Module ops 

High-level operations that clean, repair, solvate, and otherwise prepare structures.

This module groups together the public entry points for structure processing: cleaning, hydrogen addition, repairs, solvation, coordinate transforms, and topology reconstruction. Each submodule exposes a cohesive API and shares a common error type so downstream consumers can compose workflows easily.

Structs

CleanConfig

Configuration switches describing which components should be removed during cleaning.

HydroConfig

Parameters controlling hydrogen addition behavior.

SolvateConfig

Configuration parameters controlling solvent placement and ionization.

TopologyBuilder

Builder responsible for creating Topology objects from a Structure.

Transform

Collection of geometric transformation operations for structures.

Enums

Anion

Supported anion species for ionic replacement.

Cation

Supported cation species for ionic replacement.

Error

Error conditions surfaced by the operations layer.

HisStrategy

Strategies for selecting neutral histidine tautomers.

Functions

add_hydrogens

Adds hydrogens to all standard residues in-place, updating protonation states when needed.

clean_structure

Applies the cleaning rules to a mutable structure in-place.

repair_structure

Repairs every standard residue in a structure by invoking the internal repair logic.

solvate_structure

Builds a solvent box, translates the solute to the padded origin, and inserts ions.