CodonTransformer

MDAnalysis — Python library for analyzing molecular dynamics trajectories and atomic coordinate data. Supports 40+ file formats (DCD, XTC, TRR, PDB, GRO, AMBER, LAMMPS). Provides RMSD, RMSF, hydrogen

2 shared topics • 1 shared operation

MDTraj — Python library for reading, writing, and analyzing molecular dynamics trajectories. Supports 20+ formats (DCD, XTC, TRR, PDB, HDF5, NetCDF, etc.) with NumPy-native arrays. Provides RMSD, RMSF

2 shared topics • 1 shared operation

NAMD — high-performance parallel molecular dynamics for large biomolecular systems. Runs on CPU clusters and GPUs with CHARMM and AMBER force fields. Supports explicit/implicit solvent, enhanced sampl

2 shared topics • 1 shared operation

Use when working with ProteinShake, a Python library for protein 3D structure datasets and benchmark tasks that can be converted to graph, point-cloud, or voxel representations and loaded into PyTorch

2 shared topics • 1 shared operation

h5py — the standard Pythonic interface to HDF5 binary data format. Provides hierarchical storage for large numerical datasets with seamless NumPy integration. Supports compression (GZIP, LZF, SZIP), c

1 shared topic • 2 shared operations