namdtools 0.4.2__tar.gz → 0.4.4.dev0__tar.gz

namdtools-0.4.4.dev0/.gitattributes

@@ -0,0 +1 @@
+namdtools/_version.py export-subst

namdtools-0.4.4.dev0/.github/workflows/tests.yml

@@ -0,0 +1,30 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install namdtools
+        run: pip install -e ".[dev]"
+
+      - name: Run tests
+        run: pytest tests/ -v

namdtools-0.4.4.dev0/.gitignore

@@ -0,0 +1,9 @@
+/build/
+/dist/
+.hypothesis/
+.hypothesis/*
+/.idea/
+/namdtools.egg-info/
+__pycache__/
+__pycache__/*
+/_scripts/

namdtools-0.4.4.dev0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Lockhart Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

namdtools-0.4.4.dev0/PKG-INFO

@@ -0,0 +1,47 @@
+Metadata-Version: 2.4
+Name: namdtools
+Version: 0.4.4.dev0
+Summary: Python tools for NAMD
+Author-email: "C. Lockhart" <clockha2@gmu.edu>
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fpathlib>=0.1.3
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: polars
+Requires-Dist: sympy
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: sphinx-copybutton; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Dynamic: license-file
+
+
+a Python interface to NAMD  
+http://www.ks.uiuc.edu/Research/namd/
+
+<!--*master:*-->
+<span style="white-space: nowrap;">
+    <a href="https://pypi.org/project/namdtools/"><img src="https://img.shields.io/pypi/v/namdtools" /></a>
+    <a href="https://travis-ci.com/github/LockhartLab/namdtools"><img src="https://img.shields.io/travis/com/lockhartlab/namdtools/master" /></a>
+</span>
+
+<hr>
+
+note that this package is **still in development**  
+at this stage, I'm only building thing as they come to mind  
+version 1.0 will be the first major release  
+until then, consider this code heavily volatile
+
+yet, install simply by calling ```pip install namdtools```
+
+<hr>
+
+Related Packages
+----------------
+https://github.com/sunhwan/NAMD-replica  
+https://github.com/bio-phys/MDBenchmark  
+https://github.com/radakb/pynamd/

namdtools-0.4.4.dev0/README.md

@@ -0,0 +1,26 @@
+
+a Python interface to NAMD  
+http://www.ks.uiuc.edu/Research/namd/
+
+<!--*master:*-->
+<span style="white-space: nowrap;">
+    <a href="https://pypi.org/project/namdtools/"><img src="https://img.shields.io/pypi/v/namdtools" /></a>
+    <a href="https://travis-ci.com/github/LockhartLab/namdtools"><img src="https://img.shields.io/travis/com/lockhartlab/namdtools/master" /></a>
+</span>
+
+<hr>
+
+note that this package is **still in development**  
+at this stage, I'm only building thing as they come to mind  
+version 1.0 will be the first major release  
+until then, consider this code heavily volatile
+
+yet, install simply by calling ```pip install namdtools```
+
+<hr>
+
+Related Packages
+----------------
+https://github.com/sunhwan/NAMD-replica  
+https://github.com/bio-phys/MDBenchmark  
+https://github.com/radakb/pynamd/

namdtools-0.4.4.dev0/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+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)

namdtools-0.4.4.dev0/docs/build/html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 49fbd4360841f4223712a8c96171aed4
+tags: 645f666f9bcd5a90fca523b33c5a78b7

namdtools-0.4.4.dev0/docs/build/html/_modules/index.html

@@ -0,0 +1,72 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Overview: module code &#8212; namdtools 0.4.3.dev4 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=8f2a1f02" />
+    <link rel="stylesheet" type="text/css" href="../_static/nature.css?v=279e0f84" />
+    <script src="../_static/documentation_options.js?v=44170b8a"></script>
+    <script src="../_static/doctools.js?v=fd6eb6e6"></script>
+    <script src="../_static/sphinx_highlight.js?v=6ffebe34"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+  </head><body>
+    <div class="related" role="navigation" aria-label="Related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="nav-item nav-item-0"><a href="../index.html">namdtools 0.4.3.dev4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Overview: module code</a></li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="namdtools/pme.html">namdtools.pme</a></li>
+<li><a href="namdtools/read.html">namdtools.read</a></li>
+</ul>
+
+            <div class="clearer"></div>
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
+        <div class="sphinxsidebarwrapper">
+<search id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="Related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="nav-item nav-item-0"><a href="../index.html">namdtools 0.4.3.dev4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Overview: module code</a></li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+    &#169; Copyright 2020, Lockhart Lab.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 9.1.0.
+    </div>
+  </body>
+</html>

namdtools-0.4.4.dev0/docs/build/html/_modules/namdtools/pme.html

@@ -0,0 +1,114 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>namdtools.pme &#8212; namdtools 0.4.3.dev4 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=8f2a1f02" />
+    <link rel="stylesheet" type="text/css" href="../../_static/nature.css?v=279e0f84" />
+    <script src="../../_static/documentation_options.js?v=44170b8a"></script>
+    <script src="../../_static/doctools.js?v=fd6eb6e6"></script>
+    <script src="../../_static/sphinx_highlight.js?v=6ffebe34"></script>
+    <link rel="index" title="Index" href="../../genindex.html" />
+    <link rel="search" title="Search" href="../../search.html" /> 
+  </head><body>
+    <div class="related" role="navigation" aria-label="Related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">namdtools 0.4.3.dev4 documentation</a> &#187;</li>
+          <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">namdtools.pme</a></li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <h1>Source code for namdtools.pme</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+
+
+<div class="viewcode-block" id="get_pme_size">
+<a class="viewcode-back" href="../../api/generated/namdtools.pme.get_pme_size.html#namdtools.pme.get_pme_size">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">get_pme_size</span><span class="p">(</span><span class="n">a</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">"""</span>
+<span class="sd">    Given a box length, figure out the grid size for PME. We are looking for the PME size that's ~1 grid spacing, while</span>
+<span class="sd">    with only small prime factors 2, 3, and 5.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    a : numeric</span>
+<span class="sd">        Size of box length.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    int</span>
+<span class="sd">        Size of PME grid length.</span>
+<span class="sd">    """</span>
+
+    <span class="c1"># To reduce runtime, import this here</span>
+    <span class="kn">from</span><span class="w"> </span><span class="nn">sympy.ntheory</span><span class="w"> </span><span class="kn">import</span> <span class="n">factorint</span>
+
+    <span class="c1"># If a is a decimal, round up</span>
+    <span class="n">a</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">ceil</span><span class="p">(</span><span class="n">a</span><span class="p">))</span>
+
+    <span class="c1"># We want to find larger number that has only factors 2, 3, and 5</span>
+    <span class="c1"># noinspection PyShadowingNames</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">_has_only_factors</span><span class="p">(</span><span class="n">a</span><span class="p">):</span>
+        <span class="n">factors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">factorint</span><span class="p">(</span><span class="n">a</span><span class="p">)</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
+        <span class="k">for</span> <span class="n">factor</span> <span class="ow">in</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">5</span><span class="p">]:</span>
+            <span class="n">factors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">factors</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">factors</span> <span class="o">==</span> <span class="n">factor</span><span class="p">))</span>
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">factors</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span>
+
+    <span class="c1"># Keep on increasing a until we find the right number</span>
+    <span class="k">while</span> <span class="ow">not</span> <span class="n">_has_only_factors</span><span class="p">(</span><span class="n">a</span><span class="p">):</span>
+        <span class="n">a</span> <span class="o">+=</span> <span class="mi">1</span>
+
+    <span class="c1"># Return</span>
+    <span class="k">return</span> <span class="n">a</span></div>
+
+</pre></div>
+
+            <div class="clearer"></div>
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
+        <div class="sphinxsidebarwrapper">
+<search id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="Related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">namdtools 0.4.3.dev4 documentation</a> &#187;</li>
+          <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">namdtools.pme</a></li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+    &#169; Copyright 2020, Lockhart Lab.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 9.1.0.
+    </div>
+  </body>
+</html>

namdtools-0.4.4.dev0/docs/build/html/_modules/namdtools/read.html

@@ -0,0 +1,151 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>namdtools.read &#8212; namdtools 0.4.3.dev4 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=8f2a1f02" />
+    <link rel="stylesheet" type="text/css" href="../../_static/nature.css?v=279e0f84" />
+    <script src="../../_static/documentation_options.js?v=44170b8a"></script>
+    <script src="../../_static/doctools.js?v=fd6eb6e6"></script>
+    <script src="../../_static/sphinx_highlight.js?v=6ffebe34"></script>
+    <link rel="index" title="Index" href="../../genindex.html" />
+    <link rel="search" title="Search" href="../../search.html" /> 
+  </head><body>
+    <div class="related" role="navigation" aria-label="Related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">namdtools 0.4.3.dev4 documentation</a> &#187;</li>
+          <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">namdtools.read</a></li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <h1>Source code for namdtools.read</h1><div class="highlight"><pre>
+<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">fpathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">ExpandedFPath</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">fpathlib.ext.polars</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pl</span>
+
+
+<span class="c1"># Read NAMD log file</span>
+<div class="viewcode-block" id="read_log">
+<a class="viewcode-back" href="../../api/generated/namdtools.read.read_log.html#namdtools.read.read_log">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">read_log</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">drop_etitle</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+    <span class="k">return</span> <span class="n">scan_log</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">drop_etitle</span><span class="p">)</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span></div>
+
+
+<span class="c1"># Scan NAMD log file</span>
+<span class="c1"># TODO collect(engine="streaming") is necessary when there are many globbed filed in source</span>
+<span class="c1"># this could be fixed in the future.</span>
+<div class="viewcode-block" id="scan_log">
+<a class="viewcode-back" href="../../api/generated/namdtools.read.scan_log.html#namdtools.read.scan_log">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">scan_log</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">drop_etitle</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+<span class="w">    </span><span class="sa">r</span><span class="sd">"""</span>
+<span class="sd">    Scan NAMD log file.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    source : :obj:`str`</span>
+<span class="sd">        Name of NAMD log file. </span>
+<span class="sd">    drop_etitle : :obj:`bool`</span>
+<span class="sd">        Drop the first column of the log file, which is the title of the energy term. (Default: True).</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    DataFrame</span>
+<span class="sd">    """</span>
+
+    <span class="c1"># Read in logs in `source`</span>
+    <span class="n">lf</span> <span class="o">=</span> <span class="n">pl</span><span class="o">.</span><span class="n">scan_txt</span><span class="p">(</span>
+        <span class="n">source</span><span class="p">,</span>
+        <span class="n">separator</span><span class="o">=</span><span class="sa">r</span><span class="s2">"\s+"</span><span class="p">,</span>
+        <span class="n">filter_expr</span><span class="o">=</span><span class="n">pl</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">"line"</span><span class="p">)</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">starts_with</span><span class="p">(</span><span class="s2">"ENERGY"</span><span class="p">),</span>
+    <span class="p">)</span>
+    
+    <span class="c1"># Change fields to appropriate header values</span>
+    <span class="n">columns</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s2">"etitle"</span><span class="p">,</span>
+            <span class="s2">"ts"</span><span class="p">,</span>
+            <span class="s2">"bond"</span><span class="p">,</span>
+            <span class="s2">"angle"</span><span class="p">,</span>
+            <span class="s2">"dihed"</span><span class="p">,</span>
+            <span class="s2">"imprp"</span><span class="p">,</span>
+            <span class="s2">"elect"</span><span class="p">,</span>
+            <span class="s2">"vdw"</span><span class="p">,</span>
+            <span class="s2">"boundary"</span><span class="p">,</span>
+            <span class="s2">"misc"</span><span class="p">,</span>
+            <span class="s2">"kinetic"</span><span class="p">,</span>
+            <span class="s2">"total"</span><span class="p">,</span>
+            <span class="s2">"temp"</span><span class="p">,</span>
+            <span class="s2">"potential"</span><span class="p">,</span>
+            <span class="s2">"total3"</span><span class="p">,</span>
+            <span class="s2">"tempavg"</span><span class="p">,</span>
+            <span class="s2">"pressure"</span><span class="p">,</span>
+            <span class="s2">"gpressure"</span><span class="p">,</span>
+            <span class="s2">"volume"</span><span class="p">,</span>
+            <span class="s2">"pressavg"</span><span class="p">,</span>
+            <span class="s2">"gpressavg"</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="n">fields</span> <span class="o">=</span> <span class="n">lf</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">pl</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">"^field_.*$"</span><span class="p">))</span><span class="o">.</span><span class="n">collect</span><span class="p">(</span><span class="n">engine</span><span class="o">=</span><span class="s2">"streaming"</span><span class="p">)</span><span class="o">.</span><span class="n">schema</span><span class="o">.</span><span class="n">names</span><span class="p">()</span>
+    <span class="n">n_fields</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">fields</span><span class="p">)</span>
+    <span class="k">if</span> <span class="n">n_fields</span> <span class="o">==</span> <span class="mi">16</span><span class="p">:</span>
+        <span class="n">columns</span> <span class="o">=</span> <span class="n">columns</span><span class="p">[:</span><span class="mi">16</span><span class="p">]</span>
+    <span class="k">elif</span> <span class="n">n_fields</span> <span class="o">!=</span> <span class="mi">21</span><span class="p">:</span>
+        <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"unexpected number of ENERGY fields: </span><span class="si">{</span><span class="n">n_fields</span><span class="si">}</span><span class="s2"> (expected 16 or 21)"</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+    <span class="n">lf</span> <span class="o">=</span> <span class="n">lf</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">fields</span><span class="p">,</span> <span class="n">columns</span><span class="p">)))</span>
+
+    <span class="c1"># Drop etitle?</span>
+    <span class="k">if</span> <span class="n">drop_etitle</span><span class="p">:</span>
+        <span class="n">lf</span> <span class="o">=</span> <span class="n">lf</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">"etitle"</span><span class="p">)</span>
+
+    <span class="c1"># Return</span>
+    <span class="k">return</span> <span class="n">lf</span></div>
+
+</pre></div>
+
+            <div class="clearer"></div>
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
+        <div class="sphinxsidebarwrapper">
+<search id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="Related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">namdtools 0.4.3.dev4 documentation</a> &#187;</li>
+          <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">namdtools.read</a></li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+    &#169; Copyright 2020, Lockhart Lab.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 9.1.0.
+    </div>
+  </body>
+</html>

namdtools-0.4.4.dev0/docs/build/html/_sources/api/generated/namdtools.pme.get_pme_size.rst.txt

@@ -0,0 +1,6 @@
+namdtools.pme.get\_pme\_size
+============================
+
+.. currentmodule:: namdtools.pme
+
+.. autofunction:: get_pme_size

namdtools-0.4.4.dev0/docs/build/html/_sources/api/generated/namdtools.read.read_log.rst.txt

@@ -0,0 +1,6 @@
+namdtools.read.read\_log
+========================
+
+.. currentmodule:: namdtools.read
+
+.. autofunction:: read_log

namdtools-0.4.4.dev0/docs/build/html/_sources/api/generated/namdtools.read.scan_log.rst.txt

@@ -0,0 +1,6 @@
+namdtools.read.scan\_log
+========================
+
+.. currentmodule:: namdtools.read
+
+.. autofunction:: scan_log

namdtools-0.4.4.dev0/docs/build/html/_sources/api/pme.rst.txt

@@ -0,0 +1,12 @@
+namdtools.pme
+==============
+
+.. currentmodule:: namdtools.pme
+
+Functions
+~~~~~~~~~
+
+.. autosummary::
+   :toctree: generated
+
+   get_pme_size

namdtools-0.4.4.dev0/docs/build/html/_sources/api/read.rst.txt

@@ -0,0 +1,13 @@
+namdtools.read
+==============
+
+.. currentmodule:: namdtools.read
+   
+Functions
+~~~~~~~~~
+
+.. autosummary::
+   :toctree: generated
+
+   read_log
+   scan_log

namdtools-0.4.4.dev0/docs/build/html/_sources/api.rst.txt

@@ -0,0 +1,9 @@
+
+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 1
+
+   api/pme
+   api/read

namdtools-0.4.4.dev0/docs/build/html/_sources/index.rst.txt

@@ -0,0 +1,14 @@
+
+namdtools
+=========
+
+.. toctree::
+   :maxdepth: 1
+
+   api
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`