Struct MolGraph 

pub struct MolGraph { /* private fields */ }

A dynamic molecular graph supporting ergonomic CRUD for atoms, bonds, angles, and dihedrals.

Implementations

impl MolGraph

pub fn new() -> MolGraph

Create an empty molecular graph.

pub fn add_atom(&mut self, atom: Atom) -> AtomId

Insert an atom, returning its stable handle.

pub fn remove_atom(&mut self, id: AtomId) -> Result<Atom, MolRsError>

Remove an atom and all incident bonds / angles / dihedrals.

pub fn get_atom(&self, id: AtomId) -> Result<&Atom, MolRsError>

Get a reference to an atom.

pub fn get_atom_mut(&mut self, id: AtomId) -> Result<&mut Atom, MolRsError>

Get a mutable reference to an atom.

pub fn add_bond(&mut self, a: AtomId, b: AtomId) -> Result<BondId, MolRsError>

Add a bond between two existing atoms.

pub fn remove_bond(&mut self, id: BondId) -> Result<Bond, MolRsError>

Remove a bond and update the adjacency index.

pub fn get_bond(&self, id: BondId) -> Result<&Bond, MolRsError>

Get a reference to a bond.

pub fn get_bond_mut(&mut self, id: BondId) -> Result<&mut Bond, MolRsError>

Get a mutable reference to a bond.

pub fn add_angle( &mut self, i: AtomId, j: AtomId, k: AtomId, ) -> Result<AngleId, MolRsError>

Add an angle (i-j-k, j central).

pub fn remove_angle(&mut self, id: AngleId) -> Result<Angle, MolRsError>

Remove an angle.

pub fn get_angle(&self, id: AngleId) -> Result<&Angle, MolRsError>

Get a reference to an angle.

pub fn add_dihedral( &mut self, i: AtomId, j: AtomId, k: AtomId, l: AtomId, ) -> Result<DihedralId, MolRsError>

Add a dihedral (i-j-k-l).

pub fn remove_dihedral( &mut self, id: DihedralId, ) -> Result<Dihedral, MolRsError>

Remove a dihedral.

pub fn get_dihedral(&self, id: DihedralId) -> Result<&Dihedral, MolRsError>

Get a reference to a dihedral.

pub fn atoms(&self) -> impl Iterator<Item = (AtomId, &Atom)>

Iterate over all (AtomId, &Atom) pairs.

pub fn bonds(&self) -> impl Iterator<Item = (BondId, &Bond)>

Iterate over all (BondId, &Bond) pairs.

pub fn angles(&self) -> impl Iterator<Item = (AngleId, &Angle)>

Iterate over all (AngleId, &Angle) pairs.

pub fn dihedrals(&self) -> impl Iterator<Item = (DihedralId, &Dihedral)>

Iterate over all (DihedralId, &Dihedral) pairs.

pub fn n_atoms(&self) -> usize

Number of atoms.

pub fn n_bonds(&self) -> usize

Number of bonds.

pub fn n_angles(&self) -> usize

Number of angles.

pub fn n_dihedrals(&self) -> usize

Number of dihedrals.

pub fn neighbors(&self, id: AtomId) -> impl Iterator<Item = AtomId>

Iterate over neighbor atom IDs of a given atom (via bond connectivity).

pub fn neighbor_bonds(&self, id: AtomId) -> impl Iterator<Item = (AtomId, f64)>

Iterate over (neighbor_id, bond_order) for a given atom.

Bond order is read from the "order" property (default 1.0).

pub fn translate(&mut self, delta: [f64; 3])

Translate all atoms that have x/y/z props.

pub fn rotate(&mut self, axis: [f64; 3], angle: f64, about: Option<[f64; 3]>)

Rotate all atoms that have x/y/z props around axis by angle (radians), optionally about a center point.

pub fn merge(&mut self, other: MolGraph)

Merge another MolGraph into self, consuming other. All IDs in other are remapped to new IDs in self.

pub fn to_frame(&self) -> Frame

Export to a Frame. Each unique prop key becomes a column in the "atoms" block. Bonds, angles, dihedrals become separate blocks with 0-based indices referencing atom row order.

pub fn from_frame(frame: &Frame) -> Result<MolGraph, MolRsError>

Import from a Frame. The "atoms" block columns become props; "bonds" block atomi/atomj columns become bonds.

Trait Implementations

impl Clone for MolGraph

fn clone(&self) -> MolGraph

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for MolGraph

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

Formats the value using the given formatter.

impl Default for MolGraph

fn default() -> MolGraph

Returns the “default value” for a type.