Merge branch 'master' of github.com:rigdenlab/SIMBAD

Clashes between local and master

README.rst

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+**********************************************************************
+Sequence Independent Molecular Replacement Based on Available Database
+**********************************************************************
+
+.. image:: https://readthedocs.org/projects/simbad/badge/?version=latest
+   :target: http://simbad.readthedocs.io/en/latest/?badge=latest
+   :alt: Documentation Status
+
+.. image:: https://landscape.io/github/rigdenlab/SIMBAD/master/landscape.svg?style=flat
+   :target: https://landscape.io/github/rigdenlab/SIMBAD/master
+   :alt: Code Health
+
+Documentation & Usage
++++++++++++++++++++++
+Please refer to `SIMBAD's documentation <http://simbad.readthedocs.io/en/latest/>`_
+
+Contributing
+++++++++++++
+There are two ways by which you can contribute to SIMBAD:
+
+1. Submit any suggestions to the `GitHub Issue Tracker`_, or
+2. Fork this repository, commit your changes and submit a pull request.
+
+Found a Bug?
+++++++++++++
+Please use the `GitHub Issue Tracker`_.
+
+Contributors
+++++++++++++
+
+- Adam Simpkin
+- Ronan Keegan
+- Felix Simkovic
+- Daniel Rigden
+
+
+.. _GitHub Issue Tracker: https://github.com/rigdenlab/simbad/issues

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = SIMBAD
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/custom.css

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+/*
+ * Custom CSS file extending the Bootswatch theme
+ * All CSS elements are based on bootstrap 3.3.6
+ *
+ * Author:    Felix Simkovic
+ * Date:      01/01/2017
+ * Copyright: University of Liverpool
+ */
+
+dd {
+margin-left: 30px;
+}
+
+h1 {
+font-size: 2.0em;
+}
+h2 {
+font-size: 1.8em;
+}
+h3 {
+font-size: 1.6em;
+}
+h4 {
+font-size: 1.4em;
+}
+h5 {
+font-size: 1.2em;
+}
+
+img {
+max-width: 100%;
+max-height: 100%;
+}
+
+@media print {
+a[href]:after {content: none !important;}
+}
+
+.navbar-collapse {
+padding-right: 0px;
+padding-left: 0px;
+}
+
+.nav > li > a {
+padding: 15px 30px 15px 0px;
+}
+
+.headerlink {
+visibility: hidden;
+}
+
+/* https://sphinx-argparse.readthedocs.io/en/stable/misc.html */
+.wy-table-responsive table td {
+white-space: normal !important;
+}
+.wy-table-responsive {
+overflow: visible !important;
+}
+
+/* Amino acid colors */
+.ala {color: #882D17;}
+.cys {color: #F3C300;}
+.asp {color: #875692;}
+.glu {color: #F38400;}
+.phe {color: #A1CAF1;}
+.gly {color: #BE0032;}
+.his {color: #C2B280;}
+.ile {color: #848482;}
+.lys {color: #008856;}
+.leu {color: #E68FAC;}
+.met {color: #0067A5;}
+.asn {color: #F99379;}
+.pro {color: #604E97;}
+.gln {color: #F6A600;}
+.arg {color: #B3446C;}
+.ser {color: #DCD300;}
+.thr {color: #8DB600;}
+.val {color: #654522;}
+.trp {color: #E25822;}
+.tyr {color: #2B3D26;}
+.unk {color: #000000;}
+
+.btn-example, .btn-reference a:link {color: #ffffff;}
+.btn-example, .btn-reference a:visited {color: #ffffff;}
+.btn-example, .btn-reference a:hover {
+    color: #ffffff;
+    text-decoration: none;
+}
+.btn-example, .btn-reference a:active {
+    color: #ffffff;
+    text-decoration: none;
+}
+
+.btn-default {
+background-image: -webkit-linear-gradient(#6d7070, #3a3c3d 50%, #3a3c3d);
+background-image: -o-linear-gradient(#6d7070, #3a3c3d 50%, #3a3c3d);
+background-image: -webkit-gradient(linear, left top, left bottom, from(#6d7070), color-stop(50%, #3a3c3d), to(#3a3c3d));
+background-image: linear-gradient(#6d7070, #3a3c3d 50%, #3a3c3d);
+background-repeat: no-repeat;
+filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff6d7070', endColorstr='#ff3a3c3d', GradientType=0);
+-webkit-filter: none;
+        filter: none;
+border: 1px solid #3a3c3d;
+}
+.btn-default:hover {
+background-image: -webkit-linear-gradient(#6d7070, #2b2d2d 50%, #2b2d2d);
+background-image: -o-linear-gradient(#6d7070, #2b2d2d 50%, #2b2d2d);
+background-image: -webkit-gradient(linear, left top, left bottom, from(#6d7070), color-stop(50%, #2b2d2d), to(#2b2d2d));
+background-image: linear-gradient(#6d7070, #2b2d2d 50%, #2b2d2d);
+background-repeat: no-repeat;
+filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff6d7070', endColorstr='#ff2b2d2d', GradientType=0);
+-webkit-filter: none;
+        filter: none;
+border: 1px solid #3a3c3d;
+}
+.btn-primary {
+background-image: -webkit-linear-gradient(#d60f7e, #674593 50%, #674593);
+background-image: -o-linear-gradient(#d60f7e, #674593 50%, #674593);
+background-image: -webkit-gradient(linear, left top, left bottom, from(#d60f7e), color-stop(50%, #674593), to(#674593));
+background-image: linear-gradient(#d60f7e, #674593 50%, #674593);
+background-repeat: no-repeat;
+filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd60f7e', endColorstr='#ff674593', GradientType=0);
+-webkit-filter: none;
+        filter: none;
+border: 1px solid #674593;
+}
+.btn-primary:hover {
+background-image: -webkit-linear-gradient(#d60f7e, #5a4b96 50%, #5a4b96);
+background-image: -o-linear-gradient(#d60f7e, #5a4b96 50%, #5a4b96);
+background-image: -webkit-gradient(linear, left top, left bottom, from(#d60f7e), color-stop(50%, #5a4b96), to(#5a4b96));
+background-image: linear-gradient(#d60f7e, #5a4b96 50%, #5a4b96);
+background-repeat: no-repeat;
+filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd60f7e', endColorstr='#ff5a4b96', GradientType=0);
+-webkit-filter: none;
+        filter: none;
+border: 1px solid #674593;
+}