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‎docs_1/build/doctrees/environment.pickle‎

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‎docs_1/build/doctrees/installation.doctree‎

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‎docs_1/build/html/_modules/idpet/comparison.html‎

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<title>idpet.comparison &mdash; IDPET 0.1.0 documentation</title>
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<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=b86133f3" />
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<link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=e59714d7" />
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<script src="../../_static/design-tabs.js?v=f930bc37"></script>
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<link rel="index" title="Index" href="../../genindex.html" />
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<link rel="search" title="Search" href="../../search.html" />

‎docs_1/build/html/_modules/idpet/visualization.html‎

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<title>idpet.visualization &mdash; IDPET 0.1.0 documentation</title>
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<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=b86133f3" />
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<link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=e59714d7" />
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<script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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<script src="../../_static/documentation_options.js?v=01f34227"></script>
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<script src="../../_static/doctools.js?v=9bcbadda"></script>
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<script src="../../_static/design-tabs.js?v=f930bc37"></script>
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<script src="../../_static/js/theme.js"></script>
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<link rel="index" title="Index" href="../../genindex.html" />
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<link rel="search" title="Search" href="../../search.html" />

‎docs_1/build/html/_sources/installation.rst.txt‎

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Installation
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============
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We recommend installing IDPET in a clean virtual environment to avoid package conflicts. Below are step-by-step instructions for installation using either `venv` or `conda`, along with important setup notes for MDTraj.
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Install using pip
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-----------------
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To install IDPET using pip, follow these steps:
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Step 1: (Recommended) Create a virtual environment
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Step 1: Install MDTraj
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~~~~~~~~~~~~~~~~~~~~~~
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**Using venv (standard Python):**
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IDPET is built on top of `MDTraj <https://mdtraj.org/>`_. As MDTraj can have compatibility issues on Windows OS, we recommend installing it using conda. This step can be omitted when using Linux.
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.. code-block:: bash
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.. code-block:: shell
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python -m venv idpet-env
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# Activate the environment
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# On Linux/macOS:
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source idpet-env/bin/activate
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# On Windows:
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idpet-env\Scripts\activate
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# Upgrade pip
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pip install --upgrade pip
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**Using conda:**
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.. code-block:: bash
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conda create -n idpet-env python=3.9 -y
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conda activate idpet-env
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Step 2: Install MDTraj (required)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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IDPET is built on top of `MDTraj <https://mdtraj.org/>`_. Since MDTraj can have compatibility issues on Windows, we recommend installing it via `conda`:
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.. code-block:: bash
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conda install -c conda-forge mdtraj
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Step 2: Install IDPET
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This step is **optional on Linux**, but still safe and recommended to avoid binary issues.
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Step 3: Install IDPET
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~~~~~~~~~~~~~~~~~~~~~
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Finally, you can install IDPET using pip.
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With your environment active and MDTraj installed, you can now install IDPET from PyPI:
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.. code-block:: shell
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.. code-block:: bash
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pip install idpet
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To verify the installation:
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.. code-block:: python
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import idpet
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print(idpet.__version__)
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Developer installation (optional)
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---------------------------------
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If you wish to contribute to IDPET or work with the source code, you can install it in editable mode:
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.. code-block:: bash
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git clone https://github.com/hamidrgh/idpet.git
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cd idpet
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pip install -e .
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This will install IDPET in "editable" mode so any local changes take effect immediately.
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‎docs_1/build/html/installation.html‎

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<li class="toctree-l1"><a class="reference internal" href="overview.html">Overview</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#install-using-pip">Install using pip</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#step-1-install-mdtraj">Step 1: Install MDTraj</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#step-2-install-idpet">Step 2: Install IDPET</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#step-1-recommended-create-a-virtual-environment">Step 1: (Recommended) Create a virtual environment</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#step-2-install-mdtraj-required">Step 2: Install MDTraj (required)</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#step-3-install-idpet">Step 3: Install IDPET</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="#developer-installation-optional">Developer installation (optional)</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="demo.html">Demo</a></li>
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<section id="installation">
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<h1>Installation<a class="headerlink" href="#installation" title="Link to this heading"></a></h1>
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<p>We recommend installing IDPET in a clean virtual environment to avoid package conflicts. Below are step-by-step instructions for installation using either <cite>venv</cite> or <cite>conda</cite>, along with important setup notes for MDTraj.</p>
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<section id="install-using-pip">
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<h2>Install using pip<a class="headerlink" href="#install-using-pip" title="Link to this heading"></a></h2>
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<p>To install IDPET using pip, follow these steps:</p>
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<section id="step-1-install-mdtraj">
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<h3>Step 1: Install MDTraj<a class="headerlink" href="#step-1-install-mdtraj" title="Link to this heading"></a></h3>
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<p>IDPET is built on top of <a class="reference external" href="https://mdtraj.org/">MDTraj</a>. As MDTraj can have compatibility issues on Windows OS, we recommend installing it using conda. This step can be omitted when using Linux.</p>
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<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>install<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span>mdtraj
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<section id="step-1-recommended-create-a-virtual-environment">
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<h3>Step 1: (Recommended) Create a virtual environment<a class="headerlink" href="#step-1-recommended-create-a-virtual-environment" title="Link to this heading"></a></h3>
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<p><strong>Using venv (standard Python):</strong></p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python<span class="w"> </span>-m<span class="w"> </span>venv<span class="w"> </span>idpet-env
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<span class="c1"># Activate the environment</span>
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<span class="c1"># On Linux/macOS:</span>
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<span class="nb">source</span><span class="w"> </span>idpet-env/bin/activate
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<span class="c1"># On Windows:</span>
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idpet-env<span class="se">\S</span>cripts<span class="se">\a</span>ctivate
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<span class="c1"># Upgrade pip</span>
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pip<span class="w"> </span>install<span class="w"> </span>--upgrade<span class="w"> </span>pip
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</pre></div>
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</div>
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<p><strong>Using conda:</strong></p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>idpet-env<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.9<span class="w"> </span>-y
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conda<span class="w"> </span>activate<span class="w"> </span>idpet-env
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</pre></div>
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</div>
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</section>
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<section id="step-2-install-mdtraj-required">
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<h3>Step 2: Install MDTraj (required)<a class="headerlink" href="#step-2-install-mdtraj-required" title="Link to this heading"></a></h3>
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<p>IDPET is built on top of <a class="reference external" href="https://mdtraj.org/">MDTraj</a>. Since MDTraj can have compatibility issues on Windows, we recommend installing it via <cite>conda</cite>:</p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>install<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span>mdtraj
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</pre></div>
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</div>
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<p>This step is <strong>optional on Linux</strong>, but still safe and recommended to avoid binary issues.</p>
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</section>
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<section id="step-2-install-idpet">
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<h3>Step 2: Install IDPET<a class="headerlink" href="#step-2-install-idpet" title="Link to this heading"></a></h3>
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<p>Finally, you can install IDPET using pip.</p>
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<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>idpet
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<section id="step-3-install-idpet">
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<h3>Step 3: Install IDPET<a class="headerlink" href="#step-3-install-idpet" title="Link to this heading"></a></h3>
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<p>With your environment active and MDTraj installed, you can now install IDPET from PyPI:</p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>idpet
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</pre></div>
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</div>
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<p>To verify the installation:</p>
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<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">idpet</span>
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<span class="nb">print</span><span class="p">(</span><span class="n">idpet</span><span class="o">.</span><span class="n">__version__</span><span class="p">)</span>
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</pre></div>
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</div>
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</section>
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</section>
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<section id="developer-installation-optional">
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<h2>Developer installation (optional)<a class="headerlink" href="#developer-installation-optional" title="Link to this heading"></a></h2>
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<p>If you wish to contribute to IDPET or work with the source code, you can install it in editable mode:</p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/hamidrgh/idpet.git
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<span class="nb">cd</span><span class="w"> </span>idpet
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pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span>.
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</pre></div>
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</div>
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<p>This will install IDPET in “editable” mode so any local changes take effect immediately.</p>
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</section>
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</section>
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‎docs_1/build/html/searchindex.js‎

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‎docs_1/source/installation.rst‎

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Installation
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============
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We recommend installing IDPET in a clean virtual environment to avoid package conflicts. Below are step-by-step instructions for installation using either `venv` or `conda`, along with important setup notes for MDTraj.
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Install using pip
67
-----------------
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89
To install IDPET using pip, follow these steps:
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Step 1: (Recommended) Create a virtual environment
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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11-
Step 1: Install MDTraj
12-
~~~~~~~~~~~~~~~~~~~~~~
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**Using venv (standard Python):**
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14-
IDPET is built on top of `MDTraj <https://mdtraj.org/>`_. As MDTraj can have compatibility issues on Windows OS, we recommend installing it using conda. This step can be omitted when using Linux.
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.. code-block:: bash
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.. code-block:: shell
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python -m venv idpet-env
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# Activate the environment
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# On Linux/macOS:
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source idpet-env/bin/activate
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# On Windows:
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idpet-env\Scripts\activate
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# Upgrade pip
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pip install --upgrade pip
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**Using conda:**
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.. code-block:: bash
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conda create -n idpet-env python=3.9 -y
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conda activate idpet-env
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Step 2: Install MDTraj (required)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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IDPET is built on top of `MDTraj <https://mdtraj.org/>`_. Since MDTraj can have compatibility issues on Windows, we recommend installing it via `conda`:
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.. code-block:: bash
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conda install -c conda-forge mdtraj
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Step 2: Install IDPET
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This step is **optional on Linux**, but still safe and recommended to avoid binary issues.
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Step 3: Install IDPET
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~~~~~~~~~~~~~~~~~~~~~
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Finally, you can install IDPET using pip.
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With your environment active and MDTraj installed, you can now install IDPET from PyPI:
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.. code-block:: shell
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.. code-block:: bash
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pip install idpet
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To verify the installation:
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.. code-block:: python
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import idpet
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print(idpet.__version__)
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Developer installation (optional)
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---------------------------------
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If you wish to contribute to IDPET or work with the source code, you can install it in editable mode:
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.. code-block:: bash
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git clone https://github.com/hamidrgh/idpet.git
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cd idpet
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pip install -e .
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This will install IDPET in "editable" mode so any local changes take effect immediately.
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