Struct ReadOptions 

pub struct ReadOptions {
    pub format: Format,
    pub mode: ParseMode,
    pub only_first_model: bool,
    pub only_atomic_coords: bool,
    pub perception: Perception,
    pub discard_hydrogens: bool,
    pub missing_element_policy: MissingElementPolicy,
    pub occupancy_policy: OccupancyPolicy,
    pub ambiguous_residue_boundary_policy: AmbiguousResidueBoundaryPolicy,
    pub limits: Limits,
    pub categories: CategoryFilter,
    pub input_digest: InputDigest,
}

What a read should and should not bother doing.

Fields

format: Format

Which format, or automatic detection.

mode: ParseMode

How much irregularity to tolerate.

only_first_model: bool

Read only the first model.

only_atomic_coords: bool

Read coordinates and skip everything else.

perception: Perception

Skip the perception pass that follows a read: inferred bonds, standard component annotation and secondary-structure assignment. The parse and everything the file itself records are unaffected; only what a reader would otherwise compute from the coordinates is left out.

discard_hydrogens: bool

Drop hydrogens while reading.

missing_element_policy: MissingElementPolicy

What to do when a row does not declare a valid element.

occupancy_policy: OccupancyPolicy

What to do when a recorded occupancy lies outside zero to one.

ambiguous_residue_boundary_policy: AmbiguousResidueBoundaryPolicy

What to do when mmCIF residue identifiers do not define a boundary.

limits: Limits

Ceilings that apply while reading.

categories: CategoryFilter

Which optional categories or records to read.

input_digest: InputDigest

Whether to record the SHA-256 of the bytes parsed in the structure’s entry metadata; only a result certified as computed from exactly these bytes needs it.

Implementations

impl ReadOptions

pub fn new() -> ReadOptions

Options that read everything, tolerating what the archive contains.

pub const fn format(self, format: Format) -> ReadOptions

Sets the format.

pub const fn mode(self, mode: ParseMode) -> ReadOptions

Sets how much irregularity to tolerate.

pub const fn only_first_model(self, only: bool) -> ReadOptions

Reads only the first model.

pub const fn only_atomic_coords(self, only: bool) -> ReadOptions

Reads coordinates and skips everything else.

pub const fn perceive(self, perceive: bool) -> ReadOptions

Chooses whether the perception pass runs after the parse (it does by default).

Passing false returns the structure as the file states it: file bonds and deposited secondary structure are kept, nothing is inferred from geometry.

pub const fn missing_element_policy( self, policy: MissingElementPolicy, ) -> ReadOptions

Selects an explicit policy for missing or invalid element fields.

pub const fn occupancy_policy(self, policy: OccupancyPolicy) -> ReadOptions

Selects the policy for occupancies outside zero to one.

pub const fn ambiguous_residue_boundary_policy( self, policy: AmbiguousResidueBoundaryPolicy, ) -> ReadOptions

Selects an explicit policy for ambiguous mmCIF residue boundaries.

pub const fn discard_hydrogens(self, discard: bool) -> ReadOptions

Drops hydrogens while reading.

pub fn categories(self, categories: CategoryFilter) -> ReadOptions

Restricts which optional categories (mmCIF/BinaryCIF) or records (PDB) are read. Names the structure cannot be built without are always read.

pub const fn digest_input(self, digest: bool) -> ReadOptions

Records the SHA-256 of the bytes parsed, so a result can be tied to them.

pub const fn limits(self, limits: Limits) -> ReadOptions

Sets the ceilings that apply while reading.

pub fn finish( &self, structure: Structure, findings: impl IntoIterator<Item = Diagnostic>, ) -> Result<(Structure, Vec<Diagnostic>), Vec<Diagnostic>>

Finishes a read under this option set.

Errors

Returns the ordered findings when at least one finding is an error under the selected parse mode.

Trait Implementations

impl Clone for ReadOptions

fn clone(&self) -> ReadOptions

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ReadOptions

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

Formats the value using the given formatter.

impl Default for ReadOptions

fn default() -> ReadOptions

Returns the “default value” for a type.