# API reference

Auto-generated module documentation, grouped by topic.

## Core

```{toctree}
:maxdepth: 1

moleculekit.molecule
moleculekit.readers
moleculekit.writers
moleculekit.residues
moleculekit.periodictable
moleculekit.config
```

## Atom selection

```{toctree}
:maxdepth: 1

moleculekit.atomselect.atomselect
moleculekit.atomselect.analyze
moleculekit.atomselect
moleculekit.atomselect_utils
```

## Geometry and analysis

```{toctree}
:maxdepth: 1

moleculekit.align
moleculekit.distance
moleculekit.dihedral
moleculekit.util
moleculekit.bondguesser
moleculekit.unitcell
moleculekit.wrapping
```

## Projections

```{toctree}
:maxdepth: 1

moleculekit.projections.metriccoordinate
moleculekit.projections.metricdihedral
moleculekit.projections.metricdistance
moleculekit.projections.metricfluctuation
moleculekit.projections.metricgyration
moleculekit.projections.metricplumed2
moleculekit.projections.metricrmsd
moleculekit.projections.metricsasa
moleculekit.projections.metricsecondarystructure
moleculekit.projections.metricshell
moleculekit.projections.metricsphericalcoordinate
moleculekit.projections.metrictmscore
moleculekit.projections.projection
moleculekit.projections
moleculekit.projections.util
```

## Interactions

```{toctree}
:maxdepth: 1

moleculekit.interactions.interactions
moleculekit.interactions.hbonds
moleculekit.interactions.pipi
moleculekit.interactions.cationpi
moleculekit.interactions.sigmahole
moleculekit.interactions
```

## Toolkit conversion

```{toctree}
:maxdepth: 1

moleculekit.rdkittools
```

## File formats

```{toctree}
:maxdepth: 1

moleculekit.pdbx.reader.PdbxReader
moleculekit.pdbx.writer.PdbxWriter
moleculekit.pdbx.reader.BinaryCifReader
moleculekit.pdbx.writer.BinaryCifWriter
moleculekit.pdbx.reader.PdbxContainers
moleculekit.pdbx.reader.PdbxParser
moleculekit.pdbx
moleculekit.pdbx.reader
moleculekit.pdbx.writer
moleculekit.fileformats.netcdf
moleculekit.fileformats
moleculekit.fileformats.utils
moleculekit.binpos
moleculekit.dcd
moleculekit.trr
moleculekit.xtc
```

## Tools

```{toctree}
:maxdepth: 1

moleculekit.tools.preparation
moleculekit.tools.nonstandard_residues
moleculekit.tools.preparation_customres
moleculekit.tools.mutate
moleculekit.tools.modelling
moleculekit.tools.autosegment
moleculekit.tools.backbone
moleculekit.tools.atomtyper
moleculekit.tools.detect
moleculekit.tools.docking
moleculekit.tools.graphalignment
moleculekit.tools.hhblitsprofile
moleculekit.tools.moleculechecks
moleculekit.tools.sequencestructuralalignment
moleculekit.tools.voxeldescriptors
moleculekit.tools.crystalpacking
moleculekit.tools.obabel_tools
moleculekit.tools.obabel_tools.obabel_cli
moleculekit.tools
```

## Visualization

```{toctree}
:maxdepth: 1

moleculekit.viewer
moleculekit.viewer.molstar
moleculekit.viewer.molstar.registry
moleculekit.viewer.molstar.serialize
moleculekit.viewer.molstar.server
moleculekit.vmdviewer
moleculekit.vmdgraphics
moleculekit.pymolgraphics
moleculekit.representations
```

## External resources

```{toctree}
:maxdepth: 1

moleculekit.rcsb
moleculekit.opm
```

## Small molecules

```{toctree}
:maxdepth: 1

moleculekit.smallmol
moleculekit.smallmol.smallmol
moleculekit.smallmol.smallmolcdp
moleculekit.smallmol.smallmollib
moleculekit.smallmol.util
```

## Internals and low-level modules

```{toctree}
:maxdepth: 1

moleculekit
moleculekit.cython_utils
moleculekit.bondguesser_utils
moleculekit.distance_utils
moleculekit.occupancy_utils
moleculekit.kdtree
moleculekit.openmmtools
moleculekit.tmalign
moleculekit.ply
moleculekit.ply.lex
moleculekit.ply.yacc
```