Topology
type¶Topology
¶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.Topology
()¶Topology
.Topology
(frame::Frame)¶Topology
of the given frame
.deepcopy
(topology::Topology)¶topology
.size
(topology::Topology)¶Topology
size, i.e. the current number of atoms.add_atom!
(topology::Topology, atom::Atom)¶atom
at the end of a topology
.remove_atom!
(topology::Topology, index::Integer)¶index
from a topology
.bonds_count
(topology::Topology)¶topology
.angles_count
(topology::Topology)¶topology
.dihedrals_count
(topology::Topology)¶topology
.impropers_count
(topology::Topology)¶topology
.bonds
(topology::Topology)¶topology
, in a 2 x bonds_count(topology)
array.angles
(topology::Topology)¶topology
, in a 3 x angles_count(topology)
array.dihedrals
(topology::Topology)¶topology
, in a 4 x dihedrals_count(topology)
array.impropers
(topology::Topology)¶topology
, in a 4 x impropers_count(topology)
array.add_bond!
(topology::Topology, i::Integer, j::Integer, order = nothing)¶i
and j
in the topology
, optionaly
setting the bond order
.remove_bond!
(topology::Topology, i::Integer, j::Integer)¶i
and j
in the topology
.bond_order
(topology::Topology, i::Integer, j::Integer)¶BondOrder
for the bond between atoms i
and j
in the
topology
.bond_orders
(topology::Topology)¶BondOrder
for all the bonds in the topology
.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.
count_residues
(topology::Topology)¶topology
.are_linked
(topology::Topology, first::Residue, second::Residue)¶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.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.