PydSEAMSlib: python bindings for d-SEAMS#
d-SEAMS (Deferred Structural Elucidation Analysis for
Molecular Simulations) is a tool for the analysis of molecular dynamics
trajectories which is specifically able to qualitatively classify ice structures
in both strong-confinement and bulk systems Goswami et al. [IDX_GGS20]. PydSEAMSlib makes d-SEAMS user
friendly and accessible to the larger Scientific Python ecosystem.
Note
Historically, in 2023, the project was initiated under the name PySeams, which could not be registered on PyPI due to naming similarities, so the project in 2024 switched to its current name, PydSEAMSlib.
Installation#
git clone https://github.com/d-SEAMS/PydSEAMSlib.git
cd PydSEAMSlib
We provide a conda-lock environment:
micromamba create -f conda-lock.yml -n pyseamsdev
micromamba activate pyseamsdev
Which can then be used directly for a pip install:
# Pure bindings
pip install .
# For ASE integration
pip install .[adapters]
# With tests
pip install .[testing]
# Everything
pip install .[testing,adapters,docs]
Development local builds can be prepared via meson:
meson setup bbdir --prefix=$CONDA_PREFIX --libdir=lib
meson compile install bbdir
docker installation for emulated hardware#
For arm64v8 machines, it may be easier to use the following docker image.
git clone https://github.com/RuhiRG/D-seams-docker-recipes.git
docker run -it dseamsdockerrecipes:latest /usr/bin/bash
git clone https://github.com/d-SEAMS/PydSEAMSlib.git
cd PydSEAMSlib
Subsequently, the earlier steps can be followed.
License#
MIT. For more details, including contribution guidelines visit the GitHub repo.
References#
Rohit Goswami, Amrita Goswami, and Jayant K. Singh. D-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations. Journal of Chemical Information and Modeling, 60(4):2169–2177, April 2020. doi:10.1021/acs.jcim.0c00031.
Documentation#
API Documentation