Struct chemfiles::Topology[][src]

pub struct Topology { /* fields omitted */ }
Expand description

A Topology contains the definition of all the atoms in the system, and the liaisons between the atoms (bonds, angles, dihedrals, …). It will also contain all the residues information if it is available.

Implementations

Create a new empty topology.

Example

let topology = Topology::new();
assert_eq!(topology.size(), 0);

Get a reference of the atom at the given index in this topology.

Panics

If index is out of bounds.

Example

let mut topology = Topology::new();
topology.resize(6);

let atom = topology.atom(4);
assert_eq!(atom.name(), "");

Get a mutable reference to the atom at the given index in this topology.

Panics

If index is out of bounds.

Example

let mut topology = Topology::new();
topology.resize(6);

assert_eq!(topology.atom(4).name(), "");

topology.atom_mut(4).set_name("Fe");
assert_eq!(topology.atom(4).name(), "Fe");

Get the current number of atoms in this topology.

Example

let mut topology = Topology::new();
assert_eq!(topology.size(), 0);

topology.resize(6);
assert_eq!(topology.size(), 6);

Resize this topology to hold natoms atoms, inserting dummy atoms if the new size if bigger than the old one.

Example

let mut topology = Topology::new();
assert_eq!(topology.size(), 0);

topology.resize(6);
assert_eq!(topology.size(), 6);

Add an Atom at the end of this topology

Example

let mut topology = Topology::new();
topology.add_atom(&Atom::new("Mg"));

let atom = topology.atom(0);
assert_eq!(atom.name(), "Mg");

Remove an Atom from this topology by index. This modify all the other atoms indexes.

Panics

If the index is out of bounds

Example

let mut topology = Topology::new();
topology.resize(9);
assert_eq!(topology.size(), 9);

topology.remove(7);
assert_eq!(topology.size(), 8);

Get the number of bonds in the topology.

Example

let mut topology = Topology::new();
assert_eq!(topology.bonds_count(), 0);
topology.resize(4);

topology.add_bond(0, 1);
topology.add_bond(2, 1);
topology.add_bond(2, 3);
assert_eq!(topology.bonds_count(), 3);

Get the number of angles in the topology.

Example

let mut topology = Topology::new();
assert_eq!(topology.angles_count(), 0);
topology.resize(4);

topology.add_bond(0, 1);
topology.add_bond(2, 1);
topology.add_bond(2, 3);
assert_eq!(topology.angles_count(), 2);

Get the number of dihedral angles in the topology.

Example

let mut topology = Topology::new();
assert_eq!(topology.dihedrals_count(), 0);
topology.resize(4);

topology.add_bond(0, 1);
topology.add_bond(2, 1);
topology.add_bond(2, 3);
assert_eq!(topology.dihedrals_count(), 1);

Get the number of improper dihedral angles in the topology.

Example

let mut topology = Topology::new();
assert_eq!(topology.dihedrals_count(), 0);
topology.resize(4);

topology.add_bond(0, 1);
topology.add_bond(0, 2);
topology.add_bond(0, 3);
assert_eq!(topology.impropers_count(), 1);

Get the list of bonds in the topology.

Example

let mut topology = Topology::new();
topology.resize(4);

topology.add_bond(0, 1);
topology.add_bond(2, 1);
topology.add_bond(2, 3);
assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);

Get the list of angles in the topology.

Example

let mut topology = Topology::new();
topology.resize(4);

topology.add_bond(0, 1);
topology.add_bond(2, 1);
topology.add_bond(2, 3);
assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);

Get the list of dihedral angles in the topology.

Example

let mut topology = Topology::new();
topology.resize(4);

topology.add_bond(0, 1);
topology.add_bond(2, 1);
topology.add_bond(2, 3);

assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);

Get the list of improper dihedral angles in the topology.

Example

let mut topology = Topology::new();
topology.resize(4);

topology.add_bond(0, 1);
topology.add_bond(0, 2);
topology.add_bond(0, 3);

assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);

Remove all existing bonds, angles, dihedral angles and improper dihedral angles in the topology.

Example

let mut topology = Topology::new();
assert_eq!(topology.bonds_count(), 0);
topology.resize(4);
topology.add_bond(0, 1);
topology.add_bond(0, 2);
assert_eq!(topology.bonds_count(), 2);
assert_eq!(topology.angles().len(), 1);

topology.clear_bonds();
assert!(topology.bonds().is_empty());
assert!(topology.angles().is_empty());

Add a bond between the atoms at indexes i and j in the topology.

The bond order is set to BondOrder::Unknown.

Example

let mut topology = Topology::new();
assert_eq!(topology.bonds_count(), 0);
topology.resize(4);

topology.add_bond(0, 1);
topology.add_bond(0, 2);
assert_eq!(topology.bonds_count(), 2);

assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);

Add a bond between the atoms at indexes i and j in the topology with the given bond order.

Example

let mut topology = Topology::new();
assert_eq!(topology.bonds_count(), 0);
topology.resize(2);

topology.add_bond_with_order(0, 1, BondOrder::Double);
assert_eq!(topology.bond_order(0, 1), BondOrder::Double);

Get the bond order for the bond between the atoms at indexes i and j.

Example

let mut topology = Topology::new();
assert_eq!(topology.bonds_count(), 0);
topology.resize(2);

topology.add_bond_with_order(0, 1, BondOrder::Double);
assert_eq!(topology.bond_order(0, 1), BondOrder::Double);

Get the bond order for all the bonds in the topology

Example

let mut topology = Topology::new();
assert_eq!(topology.bonds_count(), 0);
topology.resize(3);

topology.add_bond_with_order(0, 1, BondOrder::Double);
topology.add_bond_with_order(0, 2, BondOrder::Single);

assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);

Remove any existing bond between the atoms at indexes i and j in this topology.

This function does nothing if there is no bond between i and j.

Example

let mut topology = Topology::new();
assert_eq!(topology.bonds_count(), 0);
topology.resize(4);

topology.add_bond(0, 1);
topology.add_bond(1, 2);
assert_eq!(topology.bonds_count(), 2);

topology.remove_bond(0, 1);
assert_eq!(topology.bonds_count(), 1);

// Removing a bond that does not exists is fine
topology.remove_bond(0, 2);
assert_eq!(topology.bonds_count(), 1);

Get a reference to the residue at index index from this topology.

The residue index in the topology is not always the same as the residue id.

Example

let mut topology = Topology::new();
topology.add_residue(&Residue::new("water")).unwrap();

let residue = topology.residue(0).unwrap();
assert_eq!(residue.name(), "water");

Get a copy of the residue containing the atom at index index in this topology, if any.

Example

let mut topology = Topology::new();
topology.resize(8);

let mut residue = Residue::new("water");
residue.add_atom(0);
residue.add_atom(1);
residue.add_atom(2);
topology.add_residue(&residue).unwrap();

let residue = topology.residue_for_atom(0).unwrap();
assert_eq!(residue.name(), "water");

assert!(topology.residue_for_atom(6).is_none());

Get the number of residues in this topology.

Example

let mut topology = Topology::new();
assert_eq!(topology.residues_count(), 0);

topology.add_residue(&Residue::with_id("water", 0)).unwrap();
topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
assert_eq!(topology.residues_count(), 2);

Add a residue to this topology.

Errors

This function fails is the residue id is not already in the topology, or if the residue contains atoms that are already in another residue.

Example

let mut topology = Topology::new();
topology.add_residue(&Residue::new("water")).unwrap();

let residue = topology.residue(0).unwrap();
assert_eq!(residue.name(), "water");

Check if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.

Example

let mut topology = Topology::new();

topology.add_residue(&Residue::with_id("water", 0)).unwrap();
topology.add_residue(&Residue::with_id("protein", 1)).unwrap();

let first = topology.residue(0).unwrap();
let second = topology.residue(1).unwrap();
assert_eq!(topology.are_linked(&first, &second), false);

Trait Implementations

Returns a copy of the value. Read more

Performs copy-assignment from source. Read more

Executes the destructor for this type. Read more

Auto Trait Implementations

Blanket Implementations

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Mutably borrows from an owned value. Read more

Performs the conversion.

Performs the conversion.

The resulting type after obtaining ownership.

Creates owned data from borrowed data, usually by cloning. Read more

🔬 This is a nightly-only experimental API. (toowned_clone_into)

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The type returned in the event of a conversion error.

Performs the conversion.

The type returned in the event of a conversion error.

Performs the conversion.