# API reference

Auto-generated module documentation, grouped by topic. The RST stubs in this directory are produced by `sphinx-apidoc` at build time (`make rst`); they cover every public symbol in the `htmd` package.

## Top-level entry points

```{toctree}
:maxdepth: 1

htmd.ui
htmd.simlist
htmd.units
htmd.util
htmd.home
htmd.config
```

## System building

```{toctree}
:maxdepth: 1

htmd.builder
htmd.builder.builder
htmd.builder.charmm
htmd.builder.amber
htmd.builder.openmm
htmd.builder.solvate
htmd.builder.ionize
htmd.builder.loopmodeler
htmd.builder.nonstandard
```

## Membrane building

```{toctree}
:maxdepth: 1

htmd.membranebuilder
htmd.membranebuilder.build_membrane
htmd.membranebuilder.globalminimization
htmd.membranebuilder.ljfluid
htmd.membranebuilder.ringpenetration
```

## Adaptive sampling

```{toctree}
:maxdepth: 1

htmd.adaptive
htmd.adaptive.adaptive
htmd.adaptive.adaptiverun
htmd.adaptive.adaptivegoal
htmd.adaptive.adaptivegoaleg
htmd.adaptive.adaptivebandit
htmd.adaptive.util
```

## Projections (HTMD-specific)

```{toctree}
:maxdepth: 1

htmd.projections
htmd.projections.metric
htmd.projections.tica
htmd.projections.gwpca
htmd.projections.kmeanstri
```

## Clustering

```{toctree}
:maxdepth: 1

htmd.clustering
htmd.clustering.kcenters
htmd.clustering.regular
```

## MSM analysis

```{toctree}
:maxdepth: 1

htmd.metricdata
htmd.metricdatagenerator
htmd.model
htmd.kinetics
htmd.mutualinformation
htmd.pathplanning
```

## Docking

```{toctree}
:maxdepth: 1

htmd.dock
```

## Utilities / internal

```{toctree}
:maxdepth: 1

htmd.decorators
htmd.latest
htmd.license
htmd.parallelprogress
htmd.session
htmd.versionwarnings
```

```{toctree}
:hidden:

htmd
```