update docs

TIES_MD/cli.py

@@ -48,7 +48,7 @@ def main(argv=None):
     if args['--config_file']:
         config_file = args['--config_file']
         input_folder = config_file.split('/')[:-1]
-        input_folder = '/'.join(input_folder)
+        input_folder = os.path.abspath('/'.join(input_folder))
     else:
         input_folder = os.getcwd()
         config_file = input_folder+'/TIES.cfg'

TIES_MD/doc/source/API.rst

@@ -8,11 +8,21 @@ API
 ---
 
 Here we detail all the options in the API and what should be passed. The options that were previously on the command line
-can be passed into the TIES class like so::
+can be passed into the TIES class. A minimal evocation would looks like::
 
     from TIES_MD import TIES
     import os
-    md = TIES(cwd=os.path.abspath('./my_ties_sims'), windows_mask=[0,1], rep_id=0, exp_name='sys_solv')
+    md = TIES(cwd=os.path.abspath('./my_ties_sims'))
+
+``cwd`` points to where the ``TIES.cfg`` file is located and where the simulations are performed, note this must be
+an absolute path. All other arguments will be set to their default values. If we want to change all the arguments then
+the code might look like::
+
+        from TIES_MD import TIES
+        import os
+        md = TIES(cwd=os.path.abspath('./my_ties_sims'), exp_name='sys_solv', windows_mask=[0], devices=[0], rep_id=0)
+
+These arguments have the same definitions as in the :ref:`Command Line` subsection of the tutorial.
 
 Once the TIES class is constructed the options that were previously in TIES.cfg can now be set as attributes of the TIES
 class like so::
@@ -41,7 +51,7 @@ class like so::
     #How many total replicas of each window are run (we recommend at least 5).
     md.total_reps = 3
 
-    #Boolean for if we will split all replicas into separate runs. (True for maximum parallelism)
+    #Boolean for if we will split all replicas into separate runs. (Set to True for maximum parallelism)
     md.split_run = False
 
     #List for where in lambda schedule (0->1) should the electrostatic potentials begin, stop appearing.

TIES_MD/doc/source/binding_free_energies.rst

@@ -32,7 +32,7 @@ Setup
 To set up these calculation we recommend the use of ``TIES20``. This is a program designed to both build and parameterize
 hybrid ligands but also setup binding free energy calculations for the TIES protocol that can be run with ``TIES_MD``.
 ``TIES20`` can be used in `browser <https://ccs-ties.org/ties/>`_. Alternatively one can use the ``TIES20`` API to set up
-simulations. In order to use the API ``TIES20`` must be installed locally please see the :ref:`TIES20` section
+simulations. In order to use the API ``TIES20`` must be installed locally please see the `TIES20 git. <https://github.com/UCL-CCS/TIES20>`_
 for how to do this. With ``TIES20`` installed you can use the API as follows to build inputs::
 
     #ties20 imports

TIES_MD/doc/source/index.rst

@@ -28,7 +28,6 @@ Contents
     parallelization
     HPC_submissions
     theory
-    TIES20
     🚀Github <https://github.com/UCL-CCS/TIES_MD>
 
 Code Documentation

TIES_MD/doc/source/tutorial.rst

@@ -125,7 +125,7 @@ settings and the settings found in ``TIES.cfg``. The setting which can be taken
 values are as follows::
 
     [--config_file=./TIES.cfg]
-    A string for the absolute path pointing to where the TIES.cfg file is located. #THIS PATH MUST BE ABSOLUTE.
+    A string for the path pointing to where the TIES.cfg file is located.
 
     [--exp_name=complex]
     This is the name of the experiment and the prefix that TIES OpenMM will expect on the input pdb and prmtop file.

TIES_MD/tests/test_TIES.py

@@ -95,7 +95,8 @@ def test_namd_conf(self):
         args_dict = copy.deepcopy(test_args)
 
         #make a output dir
-        out_dir = os.path.join('data', 'test_replica-confs', 'tmp') #this is a relative path to make tests work anywhere
+        out_dir = os.path.join('data', 'test_replica-confs', 'tmp') #this is a relative such that CI dir structure is not
+        #in generated conf scripts therfore we can match them.
         Path(out_dir).mkdir(parents=False, exist_ok=True)
 
         #iterate over the variables that effect how confs are written

docs/API.html

@@ -87,12 +87,21 @@ <h1>TIES MD API<a class="headerlink" href="#ties-md-api" title="Permalink to thi
 <section id="api">
 <h2>API<a class="headerlink" href="#api" title="Permalink to this heading"></a></h2>
 <p>Here we detail all the options in the API and what should be passed. The options that were previously on the command line
-can be passed into the TIES class like so:</p>
+can be passed into the TIES class. A minimal evocation would looks like:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">TIES_MD</span> <span class="kn">import</span> <span class="n">TIES</span>
 <span class="kn">import</span> <span class="nn">os</span>
-<span class="n">md</span> <span class="o">=</span> <span class="n">TIES</span><span class="p">(</span><span class="n">cwd</span><span class="o">=</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="s1">&#39;./my_ties_sims&#39;</span><span class="p">),</span> <span class="n">windows_mask</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">],</span> <span class="n">rep_id</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">exp_name</span><span class="o">=</span><span class="s1">&#39;sys_solv&#39;</span><span class="p">)</span>
+<span class="n">md</span> <span class="o">=</span> <span class="n">TIES</span><span class="p">(</span><span class="n">cwd</span><span class="o">=</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="s1">&#39;./my_ties_sims&#39;</span><span class="p">))</span>
 </pre></div>
 </div>
+<p><code class="docutils literal notranslate"><span class="pre">cwd</span></code> points to where the <code class="docutils literal notranslate"><span class="pre">TIES.cfg</span></code> file is located and where the simulations are performed, note this must be
+an absolute path. All other arguments will be set to their default values. If we want to change all the arguments then
+the code might look like:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">TIES_MD</span> <span class="kn">import</span> <span class="n">TIES</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="n">md</span> <span class="o">=</span> <span class="n">TIES</span><span class="p">(</span><span class="n">cwd</span><span class="o">=</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="s1">&#39;./my_ties_sims&#39;</span><span class="p">),</span> <span class="n">exp_name</span><span class="o">=</span><span class="s1">&#39;sys_solv&#39;</span><span class="p">,</span> <span class="n">windows_mask</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">devices</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">rep_id</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>These arguments have the same definitions as in the <a class="reference internal" href="tutorial.html#command-line"><span class="std std-ref">Command Line</span></a> subsection of the tutorial.</p>
 <p>Once the TIES class is constructed the options that were previously in TIES.cfg can now be set as attributes of the TIES
 class like so:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># openmm.unit is needed to set values with units</span>
@@ -119,7 +128,7 @@ <h2>API<a class="headerlink" href="#api" title="Permalink to this heading"></
 <span class="c1">#How many total replicas of each window are run (we recommend at least 5).</span>
 <span class="n">md</span><span class="o">.</span><span class="n">total_reps</span> <span class="o">=</span> <span class="mi">3</span>
 
-<span class="c1">#Boolean for if we will split all replicas into separate runs. (True for maximum parallelism)</span>
+<span class="c1">#Boolean for if we will split all replicas into separate runs. (Set to True for maximum parallelism)</span>
 <span class="n">md</span><span class="o">.</span><span class="n">split_run</span> <span class="o">=</span> <span class="kc">False</span>
 
 <span class="c1">#List for where in lambda schedule (0-&gt;1) should the electrostatic potentials begin, stop appearing.</span>

docs/_sources/API.rst.txt

@@ -8,11 +8,21 @@ API
 ---
 
 Here we detail all the options in the API and what should be passed. The options that were previously on the command line
-can be passed into the TIES class like so::
+can be passed into the TIES class. A minimal evocation would looks like::
 
     from TIES_MD import TIES
     import os
-    md = TIES(cwd=os.path.abspath('./my_ties_sims'), windows_mask=[0,1], rep_id=0, exp_name='sys_solv')
+    md = TIES(cwd=os.path.abspath('./my_ties_sims'))
+
+``cwd`` points to where the ``TIES.cfg`` file is located and where the simulations are performed, note this must be
+an absolute path. All other arguments will be set to their default values. If we want to change all the arguments then
+the code might look like::
+
+        from TIES_MD import TIES
+        import os
+        md = TIES(cwd=os.path.abspath('./my_ties_sims'), exp_name='sys_solv', windows_mask=[0], devices=[0], rep_id=0)
+
+These arguments have the same definitions as in the :ref:`Command Line` subsection of the tutorial.
 
 Once the TIES class is constructed the options that were previously in TIES.cfg can now be set as attributes of the TIES
 class like so::
@@ -41,7 +51,7 @@ class like so::
     #How many total replicas of each window are run (we recommend at least 5).
     md.total_reps = 3
 
-    #Boolean for if we will split all replicas into separate runs. (True for maximum parallelism)
+    #Boolean for if we will split all replicas into separate runs. (Set to True for maximum parallelism)
     md.split_run = False
 
     #List for where in lambda schedule (0->1) should the electrostatic potentials begin, stop appearing.

docs/_sources/binding_free_energies.rst.txt

@@ -32,7 +32,7 @@ Setup
 To set up these calculation we recommend the use of ``TIES20``. This is a program designed to both build and parameterize
 hybrid ligands but also setup binding free energy calculations for the TIES protocol that can be run with ``TIES_MD``.
 ``TIES20`` can be used in `browser <https://ccs-ties.org/ties/>`_. Alternatively one can use the ``TIES20`` API to set up
-simulations. In order to use the API ``TIES20`` must be installed locally please see the :ref:`TIES20` section
+simulations. In order to use the API ``TIES20`` must be installed locally please see the `TIES20 git. <https://github.com/UCL-CCS/TIES20>`_
 for how to do this. With ``TIES20`` installed you can use the API as follows to build inputs::
 
     #ties20 imports

docs/_sources/index.rst.txt

@@ -28,7 +28,6 @@ Contents
     parallelization
     HPC_submissions
     theory
-    TIES20
     🚀Github <https://github.com/UCL-CCS/TIES_MD>
 
 Code Documentation

docs/_sources/tutorial.rst.txt

@@ -125,7 +125,7 @@ settings and the settings found in ``TIES.cfg``. The setting which can be taken
 values are as follows::
 
     [--config_file=./TIES.cfg]
-    A string for the absolute path pointing to where the TIES.cfg file is located. #THIS PATH MUST BE ABSOLUTE.
+    A string for the path pointing to where the TIES.cfg file is located.
 
     [--exp_name=complex]
     This is the name of the experiment and the prefix that TIES OpenMM will expect on the input pdb and prmtop file.

docs/binding_free_energies.html

@@ -109,7 +109,7 @@ <h2>Setup<a class="headerlink" href="#setup" title="Permalink to this heading">
 <p>To set up these calculation we recommend the use of <code class="docutils literal notranslate"><span class="pre">TIES20</span></code>. This is a program designed to both build and parameterize
 hybrid ligands but also setup binding free energy calculations for the TIES protocol that can be run with <code class="docutils literal notranslate"><span class="pre">TIES_MD</span></code>.
 <code class="docutils literal notranslate"><span class="pre">TIES20</span></code> can be used in <a class="reference external" href="https://ccs-ties.org/ties/">browser</a>. Alternatively one can use the <code class="docutils literal notranslate"><span class="pre">TIES20</span></code> API to set up
-simulations. In order to use the API <code class="docutils literal notranslate"><span class="pre">TIES20</span></code> must be installed locally please see the <span class="xref std std-ref">TIES20</span> section
+simulations. In order to use the API <code class="docutils literal notranslate"><span class="pre">TIES20</span></code> must be installed locally please see the <a class="reference external" href="https://github.com/UCL-CCS/TIES20">TIES20 git.</a>
 for how to do this. With <code class="docutils literal notranslate"><span class="pre">TIES20</span></code> installed you can use the API as follows to build inputs:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1">#ties20 imports</span>
 <span class="kn">from</span> <span class="nn">ties</span> <span class="kn">import</span> <span class="n">Pair</span><span class="p">,</span> <span class="n">Config</span><span class="p">,</span> <span class="n">Ligand</span><span class="p">,</span> <span class="n">Protein</span>

docs/tutorial.html

@@ -195,7 +195,7 @@ <h2>Command Line<a class="headerlink" href="#command-line" title="Permalink to t
 settings and the settings found in <code class="docutils literal notranslate"><span class="pre">TIES.cfg</span></code>. The setting which can be taken on the command line and their default
 values are as follows:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>[--config_file=./TIES.cfg]
-A string for the absolute path pointing to where the TIES.cfg file is located. #THIS PATH MUST BE ABSOLUTE.
+A string for the path pointing to where the TIES.cfg file is located.
 
 [--exp_name=complex]
 This is the name of the experiment and the prefix that TIES OpenMM will expect on the input pdb and prmtop file.