peleffy.template.impact.WritableAtom¶

class peleffy.template.impact.WritableAtom(atom)[source]¶

Writable peleffy’s Atom class

__init__(atom)[source]¶

It initializes a WritableAtom object.

Parameters

atom (a peleffy.topology.molecule.Atom) – The Atom to create the WritableAtom 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

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

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

set_OPLS_type(OPLS_type)¶

It sets the OPLS type of the atom.

Parameters

OPLS_type (str) – The OPLS type to set to this Atom object

set_PDB_name(pdb_name)¶

It sets the PDB atom name.

Parameters

pdb_name (str) – The PDB atom name to be set

set_SASA_radius(SASA_radius)¶

It sets the SASA radius of the atom.

Parameters

SASA_radius (float) – The SASA radius to set to this Atom object

set_as_branch()¶

It sets the atom as branch.

set_as_core()¶

It sets the atom as core.

set_born_radius(born_radius)¶

It sets the Born radius of the atom.

Parameters

born_radius (float) – The Born radius to set to this Atom object

set_charge(charge)¶

It sets the charge of the atom.

Parameters

charge (float) – The charge to set to this Atom object

set_coords(coords)¶

It sets the coordinates of the atom.

Parameters

coords (list) – The coordinates array to set to this Atom object

set_epsilon(epsilon)¶

It sets the epsilon of the atom.

Parameters

epsilon (float) – The epsilon to set to this Atom object

set_index(index)¶

It sets the index of the atom.

Parameters

index (int) – The index of this Atom object

set_nonpolar_alpha(nonpolar_alpha)¶

It sets the nonpolar alpha of the atom.

Parameters

nonpolar_alpha (float) – The nonpolar alpha to set to this Atom object

set_nonpolar_gamma(nonpolar_gamma)¶

It sets the nonpolar gamma of the atom.

Parameters

nonpolar_gamma (float) – The nonpolar gamma to set to this Atom object

set_parent(parent)¶

It sets the parent of the atom.

Parameters

parent (peleffy.topology.Atom) – The parent of the atom

set_sigma(sigma)¶

It sets the sigma of the atom.

Parameters

sigma (float) – The sigma to set to this Atom object

Attributes

`OPLS_type`	Atom’s OPLS type.
`PDB_name`	Atom’s PDB name.
`SASA_radius`	Atom’s SASA radius.
`born_radius`	Atom’s born radius.
`charge`	Atom’s charge.
`core`	Atom’s core char.
`epsilon`	Atom’s epsilon.
`index`	Atom’s index.
`n_writable_attrs`	The number of writable attributes this topological element has.
`name`	The name that this topological element has.
`nonpolar_alpha`	Atom’s nonpolar alpha.
`nonpolar_gamma`	Atom’s nonpolar gamma.
`parent`	Atom’s parent.
`sigma`	Atom’s sigma.
`unknown`	Atom’s unknown int.
`x`	Atom’s x coordinate.
`y`	Atom’s y coordinate.
`z`	Atom’s z coordinate.