peleffy.topology.Proper¶

class peleffy.topology.Proper(index=- 1, atom1_idx=None, atom2_idx=None, atom3_idx=None, atom4_idx=None, periodicity=None, prefactor=None, constant=None, phase=None)[source]¶

It represents a proper dihedral in the topology.

__init__(index=- 1, atom1_idx=None, atom2_idx=None, atom3_idx=None, atom4_idx=None, periodicity=None, prefactor=None, constant=None, phase=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

prefactor (int) – The prefactor of this Dihedral

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

phase (simtk.unit.Quantity) – The phase constant 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

exclude_from_14_list()[source]¶

It excludes this proper dihedral from PELE’s 1-4 list by setting the index of the third atom to negative.

include_in_14_list()[source]¶

It includes this proper dihedral in PELE’s 1-4 list.

plot()¶

It plots this Dihedral as a function of phi angle.

set_atom1_idx(index)¶

It sets atom1’s index.

Parameters

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

set_atom2_idx(index)¶

It sets atom2’s index.

Parameters

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

set_atom3_idx(index)¶

It sets atom3’s index.

Parameters

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

set_atom4_idx(index)¶

It sets atom4’s index.

Parameters

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

set_index(index)¶

It sets the index of the dihedral.

Parameters

index (int) – The index of this Dihedral object

Attributes

`atom1_idx`	Dihedral’s atom1 index.
`atom2_idx`	Dihedral’s atom2 index.
`atom3_idx`	Dihedral’s atom3 index.
`atom4_idx`	Dihedral’s atom4 index.
`constant`	Dihedral’s constant.
`exclude`
`index`	Dihedral’s index.
`n_writable_attrs`	The number of writable attributes this topological element has.
`name`	The name that this topological element has.
`periodicity`	Dihedral’s periodicity.
`phase`	Dihedral’s phase constant.
`prefactor`	Dihedral’s prefactor.