> ## Documentation Index
> Fetch the complete documentation index at: https://bagel.softnanolab.com/llms.txt
> Use this file to discover all available pages before exploring further.

# SecondaryStructureEnergy

> Energy that drives the secondary structure of the selected residues to a given type. Calculated by finding the fraction of selected residues with the wrong secondary structure. Secondary structure types include alpha-helix, beta-sheet, and coil.

## Definition

The secondary structure energy is the fraction of selected residues whose assigned secondary structure does not match the target.

$$
E_{\mathrm{SS}} = \frac{1}{N_G} \sum_{\alpha \in G} \mathbb{I}[\mathrm{SS}_\alpha \neq \mathrm{SS}_{\mathrm{target}}]
$$

* $\mathbb{I}$ is the indicator function (1 if the condition is true, 0 otherwise)
* $\mathrm{SS}_\alpha$ is the secondary structure assignment for residue $\alpha$
* $\mathrm{SS}_{\mathrm{target}}$ is the target secondary structure (alpha-helix, beta-sheet, or coil)
* $N_G$ is the number of residues in the group $G$

## Parameters

<ResponseField name="oracle" type="Oracle" required>
  The oracle to use for the energy term.
</ResponseField>

<ResponseField name="residues" type="list[Residue]" required>
  Which residues to include in the calculation.
</ResponseField>

<ResponseField name="target_secondary_structure" type="str" required>
  Which secondary structure type to drive towards. Options are 'alpha-helix', 'beta-sheet', or 'coil'.
</ResponseField>

<ResponseField name="inheritable" type="bool" default="True">
  If a new residue is added next to a residue included in this energy term, this dictates whether that new residue could then be added to this energy term.
</ResponseField>

<ResponseField name="weight" type="float" default="1.0">
  The weight of the energy term.
</ResponseField>

<ResponseField name="name" type="str | None" default="None">
  Optional name to append to the energy term name.
</ResponseField>

## Methods

### compute

**Parameters**

<ResponseField name="oracles_result" type="OraclesResultDict" required />

## Example

```python theme={null}
import numpy as np
import bagel as bg

# Create a 190-residue chain
sequence = np.random.choice(list(bg.constants.aa_dict.keys()), size=190)
residues = [bg.Residue(name=aa, chain_ID="A", index=i, mutable=True) for i, aa in enumerate(sequence)]

# Create the folding oracle
esmfold = bg.oracles.ESMFold()

# Define groups of residues that should form beta-sheets
groups = [residues[(i * 50) + 5 : (i * 50) + 35] for i in range(4)]

secondary_structure = bg.energies.SecondaryStructureEnergy(
    oracle=esmfold,
    residues=groups,
    target_secondary_structure="beta-sheet",
    weight=1.0,
)

# Add to a state
state = bg.State(
    chains=[bg.Chain(residues)],
    energy_terms=[secondary_structure],
    name="my_state",
)
```