HTMD and moleculekit

HTMD and moleculekit are two separate Python packages that work together. Knowing which package owns which feature makes both easier to navigate.

moleculekit: structures and frames

moleculekit is the lower-level library. It handles everything that lives inside a single molecular system:

• the Molecule class - per-atom arrays, the bond graph, periodic box info, and per-frame trajectory data;

• file I/O for PDB, mmCIF/BCIF, PSF, PRMTOP, XTC, DCD, TRR, NetCDF, and others;

• atom selection (string language and boolean masks);

• geometry: alignment, distances, dihedrals, RMSD/RMSF, projections, interactions;

• system preparation: protonation, non-standard residues, mutation, missing-sidechain and partial backbone repair, segmentation;

• visualization via the built-in MolStar viewer and VMD/PyMOL bridges.

If you can do it without launching a simulation, it’s probably in moleculekit.

HTMD: campaigns of simulations

HTMD builds on top of moleculekit and adds the machinery for running and analysing many simulations at once:

• System building (htmd.builder and htmd.membranebuilder): solvating, ionising, and parameterizing systems through CHARMM, AMBER, or OpenMM; placing membranes; closing loops.

• Queue-aware simulation drivers (re-exported by htmd.ui from the jobqueues package - LocalGPUQueue, LocalCPUQueue, SlurmQueue, LsfQueue, PBSQueue): launching simulations across local GPUs or HPC queueing systems with a uniform interface.

• Adaptive sampling (htmd.adaptive): driving multi-epoch campaigns whose next starting frames are chosen by an MSM built from earlier epochs - see Adaptive sampling.

• MSM analysis (htmd.simlist, htmd.metricdata, htmd.model, htmd.kinetics, htmd.clustering): the simulation-list → projection → clustering → model → kinetics pipeline; see MSM workflow.

• HTMD-specific projections (htmd.projections.metric, htmd.projections.tica, htmd.projections.gwpca): TICA / GWPCA dimensionality reduction over the per-frame features moleculekit produces.

If it involves more than one trajectory, or a job queue, it’s in HTMD.

How they cooperate

A typical HTMD workflow imports moleculekit objects indirectly through htmd.ui, which re-exports Molecule, the moleculekit projection metrics, viewer helpers, and friends:

from htmd.ui import *

mol = Molecule("3PTB")          # moleculekit Molecule
mol.view(viewer="molstar")      # moleculekit viewer

# moleculekit projection used as input to an HTMD AdaptiveMD run
metric = MetricDistance("name CA", "resname BEN", periodic="selections")

You can import directly from either package; htmd.ui exists for convenience so a single namespace covers everything you need in an analysis script.

Where to look

• moleculekit topics (reading/writing structures, atom selection, projections, system preparation) - moleculekit docs.

• HTMD topics (building, queues, adaptive sampling, MSM construction, kinetics) - this site.