Struct Interactor

pub struct Interactor {
    pub passive: HashSet<i16>,
    /* private fields */
}

Represents an interactor in a molecular system.

This struct contains information about a specific interactor, including its identification, residues, atoms, target interactions, and various parameters for interaction calculations.

Fields

passive: HashSet<i16>

Set of passive residue numbers.

Implementations

impl Interactor

pub fn new(id: u16) -> Self

Creates a new Interactor instance with default values.

This method initializes a new Interactor with the given ID and default values for all other fields. It’s marked with #[allow(clippy::too_many_arguments)] to suppress warnings about the number of fields, even though this constructor doesn’t actually take multiple arguments.

Arguments

• id - A u16 that specifies the unique identifier for the new Interactor.

Returns

A new Interactor instance with the specified ID and default values for all other fields.

pub fn is_valid(&self) -> Result<bool, &str>

Checks if the Interactor is in a valid state.

This method performs two validity checks:

1. Ensures that the target set is not empty.
2. Verifies that there’s no overlap between active and passive residues.

Returns

• Ok(true) if the Interactor is valid.
• Err(&str) with an error message if any validity check fails.

pub fn set_passive_from_active(&mut self)

Sets passive residues based on the active residues and their neighboring residues.

This method performs the following steps:

1. Opens the PDB file specified in the structure field.
2. Retrieves the residues corresponding to the active residues.
3. Performs a neighbor search to find residues within 5.0 Å of the active residues.
4. Adds these neighboring residues to the passive set.

Panics

This method will panic if:

• The structure field is None.
• There’s an error opening or parsing the PDB file.

Side Effects

This method modifies the passive set of the Interactor, adding new residues based on the neighbor search results.

Dependencies

This method relies on external functions from the structure module:

• structure::get_residues
• structure::neighbor_search
• structure::load_pdb

pub fn set_surface_as_passive(&mut self)

Sets surface residues as passive based on their solvent accessible surface area (SASA).

This method performs the following steps:

1. Opens the PDB file specified in the structure field.
2. Calculates the SASA for all residues in the structure.
3. Identifies surface residues (those with relative SASA > 0.7) on the same chain as the interactor.
4. Adds these surface residues to the passive set.

Panics

This method will panic if:

• The structure field is None.
• There’s an error opening or parsing the PDB file.

Side Effects

This method modifies the passive set of the Interactor, adding new residues based on the SASA calculation results.

Dependencies

This method relies on external functions from the sasa and structure modules:

• sasa::calculate_sasa
• structure::load_pdb

Note

The threshold for considering a residue as “surface” is set to 0.7 relative SASA. This value may need to be adjusted based on specific requirements.

pub fn remove_buried_residues(&mut self)

Removes buried residues from both active and passive sets based on solvent accessible surface area (SASA).

This method performs the following steps:

1. Opens the PDB file specified in the structure field.
2. Calculates the SASA for all residues in the structure.
3. Identifies buried residues (those with relative SASA below a certain cutoff) on the same chain as the interactor.
4. Removes these buried residues from both the active and passive sets.

Panics

This method will panic if:

• The structure field is None.
• There’s an error opening or parsing the PDB file.

Side Effects

This method modifies both the active and passive sets of the Interactor, removing residues based on the SASA calculation results.

Dependencies

This method relies on external functions from the sasa and structure module:

• sasa::calculate_sasa
• structure::load_pdb

Note

The default threshold for considering a residue as “buried” is set to 0.7 relative SASA. This can be customized by setting the filter_buried_cutoff field of the Interactor.

pub fn id(&self) -> u16

Returns the unique identifier of the Interactor.

Returns

A u16 representing the ID of the Interactor.

pub fn chain(&self) -> &str

Returns the chain identifier of the Interactor.

Returns

A string slice (&str) representing the chain of the Interactor.

pub fn active(&self) -> &HashSet<i16>

Returns a reference to the set of active residues.

Returns

A reference to a HashSet<i16> containing the active residue numbers.

pub fn active_atoms(&self) -> &Option<Vec<String>>

Returns a reference to a set of active atoms strings.

Returns

A reference to a Option<Vec<String>> containing active atom names.

pub fn passive(&self) -> &HashSet<i16>

Returns a reference to the set of passive residues.

Returns

A reference to a HashSet<i16> containing the passive residue numbers.

pub fn passive_atoms(&self) -> &Option<Vec<String>>

Returns a reference to a set of passive atoms strings.

Returns

A reference to a Option<Vec<String>> containing passive atom names.

pub fn wildcard(&self) -> &str

Returns the wildcard string associated with this Interactor.

Returns

• If a wildcard is set, returns a string slice (&str) containing the wildcard value.
• If no wildcard is set, returns an empty string slice.

Notes

• This method provides read-only access to the wildcard value.
• The wildcard is typically used to represent any residue or atom in certain contexts.

pub fn target(&self) -> &HashSet<u16>

Returns a reference to the set of target interactor IDs.

Returns

A reference to a HashSet<u16> containing the IDs of target interactors.

pub fn structure(&self) -> &str

Returns the structure file path of the Interactor.

Returns

A string slice (&str) representing the structure file path, or an empty string if not set.

pub fn set_structure(&mut self, structure: &str)

Sets the structure file path for the Interactor.

Arguments

• structure - A string slice containing the path to the structure file.

pub fn load_structure( &mut self, structure_path: &str, ) -> Result<(), Vec<PDBError>>

Loads a PDB structure from the given path and stores it.

Returns

Ok(()) on success, or Vec<PDBError> if loading failed.

pub fn pdb(&self) -> &Option<PDB>

Returns a reference to the stored PDB structure, if any.

Returns

Reference to an Option<PDB> containing the structure.

pub fn set_pdb(&mut self, pdb: PDB)

Stores a PDB structure in the Interactor.

Arguments

• pdb - The PDB structure to store

pub fn set_chain(&mut self, chain: &str)

Sets the chain identifier for the Interactor.

Arguments

• chain - A string slice containing the chain identifier.

pub fn set_active(&mut self, active: Vec<i16>)

Sets the active residues for the Interactor.

Arguments

• active - A vector of i16 values representing the active residue numbers.

pub fn set_passive(&mut self, passive: Vec<i16>)

Sets the passive residues for the Interactor.

Arguments

• passive - A vector of i16 values representing the passive residue numbers.

pub fn set_wildcard(&mut self, wildcard: &str)

Sets the wildcard string for this Interactor.

This method allows you to set or update the wildcard value associated with the Interactor.

Arguments

• wildcard - A string slice (&str) that specifies the new wildcard value.

Notes

• This method will overwrite any previously set wildcard value.
• The wildcard is stored as an owned String, so the input &str is cloned.
• An empty string is a valid wildcard value, though its interpretation may depend on the context.
• The wildcard is typically used to represent any residue or atom in certain contexts.

pub fn set_target_distance(&mut self, distance: f64)

Sets the target distance for the Interactor.

Arguments

• distance - A f64 value representing the target distance.

pub fn set_lower_margin(&mut self, margin: f64)

Sets the lower margin for the Interactor.

Arguments

• margin - A f64 value representing the lower margin.

pub fn set_upper_margin(&mut self, margin: f64)

Sets the upper margin for the Interactor.

Arguments

• margin - A f64 value representing the upper margin.

pub fn passive_from_active(&self) -> bool

Returns whether passive residues should be derived from active residues.

Returns

A bool indicating if passive residues should be derived from active ones.

pub fn surface_as_passive(&self) -> bool

Returns whether surface residues should be treated as passive.

Returns

A bool indicating if surface residues should be treated as passive.

pub fn filter_buried(&self) -> bool

Returns whether buried residues should be filtered.

Returns

A bool indicating if buried residues should be filtered.

pub fn set_filter_buried_cutoff(&mut self, cutoff: f64)

Sets whether passive residues should be derived from active residues.

Arguments

• cutoff - A f64 value representing the cutoff to filter buried residues.

pub fn add_target(&mut self, target: u16)

Adds a target interactor ID.

Arguments

• target - A u16 value representing the ID of the target interactor to add.

pub fn set_active_atoms(&mut self, atoms: Vec<String>)

Sets the active atoms for the Interactor.

Arguments

• atoms - A vector of Strings representing the active atom names.

pub fn set_passive_atoms(&mut self, atoms: Vec<String>)

Sets the passive atoms for the Interactor.

Arguments

• atoms - A vector of Strings representing the passive atom names.

pub fn create_block(&self, passive_res: Vec<PassiveResidues<'_>>) -> String

Creates a block of restraints for the Interactor.

This method generates a string representation of restraints for the Interactor, based on its active residues and the provided target residues.

Arguments

• target_res - A vector of tuples, each containing a chain identifier (&str) and a residue number (&i16) for the target residues.

Returns

A String containing the formatted block of restraints.

pub fn make_pml_string(&self, passive_res: Vec<PassiveResidues<'_>>) -> String

Trait Implementations

impl Clone for Interactor

fn clone(&self) -> Interactor

Returns a duplicate of the value.

const fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Interactor

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for Interactor

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.