fractaldna.dna_models.dnapositions.MoleculeFromAtoms¶

class fractaldna.dna_models.dnapositions.MoleculeFromAtoms(atoms)¶

Bases: object

__init__(atoms)¶: MoleculeFromAtoms(atoms) A molecule created from a dictionary of cartesian atom positions

Methods

`__init__`(atoms)	MoleculeFromAtoms(atoms) A molecule created from a dictionary of cartesian atom positions
`find_center`()	c = MoleculeFromAtoms.find_center()
`find_equivalent_half_lengths`()	l = MoleculeFromAtoms.find_equivalent_half_lengths()
`find_equivalent_radius`()	r = MoleculeFromAtoms.find_equivalent_radius()
`find_half_lengths`()	half_lengths = MoleculeFromAtoms.find_half_lengths()
`find_radius`()	r = MoleculeFromAtoms.find_radius()
`from_cylindrical`(atoms[, inverse])	Make a MoleculeFromAtoms instance from a list of atoms in cylindrical coords (r, theta, phi)
`to_plot`()	fig = MoleculeFromAtoms.to_plot()

find_center()¶

c = MoleculeFromAtoms.find_center()

Find the barycenter of the atoms that constitute this molecule

find_equivalent_half_lengths()¶

l = MoleculeFromAtoms.find_equivalent_half_lengths()

Find the half lengths scaled to give a volume equal to what the constituent molecules occupy

find_equivalent_radius()¶

r = MoleculeFromAtoms.find_equivalent_radius()

Return the radius that yields the same volume occupied by all atoms

find_half_lengths()¶

half_lengths = MoleculeFromAtoms.find_half_lengths()

Return an array of the half lengths of a box that encloses the molecule in xyz. This is not a minimum bounding volume

find_radius()¶

r = MoleculeFromAtoms.find_radius()

Return the minimum radius that encloses this molecule

classmethod from_cylindrical(atoms, inverse=False)¶

Make a MoleculeFromAtoms instance from a list of atoms in cylindrical coords (r, theta, phi)

MoleculeFromAtoms.from_cylindrical(atoms, inverse=False)

Note: Theta is in degrees

Parameters:: inverse (bool) – (default False)Set to True to generate a dyadically related base pair (negates theta and z)

to_plot()¶

fig = MoleculeFromAtoms.to_plot()

Returns a matplotlib figure instance of the molecule.