Struct chemfiles::Topology
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[src]
pub struct Topology { /* fields omitted */ }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.
Methods
impl Topology[src]
pub fn new() -> Result<Topology>[src]
Create a new empty topology.
Example
let topology = Topology::new().unwrap(); assert_eq!(topology.size(), Ok(0));
pub fn atom(&self, index: u64) -> Result<Atom>[src]
Get a copy of the atom at index index from this topology.
Example
let mut topology = Topology::new().unwrap(); topology.resize(6).unwrap(); let atom = topology.atom(4).unwrap(); assert_eq!(atom.name(), Ok(String::new()));
pub fn size(&self) -> Result<u64>[src]
Get the current number of atoms in this topology.
Example
let mut topology = Topology::new().unwrap(); assert_eq!(topology.size(), Ok(0)); topology.resize(6).unwrap(); assert_eq!(topology.size(), Ok(6));
pub fn resize(&mut self, natoms: u64) -> Result<()>[src]
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().unwrap(); assert_eq!(topology.size(), Ok(0)); topology.resize(6).unwrap(); assert_eq!(topology.size(), Ok(6));
pub fn add_atom(&mut self, atom: &Atom) -> Result<()>[src]
Add an Atom at the end of this topology
Example
let mut topology = Topology::new().unwrap(); topology.add_atom(&Atom::new("Mg").unwrap()).unwrap(); let atom = topology.atom(0).unwrap(); assert_eq!(atom.name(), Ok(String::from("Mg")));
pub fn remove(&mut self, index: u64) -> Result<()>[src]
Remove an Atom from this topology by index. This modify all the other
atoms indexes.
Example
let mut topology = Topology::new().unwrap(); topology.resize(9).unwrap(); assert_eq!(topology.size(), Ok(9)); topology.remove(7).unwrap(); assert_eq!(topology.size(), Ok(8));
pub fn bonds_count(&self) -> Result<u64>[src]
Get the number of bonds in the topology.
Example
let mut topology = Topology::new().unwrap(); assert_eq!(topology.bonds_count(), Ok(0)); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_bond(0, 1).unwrap(); topology.add_bond(2, 1).unwrap(); topology.add_bond(2, 3).unwrap(); assert_eq!(topology.bonds_count(), Ok(3));
pub fn angles_count(&self) -> Result<u64>[src]
Get the number of angles in the topology.
Example
let mut topology = Topology::new().unwrap(); assert_eq!(topology.angles_count(), Ok(0)); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_bond(0, 1).unwrap(); topology.add_bond(2, 1).unwrap(); topology.add_bond(2, 3).unwrap(); assert_eq!(topology.angles_count(), Ok(2));
pub fn dihedrals_count(&self) -> Result<u64>[src]
Get the number of dihedral angles in the topology.
Example
let mut topology = Topology::new().unwrap(); assert_eq!(topology.dihedrals_count(), Ok(0)); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_bond(0, 1).unwrap(); topology.add_bond(2, 1).unwrap(); topology.add_bond(2, 3).unwrap(); assert_eq!(topology.dihedrals_count(), Ok(1));
pub fn impropers_count(&self) -> Result<u64>[src]
Get the number of improper dihedral angles in the topology.
Example
let mut topology = Topology::new().unwrap(); assert_eq!(topology.dihedrals_count(), Ok(0)); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_bond(0, 1).unwrap(); topology.add_bond(0, 2).unwrap(); topology.add_bond(0, 3).unwrap(); assert_eq!(topology.impropers_count(), Ok(1));
pub fn bonds(&self) -> Result<Vec<[u64; 2]>>[src]
Get the list of bonds in the topology.
Example
let mut topology = Topology::new().unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_bond(0, 1).unwrap(); topology.add_bond(2, 1).unwrap(); topology.add_bond(2, 3).unwrap(); assert_eq!(topology.bonds(), Ok(vec![[0, 1], [1, 2], [2, 3]]));
pub fn angles(&self) -> Result<Vec<[u64; 3]>>[src]
Get the list of angles in the topology.
Example
let mut topology = Topology::new().unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_bond(0, 1).unwrap(); topology.add_bond(2, 1).unwrap(); topology.add_bond(2, 3).unwrap(); assert_eq!(topology.angles(), Ok(vec![[0, 1, 2], [1, 2, 3]]));
pub fn dihedrals(&self) -> Result<Vec<[u64; 4]>>[src]
Get the list of dihedral angles in the topology.
Example
let mut topology = Topology::new().unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_bond(0, 1).unwrap(); topology.add_bond(2, 1).unwrap(); topology.add_bond(2, 3).unwrap(); assert_eq!(topology.dihedrals(), Ok(vec![[0, 1, 2, 3]]));
pub fn impropers(&self) -> Result<Vec<[u64; 4]>>[src]
Get the list of improper dihedral angles in the topology.
Example
let mut topology = Topology::new().unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_bond(0, 1).unwrap(); topology.add_bond(0, 2).unwrap(); topology.add_bond(0, 3).unwrap(); assert_eq!(topology.impropers(), Ok(vec![[1, 0, 2, 3]]));
pub fn add_bond(&mut self, i: u64, j: u64) -> Result<()>[src]
Add a bond between the atoms at indexes i and j in the topology.
Example
let mut topology = Topology::new().unwrap(); assert_eq!(topology.bonds_count(), Ok(0)); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_bond(0, 1).unwrap(); topology.add_bond(0, 2).unwrap(); assert_eq!(topology.bonds_count(), Ok(2));
pub fn remove_bond(&mut self, i: u64, j: u64) -> Result<()>[src]
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().unwrap(); assert_eq!(topology.bonds_count(), Ok(0)); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_atom(&Atom::new("F").unwrap()).unwrap(); topology.add_bond(0, 1).unwrap(); topology.add_bond(1, 2).unwrap(); assert_eq!(topology.bonds_count(), Ok(2)); topology.remove_bond(0, 1).unwrap(); assert_eq!(topology.bonds_count(), Ok(1)); // Removing a bond that does not exists topology.remove_bond(0, 2).unwrap(); assert_eq!(topology.bonds_count(), Ok(1));
pub fn residue(&self, index: u64) -> Result<Residue>[src]
Get a copy of 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().unwrap(); topology.add_residue(&Residue::new("water").unwrap()).unwrap(); let residue = topology.residue(0).unwrap(); assert_eq!(residue.name(), Ok(String::from("water")));
pub fn residue_for_atom(&self, index: u64) -> Result<Option<Residue>>[src]
Get a copy of the residue containing the atom at index index in this
topology, if any.
Example
let mut topology = Topology::new().unwrap(); topology.resize(8).unwrap(); let mut residue = Residue::new("water").unwrap(); residue.add_atom(0).unwrap(); residue.add_atom(1).unwrap(); residue.add_atom(2).unwrap(); topology.add_residue(&residue).unwrap(); let residue = topology.residue_for_atom(0).unwrap().unwrap(); assert_eq!(residue.name(), Ok(String::from("water"))); let residue = topology.residue_for_atom(6).unwrap(); assert!(residue.is_none());
pub fn residues_count(&self) -> Result<u64>[src]
Get the number of residues in this topology.
Example
let mut topology = Topology::new().unwrap(); assert_eq!(topology.residues_count(), Ok(0)); topology.add_residue(&Residue::with_id("water", 0).unwrap()).unwrap(); topology.add_residue(&Residue::with_id("protein", 1).unwrap()).unwrap(); assert_eq!(topology.residues_count(), Ok(2));
pub fn add_residue(&mut self, residue: &Residue) -> Result<()>[src]
Add a residue to this topology.
The residue id must not already be in the topology, and the residue
must contain only atoms that are not already in another residue.
Example
let mut topology = Topology::new().unwrap(); topology.add_residue(&Residue::new("water").unwrap()).unwrap(); let residue = topology.residue(0).unwrap(); assert_eq!(residue.name(), Ok(String::from("water")));
pub fn are_linked(&self, first: &Residue, second: &Residue) -> Result<bool>[src]
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().unwrap(); topology.add_residue(&Residue::with_id("water", 0).unwrap()).unwrap(); topology.add_residue(&Residue::with_id("protein", 1).unwrap()).unwrap(); let first = topology.residue(0).unwrap(); let second = topology.residue(1).unwrap(); assert_eq!(topology.are_linked(&first, &second), Ok(false));
Trait Implementations
impl Clone for Topology[src]
fn clone(&self) -> Topology[src]
Returns a copy of the value. Read more
fn clone_from(&mut self, source: &Self)1.0.0[src]
Performs copy-assignment from source. Read more