Package schrodinger :: Package application :: Package matsci :: Module shapes

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Module shapes

Classes and functions to handle various shapes.

Classes

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Vertex
Class to manage vertices.

Edge
Class to manage edges.

Face
Class to manage faces.

ConvexPolyhedron
Class to manage a convex polyhedron.

Cube
Class to manage a cube.

Tetrahedron
Class to manage a tetrahedron.

Octahedron
Class to manage an octahedron.

Dodecahedron
Class to manage a dodecahedron.

Icosahedron
Class to manage an icosahedron.

Cubeoctahedron
Class to manage a cubeoctahedron.

Parallelepiped
Class to manage a parallelepiped.

Slab
Class to manage a slab.

Sphere
Class to manage a sphere.

Cylinder
Class to manage a cylinder.

Functions

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object

get_shape_object_by_name(name)
Return a shape object by name.

float

get_polygon_area(vertices)
Return the area of the specified polygon using the shoelace formula.

list

get_reference_data(data, attr, num_unique, threshold)
Return a list containing the num_unique number of unique data.

list of numpy.array

get_parallelepiped_vertices(origin, a_vec, b_vec, c_vec, center=True)
Get the vertices of the specified parallelepiped.

numpy.array

get_centroid(vertices)
Return the centroid of the provided vertices.

Variables

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__doc__ = ...

_version = '$Revision 0.0 $'

ORIGIN = [0.0, 0.0, 0.0]

X_AXIS = array([ 1., 0., 0.])

Y_AXIS = array([ 0., 1., 0.])

Z_AXIS = array([ 0., 0., 1.])

TEMPLATE_ELEMENT = 'C'

TEMPLATE_BOND_ORDER = 1

INF_NAN_THRESH = 1e-12

DISTANCE_THRESH = 0.0001

SQRT2 = 1.41421356237

INVSQRT2 = 0.707106781187

GOLDEN = 1.61803398875

INVGOLDEN = 0.61803398875

PI = 3.14159265359

PLATONIC = 'platonic'

ARCHIMEDEAN = 'archimedean'

PRISM = 'prism'

BASIC = 'basic'

POLYHEDRON_TYPES = ['platonic', 'archimedean', 'prism']

LENGTH = 'length'

AREA = 'area'

COLINEAR_THRESH = 0.25

SHAPES_NAMES_TO_OBJECTS_DICT = OrderedDict([('cube', <class 's...

__package__ = 'schrodinger.application.matsci'

Function Details

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get_shape_object_by_name(name)

Return a shape object by name.

Parameters:

name (str) - the name of the object wanted

Returns: object

the shape object

get_polygon_area(vertices)

Return the area of the specified polygon using the shoelace formula.

Parameters:

vertices (list) - contains all vertices of the polygon, each of which is a two dimensional numpy.array, i.e. x and y

Returns: float

the area of the polygon

get_reference_data(data, attr, num_unique, threshold)

Return a list containing the num_unique number of unique data. The data will be either a list of Face or a list of Edge characterized using the attr AREA or LENGTH, respectively. These will be the reference data used to orient the polyhedron.

Parameters:

data (list) - either all Face objects for a given polyhedron or all Edge objects for a given face
attr (str) - the attribute on which to characterize the data, either AREA or LENGTH
num_unique (int) - the number of symmetry unique data
threshold (float) - the threshold used to consider if two data are equivalent by attr (either Ang. or Ang.^2)

Returns: list

unique data to serve as references

get_parallelepiped_vertices(origin, a_vec, b_vec, c_vec, center=True)

Get the vertices of the specified parallelepiped.

Parameters:

origin (numpy.array) - the point of origin of the lattic vectors
a_vec (numpy.array) - the a lattice vector
b_vec (numpy.array) - the b lattice vector
c_vec (numpy.array) - the c lattice vector
center (bool) - specifies whether or not to translate the final vertices so that the centroid is at (0, 0, 0)

Returns: list of numpy.array

the vertices of the parallelepiped

get_centroid(vertices)

Return the centroid of the provided vertices.

Parameters:

vertices (list) - numpy.array array of points

Returns: numpy.array

the centroid

Variables Details

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doc

Value:

"""
Classes and functions to handle various shapes.

Copyright Schrodinger, LLC.  All rights reserved."""

SHAPES_NAMES_TO_OBJECTS_DICT

Value:

OrderedDict([('cube', <class 'schrodinger.application.matsci.shapes.Cu
be'>), ('tetrahedron', <class 'schrodinger.application.matsci.shapes.T
etrahedron'>), ('octahedron', <class 'schrodinger.application.matsci.s
hapes.Octahedron'>), ('dodecahedron', <class 'schrodinger.application.
matsci.shapes.Dodecahedron'>), ('icosahedron', <class 'schrodinger.app
lication.matsci.shapes.Icosahedron'>), ('cubeoctahedron', <class 'schr
odinger.application.matsci.shapes.Cubeoctahedron'>), ('slab', <class '
schrodinger.application.matsci.shapes.Slab'>), ('parallelepiped', <cla
...