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.

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.

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

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

Bases: schrodinger.graphics3d.common._MaestroPrimitiveMixin, schrodinger.graphics3d.common.Primitive

__init__(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

Create a polyhedron centered at center. Note that one of length, radius, or volume is needed to create the shape.

Parameters

center (list(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.
color – One of - Color object, Color name (string), or Tuple of (R, G, B) (each 0.0-1.0)
opacity (float) – 0.0 (invisible) through 1.0 (opaque). Defaults to 1.0
style (int) – LINE or FILL. Default is FILL.

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.
NotImplementedError – If the initiating subclass does not have a getVertices or getFaces method.

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

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.

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

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

getFaces(vertices)¶

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

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.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()

__init__(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

See: MaestroPolyhedronCore.__init__

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.

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

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)

# Hide the markers.
tetrahedron_grp.hide()

# Remove the markers
tetrahedron_grp.clear()

__init__(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

See: MaestroPolyhedronCore.__init__

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.

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

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.

__init__(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

See: MaestroPolyhedronCore.__init__

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.

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

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.

__init__(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

See: MaestroPolyhedronCore.__init__

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.

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

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.

__init__(center, mode, length=None, radius=None, volume=None, color='red', opacity=1.0, style=1)¶

See: MaestroPolyhedronCore.__init__

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.

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