mdtraj | Python Package Wiki

Based on how often these packages appear together in public requirements.txt files on GitHub.

multiprocessing-logging	Logger for multiprocessing applications
geomm	A simple no-nonsense library for computing common geometry on macromolecular systems.
sklearn	A set of python modules for machine learning and data mining
openmm-systems	Collection of premade molecular systems for use with OpenMM
fsspec	File-system specification
wepy	Weighted Ensemble Framework
scanpy	Single-Cell Analysis in Python.
eliot-tree	Render Eliot logs as an ASCII tree
filprofiler	A memory profiler for data batch processing applications.
anndata	Annotated Data.
scipy	SciPy: Scientific Library for Python
scikit-learn	A set of python modules for machine learning and data mining
librosa	Python module for audio and music processing
joblib	Lightweight pipelining: using Python functions as pipeline jobs.
pysal	A library of spatial analysis functions.
mlxtend	Machine Learning Library Extensions
jenks	a jenkins command-line tool
pygeoprocessing	PyGeoprocessing: Geoprocessing routines for GIS
python-louvain	Louvain algorithm for community detection

Proportion of downloaded versions in the last 3 months (only versions over 1%).

pip install mdtraj==1.9.6