schrodinger.graphics3d.polyhedron module¶

The polyhedron module allows creation and drawing of polyhedra. The body of the polyhedron is composed of faces that are composed of vertices.

Drawing is done in the current OpenGL rendering context and current OpenGL window, so you must set those prior to drawing. If you are using this with Maestro’s drawing callback mechanism the context and window are handled automatically.

Control over the vertices, faces, color, and opacity of a box are provided. However, please note that the current implementation does not ensure the passed in vertices and faces will enclose to form a volume. This must be determined in the subclass.

To draw any number of polyhedra, create the Polyhedron instances, add them to a Group instance then invoke the Group’s draw() method.

class schrodinger.graphics3d.polyhedron.Cube(*args, **keywords)¶

Bases: schrodinger.graphics3d.polyhedron.MaestroCube

This class is now deprecated. Please use MaestroCube.

class schrodinger.graphics3d.polyhedron.Dodecahedron(*args, **keywords)¶

Bases: schrodinger.graphics3d.polyhedron.MaestroDodecahedron

This class is now deprecated. Please use MaestroDodecahedron.

class schrodinger.graphics3d.polyhedron.Icosahedron(*args, **keywords)¶

Bases: schrodinger.graphics3d.polyhedron.MaestroIcosahedron

This class is now deprecated. Please use MaestroIcosahedron.

class schrodinger.graphics3d.polyhedron.MaestroCube(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

Bases: schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore

Class to draw a 3D cube in Maestro’s Workspace.

Cubes should be added to a graphics3d.common.Group, or CubeGroup, and drawing done via the Group. See the graphics3d.common.Group documentation.

API Example:

import schrodinger.maestro.maestro as maestro
import schrodinger.graphics3d.polyhedron as polyhedron

cube_group = polyhedron.Group()
st = maestro.workspace_get() # Here, st is methane.
for atom in st.atom:
    if atom.element == 'C':
        center = atom.xyz

cube = polyhedron.Cube(
    center  = center,
    mode = polyhedron.MODE_MAESTRO,
    length  = 1.828, # length between Hs
    color   = 'goldenrod',
    opacity = 1.0,
    style   = polyhedron.LINE
)
# Add the primative to the container.
cube_group.add(cube)

# Show the markers
cube.show()
cube_group.show()

# Hide the markers.
cube_group.hide()

# Remove the markers and the callback.
cube_group.clear()

getIndices()¶: :return The indices of the faces

getVertices(center, length=None, radius=None, volume=None)¶

Get a list of vertices. If the center coordinates are considered the origin the vertices will have a base on the y-plane, a vertex on the x-axis and a vertex directly in the +z-axis from the center.

Parameters:

center (list(float, float, float)) – List of 3 Angstrom values indicating the center coordinate of the tetrahedron.
length (float) – Length in Angstroms of each of the sides of the tetrahedron. Note: length or radius must be specified to create tetrahedron.
radius (float) – Circumsphere radius in Angstroms from center of tetrahedron. Note: length or radius must be specified to create tetrahedron.
volume (float) – Volume in cubed Angstroms of the object.

class schrodinger.graphics3d.polyhedron.MaestroDodecahedron(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

Bases: schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore

Class to draw a 3D dodecahedron in Maestro’s Workspace.

See Tetrahedron doc string for more details.

getIndices()¶: :return The indices of the faces

getVertices(center, length=None, radius=None, volume=None)¶

Get a list of vertices. If the center coordinates are considered the origin the vertices will have a base on the y-plane, a vertex on the x-axis and a vertex directly in the +z-axis from the center.

Parameters:

center (list(float, float, float)) – List of 3 Angstrom values indicating the center coordinate of the dodecahedron.
length (float) – Length in Angstroms of each of the sides of the dodecahedron. Note: length or radius must be specified to create dodecahedron.
radius (float) – Circumsphere radius in Angstroms from center of dodecahedron. Note: length or radius must be specified to create dodecahedron.
volume (float) – Volume in cubed Angstroms of the object.

class schrodinger.graphics3d.polyhedron.MaestroIcosahedron(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

Bases: schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore

Class to draw a 3D icosahedron in Maestro’s Workspace.

See Tetrahedron doc string for more details.

getIndices()¶: :return The indices of the faces

getVertices(center, length=None, radius=None, volume=None)¶

Get a list of vertices. If the center coordinates are considered the origin the vertices will have a base on the y-plane, a vertex on the x-axis and a vertex directly in the +z-axis from the center.

Parameters:

center (list(float, float, float)) – List of 3 Angstrom values indicating the center coordinate of the icosahedron.
length (float) – Length in Angstroms of each of the sides of the icosahedron. Note: length or radius must be specified to create icosahedron.
radius (float) – Circumsphere radius in Angstroms from center of icosahedron. Note: length or radius must be specified to create icosahedron.
volume (float) – Volume in cubed Angstroms of the object.

class schrodinger.graphics3d.polyhedron.MaestroOctahedron(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

Bases: schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore

Class to draw a 3D octahedron in Maestro’s Workspace.

See Tetrahedron doc string for more details.

getIndices()¶: :return The indices of the faces

getVertices(center, length=None, radius=None, volume=None)¶

Get a list of vertices. If the center coordinates are considered the origin the vertices will have a base on the y-plane, a vertex on the x-axis and a vertex directly in the +z-axis from the center.

Parameters:

center (list(float, float, float)) – List of 3 Angstrom values indicating the center coordinate of the tetrahedron.
length (float) – Length in Angstroms of each of the sides of the tetrahedron. Note: length or radius must be specified to create tetrahedron.
radius (float) – Circumsphere radius in Angstroms from center of tetrahedron. Note: length or radius must be specified to create tetrahedron.
volume (float) – Volume in cubed Angstroms of the object.

class schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

Bases: schrodinger.graphics3d.polyhedron.Polyhedron

getFaces(vertices)¶

Parameters:	vertices (list of lists) – List of vertices. Each member of list should be a list of 3 coords, [x,y,z]

getIndices()¶: Abstract method, defined by convention only

getVertices()¶: Abstract method, defined by convention only

updateVertices(center, length=None, radius=None, volume=None)¶

Update the vertices given a new center and size parameter. The changes will be seen the next time the object is drawn.

Parameters:	center (list(float, float, float)) – List of 3 Angstrom values indicating the center coordinate of the tetrahedron. length (float) – Length in Angstroms of each of the edges of the tetrahedron. radius (float) – Circumsphere radius in Angstroms from center of tetrahedron. volume (float) – Volume in cubed Angstroms of the object.
Raises:	RuntimeError – If a single option from `length`, `radius`, and `volume` does not have a value. ValueError – If the size parameter (`length`, `radius`, or `volume`) is not a float.

See Polyhedron.update

class schrodinger.graphics3d.polyhedron.MaestroTetrahedron(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

Bases: schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore

Class to draw a 3D tetrahedron in Maestro’s Workspace.

Tetrahedrons should be added to a graphics3d.common.Group, or TetrahedronGroup, and drawing done via the Group. See the graphics3d.common.Group documentation.

API Example:

import schrodinger.maestro.maestro as maestro
import schrodinger.graphics3d.polyhedron as polyhedron

tetrahedron_grp = polyhedron.Group()
st = maestro.workspace_get() # Here, st is methane.
for atom in st.atom:
    if atom.element == 'C':
        center = atoms.xyz

tetra = polyhedron.Tetrahedron(
    center  = center,
    length  = 1.828, # length between Hs
    color   = 'goldenrod',
    opacity = 1.0,
    style   = tetrahedron.LINE
)
# Add the primative to the container.
tetrahedron_grp.add(tetra)

# Add the draw callback.
maestro.workspace_draw_function_add(tetrahedron_grp.draw)

# Hide the markers.
tetrahedron_grp.hide()

# Remove the markers and the callback.
tetrahedron_grp.clear()
maestro.workspace_draw_function_remove(tetrahedron_grp.draw)

getIndices()¶: :return The indices of the faces

getVertices(center, length=None, radius=None, volume=None)¶

Get a list of vertices. If the center coordinates are considered the origin the vertices will have a base on the y-plane, a vertex on the x-axis and a vertex directly in the +z-axis from the center.

Parameters:

center (list(float, float, float)) – List of 3 Angstrom values indicating the center coordinate of the tetrahedron.
length (float) – Length in Angstroms of each of the sides of the tetrahedron. Note: length or radius must be specified to create tetrahedron.
radius (float) – Circumsphere radius in Angstroms from center of tetrahedron. Note: length or radius must be specified to create tetrahedron.
volume (float) – Volume in cubed Angstroms of the object.

class schrodinger.graphics3d.polyhedron.Octahedron(*args, **keywords)¶

Bases: schrodinger.graphics3d.polyhedron.MaestroOctahedron

This class is now deprecated. Please use MaestroOctahedron.

class schrodinger.graphics3d.polyhedron.Polyhedron(vertices, faces, mode, color='red', opacity=1.0, style=1)¶

Bases: schrodinger.graphics3d.common.Primitive

Class to draw a 3D polyhedron with OpenGL using the current context in whatever is the current drawable (which could be Maestro).

faces = None¶

A list containing lists of vertices that define a face of the polyhedron. These are set during the L{Polyhedron.update} method and taken from constructor argument, C{faces}.

@see: L{Polyhedron.update}

normals = None¶

The normals for the C{faces} passed in. These are calculated and set during the L{Polyhedron.update} method.

@see: L{Polyhedron._setNormals} @see: L{Polyhedron.update}

setStyle(style)¶

Sets the polyhedron’s drawing style.

Parameters:	style (Choice, FILL or LINE) – Whether to fill the polyhedron in or to leave it as lines connecting vertices.

update(vertices, faces)¶

Update the polyhedron’s shape.

Parameters:	vertices (list of lists) – List of vertices. Each member of list should be a list of 3 coords, [x,y,z] faces (list of lists) – List of faces comprising the polyhedron. Each face should be a list of at least 3 vertices.
See:	`Tetrahedron.updateVertices` for an example of usage

vertices = None¶

A list of each vertex of the polyhedron. These are set during the L{Polyhedron.update} method and taken from the constructor argument, C{vertices}.

@see: L{Polyhedron.update}

class schrodinger.graphics3d.polyhedron.Tetrahedron(*args, **keywords)¶

Bases: schrodinger.graphics3d.polyhedron.MaestroTetrahedron

This class is now deprecated. Please use MaestroTetrahedron.

schrodinger.graphics3d.polyhedron.origin_to_point(vertices, center)¶

Takes a set of vertices that have been created around the origin and translates them to the be centered around the x, y, z coordinates supplied in center.

Parameters:	vertices (list of lists (e.g. [[x1,y1,z1],[x2,y2,z2],..]) – The list of vertices around the origin center (list of floats) – The x, y, and z coordinates to center the `vertices` on

schrodinger.graphics3d.polyhedron.scale_vertices(vertices, scale)¶

Scale a set of vertices.

Parameters:	vertices (list of lists (e.g. [[x1,y1,z1],[x2,y2,z2],..]) – The list of vertices around the origin scale (float) – The scale to apply to the vertices

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