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# Changes made to source code take effect immediately, without needing to reinstall
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```python
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import ionerdss as ion
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# Example usage
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ion.nerdss()
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ion.some_function() # Replace with actual function calls to set up model and analyze results
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```
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For extended examples, see the [tutorials](https://ionerdss.readthedocs.io/en/latest/ionerdss_tutorials.html).
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### Run a quick trial with Google Colab
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Click the following link to make a copy of the iPython notebook in your Google Colab and following the instructions on the Notebook to run a quick trial of the NERDSS simulator with the usage of ionerdss to prepare the inputs from a PDB structure.
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[](https://colab.research.google.com/github/JohnsonBiophysicsLab/ionerdss/blob/main/docs/Run_NERDSS_colab.ipynb?copy=true)
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### Run a quick trial with our server
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Go to the [NERDSS server](http://18.188.233.206:5000/).
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---
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## Documentation
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-**User Guide:**[ionerdss user guide](https://ionerdss.readthedocs.io/en/latest/ionerdss_documentation.html).
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-**User Guide:**[ionerdss user guide](https://ionerdss.readthedocs.io/en/latest/ionerdss_documentation_v1_1.html).
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-**API Reference:**[API](https://ionerdss.readthedocs.io/en/latest/ionerdss.html) .Docstrings are integrated throughout the code (Google-style). You can also build the docs locally using Sphinx:
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-**API Reference:**[API](https://ionerdss.readthedocs.io/en/latest/ionerdss.html). You can also build the docs locally using Sphinx:
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```bash
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sphinx-apidoc -o docs/source ionerdss
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cd docs
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- Write clear docstrings in Google‐style to help auto‐generate documentation.
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Prompt used for chatGPT to refactor one function: `improve this python code, provide the detail google-style docstring for sphinx, standardize naming conventions:`
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2.**Code Organization**
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- Keep related functionality grouped in submodules.
This project is licensed under the GPL‐3.0 License.
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## Run a quick trial with Google Colab
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Click the following link to make a copy of the iPython notebook in your Google Colab and following the instructions on the Notebook to run a quick trial of the NERDSS simulator with the usage of ionerdss to prepare the inputs from a PDB structure.
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[](https://colab.research.google.com/github/JohnsonBiophysicsLab/ionerdss/blob/main/docs/Run_NERDSS_colab.ipynb?copy=true)
Copy file name to clipboardExpand all lines: docs/source/index.rst
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@@ -7,16 +7,19 @@ Welcome to ionerdss Documentation!
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==================================
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**NERDSS** (NonEquilibrium Reaction-Diffusion Self-assembly Simulator) is a simulator for reaction-diffusion processes.
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**ionerdss** is a Python package that streamlines setting up modelsand analyzing output from NERDSS. Input files can be generated from structures of macromolecular complexes, such as those defined in Protein Data Bank (PDB) files or based on the idealized geometries of Platonic solids. The package is designed to improve the usability and quantitative interpretation of NERDSS simulations.
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**ionerdss** is a Python package that streamlines setting up models, run NERDSS simulations, and analyzing output from NERDSS. Input files can be generated from structures of macromolecular complexes, such as those defined in Protein Data Bank (PDB) files. ionerdss is designed to improve the usability and quantitative interpretation of NERDSS simulations.
- **Protein Data Bank (PDB) files:** Converts PDB files into NERDSS input files. See the `PDB to NERDSS tutorial <pdb_to_nerdss_tutorial.html>`_ for more details.
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- **Platonic solids:** Creates NERDSS input files from idealized geometries of Platonic solids, offering two options for each of the five Platonic solids. See the `Platonic solids tutorial <model_setup_for_platonic_solid.html>`_ for more details.
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- **User designed molecules and reactions**: `JAVA GUI <java_gui_tutorial.html>`_ Allows users to define their own molecules and reactions.
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- **User designed molecules and reactions**: `JAVA GUI <java_gui_tutorial.html>`_ or `Python GUI <ionerdss_gui.html>`_ allow users to define their own molecules and reactions.
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- **Analyzing NERDSS Outputs:** Produces graphs, spreadsheets, and analyzed datasets from NERDSS outputs.
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- **Running NERDSS Simulations:** Install NERDSS, modify simulation parameters, and run simulations.
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- See the `PDB to NERDSS tutorial <pdb_to_nerdss_tutorial.html>`_ for more details.
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- **Analyzing NERDSS Outputs:** Produces graphs, and visulaizes trajectories from NERDSS outputs.
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- **Histogram Analysis:** Processes and outputs data from histogram.dat files.
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- **Complex Location Analysis:** Determines the location of specific complex sizes using PDB, restart, or input files.
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- **Transition Matrix Analysis:** Reads transition matrix files and generates various outputs.
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This documentation includes:
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- How to install and compile NERDSS
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- NERDSS and ionerdss documentation
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- How to install ionerdss
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- ionerdss Tutorials (via Jupyter notebooks)
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- How to install NERDSS and ionerdss
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- Release notes for both NERDSS and ioNERDSS
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- NERDSS and ionerdss documentation (user guides and developer guides)
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NERDSS (NonEquilibrium Reaction-Diffusion Self-assembly Simulator) requires a C++ compiler and the GNU Scientific Library (GSL). Once these prerequisites are installed, you can compile NERDSS from source.
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**0. Download the NERDSS source code from the official repository**
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.. code-block:: console
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git clone https://github.com/mjohn218/NERDSS.git
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cd NERDSS
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**1. Install a C++ Compiler**
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- macOS: Install XCode or Command Line Tools
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- Ubuntu: Install via apt, for example:
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``sudo apt-get install g++``
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.. code-block:: console
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sudo apt-get install g++
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**2. Install GNU Scientific Library (GSL) (v2.5+)**
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- macOS: Use Homebrew:
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``brew install gsl``
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.. code-block:: console
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brew install gsl
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- Ubuntu: Use apt:
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``sudo apt-get install libgsl-dev``
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.. code-block:: console
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sudo apt-get install libgsl-dev
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**3. Compile NERDSS**
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- Navigate to the main NERDSS directory
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- Run ``make serial``
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- The executable will appear in the ``./bin`` directory
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For more details on using NERDSS, see its official documentation or README.
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- Run
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.. code-block:: console
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make clean
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make serial
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- The executable `nerdss` will appear in the `./bin` directory
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For more details on using NERDSS, see its `documentation <nerdss_documentation.html>`_.
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Parallel NERDSS
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---------------
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To build NERDSS with MPI support, follow these steps:
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1. **Install a C++ Compiler with MPI support:**
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- **macOS:** Install OpenMPI with Homebrew:
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```
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brew install open-mpi
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```
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- **Ubuntu:** Install OpenMPI through apt:
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```
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sudo apt install openmpi-bin libopenmpi-dev
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```
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2. **Install GNU Scientific Library (GSL) (v2.5+):**
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