gmx_clusterByFeatures
It can be used to cluster the conformations of a molecule in a molecular dynamics trajectory using collection of features. The features could be any quantity as a function of time such as Projections of eigenvector from PCA or dihedral-PCA, distances, angles, channel radius etc.
See details at: gmx_clusterByFeatures homepage
Installation on Linux and MacOS
sudo python3 -m pip install gmx-clusterByFeaturesNo dependency on GROMACS. Install and use it.
For more details, visit download and installation section.
Usage
Command |
Function |
|---|---|
Main module to perform clustering |
|
Feature vs Feature plot to check quality of clustering |
|
Distance-matrix related calculations |
|
To visulaize/plot matrix obtained from distmat |
|
To calculate cavity/channel radius using HOLE program |
|
To calculate average and plot hole output radius file |
|
To write radius as a features for clustering |
|
To plot or write radius for clusters separately |
For more details, visit usage section.
Development Setup for conda
Following steps are for development setup. However, these steps can be used for installation using conda
# Clone the repository and setup development environment
git clone --recursive https://github.com/rjdkmr/gmx_clusterByFeatures.git
cd gmx_clusterByFeatures
conda env create -y --prefix ./venv --file environment.yaml # Create development conda environment
conda activate ./venv # Activate the environment
bash -i scripts/build_dev_setup_conda.sh # all build and setup steps are in this script1 maintainer
Metadata
1 maintainer
Release files for gmx-clusterByFeatures 0.1.30
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
Total release size: 76.3 MB
Release files / gmx_clusterbyfeatures-0.1.30-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
| Download URL | gmx_clusterbyfeatures-0.1.30-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 15.3 MB |
| Tags | CPython 3.13 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
|
SHA-256 checksum How to use checksums |
a99f305ed8027cfa12b22688ba8e61ccbe030524ee9e08c9e7f9284efddebdea
|
|
BLAKE2b-256 checksum How to use checksums |
6ffe1bb01871af848485987a636e9f402aceb10108578166e8f0910308e7fd8b
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.11.15
|
Release files / gmx_clusterbyfeatures-0.1.30-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
| Download URL | gmx_clusterbyfeatures-0.1.30-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 15.3 MB |
| Tags | CPython 3.12 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
|
SHA-256 checksum How to use checksums |
5a08f81612f6d29d8179a0164e6e87e69a5df141c454d4a5497aa7db33684d06
|
|
BLAKE2b-256 checksum How to use checksums |
fd24545adb58dd12b24bd04808a451c175e1b8712ce50356eb7ef290e0a41536
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.11.15
|
Release files / gmx_clusterbyfeatures-0.1.30-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
| Download URL | gmx_clusterbyfeatures-0.1.30-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 15.3 MB |
| Tags | CPython 3.11 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
|
SHA-256 checksum How to use checksums |
2ed9aa73d15be91d616556fdac8e8a33751425259bf5233f10f701863e99e45a
|
|
BLAKE2b-256 checksum How to use checksums |
a885c3e954c39319256a832286d2a27f9d21a4851c9f65e4cbbdd351e2d52927
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.11.15
|
Release files / gmx_clusterbyfeatures-0.1.30-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
| Download URL | gmx_clusterbyfeatures-0.1.30-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 15.2 MB |
| Tags | CPython 3.10 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
|
SHA-256 checksum How to use checksums |
dd65f3fe4805cc09c48d8ed283a7d1789343117c3d3458391d75be8d35c10915
|
|
BLAKE2b-256 checksum How to use checksums |
84775a823ff2d77d026aa1cdf0450ee128811d19be4acfacd8bb40eb63775b86
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.11.15
|
Release files / gmx_clusterbyfeatures-0.1.30-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
| Download URL | gmx_clusterbyfeatures-0.1.30-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 15.2 MB |
| Tags | CPython 3.9 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
|
SHA-256 checksum How to use checksums |
e3a11ef6957f1080d91b6a7b58751e05506eecdb08156dc7fffd8581d098d0c0
|
|
BLAKE2b-256 checksum How to use checksums |
a848084a6ae08654fbef82e1d0719554728369ebd5fae3670336811555526e69
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.11.15
|
Security for gmx-clusterByFeatures 0.1.30
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
