Topology

A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.

Possible bond orders in Chemfiles:

• Chemfiles.UnknownBond: when the bond order is not specified
• Chemfiles.SingleBond: for single bonds
• Chemfiles.DoubleBond: for double bonds
• Chemfiles.TripleBond: for triple bonds
• Chemfiles.QuadrupleBond: for quadruple bonds (present in some metals)
• Chemfiles.QuintupletBond: for qintuplet bonds (present in some metals)
• Chemfiles.AmideBond: for amide bonds
• Chemfiles.AromaticBond: for aromatic bonds

Topology(frame::Frame) -> Topology

Get a copy of the Topology of the given frame.

Topology() -> Topology

Create an empty Topology.

deepcopy(topology::Topology) -> Topology

Make a deep copy of a topology.

getindex(
    topology::Topology,
    index::Integer
) -> Chemfiles.Atom

Get the Atom at the given index of the topology. By default this creates a copy so as to be safe. To not create a copy, use @view topology[index].

See also Base.view(topology::Topology, index::Integer)

resize!(topology::Topology, size::Integer)

Resize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.

If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.

size(topology::Topology) -> Int64

Get the Topology size, i.e. the current number of atoms.

view(topology::Topology, index::Integer) -> Chemfiles.Atom

Get the Atom at the given index of the topology without creating a copy.

add_atom!(topology::Topology, atom::Chemfiles.Atom)

Add an atom at the end of a topology.

add_bond!(topology::Topology, i::Integer, j::Integer)
add_bond!(topology::Topology, i::Integer, j::Integer, order)

Add a bond between the atoms i and j in the topology, optionaly setting the bond order.

add_residue!(topology::Topology, residue::Residue)

Add a copy of 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.

angles(topology::Topology) -> Matrix{UInt64}

Get the angles in the topology, in a 3 x angles_count(topology) array.

angles_count(topology::Topology) -> Int64

Get the number of angles in the topology.

are_linked(
    topology::Topology,
    first::Residue,
    second::Residue
) -> Bool

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.

bond_order(
    topology::Topology,
    i::Integer,
    j::Integer
) -> Chemfiles.BondOrder

Get the BondOrder for the bond between atoms i and j in the topology.

bond_orders(
    topology::Topology
) -> Vector{Chemfiles.BondOrder}

Get the BondOrder for all the bonds in the topology.

bonds(topology::Topology) -> Matrix{UInt64}

Get the bonds in the topology, in a 2 x bonds_count(topology) array.

bonds_count(topology::Topology) -> Int64

Get the number of bonds in the topology.

clear_bonds!(topology::Topology)

Remove all bonds, angles and dihedral angles from this Topology.

count_residues(topology::Topology) -> Int64

Get the number of residues in the topology.

dihedrals(topology::Topology) -> Matrix{UInt64}

Get the dihedral angles in the topology, in a 4 x dihedrals_count(topology) array.

dihedrals_count(topology::Topology) -> Int64

Get the number of dihedral angles in the topology.

impropers(topology::Topology) -> Matrix{UInt64}

Get the improper angles in the topology, in a 4 x impropers_count(topology) array.

impropers_count(topology::Topology) -> Int64

Get the number of improper angles in the topology.

remove_atom!(topology::Topology, index::Integer)

Remove the atom at the given index from a topology.

remove_bond!(topology::Topology, i::Integer, j::Integer)

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