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https://github.com/mosdef-hub/mbuild

A hierarchical, component based molecule builder
https://github.com/mosdef-hub/mbuild

mbuild molecular-dynamics molecular-simulation molecule-builder mosdef python

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A hierarchical, component based molecule builder

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README 

          
## mBuild: a hierarchical, component based molecule builder



[![Gitter chat](https://badges.gitter.im/mosdef-hub/gitter.svg)](https://gitter.im/mosdef-hub/Lobby)

[![CI](https://github.com/mosdef-hub/mbuild/actions/workflows/CI.yaml/badge.svg)](https://github.com/mosdef-hub/mbuild/actions/workflows/CI.yaml)

[![Anaconda Badge](https://anaconda.org/conda-forge/mbuild/badges/version.svg)](https://anaconda.org/conda-forge/mbuild)

[![codecov](https://codecov.io/gh/mosdef-hub/mbuild/branch/master/graph/badge.svg)](https://codecov.io/gh/mosdef-hub/mbuild)



With just a few lines of mBuild code, you can assemble reusable components into

complex molecular systems for molecular dynamics simulations.



* mBuild is designed to minimize or even eliminate the need to explicitly translate and

  orient components when building systems: you simply tell it to connect two

  pieces!

* mBuild keeps track of the system's topology so you don't have to

  worry about manually defining bonds when constructing chemically bonded

  structures from smaller components.



To learn more, get started or contribute, check out our [website](http://mbuild.mosdef.org).



### mBuild within the MoSDeF Ecosystem



  mBuild within the MoSDeF Ecosystem




The `mBuild` package is part of the [Molecular Simulation Design Framework (MoSDeF) project](http://mosdef.org/).

Libraries in the MoSDeF ecosystem are designed to provide utilities neccessary to streamline

a researcher's simulation workflow. When setting up simulation studies,

we also recommend users to follow the [TRUE](https://www.tandfonline.com/doi/full/10.1080/00268976.2020.1742938)

(Transparent, Reproducible, Usable-by-others, and Extensible) standard, which is a set of common

practices meant to improve the reproducibility of computational simulation research.



Installation

------------

For full, detailed instructions, refer to the [documentation for installation](https://mbuild.mosdef.org/en/stable/getting_started/installation/installation_toc.html)



#### `conda` installation quickstart

`mBuild` is available on `conda` and can be installed as:

```bash

conda install -c conda-forge mbuild

```



#### Installing from source



Dependencies of mBuild are listed in the files ``environment.yml`` (lightweight environment specification containing minimal dependencies) and ``environment-dev.yml`` (comprehensive environment specification including optional and testing packages for developers).

The ``mbuild`` or ``mbuild-dev`` conda environments can be created with



```.. code-block:: bash

git clone https://github.com/mosdef-hub/mbuild.git

cd mbuild

# for mbuild conda environment

conda env create -f environment.yml

conda activate mbuild



# for mbuild-dev

conda env create -f environment-dev.yml

conda activate mbuild-dev



# install a non-editable version of mbuild

pip install .

```



NOTE: [openbabel](https://github.com/openbabel/openbabel) is required for some energy minimization methods in `mbuild.compound.Compound()`. It can be installed into your mBuild environment from conda-forge with `conda install -c conda-forge openbabel`; however, openbabel does not yet support python 3.13.



#### Install an editable version from source



Once all dependencies have been installed and the ``conda`` environment has been created, the ``mBuild`` itself can be installed.



``` code-block:: bash

cd mbuild

conda activate mbuild-dev # or mbuild depending on your installation

pip install -e .

```

#### Quick Start with Docker

To use `mbuild` in a jupyter-notebook that runs from a docker container with all the dependencies installed use the following command:



```sh

$ docker pull mosdef/mbuild:latest

$ docker run -it --name mbuild -p 8888:8888 mosdef/mbuild:latest su anaconda -s\

      /bin/sh -l -c "jupyter-notebook --no-browser --ip="0.0.0.0" --notebook-dir\

      /home/anaconda/mbuild-notebooks

```



Alternatively, you can also start a Bourne shell directly:

```sh

$ docker run -it --name mbuild mosdef/mbuild:latest

```



To learn more about using `mBuild` with docker, please refer to the documentation [here](https://mbuild.mosdef.org/en/latest/docker.html).



### Tutorials



*Interactive tutorials can be found here:*



[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/mosdef-hub/mbuild_tutorials/master)



Components in dashed boxes are drawn by hand using, e.g.,

[Avogadro](https://avogadro.cc/) or generated elsewhere. Each

component is wrapped as a simple python class with user defined attachment

sites, or ports. That's the "hard" part! Now mBuild can do the rest. Each component

further down the hierarchy is, again, a simple python class that describes

which piece should connect to which piece.



Ultimately, complex structures can be created with just a line or two

of code. Additionally, this approach seamlessly exposes tunable parameters within

the hierarchy so you can actually create whole families of structures simply

by adjusting a variable:



```python

import mbuild as mb

from mbuild.examples import PMPCLayer



pattern = mb.Random2DPattern(20)  # A random arrangement of 20 pieces on a 2D surface.

pmpc_layer = PMPCLayer(chain_length=20, pattern=pattern, tile_x=3, tile_y=2)

```



![Zwitterionic brushes on beta-cristobalite substrate](docs/images/pmpc.png)

### Community Recipes

Use case-specific systems can be generated via mBuild recipes.

Some users have graciously contributed recipes for particular systems, including:



* [Graphene slit pores](https://github.com/rmatsum836/Pore-Builder)

* [Nanodroplets on graphene](https://github.com/ftiet/droplet-builder)

* [Coarse-grained DNA](https://github.com/zijiewu3/mbuild_ONA)

* [Lipid bilayers](https://github.com/uppittu11/mbuild_bilayer)

* [Surface Coatings](https://github.com/daico007/surface_coatings)



### Citing mBuild



If you use this package, please cite [our paper](http://dx.doi.org/10.1007/978-981-10-1128-3_5

). The BibTeX reference is

```

@article{Klein2016mBuild,

      author = "Klein, Christoph and Sallai, János and Jones, Trevor J. and Iacovella, Christopher R. and McCabe, Clare and Cummings, Peter T.",

      title = "A Hierarchical, Component Based Approach to Screening Properties of Soft Matter",

      booktitle = "Foundations of Molecular Modeling and Simulation",

      series = "Molecular Modeling and Simulation: Applications and Perspectives",

      year = "2016",

      doi = "http://dx.doi.org/10.1007/978-981-10-1128-3_5"

}

```



### [![License](https://img.shields.io/badge/license-MIT-blue.svg)](http://opensource.org/licenses/MIT)



Various sub-portions of this library may be independently distributed under

different licenses. See those files for their specific terms.



This material is based upon work supported by the National Science Foundation under grants NSF CBET-1028374 and NSF ACI-1047828. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.