peleffy.topology.Atom

class peleffy.topology.Atom(index=- 1, core=None, OPLS_type=None, PDB_name=None, unknown=None, x=None, y=None, z=None, sigma=None, epsilon=None, charge=None, born_radius=None, SASA_radius=None, nonpolar_gamma=None, nonpolar_alpha=None, parent=None)

It represents the properties of an atom.

__init__(index=- 1, core=None, OPLS_type=None, PDB_name=None, unknown=None, x=None, y=None, z=None, sigma=None, epsilon=None, charge=None, born_radius=None, SASA_radius=None, nonpolar_gamma=None, nonpolar_alpha=None, parent=None)

It initializes an Atom object.

Parameters

• index (int) – The index of the atom

• core (bool) – Whether atom is in the core or in a branch

• OPLS_type (str) – The OPLS type of the atom

• PDB_name (str) – The PDB name of the atom

• unknown (int) – The unknown value of the atom

• x (float) – The x coordinate of the atom

• y (float) – The y coordinate of the atom

• z (float) – The z coordinate of the atom

• sigma (simtk.unit.Quantity) – The sigma parameter of the atom

• epsilon (simtk.unit.Quantity) – The epsilon parameter of the atom

• charge (simtk.unit.Quantity) – The partial charge parameter of the atom

• born_radius (simtk.unit.Quantity) – The SGB born parameter radius of the atom

• SASA_radius (simtk.unit.Quantity) – The SASA radius parameter of the atom

• nonpolar_gamma (simtk.unit.Quantity) – The nonpolar gamma parameter of the atom

• nonpolar_alpha (simtk.unit.Quantity) – The nonpolar alpha parameter of the atom

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

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_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 position.
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.