peleffy.topology.Angle

class peleffy.topology.Angle(index=- 1, atom1_idx=None, atom2_idx=None, atom3_idx=None, spring_constant=None, eq_angle=None)

It represents an angle in the topology.

__init__(index=- 1, atom1_idx=None, atom2_idx=None, atom3_idx=None, spring_constant=None, eq_angle=None)

It initiates an Angle object.

Parameters

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

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

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

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

• spring_constant (simtk.unit.Quantity) – The spring constant of this Angle

• eq_angle (simtk.unit.Quantity) – The equilibrium angle of this Angle

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

set_atom1_idx(index)

It sets atom1’s index.

Parameters

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

set_atom2_idx(index)

It sets atom2’s index.

Parameters

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

set_atom3_idx(index)

It sets atom3’s index.

Parameters

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

set_index(index)

It sets the index of the angle.

Parameters

index (int) – The index of this Angle object

Attributes

atom1_idx	Angle’s atom1 index.
atom2_idx	Angle’s atom2 index.
atom3_idx	Angle’s atom3 index.
eq_angle	Angle’s equilibrium angle.
index	Angle’s index.
n_writable_attrs	The number of writable attributes this topological element has.
name	The name that this topological element has.
spring_constant	Angle’s spring constant.