Installation

PyPI

The easiest way to install AMOFMS from the Python Package Index. You can do this using pip:

pip install amofms

Alternatively, you can also install the in-development version with:

pip install https://github.com/JiangGroup/AMOFMS/archive/main.zip

Dependencies

AMOFMS uses MDAnalysis for molecular dynamics analysis, NumPy for numerical computations, and SciPy for additional scientific computing tasks.

The following python dependencies are required for AMOFMS:

• lipyphilic==0.10.0

• matplotlib==3.4.3

• MDAnalysis==2.7.0

• networkx==3.2

• numpy==1.22.3

• pexpect==4.9.0

• Pillow==10.2.0

• pyswarms==1.3.0

• rdkit==2023.9.4

• Requests==2.31.0

• scikit_learn==1.3.2

• scipy==1.8.1

• seaborn==0.13.2

• scikit-image

• torch==2.1.2

• torch_geometric==2.4.0

• tqdm==4.66.1

• tensorboard

• openbabel

As mentioned above, the simplest way to install these packages, along with AMOFMS, is with Conda. However, it is also possible to install MDAnalysis, NumPy, and SciPy using pip, or from source. See the MDAnalysis, NumPy, and SciPy installation instructions for further information.

Note

When installing OpenBabel through PyPI, please note that there may be issues. You can install OpenBabel via conda with the following conda command:

conda install -c conda-forge openbabel

AMOFMS uses GROMACS for molecular dynamics simulations. When conducting simulations with AMOFMS, ensure that you have installed GROMACS version 2019.6 or later. Earlier GROMACS versions have not been tested. We highly recommend using GROMACS version 2021.4 for optimal performance.