coordinates

coordinates

coordinate, topology and plumed modification functions

Functions

Name	Description
break_bond_plumed	Break bond in plumed configuration file.
get_explicit_MultipleDihedrals	Takes a valid dihedral key and returns explicit
get_explicit_or_type	Takes an Interaction and associated key, InteractionTypes, Topology
is_parameterized	Parameterized topology entries have c0 and c1 attributes != None
merge_dihedrals	Merge one to two Dihedrals or -Types into a Dihedral in free-energy syntax
merge_top_moleculetypes_slow_growth	Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation
merge_top_slow_growth	Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation.
place_atom	Place an atom to new coords at the last time point of the trajectory

break_bond_plumed

coordinates.break_bond_plumed(files, breakpair, newplumed)

Break bond in plumed configuration file.

Parameters

Name	Type	Description	Default
files	TaskFiles		required
breakpair	tuple[str, str]		required

get_explicit_MultipleDihedrals

coordinates.get_explicit_MultipleDihedrals(
    dihedral_key
    mol
    dihedrals_in
    ff
    periodicity_max=6
)

Takes a valid dihedral key and returns explicit dihedral parameters for a given topology

get_explicit_or_type

coordinates.get_explicit_or_type(
    key
    interaction
    interaction_types
    mol
    periodicity=''
)

Takes an Interaction and associated key, InteractionTypes, Topology and Periodicity (for dihedrals) and returns an object with the parameters of this Interaction

is_parameterized

coordinates.is_parameterized(entry)

Parameterized topology entries have c0 and c1 attributes != None

merge_dihedrals

coordinates.merge_dihedrals(
    dihedral_key
    dihedral_a
    dihedral_b
    dihedral_types_a
    dihedral_types_b
    molA
    molB
    funct
    periodicity
)

Merge one to two Dihedrals or -Types into a Dihedral in free-energy syntax

merge_top_moleculetypes_slow_growth

coordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff, morph_pairs)

Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation

merge_top_slow_growth

coordinates.merge_top_slow_growth(topA, topB, morph_pairs)

Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation. For now this assumes that only one moleculeype is of interest.

place_atom

coordinates.place_atom(files, step, ttime=None)

Place an atom to new coords at the last time point of the trajectory