IMP::algebra Namespace Reference

See IMP.algebra Overview for more information.

Classes
class	BoundedGridRangeD
class	BoundingBoxD
	An axis-aligned bounding box. More...
class	Cone3D
class	Cylinder3D
class	DefaultEmbeddingD
struct	DenseGrid3D
class	DenseGridStorageD
class	DynamicNearestNeighbor3D
class	Ellipsoid3D
class	EuclideanVectorKDMetric
class	ExtendedGridIndexD
	An index in an infinite grid on space. More...
class	FixedXYZ
	A simple class for returning XYZ Euler angles. More...
class	FixedZXZ
	A simple class for returning ZXZ Euler angles. More...
class	FixedZYZ
	A simple class for returning ZYZ Euler angles. More...
class	GeometricPrimitiveD
class	GridD
	A voxel grid in d-dimensional space space. More...
class	GridIndexD
	Represent a real cell in a grid (one within the bounding box) More...
class	LinearFit2D
	Calculate line that fits best the input data points (Linear least squares) More...
class	LogEmbeddingD
class	MaxVectorKDMetric
class	NearestNeighborD
class	ParabolicFit2D
	Calculate parabola that fits best the input data points. More...
class	Plane3D
class	PrincipalComponentAnalysisD
class	ReferenceFrame3D
	A reference frame in 3D. More...
class	Reflection3D
	Reflect about a plane in 3D. More...
class	Rotation2D
	Stores a 2D rotation matrix. More...
class	Rotation3D
	3D rotation class. More...
class	Segment3D
struct	SparseGrid3D
class	SparseGridStorageD
struct	SparseUnboundedGrid3D
struct	SparseUnboundedGridD
class	SphereD
class	SpherePatch3D
class	SphericalVector3D
	Class to represent a 3D point in spherical coordinates. More...
class	Transformation2D
	Simple 2D transformation class. More...
class	Transformation3D
	Simple 3D transformation class. More...
class	Triangle3D
class	UnboundedGridRangeD
class	VectorD
	A Cartesian vector in D-dimensions. More...
class	VectorInputD
class	VectorInputD< 1 >
class	VectorKDMetric

Typedefs
typedef std::pair< Vector3D, double >	AxisAnglePair
typedef BoundingBoxD< 1 >	BoundingBox1D
typedef IMP::base::Vector < BoundingBox1D >	BoundingBox1Ds
typedef BoundingBoxD< 2 >	BoundingBox2D
typedef IMP::base::Vector < BoundingBox2D >	BoundingBox2Ds
typedef BoundingBoxD< 3 >	BoundingBox3D
typedef IMP::base::Vector < BoundingBox3D >	BoundingBox3Ds
typedef BoundingBoxD< 4 >	BoundingBox4D
typedef IMP::base::Vector < BoundingBox4D >	BoundingBox4Ds
typedef BoundingBoxD< 5 >	BoundingBox5D
typedef IMP::base::Vector < BoundingBox5D >	BoundingBox5Ds
typedef BoundingBoxD< 6 >	BoundingBox6D
typedef IMP::base::Vector < BoundingBox6D >	BoundingBox6Ds
typedef BoundingBoxD<-1 >	BoundingBoxKD
typedef IMP::base::Vector < BoundingBoxKD >	BoundingBoxKDs
typedef IMP::base::Vector< Cone3D >	Cone3Ds
typedef IMP::base::Vector < Cylinder3D >	Cylinder3Ds
typedef IMP::base::Vector < Ellipsoid3D >	Ellipsoid3Ds
typedef IMP::base::Vector < LinearFit2D >	LinearFit2Ds
typedef IMP::base::Vector < ParabolicFit2D >	ParabolicFit2Ds
typedef IMP::base::Vector < Plane3D >	Plane3Ds
typedef IMP::base::Vector < ReferenceFrame3D >	ReferenceFrame3Ds
typedef IMP::base::Vector < Reflection3D >	Reflection3Ds
typedef IMP::base::Vector < Rotation2D >	Rotation2Ds
typedef IMP::base::Vector < Rotation3D >	Rotation3Ds
typedef IMP::base::Vector < Segment3D >	Segment3Ds
typedef SphereD< 1 >	Sphere1D
typedef IMP::base::Vector < Sphere1D >	Sphere1Ds
typedef SphereD< 2 >	Sphere2D
typedef IMP::base::Vector < Sphere2D >	Sphere2Ds
typedef SphereD< 3 >	Sphere3D
typedef IMP::base::Vector < Sphere3D >	Sphere3Ds
typedef SphereD< 4 >	Sphere4D
typedef IMP::base::Vector < Sphere4D >	Sphere4Ds
typedef SphereD< 5 >	Sphere5D
typedef IMP::base::Vector < Sphere5D >	Sphere5Ds
typedef SphereD< 6 >	Sphere6D
typedef IMP::base::Vector < Sphere6D >	Sphere6Ds
typedef SphereD<-1 >	SphereKD
typedef IMP::base::Vector < SphereKD >	SphereKDs
typedef IMP::base::Vector < SpherePatch3D >	SpherePatch3Ds
typedef IMP::base::Vector < SphericalVector3D >	SphericalVector3Ds
typedef IMP::base::Vector < Transformation2D >	Transformation2Ds
typedef IMP::base::Vector < Transformation3D >	Transformation3Ds
typedef IMP::base::Vector < Triangle3D >	Triangle3Ds
typedef VectorD< 1 >	Vector1D
typedef base::Vector< VectorD< 1 > >	Vector1Ds
typedef VectorD< 2 >	Vector2D
typedef base::Vector< VectorD< 2 > >	Vector2Ds
typedef VectorD< 3 >	Vector3D
typedef base::Vector< VectorD< 3 > >	Vector3Ds
typedef VectorD< 4 >	Vector4D
typedef base::Vector< VectorD< 4 > >	Vector4Ds
typedef VectorD< 5 >	Vector5D
typedef base::Vector< VectorD< 5 > >	Vector5Ds
typedef VectorD< 6 >	Vector6D
typedef base::Vector< VectorD< 6 > >	Vector6Ds
typedef VectorInputD< 1 >	VectorInput1D
typedef base::Vector < VectorInputD< 1 > >	VectorInput1Ds
typedef VectorInputD< 2 >	VectorInput2D
typedef base::Vector < VectorInputD< 2 > >	VectorInput2Ds
typedef VectorInputD< 3 >	VectorInput3D
typedef base::Vector < VectorInputD< 3 > >	VectorInput3Ds
typedef VectorInputD< 4 >	VectorInput4D
typedef base::Vector < VectorInputD< 4 > >	VectorInput4Ds
typedef VectorInputD< 5 >	VectorInput5D
typedef base::Vector < VectorInputD< 5 > >	VectorInput5Ds
typedef VectorInputD< 6 >	VectorInput6D
typedef base::Vector < VectorInputD< 6 > >	VectorInput6Ds
typedef VectorInputD<-1 >	VectorInputKD
typedef base::Vector < VectorInputD<-1 > >	VectorInputKDs
typedef VectorD<-1 >	VectorKD
typedef IMP::base::Vector < IMP::base::Pointer < VectorKDMetric > >	VectorKDMetrics
typedef base::Vector< VectorD<-1 > >	VectorKDs

Functions
Rotation2D	compose (const Rotation2D &a, const Rotation2D &b)
	compose two rotations a and b More...
Transformation3D	compose (const Transformation3D &a, const Transformation3D &b)
	compose two transformations More...
Transformation2D	compose (const Transformation2D &a, const Transformation2D &b)
	compose two transformations More...
Rotation3D	compose (const Rotation3D &a, const Rotation3D &b)
Transformation3Ds	get_alignments_from_first_to_second (const PrincipalComponentAnalysisD< 3 > &pca1, const PrincipalComponentAnalysisD< 3 > &pca2)
bool	get_are_almost_equal (const double a, const double b, const double epsilon)
	Compares two values (intended for doubles) More...
bool	get_are_colinear (const Vector3D &p1, const Vector3D &p2, const Vector3D &p3)
	Return true if the three points are co-linear.
template<class Geometry >
double	get_area (const Geometry &)
	Compute the area of any surface object.
std::pair< Vector3D, double >	get_axis_and_angle (const Rotation3D &rot)
	Decompose a Rotation3D object into a rotation around an axis. More...
double	get_ball_radius_from_volume_3d (double volume)
	Return the radius of a sphere with a given volume.
template<int D>
VectorD< D >	get_basis_vector_d (unsigned int coordinate)
	Return the basis vector for the given coordinate. More...
VectorD<-1 >	get_basis_vector_kd (int D, unsigned int coordinate)
	Return a dynamically sized basis vector.
template<class Geometry >
BoundingBoxD< 3 >	get_bounding_box (const Geometry &)
	Compute the bounding box of any geometric object.
template<int D, class Storage , class Value , class Embedding >
BoundingBoxD< D >	get_bounding_box (const GridD< D, Storage, Value, Embedding > &g)
double	get_closer_power_of_2 (double x)
	Closest power of 2 for a number, not necessarily higher.
template<typename T >
T	get_constrained (const T x, const T x0, const T xF)
	Constrains a value between two given limits.
std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...
double	get_distance (const Segment3D &s, const Vector3D &p)
	Get the distance between a segment and a point. More...
double	get_distance (const Segment3D &a, const Segment3D &b)
	Get the distance between two segments. More...
double	get_distance (const Plane3D &pln, const Vector3D &p)
	Return the distance between a plane and a point in 3D. More...
template<int D>
double	get_distance (const SphereD< D > &a, const SphereD< D > &b)
	Return the distance between the two spheres if they are disjoint. More...
double	get_distance (const Rotation3D &r0, const Rotation3D &r1)
	Return a distance between the two rotations. More...
template<int D>
VectorD< D >	get_elementwise_product (const algebra::VectorD< D > &a, const algebra::VectorD< D > &b)
template<int D>
VectorD< D >	get_elementwise_product (const Ints &a, const algebra::VectorD< D > &b)
Sphere3D	get_enclosing_sphere (const Sphere3Ds &ss)
	Return a sphere containing the listed spheres. More...
Sphere3D	get_enclosing_sphere (const Vector3Ds &ss)
	Return a sphere containing the listed spheres. More...
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...
Rotation2D	get_identity_rotation_2d ()
	Builds an identity rotation in 2D.
Rotation3D	get_identity_rotation_3d ()
	Return a rotation that does not do anything. More...
Transformation2D	get_identity_transformation_2d ()
	Returns a transformation that does not do anything.
Transformation3D	get_identity_transformation_3d ()
	Return a transformation that does not do anything. More...
template<int D>
bool	get_interiors_intersect (const SphereD< D > &a, const SphereD< D > &b)
	Return true if the two balls bounded by the two spheres interesect.
Rotation3D	get_interpolated (const Rotation3D &a, const Rotation3D &b, double f)
	Interpolate between two rotations. More...
Triangle3D	get_largest_triangle (const Vector3Ds &points)
	Return the largest triangle defined by 3 points from the input. More...
template<int D, class Storage , class Value , class Embedding >
Value	get_linearly_interpolated (const GridD< D, Storage, Value, Embedding > &g, const VectorD< D > &pt)
float	get_next_larger_power_of_2 (float x)
	Closest power of 2 that can contain a number x.
double	get_next_larger_power_of_2 (double x)
	Closest power of 2 that can contain a number x.
template<int D>
VectorD< D >	get_ones_vector_d (double v=1)
	Return a vector of ones (or another constant)
VectorD<-1 >	get_ones_vector_kd (unsigned int D, double v=1)
	Return a vector of ones (or another constant)
template<int D>
double	get_power_distance (const SphereD< D > &a, const SphereD< D > &b)
	Return the power distance between the two spheres. More...
template<int D>
PrincipalComponentAnalysisD< D >	get_principal_components (const base::Vector< VectorD< D > > &ps)
	Perform principal components analysis on a set of vectors.
Transformation3D	get_random_local_transformation (Vector3D origin, double max_translation=5., double max_angle_in_rad=0.26)
	Get a local transformation. More...
Rotation2D	get_random_rotation_2d ()
	Builds an identity rotation in 2D.
Rotation3D	get_random_rotation_3d ()
	Pick a rotation at random from all possible rotations. More...
Rotation3D	get_random_rotation_3d (const Rotation3D &center, double distance)
	Pick a rotation at random near the provided one. More...
Vector3D	get_reflected (const Plane3D &pln, const Vector3D &p)
	return the point reflected about the plane
double	get_relative_projection_on_segment (const Segment3D &s, const algebra::Vector3D &p)
Rotation3D	get_rotation_about_axis (const Vector3D &axis, double angle)
	Generate a Rotation3D object from a rotation around an axis. More...
Transformation3D	get_rotation_about_point (const Vector3D &point, const Rotation3D &rotation)
	Generate a Transformation3D object from a rotation around a point. More...
Transformation2D	get_rotation_about_point (const Vector2D &point, const Rotation2D &rotation)
	Generates a Transformation2D object from a rotation around a point. More...
Rotation3D	get_rotation_from_matrix (double m00, double m01, double m02, double m10, double m11, double m12, double m20, double m21, double m22)
	Generate a Rotation3D object from a rotation matrix.
Rotation3D	get_rotation_from_vector4d (const VectorD< 4 > &v)
	Compute a rotatation from an unnormalized quaternion. More...
Rotation3D	get_rotation_from_x_y_axes (const Vector3D &x, const Vector3D &y)
Rotation3D	get_rotation_taking_first_to_second (const Vector3D &v1, const Vector3D &v2)
	Create a rotation from the first vector to the second one.
Rotation2D	get_rotation_to_x_axis (const Vector2D &v)
template<typename T >
int	get_rounded (const T &x)
	Rounds a number to next integer. More...
template<typename T >
int	get_sign (const T &x)
	Sign of a number. 1 if the number is higher or equal to 0 and -1 otherwise.
double	get_squared (double x)
template<class Geometry >
double	get_surface_area (const Geometry &)
	Compute the surface area of any volumetric object.
FloatPair	get_surface_area_and_volume (const algebra::Sphere3Ds &ss)
Transformation3D	get_transformation_3d (const Transformation2D &t2d)
	Builds a 3D transformation from a 2D one. More...
template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >
IMP::algebra::Transformation3D	get_transformation_aligning_first_to_second (const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
	Compute the rigid transform bringing the first point set to the second. More...
Transformation2D	get_transformation_aligning_pair (const Vector2Ds &set_from, const Vector2Ds &set_to)
Transformation3D	get_transformation_from_first_to_second (const ReferenceFrame3D &a, const ReferenceFrame3D &b)
Transformation3D	get_transformation_from_first_triangle_to_second (Triangle3D first_tri, Triangle3D second_tri)
	Return a transformation between two triangles.
ReferenceFrame3D	get_transformed (const ReferenceFrame3D &rf, const Transformation3D &tr)
BoundingBoxD< 3 >	get_transformed (const BoundingBoxD< 3 > &bb, const Transformation3D &tr)
	Return a bounding box containing the transformed box.
template<class Storage , class Embedding >
const Storage::Value	get_trilinearly_interpolated (const GridD< 3, Storage, typename Storage::Value, Embedding > &g, const Vector3D &v, const typename Storage::Value &outside=0)
	Use trilinear interpolation to compute a smoothed value at v. More...
Rotation3Ds	get_uniform_cover_rotations_3d (unsigned int num_points)
	Cover the space of rotations evenly. More...
algebra::Rotation3Ds	get_uniformly_sampled_rotations (double delta)
	Generates a nondegenerate set of Euler angles with a delta resolution. More...
template<unsigned int D>
SphereD< D >	get_unit_sphere_d ()
SphereD<-1 >	get_unit_sphere_kd (unsigned int d)
template<int D>
VectorD< D >	get_vector_d_geometry (const SphereD< D > &s)
template<class Geometry >
double	get_volume (const Geometry &)
	Compute the volume of any volumetric object.
template<int D>
VectorD< D >	get_zero_vector_d ()
	Return a vector of zeros.
VectorD<-1 >	get_zero_vector_kd (int D)
	Return a dynamically sized vector of zeros.
void	set_segment_3d_geometry (Segment3D &g, const Segment3D &gi)

Variables
static const double	PI = 3.1415926535897931
	the constant pi

Standard module methods
All IMP modules have a set of standard methods to help get information about the module and about files associated with the module.
std::string	get_module_version ()
std::string	get_module_name ()

Endian
IMP provides a variety of functionality to manage byte order in input and output data.
void	reversed_read (void *dest, size_t size, size_t nitems, std::ifstream &f, bool reverse)
	Reads from file in normal or reverse order. More...
void	reversed_write (const void *src, size_t size, size_t nitems, std::ofstream &f, bool reverse=false)
	Writes to a file in normal or reversed order. More...
template<class T >
void	get_swapped_endian (T &x)
	Conversion between little and big endian. Goes both ways.
bool	get_is_big_endian ()
	Returns 1 if machine is big endian else 0.
bool	get_is_little_endian ()
	Returns 1 if machine is little endian else 0.

Simple geometric IO
These functions write geometry to text files, one line per geometric primitive. Each line has the form “x y z” for points or “x y z r” for spheres. We can easily add general dimension support if requested.. Lines beginning with "#" are treated as comments.
void	write_pts (const Vector3Ds &vs, base::TextOutput out)
	Write a set of 3D vectors to a file. More...
Vector3Ds	read_pts (base::TextInput input)
	Read a set of 3D vectors from a file. More...
void	write_spheres (const Sphere3Ds &vs, base::TextOutput out)
	Write a set of 3d spheres to a file. More...
Sphere3Ds	read_spheres (base::TextInput input)
	Read a set of 3d spheres from a file. More...

Python Only
The following functions are only availale in Python as the equivalent C++ functionality is provided via template functions or in other ways that don't directly map to python.
typedef Grid3D< int, SparseGridStorage3D< int, BoundedGridStorage3D > >	SparseIntGrid3D
typedef Grid3D< int, SparseGridStorage3D< int, UnboundedGridStorage3D > >	SparseUnboundedIntGrid3D
typedef Grid3D< double, DenseGridStorage3D< double > >	DenseDoubleGrid3D
typedef Grid3D< float, DenseGridStorage3D< float > >	DenseFloatGrid3D
Transformation3D	get_transformation_aligning_first_to_second (Vector3Ds a, Vector3Ds b)

Euler Angles
There are many conventions for how to define Euler angles, based on choices of which of the x,y,z axis to use in what order and whether the rotation axis is in the body frame (and hence affected by previous rotations) or in in a fixed frame. See http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles for a general description. All Euler angles are specified in radians. The names are all rotation_from_{fixed/body}_abc() where abc is the ordering of x,y,z.
typedef IMP::base::Vector < FixedZYZ >	FixedZYZs
typedef IMP::base::Vector < FixedZXZ >	FixedZXZs
typedef IMP::base::Vector < FixedXYZ >	FixedXYZs
Rotation3D	get_rotation_from_fixed_xyz (double xr, double yr, double zr)
	Initialize a rotation in x-y-z order from three angles. More...
Rotation3D	get_rotation_from_fixed_zxz (double phi, double theta, double psi)
	Initialize a rotation from euler angles. More...
Rotation3D	get_rotation_from_fixed_zyz (double Rot, double Tilt, double Psi)
	Generate a rotation object from Euler Angles. More...
FixedZYZ	get_fixed_zyz_from_rotation (const Rotation3D &r)
	The inverse of rotation_from_fixed_zyz() More...
FixedZXZ	get_fixed_zxz_from_rotation (const Rotation3D &r)
	The inverse of rotation_from_fixed_zyz() More...
FixedXYZ	get_fixed_xyz_from_rotation (const Rotation3D &r)
	The inverse of rotation_from_fixed_xyz() More...

Shortest segments
These methods return the shortest segment connecting two geometric objects. Such segments can be used to give the direction of the derivative of the distance between the two objects. The 0 point on the segment is in the first passed object and the 1 point is in the second.
Segment3D	get_shortest_segment (const Segment3D &s, const Vector3D &p)
Segment3D	get_shortest_segment (const Segment3D &sa, const Segment3D &sb)

3D Vectors
We provide a specialization of VectorD for 3-space and several additional functions on it.
Vector3D	get_vector_product (const Vector3D &p1, const Vector3D &p2)
	Returns the vector product (cross product) of two vectors.
Vector3D	get_orthogonal_vector (const Vector3D &v)
	Return a vector that is perpendicular to the given vector. More...
Vector3D	get_centroid (const Vector3Ds &ps)
	Returns the centroid of a set of vectors.
double	get_radius_of_gyration (const Vector3Ds &ps)
	Return the radius of gyration of a set of points. More...

Vector Generators
These functions generate vector objects. Some of the methods, those with random in their name, generate a single vector chosen uniformly from the specified domain. Others, the cover methods, generate a set of points distributed (somewhat) evenly over the domain.
template<int D>
VectorD< D >	get_random_vector_in (const BoundingBoxD< D > &bb)
	Generate a random vector in a box with uniform density.
template<int D>
VectorD< D >	get_random_vector_on (const BoundingBoxD< D > &bb)
	Generate a random vector on a box with uniform density.
template<int D>
VectorD< D >	get_random_vector_in (const SphereD< D > &s)
	Generate a random vector in a sphere with uniform density.
VectorD< 2 >	get_random_vector_in (const SphereD< 2 > &s)
Vector3D	get_random_vector_in (const Cylinder3D &c)
	Generate a random vector in a cylinder with uniform density.
template<int D>
VectorD< D >	get_random_vector_on (const SphereD< D > &s)
	Generate a random vector on a sphere with uniform density.
template<int D>
base::Vector< VectorD< D > >	get_uniform_surface_cover (const SphereD< D > &s, unsigned int n)
	Generate a set of vectors which covers a sphere uniformly. More...
Vector3Ds	get_uniform_surface_cover (const Cylinder3D &cyl, int number_of_points)
	Generate a set of 3d points that uniformly cover a cylinder.
template<int D>
base::Vector< VectorD< D > >	get_uniform_upper_hemisphere_cover (const SphereD< D > &s, unsigned int n)
	Generate a set of 3D points that uniformly cover a hemisphere. More...
Vector3Ds	get_grid_surface_cover (const Cylinder3D &cyl, int number_of_cycles, int number_of_points_on_cycle)
	Generate a grid of 3d points on a cylinder surface.
Vector3Ds	get_uniform_surface_cover (const SpherePatch3D &sph, unsigned int number_of_points)
	Generate a set of 3d points that uniformly cover a patch of a sphere. More...
Vector3Ds	get_uniform_surface_cover (const Cone3D &cone, unsigned int number_of_points)
template<int D>
base::Vector< VectorD< D > >	get_grid_interior_cover_by_spacing (const BoundingBoxD< D > &bb, double s)
Vector3Ds	get_random_chain (unsigned int n, double r, const Vector3D &start=Vector3D(0, 0, 0), const Sphere3Ds &obstacles=Sphere3Ds())
	Generate a random chain with no collisions. More...

Norms
We define a number of standard, \(L^p\), norms on VectorD. \(L^1\) is the Manhattan distance, the sum of the components \(L^2\) is the standard Euclidean length \(L^{\inf}\) is the maximum of the components
template<int D>
double	get_l2_norm (const VectorD< D > &v)
template<int D>
double	get_l1_norm (const VectorD< D > &v)
template<int D>
double	get_linf_norm (const VectorD< D > &v)

Typedef Documentation

typedef BoundingBoxD<1> IMP::algebra::BoundingBox1D

Typedef for python.

Definition at line 165 of file BoundingBoxD.h.

typedef IMP::base::Vector< BoundingBox1D > IMP::algebra::BoundingBox1Ds

Pass or store a set of BoundingBox1D .

Definition at line 165 of file BoundingBoxD.h.

typedef BoundingBoxD<2> IMP::algebra::BoundingBox2D

Typedef for python.

Definition at line 165 of file BoundingBoxD.h.

typedef IMP::base::Vector< BoundingBox2D > IMP::algebra::BoundingBox2Ds

Pass or store a set of BoundingBox2D .

Definition at line 165 of file BoundingBoxD.h.

typedef BoundingBoxD<3> IMP::algebra::BoundingBox3D

Typedef for python.

Definition at line 165 of file BoundingBoxD.h.

typedef IMP::base::Vector< BoundingBox3D > IMP::algebra::BoundingBox3Ds

Pass or store a set of BoundingBox3D .

Definition at line 165 of file BoundingBoxD.h.

typedef BoundingBoxD<4> IMP::algebra::BoundingBox4D

Typedef for python.

Definition at line 165 of file BoundingBoxD.h.

typedef IMP::base::Vector< BoundingBox4D > IMP::algebra::BoundingBox4Ds

Pass or store a set of BoundingBox4D .

Definition at line 165 of file BoundingBoxD.h.

typedef BoundingBoxD<5> IMP::algebra::BoundingBox5D

Typedef for python.

Definition at line 165 of file BoundingBoxD.h.

typedef IMP::base::Vector< BoundingBox5D > IMP::algebra::BoundingBox5Ds

Pass or store a set of BoundingBox5D .

Definition at line 165 of file BoundingBoxD.h.

typedef BoundingBoxD<6> IMP::algebra::BoundingBox6D

Typedef for python.

Definition at line 165 of file BoundingBoxD.h.

typedef IMP::base::Vector< BoundingBox6D > IMP::algebra::BoundingBox6Ds

Pass or store a set of BoundingBox6D .

Definition at line 165 of file BoundingBoxD.h.

typedef BoundingBoxD<-1> IMP::algebra::BoundingBoxKD

Typedef for python.

Definition at line 165 of file BoundingBoxD.h.

typedef IMP::base::Vector< BoundingBoxKD > IMP::algebra::BoundingBoxKDs

Pass or store a set of BoundingBoxKD .

Definition at line 165 of file BoundingBoxD.h.

typedef IMP::base::Vector< Cone3D > IMP::algebra::Cone3Ds

Pass or store a set of Cone3D .

Definition at line 65 of file Cone3D.h.

typedef IMP::base::Vector< Cylinder3D > IMP::algebra::Cylinder3Ds

Pass or store a set of Cylinder3D .

Definition at line 85 of file Cylinder3D.h.

typedef Grid3D<double, DenseGridStorage3D<double> > IMP::algebra::DenseDoubleGrid3D

A grid of doubles over a region of space.

Definition at line 92 of file algebra/python_only.h.

typedef Grid3D<float, DenseGridStorage3D<float> > IMP::algebra::DenseFloatGrid3D

A grid of floats over a region of space.

Definition at line 95 of file algebra/python_only.h.

typedef IMP::base::Vector< Ellipsoid3D > IMP::algebra::Ellipsoid3Ds

Pass or store a set of Ellipsoid3D .

Definition at line 66 of file Ellipsoid3D.h.

typedef IMP::base::Vector< FixedXYZ > IMP::algebra::FixedXYZs

Pass or store a set of FixedXYZ .

Definition at line 476 of file Rotation3D.h.

typedef IMP::base::Vector< FixedZXZ > IMP::algebra::FixedZXZs

Pass or store a set of FixedZXZ .

Definition at line 452 of file Rotation3D.h.

typedef IMP::base::Vector< FixedZYZ > IMP::algebra::FixedZYZs

Pass or store a set of FixedZYZ .

Definition at line 426 of file Rotation3D.h.

typedef IMP::base::Vector< LinearFit2D > IMP::algebra::LinearFit2Ds

Pass or store a set of LinearFit2D .

Definition at line 54 of file LinearFit.h.

typedef IMP::base::Vector< ParabolicFit2D > IMP::algebra::ParabolicFit2Ds

Pass or store a set of ParabolicFit2D .

Definition at line 56 of file ParabolicFit.h.

typedef IMP::base::Vector< Plane3D > IMP::algebra::Plane3Ds

Pass or store a set of Plane3D .

Definition at line 103 of file Plane3D.h.

typedef IMP::base::Vector< ReferenceFrame3D > IMP::algebra::ReferenceFrame3Ds

Pass or store a set of ReferenceFrame3D .

Definition at line 84 of file ReferenceFrame3D.h.

typedef IMP::base::Vector< Reflection3D > IMP::algebra::Reflection3Ds

Pass or store a set of Reflection3D .

Definition at line 37 of file Reflection3D.h.

typedef IMP::base::Vector< Rotation2D > IMP::algebra::Rotation2Ds

Pass or store a set of Rotation2D .

Definition at line 123 of file Rotation2D.h.

typedef IMP::base::Vector< Rotation3D > IMP::algebra::Rotation3Ds

Pass or store a set of Rotation3D .

Definition at line 220 of file Rotation3D.h.

typedef IMP::base::Vector< Segment3D > IMP::algebra::Segment3Ds

Pass or store a set of Segment3D .

Definition at line 54 of file Segment3D.h.

typedef Grid3D<int, SparseGridStorage3D<int, BoundedGridStorage3D> > IMP::algebra::SparseIntGrid3D

A sparse grid of integers over a bounded region of space.

Definition at line 85 of file algebra/python_only.h.

typedef Grid3D<int, SparseGridStorage3D<int, UnboundedGridStorage3D> > IMP::algebra::SparseUnboundedIntGrid3D

A sparse grid of integers over all of space.

Definition at line 89 of file algebra/python_only.h.

typedef SphereD<1> IMP::algebra::Sphere1D

Typedef for python.

Definition at line 103 of file SphereD.h.

typedef IMP::base::Vector< Sphere1D > IMP::algebra::Sphere1Ds

Pass or store a set of Sphere1D .

Definition at line 103 of file SphereD.h.

typedef SphereD<2> IMP::algebra::Sphere2D

Typedef for python.

Definition at line 103 of file SphereD.h.

typedef IMP::base::Vector< Sphere2D > IMP::algebra::Sphere2Ds

Pass or store a set of Sphere2D .

Definition at line 103 of file SphereD.h.

typedef SphereD<3> IMP::algebra::Sphere3D

Typedef for python.

Definition at line 103 of file SphereD.h.

typedef IMP::base::Vector< Sphere3D > IMP::algebra::Sphere3Ds

Pass or store a set of Sphere3D .

Definition at line 103 of file SphereD.h.

typedef SphereD<4> IMP::algebra::Sphere4D

Typedef for python.

Definition at line 103 of file SphereD.h.

typedef IMP::base::Vector< Sphere4D > IMP::algebra::Sphere4Ds

Pass or store a set of Sphere4D .

Definition at line 103 of file SphereD.h.

typedef SphereD<5> IMP::algebra::Sphere5D

Typedef for python.

Definition at line 103 of file SphereD.h.

typedef IMP::base::Vector< Sphere5D > IMP::algebra::Sphere5Ds

Pass or store a set of Sphere5D .

Definition at line 103 of file SphereD.h.

typedef SphereD<6> IMP::algebra::Sphere6D

Typedef for python.

Definition at line 103 of file SphereD.h.

typedef IMP::base::Vector< Sphere6D > IMP::algebra::Sphere6Ds

Pass or store a set of Sphere6D .

Definition at line 103 of file SphereD.h.

typedef SphereD<-1> IMP::algebra::SphereKD

Typedef for python.

Definition at line 103 of file SphereD.h.

typedef IMP::base::Vector< SphereKD > IMP::algebra::SphereKDs

Pass or store a set of SphereKD .

Definition at line 103 of file SphereD.h.

typedef IMP::base::Vector< SpherePatch3D > IMP::algebra::SpherePatch3Ds

Pass or store a set of SpherePatch3D .

Definition at line 51 of file SpherePatch3D.h.

typedef IMP::base::Vector< SphericalVector3D > IMP::algebra::SphericalVector3Ds

Pass or store a set of SphericalVector3D .

Definition at line 83 of file SphericalVector3D.h.

typedef IMP::base::Vector< Transformation2D > IMP::algebra::Transformation2Ds

Pass or store a set of Transformation2D .

Definition at line 123 of file Transformation2D.h.

typedef IMP::base::Vector< Transformation3D > IMP::algebra::Transformation3Ds

Pass or store a set of Transformation3D .

Definition at line 91 of file Transformation3D.h.

typedef IMP::base::Vector< Triangle3D > IMP::algebra::Triangle3Ds

Pass or store a set of Triangle3D .

Definition at line 42 of file Triangle3D.h.

typedef VectorD<1> IMP::algebra::Vector1D

1D vector typedef for swig

Definition at line 566 of file VectorD.h.

typedef base::Vector<VectorD<1> > IMP::algebra::Vector1Ds

1D vectors typedef for swig

Definition at line 568 of file VectorD.h.

typedef VectorD<2> IMP::algebra::Vector2D

2D vector typedef for swig

Definition at line 570 of file VectorD.h.

typedef base::Vector<VectorD<2> > IMP::algebra::Vector2Ds

2D vectors typedef for swig

Definition at line 572 of file VectorD.h.

typedef VectorD<3> IMP::algebra::Vector3D

3D vector typedef for swig

Definition at line 574 of file VectorD.h.

typedef base::Vector<VectorD<3> > IMP::algebra::Vector3Ds

3D vectors typedef for swig

Definition at line 576 of file VectorD.h.

typedef VectorD<4> IMP::algebra::Vector4D

4D vector typedef for swig

Definition at line 578 of file VectorD.h.

typedef base::Vector<VectorD<4> > IMP::algebra::Vector4Ds

4D vectors typedef for swig

Definition at line 580 of file VectorD.h.

typedef VectorD<5> IMP::algebra::Vector5D

5D vector typedef for swig

Definition at line 582 of file VectorD.h.

typedef base::Vector<VectorD<5> > IMP::algebra::Vector5Ds

5D vectors typedef for swig

Definition at line 584 of file VectorD.h.

typedef VectorD<6> IMP::algebra::Vector6D

6D vector typedef for swig

Definition at line 586 of file VectorD.h.

typedef base::Vector<VectorD<6> > IMP::algebra::Vector6Ds

6D vector typedef for swig

Definition at line 588 of file VectorD.h.

typedef VectorInputD<1> IMP::algebra::VectorInput1D

Typedef for python.

Definition at line 657 of file VectorD.h.

typedef base::Vector<VectorInputD<1> > IMP::algebra::VectorInput1Ds

Typedef for python.

Definition at line 659 of file VectorD.h.

typedef VectorInputD<2> IMP::algebra::VectorInput2D

Typedef for python.

Definition at line 661 of file VectorD.h.

typedef base::Vector<VectorInputD<2> > IMP::algebra::VectorInput2Ds

Typedef for python.

Definition at line 663 of file VectorD.h.

typedef VectorInputD<3> IMP::algebra::VectorInput3D

Typedef for python.

Definition at line 665 of file VectorD.h.

typedef base::Vector<VectorInputD<3> > IMP::algebra::VectorInput3Ds

Typedef for python.

Definition at line 667 of file VectorD.h.

typedef VectorInputD<4> IMP::algebra::VectorInput4D

Typedef for python.

Definition at line 669 of file VectorD.h.

typedef base::Vector<VectorInputD<4> > IMP::algebra::VectorInput4Ds

Typedef for python.

Definition at line 671 of file VectorD.h.

typedef VectorInputD<5> IMP::algebra::VectorInput5D

Typedef for python.

Definition at line 673 of file VectorD.h.

typedef base::Vector<VectorInputD<5> > IMP::algebra::VectorInput5Ds

Typedef for python.

Definition at line 675 of file VectorD.h.

typedef VectorInputD<6> IMP::algebra::VectorInput6D

Typedef for python.

Definition at line 677 of file VectorD.h.

typedef base::Vector<VectorInputD<6> > IMP::algebra::VectorInput6Ds

Typedef for python.

Definition at line 679 of file VectorD.h.

typedef VectorInputD<-1> IMP::algebra::VectorInputKD

Typedef for python.

Definition at line 681 of file VectorD.h.

typedef base::Vector<VectorInputD<-1> > IMP::algebra::VectorInputKDs

Typedef for python.

Definition at line 683 of file VectorD.h.

typedef VectorD<-1> IMP::algebra::VectorKD

KD vector typedef for swig

Definition at line 590 of file VectorD.h.

typedef IMP::base::Vector<IMP::base::Pointer< VectorKDMetric > > IMP::algebra::VectorKDMetrics

Store a set of objects.

Definition at line 33 of file vector_metrics.h.

typedef base::Vector<VectorD<-1> > IMP::algebra::VectorKDs

KD vectors typedef for swig

Definition at line 592 of file VectorD.h.

Function Documentation

Rotation2D IMP::algebra::compose	(	const Rotation2D &	a,
		const Rotation2D &	b
	)

For any vector v (a*b)*v = a*(b*v).

Definition at line 117 of file Rotation2D.h.

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Transformation3D compose	(	const Transformation3D &	a,
		const Transformation3D &	b
	)

For any vector v (a*b)*v = a*(b*v).

Definition at line 117 of file Transformation3D.h.

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Transformation2D compose	(	const Transformation2D &	a,
		const Transformation2D &	b
	)

For any vector v (a*b)*v = a*(b*v).

Definition at line 150 of file Transformation2D.h.

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Transformation3Ds IMP::algebra::get_alignments_from_first_to_second	(	const PrincipalComponentAnalysisD< 3 > &	pca1,
		const PrincipalComponentAnalysisD< 3 > &	pca2
	)

Get all possible alignments of the first principal component system to the second one

bool IMP::algebra::get_are_almost_equal	(	const double	a,
		const double	b,
		const double	epsilon
	)

epsilon is the tolerance allowed to consider the values as equal

Definition at line 112 of file algebra/utility.h.

std::pair< Vector3D, double > get_axis_and_angle

(

const Rotation3D &

rot

)

Note

http://en.wikipedia.org/wiki/Rotation_matrix

www.euclideanspace.com/maths/geometry/rotations/conversions/ angleToQuaternion/index.htm

Returns

axis direction and rotation about the axis in Radians

template<int D>

VectorD< D > get_basis_vector_d

(

unsigned int

coordinate

)

Return the unit vector pointing in the direction of the requested coordinate. That is

get_basis_vector_d<3>(2)== Vector3D(0,0,1);

Definition at line 415 of file VectorD.h.

std::string IMP::algebra::get_data_path

(

std::string

file_name

)

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

double get_distance	(	const Segment3D &	s,
		const Vector3D &	p
	)

double get_distance	(	const Segment3D &	a,
		const Segment3D &	b
	)

double get_distance	(	const Plane3D &	pln,
		const Vector3D &	p
	)

Definition at line 82 of file Plane3D.h.

template<int D>

double get_distance	(	const SphereD< D > &	a,
		const SphereD< D > &	b
	)

If they intersect, the distances are not meaningful.

Definition at line 119 of file SphereD.h.

double get_distance	(	const Rotation3D &	r0,
		const Rotation3D &	r1
	)

The distance runs between 0 and 1. More precisely, the distance returned is distance between the two quaternion vectors properly normalized, divided by sqrt(2).

A vector with distance d from the unit vector represents a rotation of

\( \theta= \cos^{-1}\left(1-\sqrt{2}d\right)\)

Definition at line 241 of file Rotation3D.h.

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template<int D>

VectorD< D > get_elementwise_product	(	const algebra::VectorD< D > &	a,
		const algebra::VectorD< D > &	b
	)

Return the vector that is the elementwise product of the two.

Definition at line 607 of file VectorD.h.

template<int D>

VectorD< D > get_elementwise_product	(	const Ints &	a,
		const algebra::VectorD< D > &	b
	)

Return the vector that is the elementwise product of the two.

Definition at line 620 of file VectorD.h.

Sphere3D IMP::algebra::get_enclosing_sphere

(

const Sphere3Ds &

ss

)

Note

This method produces tighter bounding spheres if CGAL is used.

Sphere3D IMP::algebra::get_enclosing_sphere

(

const Vector3Ds &

ss

)

Note

This method produces tighter bounding spheres if CGAL is used.

std::string IMP::algebra::get_example_path

(

std::string

file_name

)

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb", model));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

FixedXYZ IMP::algebra::get_fixed_xyz_from_rotation

(

const Rotation3D &

r

)

See Also

rotation_from_fixed_xyz()

FixedZXZ get_fixed_zxz_from_rotation

(

const Rotation3D &

r

)

See Also

rotation_from_fixed_zxz()

FixedZYZ get_fixed_zyz_from_rotation

(

const Rotation3D &

r

)

See Also

rotation_from_fixed_zyz()

template<int D>

base::Vector<VectorD<D> > IMP::algebra::get_grid_interior_cover_by_spacing	(	const BoundingBoxD< D > &	bb,
		double	s
	)

Cover the interior of the bounding box by equal sized parallelograms of approximately full-width s, returning the list of centers of the cubes.

Definition at line 179 of file vector_generators.h.

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Rotation3D get_identity_rotation_3d

(

)

Definition at line 225 of file Rotation3D.h.

Transformation3D get_identity_transformation_3d

(

)

Definition at line 96 of file Transformation3D.h.

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Rotation3D get_interpolated	(	const Rotation3D &	a,
		const Rotation3D &	b,
		double	f
	)

It f ==0, return b, if f==1 return a.

Definition at line 509 of file Rotation3D.h.

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Triangle3D get_largest_triangle

(

const Vector3Ds &

points

)

template<int D, class Storage , class Value , class Embedding >

Value IMP::algebra::get_linearly_interpolated	(	const GridD< D, Storage, Value, Embedding > &	g,
		const VectorD< D > &	pt
	)

Get the value from the grid with linear interpolation. Values outside the bounding box are snapped to the bounding box (effectively extending the boundary values out to infinity).

Definition at line 25 of file grid_utility.h.

Vector3D IMP::algebra::get_orthogonal_vector

(

const Vector3D &

v

)

Or, if you are Israeli, it is a vertical vector.

Definition at line 42 of file Vector3D.h.

template<int D>

double get_power_distance	(	const SphereD< D > &	a,
		const SphereD< D > &	b
	)

The power distance is the square of the distance between the centers minus the sum of the square of the radii.

Definition at line 130 of file SphereD.h.

double IMP::algebra::get_radius_of_gyration

(

const Vector3Ds &

ps

)

See Also

IMP::atom::get_radius_of_gyration()

Definition at line 68 of file Vector3D.h.

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Vector3Ds IMP::algebra::get_random_chain	(	unsigned int	n,
		double	r,
		const Vector3D &	start = Vector3D(0, 0, 0),
		const Sphere3Ds &	obstacles = Sphere3Ds()
	)

This function generates a random chain, starting at (0,0,0) with n particles each with radius r. Consecutive particles are approximately distance 2r apart and no pair of particles is closer than 2r.

If an obstacles parameter is provided then chain spheres also don't intersect the obstacle spheres.

Note

The current implementation is not very clever and can be made more clever if needed.

Transformation3D IMP::algebra::get_random_local_transformation	(	Vector3D	origin,
		double	max_translation = 5.,
		double	max_angle_in_rad = 0.26
	)

Note

randomly select an axis that passes to the input point and rotate around it

Parameters

[in]	origin	the origin of the rotation
[in]	max_translation	detault value is 5
[in]	max_angle_in_rad	default value is 15 degree in radians

Rotation3D get_random_rotation_3d

(

)

Rotation3D get_random_rotation_3d	(	const Rotation3D &	center,
		double	distance
	)

This method generates a rotation that is within the provided distance of center.

Parameters

[in]	center	The center of the rotational volume
[in]	distance	See get_distance(const Rotation3D&,const Rotation3D&) for a full definition.

Note

The cost of this operation increases as distance goes to 0.

VectorD< 2 > get_random_vector_in

(

const SphereD< 2 > &

s

)

Generates a random vector in a circle with uniform density with respect to the area of the circle

Parameters

s	a 2D sphere (circle)

double IMP::algebra::get_relative_projection_on_segment	(	const Segment3D &	s,
		const algebra::Vector3D &	p
	)

Returns f, the 'relative' projection of a point p onto the line that contains s. Formally, the projection of p onto the line through s is s[0]+f*(s[1]-s[0]) f is in the range [0..1] if the projection of p is inside s.

Parameters

s	segment in 3D
p	point in 3D

Returns

the 'relative' project of p onto the line containing s

Rotation3D get_rotation_about_axis	(	const Vector3D &	axis,
		double	angle
	)

Parameters

[in]	axis	the rotation axis passes through (0,0,0)
[in]	angle	the rotation angle in radians in the clockwise direction

Note

http://en.wikipedia.org/wiki/Rotation_matrix

www.euclideanspace.com/maths/geometry/rotations/conversions/ angleToQuaternion/index.htm

Transformation3D get_rotation_about_point	(	const Vector3D &	point,
		const Rotation3D &	rotation
	)

Rotate about a point rather than the origin.

Parameters

[in]	point	Center to rotate about
[in]	rotation	The rotation to perform

Definition at line 108 of file Transformation3D.h.

Transformation2D get_rotation_about_point	(	const Vector2D &	point,
		const Rotation2D &	rotation
	)

Generates a Transformation2D to rotate about a point rather than the origin.

Parameters

[in]	point	Center to rotate about
[in]	rotation	The rotation to perform (defined taking the origin as reference, not the new point).

Definition at line 141 of file Transformation2D.h.

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Rotation3D get_rotation_from_fixed_xyz	(	double	xr,
		double	yr,
		double	zr
	)

Parameters

[in]	xr	Rotation around the X axis in radians
[in]	yr	Rotation around the Y axis in radians
[in]	zr	Rotation around the Z axis in radians

Note

The three rotations are represented in the original (fixed) coordinate frame.

Rotation3D get_rotation_from_fixed_zxz	(	double	phi,
		double	theta,
		double	psi
	)

Parameters

[in]	phi	Rotation around the Z axis in radians
[in]	theta	Rotation around the X axis in radians
[in]	psi	Rotation around the Z axis in radians

Note

The first rotation is by an angle phi about the z-axis. The second rotation is by an angle theta in [0,pi] about the former x-axis , and the third rotation is by an angle psi about the former z-axis.

Rotation3D get_rotation_from_fixed_zyz	(	double	Rot,
		double	Tilt,
		double	Psi
	)

Note

The first rotation is by an angle about the z-axis. The second rotation is by an angle about the new y-axis. The third rotation is by an angle about the new z-axis.

Parameters

[in]	Rot	First Euler angle (radians) defining the rotation (Z axis)
[in]	Tilt	Second Euler angle (radians) defining the rotation (Y axis)
[in]	Psi	Third Euler angle (radians) defining the rotation (Z axis)

Rotation3D get_rotation_from_vector4d

(

const VectorD< 4 > &

v

)

Definition at line 326 of file Rotation3D.h.

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Rotation3D IMP::algebra::get_rotation_from_x_y_axes	(	const Vector3D &	x,
		const Vector3D &	y
	)

Return the rotation which takes the native x and y axes to the given x and y axes. The two axis must be perpendicular unit vectors.

Rotation2D IMP::algebra::get_rotation_to_x_axis

(

const Vector2D &

v

)

Builds the rotation that transforms the vector X of the origin of coordinates into the given vector

Definition at line 109 of file Rotation2D.h.

template<typename T >

int IMP::algebra::get_rounded

(

const T &

x

)

The result is of type integer but the argument can be of any type. Some examples:

a = round(-0.7); // a = -1
a = round(-0.2); // a = 0
a = round(0.2); // a = 0
a = round(0.7); // a = 1

Definition at line 49 of file algebra/utility.h.

FloatPair IMP::algebra::get_surface_area_and_volume

(

const algebra::Sphere3Ds &

ss

)

Return the surface area and volume of the union of the balls bounded by the spheres. This method requires CGAL to work.

Transformation3D IMP::algebra::get_transformation_3d

(

const Transformation2D &

t2d

)

Note

The 3D transformation is built with the 2D rotation becoming a rotation around the z axis.

template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 >

IMP::algebra::Transformation3D get_transformation_aligning_first_to_second	(	const Vector3DsOrXYZs0 &	source,
		const Vector3DsOrXYZs1 &	target
	)

The points are assumed to be corresponding (that is, from[0] is aligned to to[0] etc.). The alignment computed is that which minimized the sum of squared distances between corresponding points. Return the

\[ \textit{argmin}_T \sum \left|T\left(f\left[i\right]\right)-t[i]\right|^2 \]

If the point sets lie in a 1 or 2 dimensional subspace, the alignment algorithm is unstable and not guaranteed to work. A warning is printed in this case.

See Also

Vector3D

Definition at line 46 of file geometric_alignment.h.

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Transformation3D IMP::algebra::get_transformation_aligning_first_to_second	(	Vector3Ds	a,
		Vector3Ds	b
	)

Equivalent to

IMP::algebra::get_transformation_aligning_first_to_second(a,b);

Transformation2D IMP::algebra::get_transformation_aligning_pair	(	const Vector2Ds &	set_from,
		const Vector2Ds &	set_to
	)

Builds the transformation required to obtain a set of points from the first one

Note

The function assumes that the relative distances between points are conserved.

template<class Storage , class Embedding >

const Storage::Value get_trilinearly_interpolated	(	const GridD< 3, Storage, typename Storage::Value, Embedding > &	g,
		const Vector3D &	v,
		const typename Storage::Value &	outside = 0
	)

The voxel values are assumed to be at the center of the voxel and the passed outside value is used for voxels outside the grid. The type Voxel must support get_linearly_interpolated().

See Also

get_linearly_interpolated()

Definition at line 45 of file grid_utility.h.

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Rotation3Ds IMP::algebra::get_uniform_cover_rotations_3d

(

unsigned int

num_points

)

If you care about the distance between samples instead of the number of samples, the "surface area" of the set of rotations is pi^2. If you allocate each sample a volume of 4/3 pi d^3 (to space them d apart), Then you want 3/4 pi/d^3 points.

Creates at least num_points rotations.

template<int D>

base::Vector< VectorD< D > > get_uniform_surface_cover	(	const SphereD< D > &	s,
		unsigned int	n
	)

The function is currently pretty slow, especially in non-optimized builds. Complain if this bugs you. We might be able to do better, at least in 3D.

Creates at least the requested number of points.

Note

This predicates will produce guaranteed correct results if the CGAL library is available (the results will be unreliable if it is not).

Definition at line 120 of file vector_generators.h.

Vector3Ds get_uniform_surface_cover	(	const SpherePatch3D &	sph,
		unsigned int	number_of_points
	)

Note

the implementation can be improved

template<int D>

base::Vector<VectorD<D> > IMP::algebra::get_uniform_upper_hemisphere_cover	(	const SphereD< D > &	s,
		unsigned int	n
	)

The points all lie on the upper hemisphere, eg, all their z coordinates are greater than those of the center of the sphere.

Definition at line 140 of file vector_generators.h.

algebra::Rotation3Ds IMP::algebra::get_uniformly_sampled_rotations

(

double

delta

)

Parameters

[in]

delta

sample every delta angles in radians.

Vector3Ds read_pts

(

base::TextInput

input

)

See Also

write_pts

Sphere3Ds read_spheres

(

base::TextInput

input

)

See Also

write_pts

void IMP::algebra::reversed_read	(	void *	dest,
		size_t	size,
		size_t	nitems,
		std::ifstream &	f,
		bool	reverse
	)

If the reverse parameter is true, the data will be read in reverse order.

void IMP::algebra::reversed_write	(	const void *	src,
		size_t	size,
		size_t	nitems,
		std::ofstream &	f,
		bool	reverse = false
	)

This function is the same as fread from C, but at the end there is a flag saying if data should be read in reverse order or not.

If the reverse parameter is true, the data will be written in reverse order.

void write_pts	(	const Vector3Ds &	vs,
		base::TextOutput	out
	)

See Also

read_pts

void write_spheres	(	const Sphere3Ds &	vs,
		base::TextOutput	out
	)

See Also

read_pts