug 1, 2019
diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/f7f3cf53698e4655ac8895f13fa5dea6)](https://www.codacy.com/app/dwhswenson/contact_map?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=dwhswenson/contact_map&amp;utm_campaign=Badge_Grade)
 [![Maintainability](https://api.codeclimate.com/v1/badges/84768756d594176d8da6/maintainability)](https://codeclimate.com/github/dwhswenson/contact_map/maintainability)
 
-# Contact Maps
+# Contact Map Explorer
 
 This package provides tools for analyzing and exploring contacts
 (residue-residue and atom-atom) from a trajectory generated by molecular
@@ -20,9 +20,9 @@ processes involving biomolecules. For example, an analysis of contacts can
 be particularly useful when defining bound states during a binding processes
 between proteins, DNA, and small molecules (such as potential drugs).
 
-The contacts analyzed by `contact_map` can be either intermolecular or
-intramolecular, and can be analyzed on a residue-residue basis or an
-atom-atom basis.
+The contacts analyzed by Contact Map Explorer can be either intermolecular or
+intramolecular, and can be analyzed on a residue-residue basis or an atom-atom
+basis.
 
 This package makes it very easy to answer questions like:
 
@@ -59,7 +59,7 @@ for details.
 
 ## Support and development
 
-`contact_map` is an open source project, released under the GNU LGPL,
+Contact Map Explorer is an open source project, released under the GNU LGPL,
 version 2.1 or (at your option) any later version. Development takes place
 in public at https://github.com/dwhswenson/contact_map; your contributions
 would be welcome!

diff --git a/contact_map/contact_map.py b/contact_map/contact_map.py
@@ -1,8 +1,6 @@
 """
 Contact map analysis.
 """
-# Maintainer: David W.H. Swenson (dwhs@hyperblazer.net)
-# Licensed under LGPL, version 2.1 or greater
 import collections
 import itertools
 import pickle

diff --git a/docs/conf.py b/docs/conf.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# contact_map documentation build configuration file, created by
+# Contact Map Explorer documentation build configuration file, created by
 # sphinx-quickstart on Sun Oct  8 16:23:29 2017.
 #
 # This file is execfile()d with the current directory set to its
@@ -100,9 +100,9 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'contact_map'
-copyright = u'2017-2018, David W.H. Swenson'
-author = u'David W.H. Swenson'
+project = u'Contact Map Explorer'
+copyright = u'2017-2019, David W.H. Swenson and Sander Roet'
+author = u'David W.H. Swenson and Sander Roet'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -304,8 +304,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'contact_map.tex', u'contact\\_map Documentation',
-     u'David W.H. Swenson', 'manual'),
+    (master_doc, 'contact_map.tex', u'Contact Map Explorer Documentation',
+     u'David W.H. Swenson and Sander Roet', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -346,7 +346,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'contact_map', u'contact_map Documentation',
+    (master_doc, 'contact_map', u'Contact Map Explorer Documentation',
      [author], 1)
 ]
 
@@ -361,7 +361,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'contact_map', u'contact_map Documentation',
+    (master_doc, 'contact_map', u'Contact Map Explorer Documentation',
      author, 'contact_map', 'One line description of project.',
      'Miscellaneous'),
 ]

diff --git a/docs/index.rst b/docs/index.rst
@@ -5,8 +5,8 @@
 
 .. currentmodule:: contact_map
 
-``contact_map``
-===============
+Contact Map Explorer
+====================
 
 This package provides tools for analyzing and exploring contacts
 (residue-residue and atom-atom) from a trajectory generated by molecular
@@ -18,8 +18,8 @@ processes involving biomolecules. For example, an analysis of contacts can
 be particularly useful when defining bound states during a binding processes
 between proteins, DNA, and small molecules (such as potential drugs).
 
-The contacts analyzed by ``contact_map`` can be either intermolecular or
-intramolecular, and can be analyzed on a residue-residue basis or an
+The contacts analyzed by Contact Map Explorer can be either intermolecular
+or intramolecular, and can be analyzed on a residue-residue basis or an
 atom-atom basis.
 
 This package makes it very easy to answer questions like:
@@ -45,7 +45,7 @@ representing the fraction of trajectory time that the contact was present.
 
 * :ref:`genindex`
 
-``contact_map`` is an open source project, released under the GNU LGPL,
+Contact Map Explorer is an open source project, released under the GNU LGPL,
 version 2.1 or (at your option) any later version. Development takes place
 in public at https://github.com/dwhswenson/contact_map; your contributions
 would be welcome!

diff --git a/docs/installing.rst b/docs/installing.rst
@@ -101,7 +101,7 @@ Additional functionality
 ========================
 
 Installing some additional packages will immediately enable additional
-features in ``contact_map``. To get all the functionality, install the
+features in Contact Map Explorer. To get all the functionality, install the
 packages in ``optional_installs.txt``, either with ``pip install -r
 optional_installs.txt`` or ``conda install -y --file
 optional_installs.txt``.
@@ -133,5 +133,5 @@ suite. This can be done by installing ``pytest`` (using either ``pip`` or
 
    py.test --pyargs contact_map -v
 
-This will run the tests on the installed version of ``contact_map``. All
-tests should either pass or skip.
+This will run the tests on the installed version of Contact Map Explorer.
+All tests should either pass or skip.
diff --git a/examples/concurrences.ipynb b/examples/concurrences.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "# Concurrences\n",
     "\n",
-    "One of the tools in `contact_map` is the ability to look at simultaneous contacts. The idea is that you might have a set of contacts that is likely to happen concurrently, and that this set of contacts might help you define a stable state. This is managed in `contact_map` by what we call contact concurrences.\n",
+    "One of the tools in Contact Map Explorer is the ability to look at simultaneous contacts. The idea is that you might have a set of contacts that is likely to happen concurrently, and that this set of contacts might help you define a stable state. This is managed in Contact Map Explorer by what we call contact concurrences.\n",
     "\n",
     "To start, we'll look at a trajectory of a specific inhibitor during its binding process to GSK3B."
    ]
@@ -224,7 +224,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.2"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

diff --git a/examples/contact_map.ipynb b/examples/contact_map.ipynb
@@ -6,9 +6,9 @@
    "source": [
     "# Contact Maps\n",
     "\n",
-    "The `contact_map` package includes some tricks to study contact maps in protein dynamics, based on tools in MDTraj. This notebook shows examples and serves as documentation.\n",
+    "Contact Map Explorer includes some tricks to study contact maps in protein dynamics, based on tools in MDTraj. This notebook shows examples and serves as documentation.\n",
     "\n",
-    "As an example, we'll use part of a trajectory of the KRas protein bound to GTP, which was provided by Sander Roet. KRas is a protein that plays a role in many cancers. For simplicity, the waters were removed from the trajectory (although ions are still included). To run this notebook, download the example files from https://figshare.com/s/453b1b215cf2f9270769 (total download size about 1.2 MB). Download all files, and extract in the same directory that you started Jupyer from (so that you have a directory called `5550217` in your current working directory)."
+    "As an example, we'll use part of a trajectory of the KRas protein bound to GTP, which was provided by Sander Roet. KRas is a protein that plays a role in many cancers. For simplicity, the waters were removed from the trajectory (although ions are still included). To run this notebook, download the example files from https://figshare.com/s/453b1b215cf2f9270769 (total download size about 1.2 MB). Download all files, and extract in the same directory that you started Jupyter from (so that you have a directory called `5550217` in your current working directory)."
    ]
   },
   {
@@ -1032,7 +1032,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

diff --git a/examples/contact_map_without_atom_slice.ipynb b/examples/contact_map_without_atom_slice.ipynb
@@ -282,21 +282,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.15"
+   "pygments_lexer": "ipython3",
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

diff --git a/examples/dask_contact_frequency.ipynb b/examples/dask_contact_frequency.ipynb
@@ -191,21 +191,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.14"
+   "pygments_lexer": "ipython3",
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

diff --git a/setup.py b/setup.py
@@ -1,5 +1,5 @@
 """
-setup.py for contact_map
+setup.py for Contact Map Explorer
 """
 import os
 import subprocess
@@ -104,7 +104,7 @@ def _minimal_ext_cmd(cmd):
 VERSION_PY_CONTENT = """
 # This file is automatically generated by setup.py
 \"\"\"
-Version info for contact_map.
+Version info for Contact Map Explorer.
 
 ``full_version`` gives the most information about the current state. It is
 always the short (PEP440) version string, followed by a git hash as
@@ -161,8 +161,8 @@ def write_version_py(filename):
     write_version_py(os.path.join('contact_map', 'version.py'))
     setup(
         name="contact_map",
-        author="David W.H. Swenson",
-        author_email="dwhs@hyperblazer.net",
+        author="David W.H. Swenson and Sander Roet",
+        author_email="dwhs@hyperblazer.net, sanderroet@hotmail.com",
         version=PACKAGE_VERSION,
         license="LGPL-2.1+",
         url="https://github.com/dwhswenson/contact_map",