recipe netmd

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

Homepage:

https://github.com/mazzalab/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:

1.0.0-0

depends colorama:

depends decorator:

5.1.*

depends gensim:

>=4.0.0

depends h5py:

depends hdf5:

depends ipykernel:

depends matplotlib-base:

depends nbformat:

>=4.2.0

depends networkx:

>=3.3

depends numpy:

>=1.22

depends pandas:

>=1.2.0

depends plotly:

depends pygsp:

depends python:

>=3.10,<=3.12.8

depends python-levenshtein:

depends python-louvain:

depends pyyaml:

depends ruptures:

depends scikit-learn:

depends scipy:

<1.13

depends tqdm:

depends tslearn:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install netmd

and update with::

   mamba update netmd

To create a new environment, run:

mamba create --name myenvname netmd

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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