coordinates

coordinates

coordinate, topology and plumed modification functions

Classes

Name Description
AffectedInteractions keeping track of affected interactions during the merge process to add the correct helper pairs
MoleculeTypeMerger Takes two MoleculeTypes and joins them for a smooth free-energy like parameter transition simulation

AffectedInteractions

coordinates.AffectedInteractions(
    self,
    atoms=set(),
    bonds=BondsPairSets(),
    angles=AnglesPairSets(),
    dihedrals=DihedralsPairSets(),
)

keeping track of affected interactions during the merge process to add the correct helper pairs

MoleculeTypeMerger

coordinates.MoleculeTypeMerger(self, mol_a, mol_b, ff, morse_only=False)

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

Methods

Name Description
add_helper_pairs growing/shrinking pairs are used to turn on/off
merge modiefies mol_b, the reactive moleculetype of of top_b, in place
merge_exclusions Merge exclusions by adding the exclusions from the A state to the B state
merge_pairs Merge pairs that are from the respective pairs sections of the topologies
add_helper_pairs
coordinates.MoleculeTypeMerger.add_helper_pairs()

growing/shrinking pairs are used to turn on/off LJ / non-bonded interactions. If it is for a binding event, the pair is vanishing, as it will be an exclusion once bound. If a bond is breaking, the pair interaction is slowly turned on, as it was excluded previously.

merge
coordinates.MoleculeTypeMerger.merge()

modiefies mol_b, the reactive moleculetype of of top_b, in place

merge_exclusions
coordinates.MoleculeTypeMerger.merge_exclusions()

Merge exclusions by adding the exclusions from the A state to the B state

merge_pairs
coordinates.MoleculeTypeMerger.merge_pairs()

Merge pairs that are from the respective pairs sections of the topologies

Functions

Name Description
break_bond_plumed Break bond in plumed configuration file.
get_explicit_or_type Takes an Interaction and associated key, InteractionTypes, Topology
is_parameterized Parameterized topology entries have c0 and c1 attributes != None
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
to_pairkey Turn key into a pair key

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_or_type

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

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_top_slow_growth

coordinates.merge_top_slow_growth(top_a, top_b, morse_only=False)

Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation. Modifies topB in place. All changes are contained to the Reactive moleculetype.

place_atom

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

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

to_pairkey

coordinates.to_pairkey(key)

Turn key into a pair key Takes the key for a higher ordre interaction (bond, angle, dihedral) and from this takes the outermost atoms and returns them as a key for the corresponding pair interaction by sorting them in ascending order.

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