Package Recipe 'netmd'

recipe netmd

NetMD is a computational method for identifying consensus behavior across multiple molecular dynamics simulations.

Homepage:: https://github.com/mazzalab/NetMD
Documentation:: https://mazzalab.github.io/NetMD
License:: MIT / MIT
Recipe:: /netmd/meta.yaml

Using Graph-based Embeddings and Dynamic Time Warping, *NetMD* aligns trajectories that may be temporally out of sync and pinpoints the replicas that most faithfully represent the overall ensemble behavior. This enables consistent comparisons across simulations and supports reliable characterization of system variants, making it easier to detect shared patterns and reduce the influence of outliers or simulation artifacts.

package netmd¶

Versions:

1.0.3-0, 1.0.2-0, 1.0.1-0, 1.0.0-0

Depends:

on colorama
on decorator 5.1.*
on gensim >=4.0.0
on h5py
on hdf5
on ipykernel
on matplotlib-base
on nbformat >=4.2.0
on networkx >=3.3
on numpy >=1.22
on pandas >=1.2.0
on plotly
on pygsp
on python >=3.10,<=3.12.8
on python-levenshtein
on python-louvain
on pyyaml
on ruptures
on scikit-learn
on scipy <1.13
on tqdm
on tslearn

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install netmd

to add into an existing workspace instead, run:

pixi add netmd

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install netmd

Alternatively, to install into a new environment, run:

conda create -n envname netmd

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/netmd:<tag>

(see netmd/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/netmd/README.html)