Structure Models

Structure Models for DNA Simulations are included under fractaldna.structure_models.

Long fractals can be generated using L-Strings, which can then be turned into a voxelised representation using the methods in fractaldna.structure_models.voxelisation.

Generating Hilbert Curves using L-Strings

fractaldna.structure_models.hilbert.generate_path(lstring, n=2, distance=10.0, rounding=0, pbar=False)

Generate a path from an l-string

When moving a distance smaller than 1, ensure that rounding is set correctly.

This algorithm works best when moving in integer steps and applying any scaling after generating the path.

Parameters:

  • lstring (str) – lstring describing path

  • n (int) – steps on path between forward movements

  • distance (float) – distance between points forward movements

  • rounding (int) – rounding to apply to each position

  • pbar (bool) – display a progress bar

Return type:

List[array]

Returns:

list of XYZ points

Voxelising Fractals

class fractaldna.structure_models.voxelisation.VoxelisedFractal

Class containing a voxelised representation of a fractal

Typically created using the VoxelisedFractal.fromSeed class method

fractal = VoxelisedFractal.fromSeed(‘X’, 1) fractal.fractal contains a list of ‘Voxels’ representing the DNA Path

center_fractal()

Center the fractal around (x, y, z) = (0, 0, 0)

Return type:

None

classmethod fromLString(lstring, pbar=False)

Convert an L-String into a VoxelisedFractal

Parameters:

  • lstring (str) – L-String to convert

  • pbar (bool) – Show a progress bar for generating path and voxels

Returns:

Voxelised Fractal representation

classmethod fromSeed(seed, iterations, distance=1)

Make a voxelised fractal from an L-String seed.

The available L-Strings are described in fractaldna.structure_models.hilbert

Parameters:

  • seed (str) – Seed L-String

  • iterations (int) – number of times to iterate seed

  • distance (float) – distance between voxels

Returns:

Voxelised Fractal representation

classmethod from_path(path, pbar=False)

Convert a path (a list of xyz positions) to a voxelised representation

Parameters:

  • path (Union[List[array], List[List], array]) – path to convert

  • pbar (bool) – show a progress bar if true

Returns:

Voxelised Fractal representation

to_frame(suppress_hash=False)

Convert voxelised representation to data frame

Parameters:

suppress_hash (bool) – Hide the hash in front of the ‘IDX’ column which is kept for compatibiilty with the Geant4 DNA simulation format

Returns:

Voxelised fractal as a data frame

to_plot(refine=0, batch=False)

Create a matplotlib figure instance of this fractal

fig = toPlot(refine=0, batch=False) :type refine: int :param refine: points to plot in between voxels (more points = clearer path) :type batch: bool :param batch: True to suppress automatic display of the figure

Return type:

figure

to_pretty_plot(refine=10, mayavi=False, mask=None)

Create a matplotlib figure instance of this fractal, with curved lines rather than hard corners

fig = to_pretty_plot(refine=10, batch=False)

Parameters:

  • refine (int) – points to plot in between voxels (more points = clearer path)

  • mayavi (bool) – make plot with MayaVI

  • mask (Optional[Callable]) – Callable function that returns true for voxels that should be plotted. mask is a function that should take a position three vector and return boolean True/False for any position.

to_text(sep=' ', comment='#')
Return a textual representation of the fractal as

KIND POS_X POS_Y POS_Z EUL_PSI EUL_THETA EUL_PHI

Parameters:

  • sep (str) – string to use to separate fields (default space)

  • comment (str) – string to use to denote comment in first line (default hash: #)