schrodinger.application.matsci.shapes module

Classes and functions to handle various shapes.

Copyright Schrodinger, LLC. All rights reserved.

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage vertices.\n ', '__init__': <function Vertex.__init__>, '__dict__': <attribute '__dict__' of 'Vertex' objects>, '__weakref__': <attribute '__weakref__' of 'Vertex' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage edges.\n ', '__init__': <function Edge.__init__>, 'getLength': <function Edge.getLength>, '__dict__': <attribute '__dict__' of 'Edge' objects>, '__weakref__': <attribute '__weakref__' of 'Edge' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage faces.\n ', '__init__': <function Face.__init__>, 'getEdges': <function Face.getEdges>, 'setNormal': <function Face.setNormal>, 'setArea': <function Face.setArea>, 'getReferenceEdges': <function Face.getReferenceEdges>, 'intersectSegmentAndPlane': <function Face.intersectSegmentAndPlane>, 'insideFace': <function Face.insideFace>, '__dict__': <attribute '__dict__' of 'Face' objects>, '__weakref__': <attribute '__weakref__' of 'Face' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage a convex polyhedron.\n ', '__init__': <function ConvexPolyhedron.__init__>, 'updateShape': <function ConvexPolyhedron.updateShape>, 'getVertices': <function ConvexPolyhedron.getVertices>, 'getFaces': <function ConvexPolyhedron.getFaces>, 'translateVertices': <function ConvexPolyhedron.translateVertices>, 'getSurfaceArea': <function ConvexPolyhedron.getSurfaceArea>, 'getReferenceFaces': <function ConvexPolyhedron.getReferenceFaces>, 'alignPolyhedron': <function ConvexPolyhedron.alignPolyhedron>, 'makeTemplate': <function ConvexPolyhedron.makeTemplate>, 'addPointsToTemplate': <function ConvexPolyhedron.addPointsToTemplate>, 'addAlignmentAxesToTemplate': <function ConvexPolyhedron.addAlignmentAxesToTemplate>, 'addNormalsToTemplate': <function ConvexPolyhedron.addNormalsToTemplate>, 'getSegmentPlaneIntersections': <function ConvexPolyhedron.getSegmentPlaneIntersections>, 'addSegmentPlaneIntersectionsToTemplate': <function ConvexPolyhedron.addSegmentPlaneIntersectionsToTemplate>, 'pointInside': <function ConvexPolyhedron.pointInside>, 'allFacesIntersected': <function ConvexPolyhedron.allFacesIntersected>, '__dict__': <attribute '__dict__' of 'ConvexPolyhedron' objects>, '__weakref__': <attribute '__weakref__' of 'ConvexPolyhedron' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage a cube.\n ', '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__': <function Cube.__init__>, 'getEdgeLength': <function Cube.getEdgeLength>, 'getCircumRadius': <function Cube.getCircumRadius>, 'getVolume': <function Cube.getVolume>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage a tetrahedron.\n ', '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__': <function Tetrahedron.__init__>, 'getEdgeLength': <function Tetrahedron.getEdgeLength>, 'getCircumRadius': <function Tetrahedron.getCircumRadius>, 'getVolume': <function Tetrahedron.getVolume>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage an octahedron.\n ', '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__': <function Octahedron.__init__>, 'getEdgeLength': <function Octahedron.getEdgeLength>, 'getCircumRadius': <function Octahedron.getCircumRadius>, 'getVolume': <function Octahedron.getVolume>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage a dodecahedron.\n ', '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__': <function Dodecahedron.__init__>, 'getEdgeLength': <function Dodecahedron.getEdgeLength>, 'getCircumRadius': <function Dodecahedron.getCircumRadius>, 'getVolume': <function Dodecahedron.getVolume>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage an icosahedron.\n ', '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__': <function Icosahedron.__init__>, 'getEdgeLength': <function Icosahedron.getEdgeLength>, 'getCircumRadius': <function Icosahedron.getCircumRadius>, 'getVolume': <function Icosahedron.getVolume>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage a cubeoctahedron.\n ', '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__': <function Cubeoctahedron.__init__>, 'getEdgeLength': <function Cubeoctahedron.getEdgeLength>, 'getCircumRadius': <function Cubeoctahedron.getCircumRadius>, 'getVolume': <function Cubeoctahedron.getVolume>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage a parallelepiped.\n ', '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__': <function Parallelepiped.__init__>, 'getParallelepipedVertices': <function Parallelepiped.getParallelepipedVertices>, 'getVolume': <function Parallelepiped.getVolume>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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'
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage a slab.\n ', 'NAME': 'slab', 'DEFAULT': [5.0, 10.0, 12.0], 'DESCRIPTION': ['edge a length', 'edge b length', 'edge c length'], '__init__': <function Slab.__init__>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage a sphere.\n ', 'NAME': 'sphere', 'DEFAULT': [5.0], 'DESCRIPTION': ['radius'], 'TYPE': 'basic', 'NUM_UNIQUE_EDGES': 0, 'NUM_UNIQUE_FACES': 0, '__init__': <function Sphere.__init__>, 'getVolume': <function Sphere.getVolume>, 'getSurfaceArea': <function Sphere.getSurfaceArea>, 'pointInside': <function Sphere.pointInside>, '__dict__': <attribute '__dict__' of 'Sphere' objects>, '__weakref__': <attribute '__weakref__' of 'Sphere' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.shapes', '__doc__': '\n Class to manage a cylinder.\n ', 'NAME': 'cylinder', 'DEFAULT': [5.0, 25.0], 'DESCRIPTION': ['radius', 'length'], 'TYPE': 'basic', 'NUM_UNIQUE_EDGES': 0, 'NUM_UNIQUE_FACES': 1, '__init__': <function Cylinder.__init__>, 'getVolume': <function Cylinder.getVolume>, 'getSurfaceArea': <function Cylinder.getSurfaceArea>, 'pointInside': <function Cylinder.pointInside>, '__dict__': <attribute '__dict__' of 'Cylinder' objects>, '__weakref__': <attribute '__weakref__' of 'Cylinder' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.shapes'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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