sknano.core.molecules.Molecules

class sknano.core.molecules.Molecules(molecules=None)

Base class for collection of Molecule objects.

Parameters:

molecules : {None, sequence, Molecules}, optional

if not None, then a list of Molecule instance objects or an existing Molecules instance object.

Attributes

CM	Center-of-Mass coordinates of Molecules.
M	Total mass of Molecules.
Nmolecules	Number of molecules in Molecules.
bounds	Return bounds of Molecules.
coords	Return list of Molecule coordinates.
masses	Return list of Molecule masses.
symbols	Return list of Molecule symbols.
x	Return \(x\) coordinates of Molecule objects as array.
y	Return \(y\) coordinates of Molecule objects as array.
z	Return \(z\) coordinates of Molecule objects as array.

Methods

append(item)
center_CM([axes])	Center molecules on CM coordinates.
clear()
clip_bounds(region[, center_before_clipping])	Remove molecules outside the given limits along given dimension.
copy()
count(item)
extend(other)
filter(condition[, invert])	Filter Molecules by condition.
get_coords([asdict])	Return molecule coords.
get_molecules([asarray])	Return list of Molecules.
index(item, *args)
insert(i, item)
pop([i])
remove(item)
reverse()
rezero([epsilon])	Set really really small coordinates to zero.
rezero_coords([epsilon])	Alias for Molecules.rezero.
rezero_xyz([epsilon])
rotate([angle, axis, anchor_point, ...])	Rotate Molecule position vectors.
sort([key, reverse])
translate(t[, fix_anchor_points])	Translate Molecule position vectors by Vector t.