nanome.api.structure.atom module

class Atom[source]

Bases: nanome._internal.structure.models._Atom, nanome.api.structure._deprecated.AtomDeprecated, nanome.api.structure.base.Base

Represents an Atom
class AtomRenderingMode

Bases: enum.IntEnum

Shape types an atom can be rendered as.
To be used with atom.atom_mode
Adaptive = 6
BFactor = 5
BallStick = 0
Point = 4
Stick = 1
VanDerWaals = 3
Wire = 2
acceptor
alt_loc
String of length 1. Identifier of the alternate location.
Type:str
atom_color
Color of the atom
Type:Color
atom_mode
Represents how the atom should be shown, such as ball and point or wired.
Type:AtomRenderingMode
atom_rendering
Represents if the atom should be rendered specifically.
Type:bool
atom_scale
Scale/size/radius of the atom
Type:float
bfactor
bonds
Bonds that the atom is part of
chain
Chain that the atom is part of
complex
Complex that the atom is part of
conformer_count
current_conformer
donor
exists
Represents if atom exists for calculations.
Type:bool
formal_charge
het_surfaced
in_conformer
is_het
Represents if the atom is a HET (Heteroatom - not C or H).
Type:bool
label_text
Represents the text that would show up if atom is labeled.
Type:str
labeled
Represents if the atom has a label or not. If it does, show the label.
Type:bool
molecule
Molecule that the atom is part of
name
Represents the name of the atom. Ideally, the same as symbol.
Type:str
occupancy
partial_charge
polar_hydrogen
position
Position of the atom
Type:Vector3
positions
residue
Residue that the atom is part of
selected
Represents if the atom is currently selected in the Nanome workspace.
Type:bool
serial
set_visible(value)[source]
Set the atom to be visible or invisible in Nanome.
Type:bool
surface_color
Color of the atom surface
Type:Color
surface_opacity
Opacity of the atom surface
Type:float
surface_rendering
Represents if the atom surface should be rendered specifically.
Type:bool
symbol
Represents the symbol of the atom. E.g.: C for Carbon
Type:str
vdw_radius
VDW radius of the atom in Angstrom
Type:float