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)
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)
Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation.
TODO: for now this assumes that only one moleculeype (the first, index 0) 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