schrodinger.application.matsci.shapes module¶

Classes and functions to handle various shapes.

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

Bases: object

Class to manage vertices.

__init__(index, coordinates)¶

Create a vertex instance.

Parameters

index (int) – the index of this vertex
coordinates (numpy.array) – the coordinates of this vertex

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

Bases: object

Class to manage edges.

__init__(index, vertex_1, vertex_2)¶

Create an edge instance.

Parameters

index (int) – the index of this edge
vertex_1 (Vertex) – the first vertex in this edge
vertex_2 (Vertex) – the second vertex in this edge

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.

__init__(index, indices, points, num_unique)¶

Create a face instance.

Parameters

index (int) – the index of this face
indices (list) – the indices of points making up this face
points (list of numpy.array) – the points making up this face
num_unique (int) – the number of symmetry unique edges per face

getEdges()¶

Return a list of Edge.

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

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

setArea()¶: Set the area of 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

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

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

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.

__init__(params, center, ref_face_idx, ref_face_normal_along, ref_edge_idx, ref_edge_along)¶

Create an instance.

Parameters

params (list) – list of floating point parameters defining the polyhedron
center (numpy.array) – the center of the polyhedron
ref_face_idx (int) – specifies which of this polyhedron’s available reference faces (symmetry unique faces sorted by decreasing area) to use in the alignment
ref_face_normal_along (numpy.array triple) – specifies the vector along which the reference face normal will be aligned
ref_edge_idx (int) – specifies which of the reference faces available reference edges (symmetry unique edges sorted by decreasing length) to use in the alignment
ref_edge_along (numpy.array triple) – specifies the vector along which the reference edge will be aligned

updateShape(vertices)¶

Update the shape object using the provided vertices.

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

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

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

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

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

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

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

makeTemplate()¶

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

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

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

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.

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

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

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

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

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.

NAME = 'cube'¶

DEFAULT = [5.0]¶

DESCRIPTION = ['edge length']¶

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])]¶

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]]¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 1¶

__init__(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.]))¶

Create an instance.

Parameters

scale (float) – multiplicative scaling factor
center (numpy.array) – the center of the polyhedron
ref_face_idx (int) – specifies which of this polyhedron’s available reference faces (symmetry unique faces sorted by decreasing area) to use in the alignment
ref_face_normal_along (numpy.array triple) – specifies the vector along which the reference face normal will be aligned
ref_edge_idx (int) – specifies which of the reference faces available reference edges (symmetry unique edges sorted by decreasing length) to use in the alignment
ref_edge_along (numpy.array triple) – specifies the vector along which the reference edge will be aligned

getEdgeLength(circumradius)¶

Return the edge length.

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

getCircumRadius(length)¶

Return the circumradius.

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

getVolume(length)¶

Return the volume.

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

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.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.

NAME = 'tetrahedron'¶

DEFAULT = [10.0]¶

DESCRIPTION = ['edge length']¶

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])]¶

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

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 1¶

__init__(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.]))¶

Create an instance.

Parameters

scale (float) – multiplicative scaling factor
center (numpy.array) – the center of the polyhedron
ref_face_idx (int) – specifies which of this polyhedron’s available reference faces (symmetry unique faces sorted by decreasing area) to use in the alignment
ref_face_normal_along (numpy.array triple) – specifies the vector along which the reference face normal will be aligned
ref_edge_idx (int) – specifies which of the reference faces available reference edges (symmetry unique edges sorted by decreasing length) to use in the alignment
ref_edge_along (numpy.array triple) – specifies the vector along which the reference edge will be aligned

getEdgeLength(circumradius)¶

Return the edge length.

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

getCircumRadius(length)¶

Return the circumradius.

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

getVolume(length)¶

Return the volume.

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

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.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.

NAME = 'octahedron'¶

DEFAULT = [8.0]¶

DESCRIPTION = ['edge length']¶

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])]¶

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]]¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 1¶

__init__(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.]))¶

Create an instance.

Parameters

scale (float) – multiplicative scaling factor
center (numpy.array) – the center of the polyhedron
ref_face_idx (int) – specifies which of this polyhedron’s available reference faces (symmetry unique faces sorted by decreasing area) to use in the alignment
ref_face_normal_along (numpy.array triple) – specifies the vector along which the reference face normal will be aligned
ref_edge_idx (int) – specifies which of the reference faces available reference edges (symmetry unique edges sorted by decreasing length) to use in the alignment
ref_edge_along (numpy.array triple) – specifies the vector along which the reference edge will be aligned

getEdgeLength(circumradius)¶

Return the edge length.

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

getCircumRadius(length)¶

Return the circumradius.

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

getVolume(length)¶

Return the volume.

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

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.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.

NAME = 'dodecahedron'¶

DEFAULT = [3.0]¶

DESCRIPTION = ['edge length']¶

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 ])]¶

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]]¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 1¶

__init__(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.]))¶

Create an instance.

Parameters

scale (float) – multiplicative scaling factor
center (numpy.array) – the center of the polyhedron
ref_face_idx (int) – specifies which of this polyhedron’s available reference faces (symmetry unique faces sorted by decreasing area) to use in the alignment
ref_face_normal_along (numpy.array triple) – specifies the vector along which the reference face normal will be aligned
ref_edge_idx (int) – specifies which of the reference faces available reference edges (symmetry unique edges sorted by decreasing length) to use in the alignment
ref_edge_along (numpy.array triple) – specifies the vector along which the reference edge will be aligned

getEdgeLength(circumradius)¶

Return the edge length.

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

getCircumRadius(length)¶

Return the circumradius.

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

getVolume(length)¶

Return the volume.

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

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.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.

NAME = 'icosahedron'¶

DEFAULT = [5.0]¶

DESCRIPTION = ['edge length']¶

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 ])]¶

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]]¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 1¶

__init__(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.]))¶

Create an instance.

Parameters

scale (float) – multiplicative scaling factor
center (numpy.array) – the center of the polyhedron
ref_face_idx (int) – specifies which of this polyhedron’s available reference faces (symmetry unique faces sorted by decreasing area) to use in the alignment
ref_face_normal_along (numpy.array triple) – specifies the vector along which the reference face normal will be aligned
ref_edge_idx (int) – specifies which of the reference faces available reference edges (symmetry unique edges sorted by decreasing length) to use in the alignment
ref_edge_along (numpy.array triple) – specifies the vector along which the reference edge will be aligned

getEdgeLength(circumradius)¶

Return the edge length.

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

getCircumRadius(length)¶

Return the circumradius.

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

getVolume(length)¶

Return the volume.

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

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.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.

NAME = 'cubeoctahedron'¶

DEFAULT = [5.0]¶

DESCRIPTION = ['edge length']¶

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])]¶

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]]¶

NUM_UNIQUE_EDGES = 1¶

NUM_UNIQUE_FACES = 2¶

__init__(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.]))¶

Create an instance.

Parameters

scale (float) – multiplicative scaling factor
center (numpy.array) – the center of the polyhedron
ref_face_idx (int) – specifies which of this polyhedron’s available reference faces (symmetry unique faces sorted by decreasing area) to use in the alignment
ref_face_normal_along (numpy.array triple) – specifies the vector along which the reference face normal will be aligned
ref_edge_idx (int) – specifies which of the reference faces available reference edges (symmetry unique edges sorted by decreasing length) to use in the alignment
ref_edge_along (numpy.array triple) – specifies the vector along which the reference edge will be aligned

getEdgeLength(circumradius)¶

Return the edge length.

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

getCircumRadius(length)¶

Return the circumradius.

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

getVolume(length)¶

Return the volume.

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

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.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.

NAME = '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']¶

TYPE = 'prism'¶

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]]¶

NUM_UNIQUE_EDGES = 2¶

NUM_UNIQUE_FACES = 3¶

__init__(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.]))¶

Create an instance.

Parameters

a_param (float) – the length of the parallelepiped along edge a
b_param (float) – the length of the parallelepiped along edge b
c_param (float) – the length of the parallelepiped along edge c
alpha_param (float) – the angle between edges b and c
beta_param (float) – the angle between edges a and c
gamma_param (float) – the angle between edges a and b
center (numpy.array) – the center of the polyhedron
ref_face_idx (int) – specifies which of this polyhedron’s available reference faces (symmetry unique faces sorted by decreasing area) to use in the alignment
ref_face_normal_along (numpy.array triple) – specifies the vector along which the reference face normal will be aligned
ref_edge_idx (int) – specifies which of the reference faces available reference edges (symmetry unique edges sorted by decreasing length) to use in the alignment
ref_edge_along (numpy.array triple) – specifies the vector along which the reference edge will be aligned

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

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.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.

NAME = 'slab'¶

DEFAULT = [5.0, 10.0, 12.0]¶

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

__init__(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.]))¶

Create an instance.

Parameters

a_param (float) – the length of the parallelepiped along edge a
b_param (float) – the length of the parallelepiped along edge b
c_param (float) – the length of the parallelepiped along edge c
center (numpy.array) – the center of the polyhedron
ref_face_idx (int) – specifies which of this polyhedron’s available reference faces (symmetry unique faces sorted by decreasing area) to use in the alignment
ref_face_normal_along (numpy.array triple) – specifies the vector along which the reference face normal will be aligned
ref_edge_idx (int) – specifies which of the reference faces available reference edges (symmetry unique edges sorted by decreasing length) to use in the alignment
ref_edge_along (numpy.array triple) – specifies the vector along which the reference edge will be aligned

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]]¶

NUM_UNIQUE_EDGES = 2¶

NUM_UNIQUE_FACES = 3¶

TYPE = 'prism'¶

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

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

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

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

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.Sphere(radius, center=[0.0, 0.0, 0.0])¶

Bases: object

Class to manage a sphere.

NAME = 'sphere'¶

DEFAULT = [5.0]¶

DESCRIPTION = ['radius']¶

TYPE = 'basic'¶

NUM_UNIQUE_EDGES = 0¶

NUM_UNIQUE_FACES = 0¶

__init__(radius, center=[0.0, 0.0, 0.0])¶

Create an instance.

Parameters

radius (float) – the radius of the sphere
center (numpy.array) – the center of the sphere

getVolume(radius)¶

Return the volume.

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

getSurfaceArea(radius)¶

Return the surface area.

Parameters: radius (float) – radius in Angstrom
Return type: float
Returns: surface area in square 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.Cylinder(radius, length, center=[0.0, 0.0, 0.0])¶

Bases: object

Class to manage a cylinder.

NAME = 'cylinder'¶

DEFAULT = [5.0, 25.0]¶

DESCRIPTION = ['radius', 'length']¶

TYPE = 'basic'¶

NUM_UNIQUE_EDGES = 0¶

NUM_UNIQUE_FACES = 1¶

__init__(radius, length, center=[0.0, 0.0, 0.0])¶

Create an instance.

Parameters

radius (float) – the radius of the cylinder
length (float) – the length of the cylinder
center (numpy.array) – the center of the cylinder

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

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

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

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

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_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_centroid(vertices)¶

Return the centroid of the provided vertices.

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