Commit 00e03dc3 authored by pjropp's avatar pjropp

Rebuilt documentation

parent 2ef2119f
......@@ -141,7 +141,7 @@ pair.</li>
<code class="descname">create_bonds_by_distance</code><span class="sig-paren">(</span><em>remove_old_bond_data=True</em>, <em>delete_excessive_bonds=True</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.AtomsAndBonds.AtomsAndBonds.create_bonds_by_distance" title="Permalink to this definition"></a></dt>
<dd><p>Determines which atoms are bound to each other based on their
proximity.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.18.1)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.19.0)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Should be called via the wrapper function
<a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.create_bonds_by_distance" title="scoria.Molecule.Molecule.create_bonds_by_distance"><code class="xref py py-meth docutils literal"><span class="pre">create_bonds_by_distance()</span></code></a>.</p>
<table class="docutils field-list" frame="void" rules="none">
......@@ -202,7 +202,7 @@ pair.</li>
<code class="descname">get_index_of_first_bond_partner_of_element</code><span class="sig-paren">(</span><em>atom_index</em>, <em>the_element</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.AtomsAndBonds.AtomsAndBonds.get_index_of_first_bond_partner_of_element" title="Permalink to this definition"></a></dt>
<dd><p>For a given atom of interest, returns the index of the first
neighbor of a specified element.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref py py-mod docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.18.1)"><code class="xref py py-mod docutils literal"><span class="pre">scipy.spatial</span></code></a> libraries.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref py py-mod docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.19.0)"><code class="xref py py-mod docutils literal"><span class="pre">scipy.spatial</span></code></a> libraries.</p>
<p>Should be called via the wrapper function
<a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.get_index_of_first_bond_partner_of_element" title="scoria.Molecule.Molecule.get_index_of_first_bond_partner_of_element"><code class="xref py py-meth docutils literal"><span class="pre">get_index_of_first_bond_partner_of_element()</span></code></a>.</p>
<table class="docutils field-list" frame="void" rules="none">
......
......@@ -73,7 +73,7 @@ object.</p>
<dd><p>Allows import of molecular structure with MDAnalysis.</p>
<p>Requires the <code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code> library.</p>
<p>Should be called via the wrapper function
<code class="xref py py-meth docutils literal"><span class="pre">load_via_MDAnalysis()</span></code></p>
<a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.load_MDAnalysis_into" title="scoria.Molecule.Molecule.load_MDAnalysis_into"><code class="xref py py-meth docutils literal"><span class="pre">load_MDAnalysis_into()</span></code></a></p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
......@@ -91,7 +91,7 @@ inizalize a MDAnalysis.Universe object.</td>
<dd><p>Allows import of molecular structure from an MDAnalysis object.</p>
<p>Requires the <code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code> library.</p>
<p>Should be called via the wrapper function
<code class="xref py py-meth docutils literal"><span class="pre">load_via_MDAnalysis()</span></code></p>
<a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.load_MDAnalysis_into" title="scoria.Molecule.Molecule.load_MDAnalysis_into"><code class="xref py py-meth docutils literal"><span class="pre">load_MDAnalysis_into()</span></code></a></p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
......
......@@ -156,7 +156,7 @@ residue names.</p>
<dd><p>Identifies spheres that bound (encompass) the entire molecule, the
chains, and the residues. This information is stored in
scoria.Molecule.Molecule.hierarchy.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.18.1)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.19.0)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Wrapper function for
<a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.define_molecule_chain_residue_spherical_boundaries" title="scoria.Molecule.Molecule.define_molecule_chain_residue_spherical_boundaries"><code class="xref py py-meth docutils literal"><span class="pre">define_molecule_chain_residue_spherical_boundaries()</span></code></a></p>
</dd></dl>
......@@ -350,7 +350,7 @@ and (max_x, max_y, max_z), that bound the molecule.</p>
<dt id="scoria.Information.Information.get_bounding_sphere">
<code class="descname">get_bounding_sphere</code><span class="sig-paren">(</span><em>selection=None</em>, <em>padding=0.0</em>, <em>frame=None</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.Information.Information.get_bounding_sphere" title="Permalink to this definition"></a></dt>
<dd><p>Calculates a sphere that bounds (encompasses) a set of atoms.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.18.1)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.19.0)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Wrapper function for <a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.get_bounding_sphere" title="scoria.Molecule.Molecule.get_bounding_sphere"><code class="xref py py-meth docutils literal"><span class="pre">get_bounding_sphere()</span></code></a></p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
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......@@ -72,7 +72,7 @@ scoria.Molecule objects.</p>
<code class="descname">get_distance_to_another_molecules</code><span class="sig-paren">(</span><em>other_molecules</em>, <em>pairwise_comparison=True</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.OtherMolecules.OtherMolecules.get_distance_to_another_molecules" title="Permalink to this definition"></a></dt>
<dd><p>Computes the minimum distance between any of the atoms of this
molecular model and any of the atoms of a second specified model.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.18.1)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.19.0)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Wrapper function for <a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.get_distance_to_another_molecules" title="scoria.Molecule.Molecule.get_distance_to_another_molecules"><code class="xref py py-meth docutils literal"><span class="pre">get_distance_to_another_molecules()</span></code></a></p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
......@@ -166,7 +166,7 @@ the speed and accuracy of docking with a new scoring function,
efficient optimization, and multithreading,&#8221;&#8221; by Oleg Trott and Arthur
J. Olson. Note: Identical means the order of the atoms is the same as
well.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.18.1)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.19.0)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Wrapper function for <a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.get_rmsd_heuristic" title="scoria.Molecule.Molecule.get_rmsd_heuristic"><code class="xref py py-meth docutils literal"><span class="pre">get_rmsd_heuristic()</span></code></a></p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
......@@ -222,7 +222,7 @@ this model combined with the atoms of other_molecules.</td>
<code class="descname">steric_clash_with_another_molecules</code><span class="sig-paren">(</span><em>other_mol</em>, <em>cutoff</em>, <em>pairwise_comparison=True</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.OtherMolecules.OtherMolecules.steric_clash_with_another_molecules" title="Permalink to this definition"></a></dt>
<dd><p>Detects steric clashes between the scoria.Molecule (self) and
another scoria.Molecule.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.18.1)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.19.0)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Wrapper function for <a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.steric_clash_with_another_molecules" title="scoria.Molecule.Molecule.steric_clash_with_another_molecules"><code class="xref py py-meth docutils literal"><span class="pre">steric_clash_with_another_molecules()</span></code></a></p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
......
......@@ -176,7 +176,7 @@ segments of the documentation together. Connections can be made to
classes, <a class="reference internal" href="Molecule.html#module-scoria.Molecule" title="scoria.Molecule"><code class="xref py py-class docutils literal"><span class="pre">scoria.Molecule</span></code></a>, or to specific functions,
<a class="reference internal" href="FileIO.html#scoria.FileIO.FileIO.load_pdb_into" title="scoria.FileIO.FileIO.load_pdb_into"><code class="xref py py-func docutils literal"><span class="pre">load_pdb_into()</span></code></a>. They can also be used
to link to definitions outside the documentation base, such as linking
to the <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.18.1)"><code class="xref any docutils literal"><span class="pre">scipy.spatial</span></code></a> module. Note: to link to outside
to the <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.19.0)"><code class="xref any docutils literal"><span class="pre">scipy.spatial</span></code></a> module. Note: to link to outside
documentation libraries, the url of the library must be added to the
sphinx configuration file. Additionally, adding a tilde before a long
function definition will truncate to show just the last section.</p>
......
......@@ -249,7 +249,7 @@ residue as any of the atoms of the user-defined selection.</td>
<code class="descname">select_atoms_near_other_selection</code><span class="sig-paren">(</span><em>selection</em>, <em>cutoff</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.Selections.Selections.select_atoms_near_other_selection" title="Permalink to this definition"></a></dt>
<dd><p>Selects all atoms that are near the atoms of a user-defined
selection.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.18.1)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.19.0)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Should be called via the wrapper function
<a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.select_atoms_near_other_selection" title="scoria.Molecule.Molecule.select_atoms_near_other_selection"><code class="xref py py-meth docutils literal"><span class="pre">select_atoms_near_other_selection()</span></code></a>.</p>
<table class="docutils field-list" frame="void" rules="none">
......@@ -306,7 +306,7 @@ in the branch, used to establish directionality</li>
<code class="descname">select_close_atoms_from_different_molecules</code><span class="sig-paren">(</span><em>other_mol</em>, <em>cutoff</em>, <em>pairwise_comparison=True</em>, <em>terminate_early=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.Selections.Selections.select_close_atoms_from_different_molecules" title="Permalink to this definition"></a></dt>
<dd><p>Effectively detects steric clashes between self and another
scoria.Molecule.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.18.1)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Requires the <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/index.html#module-numpy" title="(in NumPy v1.12)"><code class="xref any docutils literal"><span class="pre">numpy</span></code></a> and <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/spatial.html#module-scipy.spatial" title="(in SciPy v0.19.0)"><code class="xref any docutils literal"><span class="pre">scipy</span></code></a> libraries.</p>
<p>Should be called via the wrapper function
<a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.select_close_atoms_from_different_molecules" title="scoria.Molecule.Molecule.select_close_atoms_from_different_molecules"><code class="xref py py-meth docutils literal"><span class="pre">select_close_atoms_from_different_molecules()</span></code></a>.</p>
<table class="docutils field-list" frame="void" rules="none">
......
......@@ -1097,6 +1097,12 @@
<dt><a href="Manipulation.html#scoria.Manipulation.Manipulation.set_coordinate_undo_point">set_coordinate_undo_point() (scoria.Manipulation.Manipulation method)</a>
</dt>
<dd><dl>
<dt><a href="Molecule.html#scoria.Molecule.Molecule.set_coordinate_undo_point">(scoria.Molecule.Molecule method)</a>
</dt>
</dl></dd>
<dt><a href="Information.html#scoria.Information.Information.set_coordinates">set_coordinates() (scoria.Information.Information method)</a>
</dt>
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