From ecc8b16c91d87fb8672bbe07d1525446ca512b3a Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Mon, 3 Jun 2019 14:40:55 +0200 Subject: [PATCH 1/4] Rename to Contact Map Explorer --- README.md | 10 +++++----- docs/conf.py | 16 ++++++++-------- docs/index.rst | 10 +++++----- docs/installing.rst | 6 +++--- examples/concurrences.ipynb | 4 ++-- examples/contact_map.ipynb | 6 +++--- examples/contact_map_without_atom_slice.ipynb | 10 +++++----- examples/dask_contact_frequency.ipynb | 10 +++++----- setup.py | 4 ++-- 9 files changed, 38 insertions(+), 38 deletions(-) diff --git a/README.md b/README.md index b3c6c99..0389f4c 100644 --- 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&utm_medium=referral&utm_content=dwhswenson/contact_map&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/docs/conf.py b/docs/conf.py index 72bc1d2..0edcb3c 100644 --- 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, 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 index 0a89e91..d8bd08f 100644 --- 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 index 07aaab9..13d24a2 100644 --- 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 index 71c1e2f..895da5d 100644 --- 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 index 8130622..55d6df1 100644 --- 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 index 98de8a0..59cef36 100644 --- 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 index a6077dd..bb58479 100644 --- 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 index 1ec9534..052a221 100644 --- 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 From 63ac227c5a97f8f5c53a26b7b79acb1b812fd51b Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Fri, 2 Aug 2019 00:46:23 +0200 Subject: [PATCH 2/4] Update setup.py author info --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 352a47e..9934e96 100644 --- a/setup.py +++ b/setup.py @@ -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, sroet@hotmail.com", version=PACKAGE_VERSION, license="LGPL-2.1+", url="http://github.com/dwhswenson/contact_map", From f8ebbc40c4db7c62d79b9ec4a9ebf19cdd6ecda3 Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Fri, 2 Aug 2019 00:52:05 +0200 Subject: [PATCH 3/4] use Sander's *actual* email address --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9934e96..b24a7d4 100644 --- a/setup.py +++ b/setup.py @@ -162,7 +162,7 @@ def write_version_py(filename): setup( name="contact_map", author="David W.H. Swenson and Sander Roet", - author_email="dwhs@hyperblazer.net, sroet@hotmail.com", + author_email="dwhs@hyperblazer.net, sanderroet@hotmail.com", version=PACKAGE_VERSION, license="LGPL-2.1+", url="http://github.com/dwhswenson/contact_map", From 98c9edb9412d1b05a4732661362bca3062dfb47d Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Mon, 5 Aug 2019 12:13:02 +0200 Subject: [PATCH 4/4] remove maintainer/license info from contact_map.py --- contact_map/contact_map.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/contact_map/contact_map.py b/contact_map/contact_map.py index 7c145f1..7f730eb 100644 --- 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