peleffy.topology.elements.OFFProper

class peleffy.topology.elements.OFFProper(index=- 1, atom1_idx=None, atom2_idx=None, atom3_idx=None, atom4_idx=None, periodicity=None, phase=None, k=None, idivf=None)[source]

It represents a proper dihedral in the Open Force Field’s topology.

__init__(index=- 1, atom1_idx=None, atom2_idx=None, atom3_idx=None, atom4_idx=None, periodicity=None, phase=None, k=None, idivf=None)

It initiates an Dihedral object.

Parameters

  • index (int) – The index of this Dihedral object

  • atom1_idx (int) – The index of the first atom involved in this Dihedral

  • atom2_idx (int) – The index of the second atom involved in this Dihedral

  • atom3_idx (int) – The index of the third atom involved in this Dihedral

  • atom4_idx (int) – The index of the fourth atom involved in this Dihedral

  • periodicity (int) – The periodicity of this Dihedral

  • phase (simtk.unit.Quantity) – The phase of this Dihedral

  • k (simtk.unit.Quantity) – The constant of this Dihedral

  • idivf (int) – The idivf of this Dihedral

apply_lambda(attributes_to_modify, lambda_value, reverse=False, final_state=None)

Given a lambda value, it modifies a set of attributes of this topological element. A lambda equal to 0 will keep the original attributes of this topological element. A lambda equal to 1 will remove completely the effects of the attributes. This behavior will be the opposite when reverse is set to True.

Parameters

  • attributes_to_modify (list[str]) – The list attribute names that will be modified

  • lambda_value (float) – A value between 0 and 1 that defined the lambda to apply to the attributes

  • reverse (bool) – When set to true the effects of lambda will be the opposite

  • final_state (a peleffy.topology.topology._TopologyElement object) – The topology element that represents the final state when lambda equals 1.0. Default is None, which means that the final state is not defined and therefore the topological element will disappear or will start from scratch

plot()

It plots this Dihedral as a function of phi angle.

to_PELE()

It converts this Open Force Field Dihedral object into a PELE-compatible one.

Returns

PELE_dihedral – The PELE-compatible Dihedral object

Return type

a Dihedral

Attributes

n_writable_attrs

The number of writable attributes this topological element has.

name

The name that this topological element has.