schrodinger.application.matsci.shapes module¶

Classes and functions to handle various shapes.

class schrodinger.application.matsci.shapes.ConvexPolyhedron(params, center, ref_face_idx, ref_face_normal_along, ref_edge_idx, ref_edge_along)¶

Bases: object

Class to manage a convex polyhedron.

addAlignmentAxesToTemplate()¶: Add unit vectors that mark the primary and secondary alignment axes to the template.

addNormalsToTemplate()¶: Add the normals of this convex polyhedron to its template.

addPointsToTemplate(points)¶

Add the specified points to this convex polyhedron’s template.

Parameters:	points (list of numpy.array) – contains the points to be added to the template for this convex polyhedron

addSegmentPlaneIntersectionsToTemplate(line_start, line_end)¶

Add to this polyhedron’s template the intersection points of the specified line segment and the planes containing the faces. Also draw connections between these points and the centers of the faces containing the planes that are being intersected.

Parameters:	line_start (numpy.array) – the start of the line segment line_end (numpy.array) – the end of the line segment

alignPolyhedron(vertices, face_vector, face_along, edge_vector, edge_along)¶

Return the polyhedron vertices rotated so as to align the face and edge vectors.

Parameters:	vertices (list) – list of Vertex face_vector (numpy.array triple) – the normal of the reference face to be rotated face_along (numpy.array triple) – the vector onto which the face normal will be rotated edge_vector (numpy.array triple) – the vector of the reference edge to be rotated edge_along (numpy.array triple) – the vector onto which the edge vector will be rotated, it is actually this vector’s component that is perpendicular to face_along that is used in the alignment, this is to safeguard against the case where edge_along and face_along are not perpendicular, if they are the same an exception is raised
Return type:	list
Returns:	list of rotated Vertex

allFacesIntersected()¶

Return True if all faces, not the planes containing those faces but the actual faces, of this convex polyhedron have been intersected at least once given all pointInside queries performed thus far.

Return type:	bool
Returns:	True if all faces have been intersected, False otherwise

getFaces(vertices, all_indices, num_unique)¶

Create face data for the polyhedron.

Parameters:	vertices (list) – list of scaled Vertex all_indices (list) – contains sub-lists specifying the vertex indices for each face num_unique (int) – the number of symmetry unique edges per face
Return type:	list
Returns:	a list of Face

getReferenceFaces(faces, num_unique)¶

Return a list containing the num_unique number of unique faces. These will be the reference faces used to orient the polyhedron.

Parameters:	faces (list) – all Face objects for this polyhedron num_unique (int) – the number of symmetry unique faces per polyhedron
Return type:	list
Returns:	unique Face objects to serve as references

getSegmentPlaneIntersections(line_start, line_end)¶

Return a two lists (1) of points where the given line segment intersects the planes containing this polyhedron’s faces and (2) the centers of the faces whose planes are being intersected.

Parameters:	line_start (numpy.array) – the start of the line segment line_end (numpy.array) – the end of the line segment
Return type:	two lists of numpy.array
Returns:	the intersection points and the centers of faces whose planes are being intersected

getSurfaceArea(faces)¶

Return the surface area of the polyhedron.

Parameters:	faces (list) – all Face objects for this polyhedron
Return type:	float
Returns:	the surface area in Ang.^2

getVertices(vertices, scale=1.0)¶

Create vertex data for the polyhedron, including an option to scale all vertices using a multiplicative factor.

Parameters:	vertices (list) – list of numpy.array triples specifying the vertices of this polyhedron scale (float) – multiplicative factor used to scale all vertices
Return type:	list
Returns:	a list of scaled Vertex

makeTemplate()¶

Create a template, i.e. structure object, for this convex polyhedron.

Return type:	`schrodinger.structure.Structure`
Returns:	the template structure

pointInside(point)¶

Return True if the query point is either on or inside of this convex polyhedron.

Parameters:	point (numpy.array) – the point in question
Return type:	bool
Returns:	True if the point in question is either on or inside this polyhedron, False otherwise

translateVertices(vertices, vector)¶

Translate the vertices by adding the specified vector.

Parameters:	vertices (list) – list of scaled Vertex vector (numpy.array triple) – the vector used to translate the vertices

updateShape(vertices)¶

Update the shape object using the provided vertices.

Parameters:	vertices (list) – list of Vertex with new coordinates

class schrodinger.application.matsci.shapes.Cube(scale, center=[0.0, 0.0, 0.0], ref_face_idx=1, ref_face_normal_along=array([ 0., 0., 1.]), ref_edge_idx=1, ref_edge_along=array([ 1., 0., 0.]))¶

Bases: schrodinger.application.matsci.shapes.ConvexPolyhedron

Class to manage a cube.

DEFAULT = [5.0]¶

DESCRIPTION = ['edge length']¶

INDICES = [[1, 3, 4, 2], [5, 1, 2, 6], [7, 5, 6, 8], [3, 7, 8, 4], [1, 5, 7, 3], [4, 8, 6, 2]]¶

NAME = 'cube'¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 1¶

TYPE = 'platonic'¶

VERTICES = [array([ 0.5, 0.5, 0.5]), array([ 0.5, 0.5, -0.5]), array([ 0.5, -0.5, 0.5]), array([ 0.5, -0.5, -0.5]), array([-0.5, 0.5, 0.5]), array([-0.5, 0.5, -0.5]), array([-0.5, -0.5, 0.5]), array([-0.5, -0.5, -0.5])]¶

getCircumRadius(length)¶

Return the circumradius.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	circumradius in Angstrom

getEdgeLength(circumradius)¶

Return the edge length.

Parameters:	circumradius (float) – circumradius in Angstrom
Return type:	float
Returns:	edge length in Angstrom

getVolume(length)¶

Return the volume.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	volume in cubic Angstrom

vertex = [-1.0, -1.0, -1.0]¶

class schrodinger.application.matsci.shapes.Cubeoctahedron(scale, center=[0.0, 0.0, 0.0], ref_face_idx=1, ref_face_normal_along=array([ 0., 0., 1.]), ref_edge_idx=1, ref_edge_along=array([ 1., 0., 0.]))¶

Bases: schrodinger.application.matsci.shapes.ConvexPolyhedron

Class to manage a cubeoctahedron.

DEFAULT = [5.0]¶

DESCRIPTION = ['edge length']¶

INDICES = [[2, 5, 11], [1, 9, 5], [5, 9, 7, 11], [11, 7, 4], [11, 4, 12, 2], [2, 12, 6], [2, 6, 1, 5], [1, 10, 3, 9], [9, 3, 7], [7, 3, 8, 4], [4, 8, 12], [12, 8, 10, 6], [6, 10, 1], [10, 8, 3]]¶

NAME = 'cubeoctahedron'¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 2¶

TYPE = 'archimedean'¶

VERTICES = [array([ 0.70710678, 0.70710678, 0. ]), array([ 0.70710678, -0.70710678, 0. ]), array([-0.70710678, 0.70710678, 0. ]), array([-0.70710678, -0.70710678, 0. ]), array([ 0.70710678, 0. , 0.70710678]), array([ 0.70710678, 0. , -0.70710678]), array([-0.70710678, 0. , 0.70710678]), array([-0.70710678, 0. , -0.70710678]), array([ 0. , 0.70710678, 0.70710678]), array([ 0. , 0.70710678, -0.70710678]), array([ 0. , -0.70710678, 0.70710678]), array([ 0. , -0.70710678, -0.70710678])]¶

getCircumRadius(length)¶

Return the circumradius.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	circumradius in Angstrom

getEdgeLength(circumradius)¶

Return the edge length.

Parameters:	circumradius (float) – circumradius in Angstrom
Return type:	float
Returns:	edge length in Angstrom

getVolume(length)¶

Return the volume.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	volume in cubic Angstrom

vertex = [0.0, -1.0, -1.0]¶

class schrodinger.application.matsci.shapes.Cylinder(radius, length, center=[0.0, 0.0, 0.0])¶

Bases: object

Class to manage a cylinder.

DEFAULT = [5.0, 25.0]¶

DESCRIPTION = ['radius', 'length']¶

NAME = 'cylinder'¶

NUM_UNIQUE_EDGES = 0¶

NUM_UNIQUE_FACES = 1¶

TYPE = 'basic'¶

getSurfaceArea(radius, length)¶

Return the surface area.

Parameters:	radius (float) – radius in Angstrom length (float) – length in Angstrom
Return type:	float
Returns:	surface area in square Angstrom

getVolume(radius, length)¶

Return the volume.

Parameters:	radius (float) – radius in Angstrom length (float) – length in Angstrom
Return type:	float
Returns:	volume in cubic Angstrom

pointInside(point)¶

Return True if the query point is either on or inside of this cylinder.

Parameters:	point (numpy.array) – the point in question
Return type:	bool
Returns:	True if the point in question is either on or inside this cylinder, False otherwise

class schrodinger.application.matsci.shapes.Dodecahedron(scale, center=[0.0, 0.0, 0.0], ref_face_idx=1, ref_face_normal_along=array([ 0., 0., 1.]), ref_edge_idx=1, ref_edge_along=array([ 1., 0., 0.]))¶

Bases: schrodinger.application.matsci.shapes.ConvexPolyhedron

Class to manage a dodecahedron.

DEFAULT = [3.0]¶

DESCRIPTION = ['edge length']¶

INDICES = [[6, 15, 13, 2, 10], [20, 6, 10, 12, 8], [19, 20, 8, 16, 7], [5, 19, 7, 11, 9], [15, 5, 9, 1, 13], [20, 19, 5, 15, 6], [10, 2, 18, 4, 12], [8, 12, 4, 14, 16], [7, 16, 14, 3, 11], [9, 11, 3, 17, 1], [13, 1, 17, 18, 2], [4, 18, 17, 3, 14]]¶

NAME = 'dodecahedron'¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 1¶

TYPE = 'platonic'¶

VERTICES = [array([ 0.80901699, 0.80901699, 0.80901699]), array([ 0.80901699, 0.80901699, -0.80901699]), array([ 0.80901699, -0.80901699, 0.80901699]), array([ 0.80901699, -0.80901699, -0.80901699]), array([-0.80901699, 0.80901699, 0.80901699]), array([-0.80901699, 0.80901699, -0.80901699]), array([-0.80901699, -0.80901699, 0.80901699]), array([-0.80901699, -0.80901699, -0.80901699]), array([ 0. , 0.5 , 1.30901699]), array([ 0. , 0.5 , -1.30901699]), array([ 0. , -0.5 , 1.30901699]), array([ 0. , -0.5 , -1.30901699]), array([ 0.5 , 1.30901699, 0. ]), array([ 0.5 , -1.30901699, 0. ]), array([-0.5 , 1.30901699, 0. ]), array([-0.5 , -1.30901699, 0. ]), array([ 1.30901699, 0. , 0.5 ]), array([ 1.30901699, 0. , -0.5 ]), array([-1.30901699, 0. , 0.5 ]), array([-1.30901699, 0. , -0.5 ])]¶

getCircumRadius(length)¶

Return the circumradius.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	circumradius in Angstrom

getEdgeLength(circumradius)¶

Return the edge length.

Parameters:	circumradius (float) – circumradius in Angstrom
Return type:	float
Returns:	edge length in Angstrom

getVolume(length)¶

Return the volume.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	volume in cubic Angstrom

vertex = [-1.618033988749895, 0.0, -0.6180339887498948]¶

class schrodinger.application.matsci.shapes.Edge(index, vertex_1, vertex_2)¶

Bases: object

Class to manage edges.

getLength()¶

Return the edge length.

Return type:	float
Returns:	the edge length in Ang.

class schrodinger.application.matsci.shapes.Face(index, indices, points, num_unique)¶

Bases: object

Class to manage faces.

getEdges()¶

Return a list of Edge.

Return type:	list
Returns:	contains all Edge for this face

getReferenceEdges(edges, num_unique)¶

Return a list containing the num_unique number of unique edges. These will be the reference edges used to orient the reference face of the polyhedron.

Parameters:	edges (list) – all Edge objects for this face num_unique (int) – the number of symmetry unique edges per face
Return type:	list
Returns:	unique Edge objects to serve as references

insideFace(point)¶

Return true if the query point lies on or inside the boundaries of this face, false otherwise.

Parameters:	point (numpy.array) – a query point
Return type:	bool
Returns:	true if the query point lies on or inside the face boundaries, false otherwise

intersectSegmentAndPlane(line_start, line_end, inf_nan_thresh=1e-12, distance_thresh=0.0001)¶

Return the intersection point of the specified line segment and the plane in which this face resides or return None if there is no intersection.

Parameters:	line_start (numpy.array) – the starting point of the line segment line_end (numpy.array) – the ending point of the line segment inf_nan_thresh (float) – this parameter handles numerical precision for inf and nan cases distance_thresh (float) – this parameter controls how the intersection of line segment end-points and a plane are handled for cases where one of the end-points lies in (or near) the plane (see the comment near the module level constant DISTANCE_THRESH)
Return type:	numpy.array or None
Returns:	the single point of intersection along the line segment or None if there is no intersection

setArea()¶: Set the area of this face.

setNormal()¶: Set the normal to this face.

class schrodinger.application.matsci.shapes.Icosahedron(scale, center=[0.0, 0.0, 0.0], ref_face_idx=1, ref_face_normal_along=array([ 0., 0., 1.]), ref_edge_idx=1, ref_edge_along=array([ 1., 0., 0.]))¶

Bases: schrodinger.application.matsci.shapes.ConvexPolyhedron

Class to manage an icosahedron.

DEFAULT = [5.0]¶

DESCRIPTION = ['edge length']¶

INDICES = [[2, 4, 12], [2, 12, 7], [2, 7, 5], [2, 5, 10], [2, 10, 4], [4, 10, 6], [4, 6, 8], [12, 4, 8], [12, 8, 11], [7, 12, 11], [7, 11, 1], [5, 7, 1], [5, 1, 9], [10, 5, 9], [10, 9, 6], [8, 6, 3], [11, 8, 3], [1, 11, 3], [9, 1, 3], [6, 9, 3]]¶

NAME = 'icosahedron'¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 1¶

TYPE = 'platonic'¶

VERTICES = [array([ 0. , 0.5 , 0.80901699]), array([ 0. , 0.5 , -0.80901699]), array([ 0. , -0.5 , 0.80901699]), array([ 0. , -0.5 , -0.80901699]), array([ 0.5 , 0.80901699, 0. ]), array([ 0.5 , -0.80901699, 0. ]), array([-0.5 , 0.80901699, 0. ]), array([-0.5 , -0.80901699, 0. ]), array([ 0.80901699, 0. , 0.5 ]), array([ 0.80901699, 0. , -0.5 ]), array([-0.80901699, 0. , 0.5 ]), array([-0.80901699, 0. , -0.5 ])]¶

getCircumRadius(length)¶

Return the circumradius.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	circumradius in Angstrom

getEdgeLength(circumradius)¶

Return the edge length.

Parameters:	circumradius (float) – circumradius in Angstrom
Return type:	float
Returns:	edge length in Angstrom

getVolume(length)¶

Return the volume.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	volume in cubic Angstrom

vertex = [-1.618033988749895, 0.0, -1.0]¶

class schrodinger.application.matsci.shapes.Octahedron(scale, center=[0.0, 0.0, 0.0], ref_face_idx=1, ref_face_normal_along=array([ 0., 0., 1.]), ref_edge_idx=1, ref_edge_along=array([ 1., 0., 0.]))¶

Bases: schrodinger.application.matsci.shapes.ConvexPolyhedron

Class to manage an octahedron.

DEFAULT = [8.0]¶

DESCRIPTION = ['edge length']¶

INDICES = [[6, 2, 3], [4, 2, 6], [5, 2, 4], [3, 2, 5], [6, 3, 1], [4, 6, 1], [5, 4, 1], [3, 5, 1]]¶

NAME = 'octahedron'¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 1¶

TYPE = 'platonic'¶

VERTICES = [array([ 0.70710678, 0. , 0. ]), array([-0.70710678, 0. , 0. ]), array([ 0. , 0.70710678, 0. ]), array([ 0. , -0.70710678, 0. ]), array([ 0. , 0. , 0.70710678]), array([ 0. , 0. , -0.70710678])]¶

getCircumRadius(length)¶

Return the circumradius.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	circumradius in Angstrom

getEdgeLength(circumradius)¶

Return the edge length.

Parameters:	circumradius (float) – circumradius in Angstrom
Return type:	float
Returns:	edge length in Angstrom

getVolume(length)¶

Return the volume.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	volume in cubic Angstrom

vertex = [0.0, 0.0, -1.0]¶

class schrodinger.application.matsci.shapes.Parallelepiped(a_param, b_param, c_param, alpha_param, beta_param, gamma_param, center=[0.0, 0.0, 0.0], ref_face_idx=1, ref_face_normal_along=array([ 0., 0., 1.]), ref_edge_idx=1, ref_edge_along=array([ 1., 0., 0.]))¶

Bases: schrodinger.application.matsci.shapes.ConvexPolyhedron

Class to manage a parallelepiped.

DEFAULT = [5.0, 10.0, 12.0, 60.0, 45.0, 80.0]¶

DESCRIPTION = ['edge a length', 'edge b length', 'edge c length', 'edge-edge b-c angle', 'edge-edge a-c angle', 'edge-edge a-b angle']¶

INDICES = [[1, 4, 3, 2], [5, 1, 2, 6], [4, 8, 7, 3], [8, 5, 6, 7], [8, 4, 1, 5], [6, 2, 3, 7]]¶

NAME = 'parallelepiped'¶

NUM_UNIQUE_EDGES = 2¶

NUM_UNIQUE_FACES = 3¶

TYPE = 'prism'¶

getParallelepipedVertices(origin, a_vec, b_vec, c_vec)¶

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
Return type:	list of numpy.array
Returns:	the vertices of the parallelepiped

getVolume(a_vec, b_vec, c_vec)¶

Return the volume.

Parameters:	a_vec (numpy.array) – the a lattice vector b_vec (numpy.array) – the b lattice vector c_vec (numpy.array) – the c lattice vector
Return type:	float
Returns:	volume in cubic Angstrom

class schrodinger.application.matsci.shapes.Slab(a_param, b_param, c_param, center=[0.0, 0.0, 0.0], ref_face_idx=1, ref_face_normal_along=array([ 0., 0., 1.]), ref_edge_idx=1, ref_edge_along=array([ 1., 0., 0.]))¶

Bases: schrodinger.application.matsci.shapes.Parallelepiped, schrodinger.application.matsci.shapes.ConvexPolyhedron

Class to manage a slab.

DEFAULT = [5.0, 10.0, 12.0]¶

DESCRIPTION = ['edge a length', 'edge b length', 'edge c length']¶

NAME = 'slab'¶

class schrodinger.application.matsci.shapes.Sphere(radius, center=[0.0, 0.0, 0.0])¶

Bases: object

Class to manage a sphere.

DEFAULT = [5.0]¶

DESCRIPTION = ['radius']¶

NAME = 'sphere'¶

NUM_UNIQUE_EDGES = 0¶

NUM_UNIQUE_FACES = 0¶

TYPE = 'basic'¶

getSurfaceArea(radius)¶

Return the surface area.

Parameters:	radius (float) – radius in Angstrom
Return type:	float
Returns:	surface area in square Angstrom

getVolume(radius)¶

Return the volume.

Parameters:	radius (float) – radius in Angstrom
Return type:	float
Returns:	volume in cubic Angstrom

pointInside(point)¶

Return True if the query point is either on or inside of this sphere.

Parameters:	point (numpy.array) – the point in question
Return type:	bool
Returns:	True if the point in question is either on or inside this sphere, False otherwise

class schrodinger.application.matsci.shapes.Tetrahedron(scale, center=[0.0, 0.0, 0.0], ref_face_idx=1, ref_face_normal_along=array([ 0., 0., 1.]), ref_edge_idx=1, ref_edge_along=array([ 1., 0., 0.]))¶

Bases: schrodinger.application.matsci.shapes.ConvexPolyhedron

Class to manage a tetrahedron.

DEFAULT = [10.0]¶

DESCRIPTION = ['edge length']¶

INDICES = [[1, 4, 2], [3, 4, 1], [2, 4, 3], [1, 2, 3]]¶

NAME = 'tetrahedron'¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 1¶

TYPE = 'platonic'¶

VERTICES = [array([ 0.5 , 0. , -0.35355339]), array([-0.5 , 0. , -0.35355339]), array([ 0. , 0.5 , 0.35355339]), array([ 0. , -0.5 , 0.35355339])]¶

getCircumRadius(length)¶

Return the circumradius.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	circumradius in Angstrom

getEdgeLength(circumradius)¶

Return the edge length.

Parameters:	circumradius (float) – circumradius in Angstrom
Return type:	float
Returns:	edge length in Angstrom

getVolume(length)¶

Return the volume.

Parameters:	length (float) – length in Angstrom
Return type:	float
Returns:	volume in cubic Angstrom

vertex = [0.0, -1.0, 0.7071067811865475]¶

class schrodinger.application.matsci.shapes.Vertex(index, coordinates)¶

Bases: object

Class to manage vertices.

schrodinger.application.matsci.shapes.get_centroid(vertices)¶

Return the centroid of the provided vertices.

Parameters:	vertices (list) – numpy.array array of points
Return type:	numpy.array
Returns:	the centroid

schrodinger.application.matsci.shapes.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)
Return type:	list of numpy.array
Returns:	the vertices of the parallelepiped

schrodinger.application.matsci.shapes.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
Return type:	float
Returns:	the area of the polygon

schrodinger.application.matsci.shapes.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)
Return type:	list
Returns:	unique data to serve as references

schrodinger.application.matsci.shapes.get_shape_object_by_name(name)¶

Return a shape object by name.

Parameters:	name (str) – the name of the object wanted
Return type:	object
Returns:	the shape object

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schrodinger.application.matsci.shapes module¶