Struct Structure 

pub struct Structure { /* private fields */ }

A crystal structure.

Implementations

impl Structure

pub fn bond_graph(&self) -> Result<BondGraph, Error>

Perceives bonds with the default rules.

Errors

Returns the errors of perceive_bonds.

impl Structure

pub fn as_p1(&self) -> Result<Self, Error>

Returns this structure as an explicit P1 structure.

A structure that is already P1 is cloned. Otherwise the cell is expanded with its operations, the operations are dropped and the original site metadata (occupancy, displacement parameters, charge and props) is kept. Structure::supercell uses this so a supercell of a symmetric structure contains the whole cell, not only the asymmetric unit.

Errors

Returns the errors of the P1 expansion or of the rebuilt sites.

impl Structure

pub fn p1(&self) -> Result<P1Cell, Error>

Expands this structure to P1 with the default tolerance.

Errors

Returns the errors of P1Cell::expand.

impl Structure

pub fn cell_contents(&self) -> Vec<(String, f64)>

Cell contents as (element, occupancy sum) in first-appearance order, counted on the whole cell (the P1 expansion when the structure has symmetry operations).

pub fn formula(&self) -> String

Formula string, for example Fe2 O3 or C0.5.

pub fn cell_mass(&self) -> Result<f64, Error>

Mass of the whole cell contents in unified atomic mass units.

Errors

Returns an error if a site element is missing from the element table.

pub fn molar_mass(&self) -> Result<f64, Error>

Molar mass of the cell contents in g/mol.

Errors

Returns the errors of Structure::cell_mass.

pub fn density(&self) -> Result<f64, Error>

Density in g/cm3 of the whole cell (the P1 expansion when the structure has symmetry operations).

Errors

Returns the errors of Structure::cell_mass.

pub fn z(&self) -> u32

Number of formula units in the cell: the greatest common divisor of the element counts of the whole cell, or 1 when a count is not an integer.

pub fn total_charge(&self) -> f64

Sum of occupancy * charge over the atoms of the whole cell.

pub fn charge_balance(&self) -> f64

Charge balance, the same as Structure::total_charge.

impl Structure

pub fn name(&self) -> &str

Structure name.

pub fn lattice(&self) -> &Lattice

Unit cell.

pub fn hall(&self) -> &str

Hall symbol of the space group; P 1 for a P1 structure.

pub fn sites(&self) -> &[Site]

Asymmetric-unit sites.

pub fn operations(&self) -> &[SymOp]

Explicit symmetry operations; empty means identity only.

pub fn explicit_bonds(&self) -> &[ExplicitBond]

User bonds and removals applied after perception.

pub fn topology_bonds(&self) -> &[TopologyBond]

Topology edges, kept separate from chemical bonds.

pub fn metadata(&self) -> &BTreeMap<String, Value>

Open structure metadata.

pub fn is_p1(&self) -> bool

Whether the structure is P1: the Hall symbol is P 1 (or empty) and every operation is the identity. A CIF may carry an explicit operation loop without a space-group symbol; such a file is not P1 even though its Hall symbol defaults to P 1.

pub fn cart_sites(&self) -> Vec<[f64; 3]>

Cartesian coordinates of the asymmetric sites.

pub fn warnings(&self) -> Vec<StructureWarning>

Structured warnings collected from the structure metadata.

pub fn summary(&self) -> Result<StructureSummary, Error>

Summary used by the CLI, Python and WASM info surfaces.

Errors

Returns the errors of Structure::density.

pub fn with_name(self, name: impl Into<String>) -> Self

Copy with a new name.

pub fn with_lattice(self, lattice: Lattice) -> Self

Copy with a new lattice.

pub fn with_site(self, site: Site) -> Self

Copy with one more site.

pub fn molecule( name: impl Into<String>, points: &[(String, [f64; 3])], padding: f64, ) -> Result<Self, Error>

A non-periodic molecule in a padded P1 box.

Errors

Returns Error::InvalidInput for no points, a non-positive padding, or a point whose element is unknown.

impl Structure

pub fn to_document(&self) -> StructureDocument

Wraps this structure in the versioned document envelope.

impl Structure

pub fn supercell(&self, na: u32, nb: u32, nc: u32) -> Result<Self, Error>

Builds an na x nb x nc supercell as a P1 structure.

Errors

Returns Error::InvalidInput for zero repeats, or Error::LimitExceeded when the estimate exceeds the hard limit.

pub fn supercell_with_limits( &self, na: u32, nb: u32, nc: u32, limits: &Limits, ) -> Result<Self, Error>

Builds an na x nb x nc supercell with an explicit limits profile.

Errors

Returns Error::InvalidInput for zero repeats, or Error::LimitExceeded when the estimate exceeds the profile’s hard limit.

pub fn supercell_matrix(&self, p: [[f64; 3]; 3]) -> Result<Self, Error>

Builds a supercell from a positive integer transformation matrix.

Rows of p are the new vectors in units of the old ones.

Errors

Returns Error::InvalidInput for non-integer, singular or negative determinant matrices, or Error::LimitExceeded for a refused size.

pub fn supercell_matrix_with_limits( &self, p: [[f64; 3]; 3], limits: &Limits, ) -> Result<Self, Error>

Builds a supercell with an explicit limits profile.

Errors

Returns Error::InvalidInput for non-integer, singular or negative determinant matrices, or Error::LimitExceeded for a refused size.

pub fn origin_shift(&self, delta: [f64; 3]) -> Result<Self, Error>

Shifts the origin by a fractional vector and rewraps the sites.

Errors

Returns Error::InvalidInput for non-finite shifts.

impl Structure

pub fn finite_cell(&self, tolerance: f64) -> Result<Self, Error>

Atoms of one finite cell, including images on faces, edges and corners.

Errors

Returns Error::InvalidInput for a negative tolerance.

Trait Implementations

impl Clone for Structure

fn clone(&self) -> Self

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Structure

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for Structure

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

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl PartialEq for Structure

fn eq(&self, other: &Self) -> bool

Equality operator ==.

fn ne(&self, other: &Rhs) -> bool

Inequality operator !=.

impl Serialize for Structure

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl StructuralPartialEq for Structure