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(
    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(mol_a, mol_b, ff, morse_only=False)

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

mol_a is modified in place.

Methods

Name	Description
add_helper_pairs	growing/shrinking pairs are used to turn on/off
amber_fix	Amber fix for breaking/binding atom types without LJ potential
merge	modiefies mol_a, the reactive moleculetype of of top_a, in place
merge_exclusions	Merge exclusions by adding the exclusions from the B state to the A 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.

amber_fix

coordinates.MoleculeTypeMerger.amber_fix()

Amber fix for breaking/binding atom types without LJ potential

merge

coordinates.MoleculeTypeMerger.merge()

modiefies mol_a, the reactive moleculetype of of top_a, in place

merge_exclusions

coordinates.MoleculeTypeMerger.merge_exclusions()

Merge exclusions by adding the exclusions from the B state to the A 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='',
)

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.