synth-dynamics 0.1.0__tar.gz

synth_dynamics-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 George Elkins
+
+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.

synth_dynamics-0.1.0/MANIFEST.in

@@ -0,0 +1,9 @@
+include LICENSE
+include README.md
+recursive-include docs *
+recursive-include examples *.py
+recursive-include tests *.py
+exclude .gitignore
+exclude GEMINI.md
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

synth_dynamics-0.1.0/PKG-INFO

@@ -0,0 +1,100 @@
+Metadata-Version: 2.4
+Name: synth-dynamics
+Version: 0.1.0
+Summary: Time-Resolved Ensemble Generator using Coarse-Grained ENM Langevin Dynamics
+Author: George Elkins
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/georgeelkins/synth-dynamics
+Project-URL: Repository, https://github.com/georgeelkins/synth-dynamics
+Project-URL: Documentation, https://synth-dynamics.readthedocs.io/
+Project-URL: Bug Tracker, https://github.com/georgeelkins/synth-dynamics/issues
+Keywords: molecular-dynamics,protein-dynamics,ANM,Langevin,ensemble-generation
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: MDAnalysis
+Requires-Dist: scipy
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Dynamic: license-file
+
+# synth-dynamics: Time-Resolved Ensemble Generator
+
+`synth-dynamics` is a fast, lightweight molecular dynamics engine designed to generate meaningful conformational ensembles of proteins. Unlike full-atom simulations (like GROMACS or Amber), `synth-dynamics` uses a **Coarse-Grained Anisotropic Network Model (ANM)** and **Langevin dynamics** to capture the essential global motions of proteins with minimal computational overhead.
+
+This tool is designed to bridge the gap between static structures and time-averaged experimental observables, such as NMR relaxation parameters, SAXS Kratky plots, or FRET efficiency distributions.
+
+## Key Features
+
+- **Coarse-Grained Simulation**: Models proteins using C-alpha atoms and harmonic "spring" networks.
+- **Fast Langevin Engine**: Propagates coordinates using a stable, overdamped Langevin integrator.
+- **Experimental Integration**: Perfect for generating the structural ensembles needed for `synth-nmr` or `synth-saxs`.
+- **Easy to Use**: Simple API for loading PDBs, configuring forcefields, and running simulations.
+- **Extensively Tested**: 100% test coverage ensuring reliability and correctness.
+
+## Installation
+
+`synth-dynamics` requires Python 3.10+ and the following dependencies:
+
+```bash
+pip install numpy MDAnalysis scipy
+```
+
+To install the documentation theme:
+```bash
+pip install sphinx_rtd_theme
+```
+
+## Quick Start
+
+Running a simulation is straightforward:
+
+```python
+from synth_dynamics import System, ANMForceField, LangevinIntegrator, Simulation
+
+# 1. Load the system (automatically filters for C-alpha atoms)
+system = System("protein.pdb")
+
+# 2. Define the Anisotropic Network Model forcefield
+# Cutoff (15A) and spring constant determine the flexibility
+ff = ANMForceField(system.equilibrium_coords, cutoff=15.0, spring_constant=1.0)
+
+# 3. Initialize the Langevin integrator (dt in fs, T in Kelvin)
+integrator = LangevinIntegrator(dt=0.1, temperature=300.0, friction=1.0)
+
+# 4. Run and save the trajectory
+sim = Simulation(system, ff, integrator)
+sim.run(n_steps=1000, output_path="trajectory.dcd", stride=10)
+```
+
+## Documentation
+
+Full API documentation and usage guides are available in the `docs/` directory. You can build the HTML documentation locally:
+
+```bash
+cd docs
+sphinx-build -b html . _build/html
+```
+
+## Testing
+
+To run the test suite and verify coverage:
+
+```bash
+PYTHONPATH=. pytest --cov=synth_dynamics tests/
+```
+
+## License
+
+This project is licensed under the MIT License - see the LICENSE file for details (if applicable).

synth_dynamics-0.1.0/README.md

@@ -0,0 +1,69 @@
+# synth-dynamics: Time-Resolved Ensemble Generator
+
+`synth-dynamics` is a fast, lightweight molecular dynamics engine designed to generate meaningful conformational ensembles of proteins. Unlike full-atom simulations (like GROMACS or Amber), `synth-dynamics` uses a **Coarse-Grained Anisotropic Network Model (ANM)** and **Langevin dynamics** to capture the essential global motions of proteins with minimal computational overhead.
+
+This tool is designed to bridge the gap between static structures and time-averaged experimental observables, such as NMR relaxation parameters, SAXS Kratky plots, or FRET efficiency distributions.
+
+## Key Features
+
+- **Coarse-Grained Simulation**: Models proteins using C-alpha atoms and harmonic "spring" networks.
+- **Fast Langevin Engine**: Propagates coordinates using a stable, overdamped Langevin integrator.
+- **Experimental Integration**: Perfect for generating the structural ensembles needed for `synth-nmr` or `synth-saxs`.
+- **Easy to Use**: Simple API for loading PDBs, configuring forcefields, and running simulations.
+- **Extensively Tested**: 100% test coverage ensuring reliability and correctness.
+
+## Installation
+
+`synth-dynamics` requires Python 3.10+ and the following dependencies:
+
+```bash
+pip install numpy MDAnalysis scipy
+```
+
+To install the documentation theme:
+```bash
+pip install sphinx_rtd_theme
+```
+
+## Quick Start
+
+Running a simulation is straightforward:
+
+```python
+from synth_dynamics import System, ANMForceField, LangevinIntegrator, Simulation
+
+# 1. Load the system (automatically filters for C-alpha atoms)
+system = System("protein.pdb")
+
+# 2. Define the Anisotropic Network Model forcefield
+# Cutoff (15A) and spring constant determine the flexibility
+ff = ANMForceField(system.equilibrium_coords, cutoff=15.0, spring_constant=1.0)
+
+# 3. Initialize the Langevin integrator (dt in fs, T in Kelvin)
+integrator = LangevinIntegrator(dt=0.1, temperature=300.0, friction=1.0)
+
+# 4. Run and save the trajectory
+sim = Simulation(system, ff, integrator)
+sim.run(n_steps=1000, output_path="trajectory.dcd", stride=10)
+```
+
+## Documentation
+
+Full API documentation and usage guides are available in the `docs/` directory. You can build the HTML documentation locally:
+
+```bash
+cd docs
+sphinx-build -b html . _build/html
+```
+
+## Testing
+
+To run the test suite and verify coverage:
+
+```bash
+PYTHONPATH=. pytest --cov=synth_dynamics tests/
+```
+
+## License
+
+This project is licensed under the MIT License - see the LICENSE file for details (if applicable).

synth_dynamics-0.1.0/docs/_build/html/.buildinfo

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+# 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: 5875c7d6db8e2e88875e7229d2847c52
+tags: 645f666f9bcd5a90fca523b33c5a78b7

synth_dynamics-0.1.0/docs/_build/html/_modules/index.html

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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="synth_dynamics/forcefield.html">synth_dynamics.forcefield</a></li>
+<li><a href="synth_dynamics/integrator.html">synth_dynamics.integrator</a></li>
+<li><a href="synth_dynamics/simulation.html">synth_dynamics.simulation</a></li>
+<li><a href="synth_dynamics/system.html">synth_dynamics.system</a></li>
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synth_dynamics-0.1.0/docs/_build/html/_modules/synth_dynamics/forcefield.html

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+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../../">
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+  <meta charset="utf-8" />
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+             
+  <h1>Source code for synth_dynamics.forcefield</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>
+<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.spatial.distance</span><span class="w"> </span><span class="kn">import</span> <span class="n">pdist</span><span class="p">,</span> <span class="n">squareform</span>
+
+<div class="viewcode-block" id="ANMForceField">
+<a class="viewcode-back" href="../../api.html#synth_dynamics.ANMForceField">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">ANMForceField</span><span class="p">:</span>
+    <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">equilibrium_coords</span><span class="p">,</span> <span class="n">cutoff</span><span class="o">=</span><span class="mf">15.0</span><span class="p">,</span> <span class="n">spring_constant</span><span class="o">=</span><span class="mf">1.0</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Anisotropic Network Model Force Field.</span>
+<span class="sd">        </span>
+<span class="sd">        Args:</span>
+<span class="sd">            equilibrium_coords: (N, 3) array of C-alpha equilibrium positions.</span>
+<span class="sd">            cutoff: Distance cutoff for interactions in Angstroms.</span>
+<span class="sd">            spring_constant: Uniform spring constant k.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">x0</span> <span class="o">=</span> <span class="n">equilibrium_coords</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cutoff</span> <span class="o">=</span> <span class="n">cutoff</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">k</span> <span class="o">=</span> <span class="n">spring_constant</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">n_atoms</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">equilibrium_coords</span><span class="p">)</span>
+        
+        <span class="c1"># Precompute equilibrium distances and adjacency matrix</span>
+        <span class="n">dist_matrix</span> <span class="o">=</span> <span class="n">squareform</span><span class="p">(</span><span class="n">pdist</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x0</span><span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">adj</span> <span class="o">=</span> <span class="p">(</span><span class="n">dist_matrix</span> <span class="o">&lt;</span> <span class="n">cutoff</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">dist_matrix</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">r0</span> <span class="o">=</span> <span class="n">dist_matrix</span>
+
+<div class="viewcode-block" id="ANMForceField.compute_forces">
+<a class="viewcode-back" href="../../api.html#synth_dynamics.ANMForceField.compute_forces">[docs]</a>
+    <span class="k">def</span><span class="w"> </span><span class="nf">compute_forces</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">current_coords</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Computes the harmonic forces on each atom.</span>
+<span class="sd">        </span>
+<span class="sd">        Args:</span>
+<span class="sd">            current_coords: (N, 3) array of current positions.</span>
+<span class="sd">        Returns:</span>
+<span class="sd">            forces: (N, 3) array of forces.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Calculate current distances and difference vectors</span>
+        <span class="c1"># diff[i, j] = r_i - r_j</span>
+        <span class="n">diff</span> <span class="o">=</span> <span class="n">current_coords</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,</span> <span class="p">:]</span> <span class="o">-</span> <span class="n">current_coords</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,</span> <span class="p">:,</span> <span class="p">:]</span>
+        <span class="n">dist</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">norm</span><span class="p">(</span><span class="n">diff</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
+        
+        <span class="c1"># Avoid division by zero</span>
+        <span class="n">dist_inv</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span>
+        <span class="n">mask</span> <span class="o">=</span> <span class="n">dist</span> <span class="o">&gt;</span> <span class="mi">0</span>
+        <span class="n">dist_inv</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">/</span> <span class="n">dist</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span>
+        
+        <span class="c1"># Force magnitude matrix: F_ij = -k * (r_ij - r0_ij)</span>
+        <span class="c1"># We only care about pairs in the adjacency matrix</span>
+        <span class="n">force_mag</span> <span class="o">=</span> <span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">k</span> <span class="o">*</span> <span class="p">(</span><span class="n">dist</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">r0</span><span class="p">)</span>
+        
+        <span class="c1"># Full force vector matrix: F_vec_ij = F_ij * (diff_ij / dist_ij)</span>
+        <span class="c1"># Shape: (N, N, 3)</span>
+        <span class="n">force_vecs</span> <span class="o">=</span> <span class="p">(</span><span class="n">force_mag</span> <span class="o">*</span> <span class="n">dist_inv</span><span class="p">)[:,</span> <span class="p">:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">]</span> <span class="o">*</span> <span class="n">diff</span>
+        
+        <span class="c1"># Zero out inactive interactions</span>
+        <span class="n">force_vecs</span><span class="p">[</span><span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">adj</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
+        
+        <span class="c1"># Total force on atom i is sum over j</span>
+        <span class="n">forces</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">force_vecs</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+                
+        <span class="k">return</span> <span class="n">forces</span></div>
+</div>
+
+</pre></div>
+
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