peleffy.topology.Bond

class peleffy.topology.Bond(index=- 1, atom1_idx=None, atom2_idx=None, spring_constant=None, eq_dist=None)

It represents a bond in the topology.

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

It initiates a Bond object.

Parameters

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

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

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

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

• eq_dist (simtk.unit.Quantity) – The equilibrium distance of this Bond

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 Bond

set_atom2_idx(index)

It sets atom2’s index.

Parameters

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

set_index(index)

It sets the index of the bond.

Parameters

index (int) – The index of this Bond object

Attributes

atom1_idx	Bond’s atom1 index.
atom2_idx	Bond’s atom2 index.
eq_dist	Bond’s equilibrium distance.
index	Bond’s index.
n_writable_attrs	The number of writable attributes this topological element has.
name	The name that this topological element has.
spring_constant	Bond’s spring constant.