peleffy.template.impact.WritableProper¶

class peleffy.template.impact.WritableProper(proper)[source]¶

Writable peleffy’s Proper class

__init__(proper)[source]¶

It initializes a WritableProper object.

Parameters

proper (a peleffy.topology.Proper) – The Proper to create the WritableProper with

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

static dummy_to_writable(f)¶

It converts a returned DummyAtom to a WritableAtom.

Parameters

f (function) – The function to apply the decorator to

Returns

out – A WritableAtom object

Return type

WritableAtom

exclude_from_14_list()¶

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

static in_angstrom(f)¶

It expresses a simtk.unit.Quantity in angstroms.

Parameters

f (function) – The function to apply the decorator to

Returns

out – simtk.unit.Quantity expressed in angstroms

Return type

float

static in_deg(f)¶

It expresses a simtk.unit.Quantity in degrees.

Parameters

f (function) – The function to apply the decorator to

Returns

out – simtk.unit.Quantity expressed in degrees

Return type

float

static in_elementarycharge(f)¶

It expresses a simtk.unit.Quantity in elementary charges.

Parameters

f (function) – The function to apply the decorator to

Returns

out – simtk.unit.Quantity expressed in elementary charges

Return type

float

static in_kcal_angstrom2mol(f)¶

It expresses a simtk.unit.Quantity in kcal/angstrom2mol.

Parameters

f (function) – The function to apply the decorator to

Returns

out – simtk.unit.Quantity expressed in kcal/angstrom2mol

Return type

float

static in_kcal_rad2mol(f)¶

It expresses a simtk.unit.Quantity in kcal/rad2mol.

Parameters

f (function) – The function to apply the decorator to

Returns

out – simtk.unit.Quantity expressed in kcal/rad2mol

Return type

float

static in_kcalmol(f)¶

It expresses a simtk.unit.Quantity in kcal/mol.

Parameters

f (function) – The function to apply the decorator to

Returns

out – simtk.unit.Quantity expressed in kcal/mol

Return type

float

include_in_14_list()¶

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

static none_to_dummy(f)¶

It converts a returned None to a DummyAtom.

Parameters

f (function) – The function to apply the decorator to

Returns

out – A DummyAtom object

Return type

DummyAtom

static none_to_zero(f)¶

It converts a returned None to zero.

Parameters

f (function) – The function to apply the decorator to

Returns

out – It is set to zero in case that it is None

Return type

function’s output

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`	Proper’s atom1 index.
`atom2_idx`	Proper’s atom2 index.
`atom3_idx`	Proper’s atom3 index.
`atom4_idx`	Proper’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.