# Compare Module

## Core

```{eval-rst}
.. automodule:: polyzymd.compare.core.base
   :members:
   :undoc-members:
   :show-inheritance:
```

```{eval-rst}
.. automodule:: polyzymd.compare.core.registry
   :members:
   :undoc-members:
   :show-inheritance:
```

## Configuration

```{eval-rst}
.. automodule:: polyzymd.compare.config
   :members:
   :undoc-members:
   :show-inheritance:
```

## Settings

```{eval-rst}
.. automodule:: polyzymd.compare.settings
   :members:
   :undoc-members:
   :show-inheritance:
```

## Statistics

```{eval-rst}
.. automodule:: polyzymd.compare.statistics
   :members:
   :undoc-members:
   :show-inheritance:
```

## Comparators

### Contacts

```{eval-rst}
.. automodule:: polyzymd.compare.comparators.contacts
   :members:
   :undoc-members:
   :show-inheritance:
```

### RMSF

```{eval-rst}
.. automodule:: polyzymd.compare.comparators.rmsf
   :members:
   :undoc-members:
   :show-inheritance:
```

### Triad

```{eval-rst}
.. automodule:: polyzymd.compare.comparators.triad
   :members:
   :undoc-members:
   :show-inheritance:
```

### Distances

```{eval-rst}
.. automodule:: polyzymd.compare.comparators.distances
   :members:
   :undoc-members:
   :show-inheritance:
```

### Exposure Dynamics

```{eval-rst}
.. automodule:: polyzymd.compare.comparators.exposure
   :members:
   :undoc-members:
   :show-inheritance:
```

### Binding Free Energy

```{eval-rst}
.. automodule:: polyzymd.compare.comparators.binding_free_energy
   :members:
   :undoc-members:
   :show-inheritance:
```

### Polymer Affinity Score

```{eval-rst}
.. automodule:: polyzymd.compare.comparators.polymer_affinity
   :members:
   :undoc-members:
   :show-inheritance:
```

## Results

Common result modules live under `polyzymd.compare.results`.

Stable result families include:

- `polyzymd.compare.results.rmsf`
- `polyzymd.compare.results.triad`
- `polyzymd.compare.results.contacts`
- `polyzymd.compare.results.distances`
- `polyzymd.compare.results.secondary_structure`

```{eval-rst}
.. automodule:: polyzymd.compare.results.binding_free_energy
   :members:
   :undoc-members:
   :show-inheritance:
```

```{eval-rst}
.. automodule:: polyzymd.compare.results.exposure
   :members:
   :undoc-members:
   :show-inheritance:
```

```{eval-rst}
.. automodule:: polyzymd.compare.results.polymer_affinity
   :members:
   :undoc-members:
   :show-inheritance:
```

## Formatters

```{eval-rst}
.. automodule:: polyzymd.compare.binding_free_energy_formatters
   :members:
   :undoc-members:
   :show-inheritance:
```

```{eval-rst}
.. automodule:: polyzymd.compare.polymer_affinity_formatters
   :members:
   :undoc-members:
   :show-inheritance:
```

## Plotters

```{eval-rst}
.. automodule:: polyzymd.compare.plotters.binding_free_energy
   :members:
   :undoc-members:
   :show-inheritance:
```

```{eval-rst}
.. automodule:: polyzymd.compare.plotters.exposure
   :members:
   :undoc-members:
   :show-inheritance:
```

```{eval-rst}
.. automodule:: polyzymd.compare.plotters.polymer_affinity
   :members:
   :undoc-members:
   :show-inheritance:
```

## CLI

```{eval-rst}
.. automodule:: polyzymd.compare.cli
   :members:
   :undoc-members:
   :show-inheritance:
```