fractaldna.dna_models.molecules.Thymine¶

class fractaldna.dna_models.molecules.Thymine(strand=-1, chain=-1, position=array([0., 0., 0.]), rotation=array([0., 0., 0.]), index=0)¶

Bases: Molecule

Thymine molecule

Parameters:

strand (int) – strand ID
chain (int) – Chain ID
position (array) – position array (3-vector)
rotation (array) – rotation array (euler angles)
index (int) – base pait index

__init__(strand=-1, chain=-1, position=array([0., 0., 0.]), rotation=array([0., 0., 0.]), index=0)¶: constructor

Methods

`__init__`([strand, chain, position, ...])	constructor
`point_in_molecule`(point)	Assert whether a point (x, y, z) is inside the molecule.
`rotate`(rotation)	Rotate molecule by [X_angle, Y_angle, Z_angle]
`to_series`()	Convert molecule to a pandas series
`to_text`([seperator])	Return a text description of the molecule Molecule.toText(seperator=" ")
`translate`(translation)	type translation: `array`

point_in_molecule(point)¶

Assert whether a point (x, y, z) is inside the molecule.

Param:: point (x, y, z)
Return type:: bool
Returns:: True/False point in molecule

rotate(rotation)¶

Rotate molecule by [X_angle, Y_angle, Z_angle]

Parameters:: rotation (array) – Euler angles for rotation
Return type:: None

to_series()¶

Convert molecule to a pandas series

Return type:: Series
Returns:: Series representation of the molecule

to_text(seperator=' ')¶

Return a text description of the molecule Molecule.toText(seperator=” “)

Parameters:: seperator (str) – seperation character
Return type:: str

translate(translation)¶

Parameters:: translation (array) – Translate the molecule by (x, y, z)
Return type:: None