ipymd.visualise package

Submodules

ipymd.visualise.visualise_sim module

Created on Sun May 1 23:47:03 2016

@author: cjs14

class ipymd.visualise.visualise_sim.Visualise_Sim(units='real')[source]

Bases: object

For units real, these are the units:

mass = grams/mole distance = Angstroms time = femtoseconds energy = Kcal/mole velocity = Angstroms/femtosecond force = Kcal/mole-Angstrom torque = Kcal/mole temperature = Kelvin pressure = atmospheres dynamic viscosity = Poise charge = multiple of electron charge (1.0 is a proton) dipole = charge*Angstroms electric field = volts/Angstrom density = gram/cm^dim
add_atoms(atoms_df, spheres=True, illustrate=False)[source]

add atoms to visualisation

atoms_df : pandas.DataFrame
a table of atom data, must contain columns; x, y, z, radius, color and transparency
spheres : bool
whether the atoms are rendered as spheres or points
illustrate : str
if True, atom shading is more indicative of an illustration
add_axes(axes=[[1, 0, 0], [0, 1, 0], [0, 0, 1]], length=1.0, offset=(-1.2, 0.2), colors=('red', 'green', 'blue'), width=1.5)[source]

add axes

axes : np.array(3,3)
to turn off axes, set to None
axes_offset : tuple
x, y offset from top top-left atom
add_bonds(atoms_df, bonds_df, cylinders=False, illustrate=False, linewidth=5)[source]

add bonds to visualisation

atoms_df : pandas.DataFrame
a table of atom data, must contain columns; x, y, z
bonds_df : list
a table of bond data, must contain; start, end, radius, color, transparency to/from refer to the atoms_df iloc (not necessarily the index number!)
cylinders : bool
whether the bonds are rendered as cylinders or lines
illustrate : str
if True, atom shading is more indicative of an illustration
add_box(a, b, c, origin=[0, 0, 0], color='black', width=1)[source]

add wireframed box to visualisation

a : np.ndarray(3, dtype=float)
The a vectors representing the sides of the box.
b : np.ndarray(3, dtype=float)
The b vectors representing the sides of the box.
c : np.ndarray(3, dtype=float)
The c vectors representing the sides of the box.
origin : np.ndarray((3,3), dtype=float), default to zero
The origin of the box.
color : str
the color of the wireframe, in chemlab colors
add_box_from_meta(meta, color='black', width=1)[source]

a shortcut for adding boxes using a panda.Series containing a,b,c,origin

add_hexagon(vectors, origin=<Mock object>, color='black', width=1)[source]

add wireframed hexagonal prism to visualisation

vectors : np.ndarray((2,3), dtype=float)
The two vectors representing the orthogonal a,c directions.
origin : np.ndarray((3,3), dtype=float), default to zero
The origin of the hexagon (representing center of hexagon)
color : str
the color of the wireframe, in chemlab colors
add_plane(vectors, origin=<Mock object>, rev_normal=False, color='red', alpha=1.0)[source]

add square plane to visualisation

vectors : np.ndarray((2,3), dtype=float)
The two vectors representing the edges of the plane.
origin : np.ndarray((3,3), dtype=float), default to zero
The origin of the plane.
rev_normal : bool
whether to reverse direction of normal (for lighting calculations)
color : str
the color of the plane, in chemlab colors
basic_vis(atoms_df=None, meta=None, spheres=True, illustrate=False, xrot=0, yrot=0, zrot=0, fov=10.0, axes=<Mock object>, axes_length=1.0, axes_offset=(-1.2, 0.2), size=400, quality=5)[source]

basic visualisation shortcut

invoking add_atoms, add_box (if meta), add_axes, get_image and visualise functions

create_textline_image(text, fontsize=10, color=(0, 0, 0), background=(255, 255, 255), boxsize=(1000, 20))[source]

create a PIL image from a line of text

get_image(xrot=0, yrot=0, zrot=0, fov=5.0, size=400, quality=5, zoom_extents=None, trim_whitespace=True)[source]

get image of visualisation

NB: x-axis horizontal, y-axis vertical, z-axis out of page

Parameters:
  • rotx (float) – rotation about x (degrees)
  • roty (float) – rotation about y (degrees)
  • rotz (float) – rotation about z (degrees)
  • fov (float) – field of view angle (degrees)
  • size (float) – size of image
  • quality (float) – quality of image (pixels per point), note: higher quality will take longer to render
  • zoom_extents (None or np.ndarray((N, 3))) – define an array of points to autozoom image, if None then computed automatically
  • trim_whitespace (bool) – whether to trim whitspace around image
Returns:

image
Return type:

PIL.Image
open_qtview(xrot=0, yrot=0, zrot=0, fov=5.0, thickness=1, zoom_extents=None)[source]

open a qt viewer of the objects

Parameters:
  • rotx (float) – rotation about x (degrees)
  • roty (float) – rotation about y (degrees)
  • rotz (float) – rotation about z (degrees)
  • fov (float) – field of view angle (degrees)
  • thickness (float) – multiplier for thickness of lines for some objects
  • zoom_extents (None or np.ndarray((N, 3))) – define an array of points to autozoom image, if None then computed automatically
Returns:

viewer – the qt viewing window
Return type:

PyQt4.QtGui.QMainWindow
remove_all_objects()[source]
remove_atoms(n=1)[source]

remove the last n sets of atoms to be added

remove_bonds(n=1)[source]

remove the last n sets of bonds to be added

remove_boxes(n=1)[source]

remove the last n boxes to be added

remove_hexagons(n=1)[source]

remove the last n boxes to be added

remove_planes(n=1)[source]

remove the last n planes to be added

visualise(images, columns=1, width=None, height=None)[source]

visualise image(s) in IPython

When this object is returned by an input cell or passed to the display function, it will result in the image being displayed in the frontend.

Parameters:
  • images (list/single PIL.Image or (x,y)) – (x,y) denotes a blank space of size x,y e.g. [img1,(100,0),img2]
  • columns (int) – number of image columns
  • width (int) – Width to which to constrain the image in html
  • height (int) – Height to which to constrain the image in html
Returns:

image
Return type:

IPython.display.Image

Module contents