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IMP Reference Guide
2.11.0
The Integrative Modeling Platform
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General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP modules. More...
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP modules.
IMP has a number of geometric primitives. They support the following namespace functions as appropriate
In addition, they cannot be compared against one another due to floating point implementation issues (eg Vector3D v=v2 does not imply v==v2).
Geometric primitives are not put into a defined state by their constructor. Such classes mimic POD types (int, float etc) in C++ and are optimized for efficiency. All operations on a default initialized instance other than assigning to it from a non-default initialized instance should be assumed to be invalid.
Many of the geometric primitives and operations in IMP are written to work in any dimension. In C++, this is implemented via templates (such as IMP::algebra::VectorD). In the Python side, the different dimensions are named explicitly instead. That means, a 2-D point is IMP::algebra::VectorD<2> in C++, and IMP::algebra::Vector2D in Python and the function IMP::algebra::get_basis_vector_d<3>() in C++ becomes IMP.algebra.get_basis_vector_3d() in Python. Similarly, a collection of 2D points is IMP::Vector<IMP::algebra::VectorD<2> > in C++ and IMP.algebra.Vector2Ds in Python, which as with all collections, look like Python lists. For convenience, we provide typedefs in C++ to the IMP::algebra::Vector2D and IMP::algebra::Vector2Ds style names.
Geometry in IMP can be stored in a variety of ways. For example, a point in 3D can be stored using an IMP::algebra::VectorD<3> or using an IMP::core::XYZ particle. It is often useful to be able to write algorithms that work on sets of points without worrying how they are stored, the Generic Geometry layer provides that. It works using a set of functions get_vector_3d() and set_vector_3d() which manipulate the geometry in terms of the IMP::algebra representation of the geometry in question. That is, get_vector_3d() returns a IMP::algebra::VectorD<3> for both an IMP::algebra::Vector3D and a IMP::core::XYZ. Algorithms take their arguments as C++ templates and use the generic geometry methods to manipulate the geometry. And versions of the function for both types of storage are exported to Python, so one could also write generic functions in Python.
For example, IMP::atom::get_rmsd() takes any combination of IMP::algebra::Vector3Ds or IMP::core::XYZs or IMP::core::XYZsTemp as arguments. Versions for all combinations of those are exported to Python.
ANN is a library implementing fast nearest neighbor searches. Certain data structures will be faster if it is installed. While compilation of the library from source is quite straightforward, it is not available as a package for common platforms. In addition, ANN must be built as a shared library rather than a static library.
Author(s): Daniel Russel, Keren Lasker, Ben Webb, Javier Angel Velázquez-Muriel
Maintainer: benmwebb
License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Publications:
Classes | |
| class | BoundedGridRangeD |
| class | BoundingBoxD |
| An axis-aligned bounding box. More... | |
| class | Cone3D |
| Represent a cone in 3D. More... | |
| class | ConnollySurfacePoint |
| Represent a point on the Connolly surface. More... | |
| class | Cylinder3D |
| Represent a cylinder in 3D. More... | |
| class | DefaultEmbeddingD |
| Embed a grid as an evenly spaced axis aligned grid. More... | |
| struct | DenseFloatLogGridKD |
| struct | DenseGrid3D |
| A dense grid of values. More... | |
| class | DenseGridStorageD |
| struct | DenseIntLogGrid3D |
| class | DynamicNearestNeighbor3D |
| Provide an incremental nearest neighbor search function. More... | |
| class | Ellipsoid3D |
| Represent an ellipsoid in 3D. More... | |
| class | EuclideanVectorKDMetric |
| The l2 norm on the distance vector. More... | |
| class | ExtendedGridIndexD |
| An index in an infinite grid on space. More... | |
| class | FixedXYZ |
| A simple class for returning XYZ Euler angles. More... | |
| class | Gaussian3D |
| A Gaussian distribution in 3D. More... | |
| class | GeometricPrimitiveD |
| Base class for geometric types. More... | |
| class | GridD |
| A voxel grid in d-dimensional space. More... | |
| class | GridIndexD |
| Represent a real cell in a grid (one within the bounding box) More... | |
| class | Line3D |
| Simple implementation of lines in 3D. More... | |
| class | LinearFit2D |
| Calculate line that fits best the input data points (Linear least squares) More... | |
| class | LogEmbeddingD |
| class | MaxVectorKDMetric |
| class | NearestNeighborD |
| Build a structure for finding nearest neighbors. More... | |
| class | ParabolicFit2D |
| Calculate parabola that fits best the input data points. More... | |
| class | Plane3D |
| Represent a plane in 3D. More... | |
| class | PrincipalComponentAnalysisD |
| Represent an eigen analysis of some data. More... | |
| class | ReferenceFrame3D |
| A reference frame in 3D. More... | |
| class | Reflection3D |
| Reflect about a plane in 3D. More... | |
| class | Rotation2D |
| Represent a rotation in 2D space. More... | |
| class | Rotation3D |
| 3D rotation class. More... | |
| class | Segment3D |
| Simple implementation of segments in 3D. More... | |
| struct | SparseGrid3D |
| A sparse grid of values. More... | |
| class | SparseGridStorageD |
| struct | SparseUnboundedGrid3D |
| A sparse, infinite grid of values. More... | |
| struct | SparseUnboundedGridD |
| A sparse, infinite grid of values. More... | |
| class | SphereD |
| Represent a sphere in D-dimensions. More... | |
| class | SpherePatch3D |
| A sphere patch is defined as all points above the plane and on the sphere. More... | |
| class | SphericalVector3D |
| Class to represent a 3D point in spherical coordinates. More... | |
| class | Torus3D |
| Represent a torus in 3D. More... | |
| class | Transformation2D |
| Simple 2D transformation class. More... | |
| class | Transformation3D |
| Simple 3D transformation class. More... | |
| class | Triangle3D |
| Represent a triangle in 3D. More... | |
| class | UnboundedGridRangeD |
| class | VectorBaseD |
| A Cartesian vector in D-dimensions. More... | |
| class | VectorD |
| A Cartesian vector in D-dimensions. More... | |
| class | VectorKDMetric |
| The base class for a metric on VectorKDs. More... | |
Functions | |
| template<int D> | |
| int | compare (const VectorD< D > &a, const VectorD< D > &b) |
| lexicographic comparison of two vectors More... | |
| 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) |
| Get all alignments of the first principal component system to the second one. More... | |
| double | get_angle (const Line3D &a, const Line3D &b) |
| Get angle in radians between two lines around their closest points. More... | |
| bool | get_are_almost_equal (const double a, const double b, const double epsilon) |
| Compare two values for "almost equal" (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. More... | |
| template<class Geometry > | |
| double | get_area (const Geometry &) |
| Compute the area of any surface object. More... | |
| 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. More... | |
| 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. More... | |
| template<class Geometry > | |
| BoundingBoxD< 3 > | get_bounding_box (const Geometry &) |
| Compute the bounding box of any geometric object. More... | |
| 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. More... | |
| ConnollySurfacePoints | get_connolly_surface (const algebra::Sphere3Ds &spheres, double density, double probe_radius) |
| template<typename T > | |
| T | get_constrained (const T x, const T x0, const T xF) |
| Constrain a value between two given limits. More... | |
| Eigen::Matrix3d | get_covariance (const Gaussian3D &g) |
| template<unsigned int D> | |
| BoundingBoxD< D > | get_cube_d (double radius) |
Cube with radius of length radius. More... | |
| BoundingBoxD<-1 > | get_cube_kd (unsigned int d, double radius) |
Cube with radius of length side. More... | |
| double | get_distance (const Segment3D &s, const Vector3D &p) |
| Get the distance between a segment and a point. More... | |
| double | get_distance (const Plane3D &pln, const Vector3D &p) |
| Return the distance between a plane and a point in 3D. More... | |
| double | get_distance (const Segment3D &a, const Segment3D &b) |
| Get the distance between two segments. More... | |
| double | get_distance (const Line3D &s, const Vector3D &p) |
| Get closest distance between a line and a point. More... | |
| double | get_distance (const Line3D &a, const Line3D &b) |
| Get the closest distance between two lines. 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... | |
| template<int D> | |
| double | get_distance (const VectorD< D > &v1, const VectorD< D > &v2) |
| Compute the distance between two vectors. More... | |
| double | get_distance (const Rotation3D &r0, const Rotation3D &r1) |
| Return a distance between the two rotations. More... | |
| IntPairs | get_edges (const BoundingBoxD< 3 > &) |
| Return the edges of the box as indices into the vertices list. More... | |
| 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. More... | |
| 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. More... | |
| 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 vectors. More... | |
| Gaussian3D | get_gaussian_from_covariance (const Eigen::Matrix3d &covariance, const Vector3D ¢er) |
| Return a Gaussian centered at the origin from a covariance matrix. More... | |
| Eigen::MatrixXd | get_gradient_of_composed_with_respect_to_first (const Rotation3D &q, const Rotation3D &p, bool projected=true) |
| Get gradient of quaternion product with respect to first quaternion. More... | |
| Eigen::MatrixXd | get_gradient_of_composed_with_respect_to_second (const Rotation3D &q, const Rotation3D &p, bool projected=true) |
| Get gradient of quaternion product with respect to second quaternion. More... | |
| Rotation2D | get_identity_rotation_2d () |
| Build an identity rotation in 2D. More... | |
| Rotation3D | get_identity_rotation_3d () |
| Return a rotation that does not do anything. More... | |
| Transformation2D | get_identity_transformation_2d () |
| Return a transformation that does not do anything. More... | |
| 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 intersect. More... | |
| template<int D> | |
| bool | get_interiors_intersect (const BoundingBoxD< D > &a, const BoundingBoxD< D > &b) |
| Return true if they intersect. More... | |
| Rotation3D | get_interpolated (const Rotation3D &a, const Rotation3D &b, double f) |
| Interpolate between two rotations. More... | |
| template<int D> | |
| BoundingBoxD< D > | get_intersection (const BoundingBoxD< D > &a, const BoundingBoxD< D > &b) |
| Return the intersecting bounding box. 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) |
| Get the value from the grid with linear interpolation. More... | |
| template<class VT > | |
| double | get_magnitude_and_normalize_in_place (VT &vt) |
| Returns the magnitude of vt and turns it to a unit vector in place. More... | |
| template<int D> | |
| double | get_maximum_length (const BoundingBoxD< D > &a) |
| Return the maximum axis aligned extent. More... | |
| float | get_next_larger_power_of_2 (float x) |
| Closest power of 2 that can contain a number x. More... | |
| double | get_next_larger_power_of_2 (double x) |
| Closest power of 2 that can contain a number x. More... | |
| template<int D> | |
| VectorD< D > | get_ones_vector_d (double v=1) |
| Return a vector of ones (or another constant) More... | |
| template<int D> | |
| VectorD< D > | get_ones_vector_kd (unsigned int Di, double v=1) |
| Return a vector of ones (or another constant) More... | |
| 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 Vector< VectorD< D > > &ps) |
| Perform principal components analysis on a set of vectors. More... | |
| Vector3D | get_projected (const Line3D &l, const Vector3D &p) |
| Project a point onto the line. More... | |
| algebra::Segment3D | get_projected (const Line3D &l, const algebra::Segment3D &s) |
| Project a segment onto a line. More... | |
| 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 () |
| Build an identity rotation in 2D. More... | |
| Rotation3D | get_random_rotation_3d () |
| Pick a rotation at random from all possible rotations. More... | |
| Rotation3D | get_random_rotation_3d (const Rotation3D ¢er, double distance) |
| Pick a rotation at random near the provided one. More... | |
| DenseGrid3D< double > | get_rasterized (const Gaussian3Ds &gmm, const Floats &weights, double cell_width, const BoundingBox3D &bb) |
| Rasterize the Gaussians to a grid. More... | |
| DenseGrid3D< double > | get_rasterized_fast (const Gaussian3Ds &gmm, const Floats &weights, double cell_width, const BoundingBox3D &bb, double factor=2.5) |
| Rasterize the Gaussians to a grid. More... | |
| Vector3D | get_reflected (const Plane3D &pln, const Vector3D &p) |
| Return the point reflected about the plane. More... | |
| double | get_relative_projection_on_segment (const Segment3D &s, const algebra::Vector3D &p) |
| Return the 'relative' projection of a point p onto the line that contains s. More... | |
| template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 > | |
| double | get_rmsd (const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2) |
| template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 > | |
| double | get_rmsd_transforming_first (const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2) |
| Calculate the root mean square deviation between two sets of 3D points. More... | |
| Rotation3D | get_rotation_about_axis (const Vector3D &axis, double angle) |
| Generate a Rotation3D object from a rotation around an axis. More... | |
| Rotation3D | get_rotation_about_normalized_axis (const Vector3D &axis_norm, double angle) |
| 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) |
| Generate 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. More... | |
| Rotation3D | get_rotation_from_matrix (Eigen::Matrix3d m) |
| Generate a Rotation3D object from a rotation matrix. More... | |
| Rotation3D | get_rotation_from_vector4d (const VectorD< 4 > &v) |
| Compute a rotation 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. More... | |
| 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... | |
| algebra::Segment3D | get_segment_connecting_first_to_second (const Line3D &a, const Line3D &b) |
| Get shortest possible segment from the first line to the second. 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. More... | |
| Sphere3Ds | get_simplified_from_volume (Sphere3Ds in, double maximum_allowed_error_angstroms) |
| Get a set of balls that approximates the surface of the passed set. More... | |
| double | get_squared (double x) |
| template<int D> | |
| double | get_squared_distance (const VectorD< D > &v1, const VectorD< D > &v2) |
| Compute the squared distance between two vectors. More... | |
| template<class Geometry > | |
| double | get_surface_area (const Geometry &) |
| Compute the surface area of any volumetric object. More... | |
| FloatPair | get_surface_area_and_volume (const algebra::Sphere3Ds &ss) |
| Get surface area & volume of the union of the balls bounded by the spheres. More... | |
| Transformation3D | get_transformation_3d (const Transformation2D &t2d) |
| Build 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. More... | |
| 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. More... | |
| algebra::Line3D | get_transformed (const algebra::Line3D &l, const Transformation3D &tr) |
| 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... | |
| Vector3Ds | get_uniform_surface_cover (const Sphere3Ds &in, double points_per_square_angstrom) |
| algebra::Rotation3Ds | get_uniformly_sampled_rotations (double delta) |
| Generates a nondegenerate set of Euler angles with a delta resolution. More... | |
| template<int D> | |
| BoundingBoxD< D > | get_union (BoundingBoxD< D > a, const BoundingBoxD< D > &b) |
| Return the union bounding box. More... | |
| template<unsigned int D> | |
| BoundingBoxD< D > | get_unit_bounding_box_d () |
| Box with radius one. More... | |
| BoundingBoxD<-1 > | get_unit_bounding_box_kd (unsigned int d) |
| Box with radius one. More... | |
| template<unsigned int D> | |
| SphereD< D > | get_unit_sphere_d () |
| SphereD<-1 > | get_unit_sphere_kd (unsigned int d) |
| template<class VT > | |
| VT | get_unit_vector (VT vt) |
| Returns a unit vector pointing at the same direction as this vector. More... | |
| template<int D> | |
| VectorD< D > | get_vector_geometry (const SphereD< D > &s) |
| template<class C > | |
| const VectorD< C::DIMENSION > & | get_vector_geometry (const C &g) |
| template<int D> | |
| Vector< VectorD< D > > | get_vertices (const BoundingBoxD< D > &bb) |
| Return a list of the 2^D bounding points for the bounding box. More... | |
| template<int D> | |
| double | get_volume (const BoundingBoxD< D > &bb) |
| See BoundingBoxD. More... | |
| template<class Geometry > | |
| double | get_volume (const Geometry &) |
| Compute the volume of any volumetric object. More... | |
| template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 > | |
| double | get_weighted_rmsd (const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const Floats &weights) |
| template<class Vector3DsOrXYZs0 , class Vector3DsOrXYZs1 > | |
| double | get_weighted_rmsd_transforming_first (const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const Floats &weights) |
| template<int D> | |
| VectorD< D > | get_zero_vector_d () |
| Return a vector of zeros. More... | |
| template<int D> | |
| VectorD< D > | get_zero_vector_kd (int Di) |
| Return a dynamically sized vector of zeros. More... | |
| template<int D> | |
| VectorD< D > | operator* (double s, VectorD< D > o) |
| void | set_line_3d_geometry (Line3D &g, const Line3D &gi) |
| void | set_segment_3d_geometry (Segment3D &g, const Segment3D &gi) |
| template<class C , class E > | |
| void | set_vector_geometry (C &g, const E &v) |
Variables | |
| static const double | PI = 3.1415926535897931 |
| the constant pi More... | |
Standard module functions | |
All | |
| std::string | get_module_version () |
| std::string | get_module_name () |
| std::string | get_data_path (std::string file_name) |
| Return the full path to one of this module's data files. More... | |
| std::string | get_example_path (std::string file_name) |
| Return the full path to one of this module's example files. More... | |
Endian | |
| |
| 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... | |
| bool | get_is_big_endian () |
| Returns 1 if machine is big endian else 0. More... | |
| bool | get_is_little_endian () |
| Returns 1 if machine is little endian else 0. More... | |
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, TextOutput out) |
| Write a set of 3D vectors to a file. More... | |
| Vector3Ds | read_pts (TextInput input) |
| Read a set of 3D vectors from a file. More... | |
| void | write_spheres (const Sphere3Ds &vs, TextOutput out) |
| Write a set of 3D spheres to a file. More... | |
| Sphere3Ds | read_spheres (TextInput input) |
| Read a set of 3D spheres from a file. More... | |
Python Only | |
The following functions are only available 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.
| |
| typedef IMP::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... | |
| 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) |
| Return the vector product (cross product) of two vectors. More... | |
| Vector3D | get_orthogonal_vector (const Vector3D &v) |
| Return a vector that is perpendicular to the given vector. More... | |
| Vector3D | get_centroid (const Vector3Ds &ps) |
| Return the centroid of a set of vectors. More... | |
| 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. More... | |
| template<int D> | |
| VectorD< D > | get_random_vector_on (const BoundingBoxD< D > &bb) |
| Generate a random vector on a box with uniform density. More... | |
| template<int D> | |
| VectorD< D > | get_random_vector_in (const SphereD< D > &s) |
| Generate a random vector in a sphere with uniform density. More... | |
| 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. More... | |
| VectorD< 3 > | get_random_vector_on_unit_sphere () |
| template<int D> | |
| VectorD< D > | get_random_vector_on (const SphereD< D > &s) |
| Generate a random vector on a sphere with uniform density. More... | |
| template<int D> | |
| 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. More... | |
| template<int D> | |
| 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. More... | |
| 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> | |
| 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.
| |
| 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 BoundingBoxD<1> IMP::algebra::BoundingBox1D |
Typedef for Python.
Definition at line 176 of file BoundingBoxD.h.
| typedef IMP::Vector< BoundingBox1D > IMP::algebra::BoundingBox1Ds |
Pass or store a set of BoundingBox1D .
Definition at line 176 of file BoundingBoxD.h.
| typedef BoundingBoxD<2> IMP::algebra::BoundingBox2D |
Typedef for Python.
Definition at line 176 of file BoundingBoxD.h.
| typedef IMP::Vector< BoundingBox2D > IMP::algebra::BoundingBox2Ds |
Pass or store a set of BoundingBox2D .
Definition at line 176 of file BoundingBoxD.h.
| typedef BoundingBoxD<3> IMP::algebra::BoundingBox3D |
Typedef for Python.
Definition at line 176 of file BoundingBoxD.h.
| typedef IMP::Vector< BoundingBox3D > IMP::algebra::BoundingBox3Ds |
Pass or store a set of BoundingBox3D .
Definition at line 176 of file BoundingBoxD.h.
| typedef BoundingBoxD<4> IMP::algebra::BoundingBox4D |
Typedef for Python.
Definition at line 176 of file BoundingBoxD.h.
| typedef IMP::Vector< BoundingBox4D > IMP::algebra::BoundingBox4Ds |
Pass or store a set of BoundingBox4D .
Definition at line 176 of file BoundingBoxD.h.
| typedef BoundingBoxD<5> IMP::algebra::BoundingBox5D |
Typedef for Python.
Definition at line 176 of file BoundingBoxD.h.
| typedef IMP::Vector< BoundingBox5D > IMP::algebra::BoundingBox5Ds |
Pass or store a set of BoundingBox5D .
Definition at line 176 of file BoundingBoxD.h.
| typedef BoundingBoxD<6> IMP::algebra::BoundingBox6D |
Typedef for Python.
Definition at line 176 of file BoundingBoxD.h.
| typedef IMP::Vector< BoundingBox6D > IMP::algebra::BoundingBox6Ds |
Pass or store a set of BoundingBox6D .
Definition at line 176 of file BoundingBoxD.h.
| typedef BoundingBoxD<-1> IMP::algebra::BoundingBoxKD |
Typedef for Python.
Definition at line 176 of file BoundingBoxD.h.
| typedef IMP::Vector< BoundingBoxKD > IMP::algebra::BoundingBoxKDs |
Pass or store a set of BoundingBoxKD .
Definition at line 176 of file BoundingBoxD.h.
| typedef IMP::Vector< Cone3D > IMP::algebra::Cone3Ds |
Pass or store a set of ConnollySurfacePoint .
Definition at line 46 of file algebra/connolly_surface.h.
| typedef IMP::Vector< Cylinder3D > IMP::algebra::Cylinder3Ds |
Pass or store a set of Cylinder3D .
Definition at line 78 of file Cylinder3D.h.
| typedef Grid3D<double, DenseGridStorage3D<double> > IMP::algebra::DenseDoubleGrid3D |
A grid of doubles over a region of space.
Definition at line 91 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 94 of file algebra/python_only.h.
| typedef IMP::Vector< Ellipsoid3D > IMP::algebra::Ellipsoid3Ds |
Pass or store a set of Ellipsoid3D .
Definition at line 46 of file Ellipsoid3D.h.
| typedef IMP::Vector< FixedXYZ > IMP::algebra::FixedXYZs |
Pass or store a set of FixedXYZ .
Definition at line 530 of file Rotation3D.h.
| typedef IMP::Vector< Gaussian3D > IMP::algebra::Gaussian3Ds |
Pass or store a set of Gaussian3D .
Definition at line 43 of file Gaussian3D.h.
| typedef IMP::Vector< Line3D > IMP::algebra::Line3Ds |
| typedef IMP::Vector< LinearFit2D > IMP::algebra::LinearFit2Ds |
Pass or store a set of LinearFit2D .
Definition at line 52 of file LinearFit.h.
Pass or store a set of ParabolicFit2D .
Definition at line 54 of file ParabolicFit.h.
| typedef IMP::Vector< Plane3D > IMP::algebra::Plane3Ds |
Pass or store a set of ReferenceFrame3D .
Definition at line 95 of file ReferenceFrame3D.h.
| typedef IMP::Vector< Reflection3D > IMP::algebra::Reflection3Ds |
Pass or store a set of Reflection3D .
Definition at line 32 of file Reflection3D.h.
| typedef IMP::Vector< Rotation2D > IMP::algebra::Rotation2Ds |
Pass or store a set of Rotation2D .
Definition at line 114 of file Rotation2D.h.
| typedef IMP::Vector< Rotation3D > IMP::algebra::Rotation3Ds |
Pass or store a set of Rotation3D .
Definition at line 272 of file Rotation3D.h.
| typedef IMP::Vector< Segment3D > IMP::algebra::Segment3Ds |
Pass or store a set of Segment3D .
Definition at line 46 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 84 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 88 of file algebra/python_only.h.
| typedef SphereD<1> IMP::algebra::Sphere1D |
| typedef IMP::Vector< Sphere1D > IMP::algebra::Sphere1Ds |
| typedef SphereD<2> IMP::algebra::Sphere2D |
| typedef IMP::Vector< Sphere2D > IMP::algebra::Sphere2Ds |
| typedef SphereD<3> IMP::algebra::Sphere3D |
| typedef IMP::Vector< Sphere3D > IMP::algebra::Sphere3Ds |
| typedef SphereD<4> IMP::algebra::Sphere4D |
| typedef IMP::Vector< Sphere4D > IMP::algebra::Sphere4Ds |
| typedef SphereD<5> IMP::algebra::Sphere5D |
| typedef IMP::Vector< Sphere5D > IMP::algebra::Sphere5Ds |
| typedef SphereD<6> IMP::algebra::Sphere6D |
| typedef IMP::Vector< Sphere6D > IMP::algebra::Sphere6Ds |
| typedef SphereD<-1> IMP::algebra::SphereKD |
| typedef IMP::Vector< SphereKD > IMP::algebra::SphereKDs |
| typedef IMP::Vector< SpherePatch3D > IMP::algebra::SpherePatch3Ds |
Pass or store a set of SpherePatch3D .
Definition at line 48 of file SpherePatch3D.h.
Pass or store a set of SphericalVector3D .
Definition at line 78 of file SphericalVector3D.h.
| typedef IMP::Vector< Torus3D > IMP::algebra::Torus3Ds |
Pass or store a set of Transformation2D .
Definition at line 118 of file Transformation2D.h.
Pass or store a set of Transformation3D .
Definition at line 98 of file Transformation3D.h.
| typedef IMP::Vector< Triangle3D > IMP::algebra::Triangle3Ds |
Pass or store a set of Triangle3D .
Definition at line 41 of file Triangle3D.h.
| typedef VectorD<1> IMP::algebra::Vector1D |
| typedef Vector<VectorD<1> > IMP::algebra::Vector1Ds |
| typedef VectorD<2> IMP::algebra::Vector2D |
| typedef Vector<VectorD<2> > IMP::algebra::Vector2Ds |
| typedef VectorD<3> IMP::algebra::Vector3D |
| typedef Vector<VectorD<3> > IMP::algebra::Vector3Ds |
| typedef VectorD<4> IMP::algebra::Vector4D |
| typedef Vector<VectorD<4> > IMP::algebra::Vector4Ds |
| typedef VectorD<5> IMP::algebra::Vector5D |
| typedef Vector<VectorD<5> > IMP::algebra::Vector5Ds |
| typedef VectorD<6> IMP::algebra::Vector6D |
| typedef Vector<VectorD<6> > IMP::algebra::Vector6Ds |
| typedef VectorD<-1> IMP::algebra::VectorKD |
A vector of reference-counting object pointers.
Definition at line 31 of file vector_metrics.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 31 of file vector_metrics.h.
| typedef Vector<VectorD<-1> > IMP::algebra::VectorKDs |
| int IMP::algebra::compare | ( | const VectorD< D > & | a, |
| const VectorD< D > & | b | ||
| ) |
| Rotation2D IMP::algebra::compose | ( | const Rotation2D & | a, |
| const Rotation2D & | b | ||
| ) |
Compose two rotations a and b.
For any vector v (a*b)*v = a*(b*v).
Definition at line 108 of file Rotation2D.h.
Here is the call graph for this function:| Transformation3D IMP::algebra::compose | ( | const Transformation3D & | a, |
| const Transformation3D & | b | ||
| ) |
Compose two transformations.
For any vector v (a*b)*v = a*(b*v).
Definition at line 122 of file Transformation3D.h.
Here is the call graph for this function:| Transformation2D IMP::algebra::compose | ( | const Transformation2D & | a, |
| const Transformation2D & | b | ||
| ) |
Compose two transformations.
For any vector v (a*b)*v = a*(b*v).
Definition at line 144 of file Transformation2D.h.
Here is the call graph for this function:| Rotation3D IMP::algebra::compose | ( | const Rotation3D & | a, |
| const Rotation3D & | b | ||
| ) |
Definition at line 448 of file Rotation3D.h.
| Transformation3Ds IMP::algebra::get_alignments_from_first_to_second | ( | const PrincipalComponentAnalysisD< 3 > & | pca1, |
| const PrincipalComponentAnalysisD< 3 > & | pca2 | ||
| ) |
Get all alignments of the first principal component system to the second one.
| double IMP::algebra::get_angle | ( | const Line3D & | a, |
| const Line3D & | b | ||
| ) |
Get angle in radians between two lines around their closest points.
| bool IMP::algebra::get_are_almost_equal | ( | const double | a, |
| const double | b, | ||
| const double | epsilon | ||
| ) |
Compare two values for "almost equal" (intended for doubles)
epsilon is the tolerance allowed to consider the values as equal
Definition at line 107 of file algebra/utility.h.
| bool IMP::algebra::get_are_colinear | ( | const Vector3D & | p1, |
| const Vector3D & | p2, | ||
| const Vector3D & | p3 | ||
| ) |
Return true if the three points are co-linear.
| double IMP::algebra::get_area | ( | const Geometry & | ) |
Compute the area of any surface object.
| std::pair<Vector3D, double> IMP::algebra::get_axis_and_angle | ( | const Rotation3D & | rot | ) |
Decompose a Rotation3D object into a rotation around an axis.
For all identity rotations, returns the axis [1,0,0] and the angle 0.0.
| double IMP::algebra::get_ball_radius_from_volume_3d | ( | double | volume | ) |
Return the radius of a sphere with a given volume.
Definition at line 35 of file Sphere3D.h.
| VectorD<D> IMP::algebra::get_basis_vector_d | ( | unsigned int | coordinate | ) |
| VectorD<-1> IMP::algebra::get_basis_vector_kd | ( | int | D, |
| unsigned int | coordinate | ||
| ) |
| BoundingBoxD<3> IMP::algebra::get_bounding_box | ( | const Geometry & | ) |
Compute the bounding box of any geometric object.
| Vector3D IMP::algebra::get_centroid | ( | const Vector3Ds & | ps | ) |
| double IMP::algebra::get_closer_power_of_2 | ( | double | x | ) |
Closest power of 2 for a number, not necessarily higher.
Definition at line 90 of file algebra/utility.h.
| ConnollySurfacePoints IMP::algebra::get_connolly_surface | ( | const algebra::Sphere3Ds & | spheres, |
| double | density, | ||
| double | probe_radius | ||
| ) |
The algorithm is taken from Connolly's original MS program, which is freely distributable and Copyright 1983, Michael Connolly.
M.L. Connolly, "Solvent-accessible surfaces of proteins and nucleic acids", Science, 221, p709-713 (1983).
M.L. Connolly, "Analytical molecular surface calculation", J. Appl. Cryst. 16, p548-558 (1983).
See also get_uniform_surface_cover(const IMP::algebra::Sphere3Ds&, double) for a faster alternative.
| T IMP::algebra::get_constrained | ( | const T | x, |
| const T | x0, | ||
| const T | xF | ||
| ) |
Constrain a value between two given limits.
Definition at line 65 of file algebra/utility.h.
| Eigen::Matrix3d IMP::algebra::get_covariance | ( | const Gaussian3D & | g | ) |
Return the covariance matrix from a given set of standard deviations in the passed reference frame.
| BoundingBoxD<D> IMP::algebra::get_cube_d | ( | double | radius | ) |
Cube with radius of length radius.
Definition at line 194 of file BoundingBoxD.h.
| BoundingBoxD<-1> IMP::algebra::get_cube_kd | ( | unsigned int | d, |
| double | radius | ||
| ) |
Cube with radius of length side.
Definition at line 201 of file BoundingBoxD.h.
Here is the call graph for this function:| std::string IMP::algebra::get_data_path | ( | std::string | file_name | ) |
Return the full path to one of this module's data files.
To read the data file "data_library" that was placed in the data directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.
| double IMP::algebra::get_distance | ( | const Segment3D & | s, |
| const Vector3D & | p | ||
| ) |
Get the distance between a segment and a point.
| double IMP::algebra::get_distance | ( | const Plane3D & | pln, |
| const Vector3D & | p | ||
| ) |
| double IMP::algebra::get_distance | ( | const Segment3D & | a, |
| const Segment3D & | b | ||
| ) |
Get the distance between two segments.
| double IMP::algebra::get_distance | ( | const Line3D & | s, |
| const Vector3D & | p | ||
| ) |
Get closest distance between a line and a point.
| double IMP::algebra::get_distance | ( | const Line3D & | a, |
| const Line3D & | b | ||
| ) |
Get the closest distance between two lines.
| double IMP::algebra::get_distance | ( | const SphereD< D > & | a, |
| const SphereD< D > & | b | ||
| ) |
| double IMP::algebra::get_distance | ( | const VectorD< D > & | v1, |
| const VectorD< D > & | v2 | ||
| ) |
| double IMP::algebra::get_distance | ( | const Rotation3D & | r0, |
| const Rotation3D & | r1 | ||
| ) |
Return a distance between the two rotations.
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 323 of file Rotation3D.h.
Here is the call graph for this function:| IntPairs IMP::algebra::get_edges | ( | const BoundingBoxD< 3 > & | ) |
Return the edges of the box as indices into the vertices list.
Definition at line 307 of file BoundingBoxD.h.
| VectorD<D> IMP::algebra::get_elementwise_product | ( | const algebra::VectorD< D > & | a, |
| const algebra::VectorD< D > & | b | ||
| ) |
| VectorD<D> IMP::algebra::get_elementwise_product | ( | const Ints & | a, |
| const algebra::VectorD< D > & | b | ||
| ) |
| Sphere3D IMP::algebra::get_enclosing_sphere | ( | const Sphere3Ds & | ss | ) |
Return a sphere containing the listed spheres.
| Sphere3D IMP::algebra::get_enclosing_sphere | ( | const Vector3Ds & | ss | ) |
| std::string IMP::algebra::get_example_path | ( | std::string | file_name | ) |
Return the full path to one of this module's example files.
To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.
| FixedXYZ IMP::algebra::get_fixed_xyz_from_rotation | ( | const Rotation3D & | r | ) |
The inverse of rotation_from_fixed_xyz()
| Gaussian3D IMP::algebra::get_gaussian_from_covariance | ( | const Eigen::Matrix3d & | covariance, |
| const Vector3D & | center | ||
| ) |
Return a Gaussian centered at the origin from a covariance matrix.
| Eigen::MatrixXd IMP::algebra::get_gradient_of_composed_with_respect_to_first | ( | const Rotation3D & | q, |
| const Rotation3D & | p, | ||
| bool | projected = true |
||
| ) |
Get gradient of quaternion product with respect to first quaternion.
Given the rotation \(R(p)\) followed by \(R(q)\), where \(p\) and \(q\) are quaternions, the quaternion of the composed rotation \(R(s)=R(q) R(p)\) can be expressed through the Hamilton product of the two quaternions \(s(q,p) = q p\). This function returns the matrix \(M = \nabla_q s(q, p)\) with elements \(M_{ij}=\frac{d s_i}{d q_j}\).
| [in] | q | rotation corresponding to first quaternion |
| [in] | p | rotation corresponding to second quaternion |
| [in] | projected | project derivative onto tangent space to \(q\). Equivalent to differentiating wrt \(\frac{q_i}{\|q\|}\) instead of \(q_i\). |
| Eigen::MatrixXd IMP::algebra::get_gradient_of_composed_with_respect_to_second | ( | const Rotation3D & | q, |
| const Rotation3D & | p, | ||
| bool | projected = true |
||
| ) |
Get gradient of quaternion product with respect to second quaternion.
Given the rotation \(R(p)\) followed by \(R(q)\), where \(p\) and \(q\) are quaternions, the quaternion of the composed rotation \(R(s)=R(q) R(p)\) can be expressed through the Hamilton product of the two quaternions \(s(q,p) = q p\). This function returns the matrix \(\nabla_p s(q, p)\) with elements \(M_{ij}=\frac{d s_i}{d p_j}\).
| [in] | q | rotation corresponding to first quaternion |
| [in] | p | rotation corresponding to second quaternion |
| [in] | projected | project derivative onto tangent space to \(p\). Equivalent to differentiating wrt \(\frac{p_i}{\|p\|}\) instead of \(p_i\). |
| 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 170 of file vector_generators.h.
Here is the call graph for this function:| Vector3Ds IMP::algebra::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.
| Rotation2D IMP::algebra::get_identity_rotation_2d | ( | ) |
Build an identity rotation in 2D.
Definition at line 90 of file Rotation2D.h.
| Rotation3D IMP::algebra::get_identity_rotation_3d | ( | ) |
Return a rotation that does not do anything.
Definition at line 309 of file Rotation3D.h.
| Transformation2D IMP::algebra::get_identity_transformation_2d | ( | ) |
Return a transformation that does not do anything.
Definition at line 123 of file Transformation2D.h.
Here is the call graph for this function:| Transformation3D IMP::algebra::get_identity_transformation_3d | ( | ) |
Return a transformation that does not do anything.
Definition at line 102 of file Transformation3D.h.
Here is the call graph for this function:| bool IMP::algebra::get_interiors_intersect | ( | const SphereD< D > & | a, |
| const SphereD< D > & | b | ||
| ) |
| bool IMP::algebra::get_interiors_intersect | ( | const BoundingBoxD< D > & | a, |
| const BoundingBoxD< D > & | b | ||
| ) |
Return true if they intersect.
Definition at line 209 of file BoundingBoxD.h.
Here is the call graph for this function:| Rotation3D IMP::algebra::get_interpolated | ( | const Rotation3D & | a, |
| const Rotation3D & | b, | ||
| double | f | ||
| ) |
Interpolate between two rotations.
It f ==0, return b, if f==1 return a.
Definition at line 545 of file Rotation3D.h.
Here is the call graph for this function:| BoundingBoxD<D> IMP::algebra::get_intersection | ( | const BoundingBoxD< D > & | a, |
| const BoundingBoxD< D > & | b | ||
| ) |
Return the intersecting bounding box.
Definition at line 223 of file BoundingBoxD.h.
Here is the call graph for this function:| bool IMP::algebra::get_is_big_endian | ( | ) |
Returns 1 if machine is big endian else 0.
| bool IMP::algebra::get_is_little_endian | ( | ) |
Returns 1 if machine is little endian else 0.
| Triangle3D IMP::algebra::get_largest_triangle | ( | const Vector3Ds & | points | ) |
Return the largest triangle defined by 3 points from the input.
| 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 23 of file grid_utility.h.
| double IMP::algebra::get_magnitude_and_normalize_in_place | ( | VT & | vt | ) |
Returns the magnitude of vt and turns it to a unit vector in place.
Definition at line 260 of file VectorBaseD.h.
Here is the call graph for this function:| double IMP::algebra::get_maximum_length | ( | const BoundingBoxD< D > & | a | ) |
Return the maximum axis aligned extent.
Definition at line 262 of file BoundingBoxD.h.
Here is the call graph for this function:| float IMP::algebra::get_next_larger_power_of_2 | ( | float | x | ) |
Closest power of 2 that can contain a number x.
Definition at line 72 of file algebra/utility.h.
| double IMP::algebra::get_next_larger_power_of_2 | ( | double | x | ) |
Closest power of 2 that can contain a number x.
Definition at line 81 of file algebra/utility.h.
| VectorD<D> IMP::algebra::get_ones_vector_d | ( | double | v = 1 | ) |
| VectorD<-1 > IMP::algebra::get_ones_vector_kd | ( | unsigned int | Di, |
| double | v = 1 |
||
| ) |
| Vector3D IMP::algebra::get_orthogonal_vector | ( | const Vector3D & | v | ) |
Return a vector that is perpendicular to the given vector.
Definition at line 51 of file Vector3D.h.
| double IMP::algebra::get_power_distance | ( | const SphereD< D > & | a, |
| const SphereD< D > & | b | ||
| ) |
| PrincipalComponentAnalysisD<D> IMP::algebra::get_principal_components | ( | const Vector< VectorD< D > > & | ps | ) |
Perform principal components analysis on a set of vectors.
Definition at line 109 of file eigen_analysis.h.
Here is the call graph for this function:| Vector3D IMP::algebra::get_projected | ( | const Line3D & | l, |
| const Vector3D & | p | ||
| ) |
Project a point onto the line.
This is equivalent to the point on the line closest to the provided point.
| algebra::Segment3D IMP::algebra::get_projected | ( | const Line3D & | l, |
| const algebra::Segment3D & | s | ||
| ) |
Project a segment onto a line.
| double IMP::algebra::get_radius_of_gyration | ( | const Vector3Ds & | ps | ) |
Return the radius of gyration of a set of points.
Definition at line 77 of file Vector3D.h.
Here is the call graph for this function:| Vector3Ds IMP::algebra::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.
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.
| Transformation3D IMP::algebra::get_random_local_transformation | ( | Vector3D | origin, |
| double | max_translation = 5., |
||
| double | max_angle_in_rad = 0.26 |
||
| ) |
Get a local transformation.
| [in] | origin | the origin of the rotation |
| [in] | max_translation | default value is 5 |
| [in] | max_angle_in_rad | default value is 15 degree in radians |
| Rotation2D IMP::algebra::get_random_rotation_2d | ( | ) |
Build an identity rotation in 2D.
Definition at line 93 of file Rotation2D.h.
| Rotation3D IMP::algebra::get_random_rotation_3d | ( | ) |
Pick a rotation at random from all possible rotations.
| Rotation3D IMP::algebra::get_random_rotation_3d | ( | const Rotation3D & | center, |
| double | distance | ||
| ) |
Pick a rotation at random near the provided one.
This method generates a rotation that is within the provided distance of center.
| [in] | center | The center of the rotational volume |
| [in] | distance | See get_distance(const Rotation3D&,const Rotation3D&) for a full definition. |
| VectorD<D> IMP::algebra::get_random_vector_in | ( | const BoundingBoxD< D > & | bb | ) |
Generate a random vector in a box with uniform density.
Definition at line 39 of file vector_generators.h.
Here is the call graph for this function:| VectorD<D> IMP::algebra::get_random_vector_in | ( | const SphereD< D > & | s | ) |
Generate a random vector in a sphere with uniform density.
Definition at line 57 of file vector_generators.h.
Here is the call graph for this function:| VectorD<2> IMP::algebra::get_random_vector_in | ( | const SphereD< 2 > & | s | ) |
| Vector3D IMP::algebra::get_random_vector_in | ( | const Cylinder3D & | c | ) |
Generate a random vector in a cylinder with uniform density.
| VectorD<D> IMP::algebra::get_random_vector_on | ( | const BoundingBoxD< D > & | bb | ) |
Generate a random vector on a box with uniform density.
Definition at line 48 of file vector_generators.h.
| VectorD<D> IMP::algebra::get_random_vector_on | ( | const SphereD< D > & | s | ) |
Generate a random vector on a sphere with uniform density.
Definition at line 100 of file vector_generators.h.
| VectorD<3> IMP::algebra::get_random_vector_on_unit_sphere | ( | ) |
returns a random vector on a sphere of radius 1 with uniform density and implementation optimized for the 3D + unit vector case
Definition at line 91 of file vector_generators.h.
| DenseGrid3D<double> IMP::algebra::get_rasterized | ( | const Gaussian3Ds & | gmm, |
| const Floats & | weights, | ||
| double | cell_width, | ||
| const BoundingBox3D & | bb | ||
| ) |
Rasterize the Gaussians to a grid.
| DenseGrid3D<double> IMP::algebra::get_rasterized_fast | ( | const Gaussian3Ds & | gmm, |
| const Floats & | weights, | ||
| double | cell_width, | ||
| const BoundingBox3D & | bb, | ||
| double | factor = 2.5 |
||
| ) |
Rasterize the Gaussians to a grid.
The result is an approximation, but is obtained significantly faster. Good for quickly checking a GMM.
| Vector3D IMP::algebra::get_reflected | ( | const Plane3D & | pln, |
| const Vector3D & | p | ||
| ) |
| double IMP::algebra::get_relative_projection_on_segment | ( | const Segment3D & | s, |
| const algebra::Vector3D & | p | ||
| ) |
Return 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.
| s | segment in 3D |
| p | point in 3D |
| double IMP::algebra::get_rmsd | ( | const Vector3DsOrXYZs0 & | m1, |
| const Vector3DsOrXYZs1 & | m2 | ||
| ) |
See get_rmsd_transforming_first().
Definition at line 47 of file algebra/distance.h.
Here is the call graph for this function:| double IMP::algebra::get_rmsd_transforming_first | ( | const Transformation3D & | tr, |
| const Vector3DsOrXYZs0 & | m1, | ||
| const Vector3DsOrXYZs1 & | m2 | ||
| ) |
Calculate the root mean square deviation between two sets of 3D points.
See generic geometry for more information.
Definition at line 27 of file algebra/distance.h.
Here is the call graph for this function:| Rotation3D IMP::algebra::get_rotation_about_axis | ( | const Vector3D & | axis, |
| double | angle | ||
| ) |
Generate a Rotation3D object from a rotation around an axis.
| [in] | axis | the rotation axis passes through (0,0,0) |
| [in] | angle | the rotation angle in radians in the clockwise direction |
Definition at line 374 of file Rotation3D.h.
Here is the call graph for this function:| Rotation3D IMP::algebra::get_rotation_about_normalized_axis | ( | const Vector3D & | axis_norm, |
| double | angle | ||
| ) |
Generate a Rotation3D object from a rotation around an axis that is assumed to be normalized
| [in] | axis_norm | the normalized rotation axis passing through (0,0,0) |
| [in] | angle | the rotation angle in radians in the clockwise direction |
Definition at line 348 of file Rotation3D.h.
| Transformation3D IMP::algebra::get_rotation_about_point | ( | const Vector3D & | point, |
| const Rotation3D & | rotation | ||
| ) |
Generate a Transformation3D object from a rotation around a point.
Rotate about a point rather than the origin.
| [in] | point | Center to rotate about |
| [in] | rotation | The rotation to perform |
Definition at line 113 of file Transformation3D.h.
| Transformation2D IMP::algebra::get_rotation_about_point | ( | const Vector2D & | point, |
| const Rotation2D & | rotation | ||
| ) |
Generate a Transformation2D object from a rotation around a point.
Generate a Transformation2D to rotate about a point rather than the origin.
| [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 135 of file Transformation2D.h.
Here is the call graph for this function:| Rotation3D IMP::algebra::get_rotation_from_fixed_xyz | ( | double | xr, |
| double | yr, | ||
| double | zr | ||
| ) |
Initialize a rotation in x-y-z order from three angles.
| [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 |
| Rotation3D IMP::algebra::get_rotation_from_fixed_zxz | ( | double | phi, |
| double | theta, | ||
| double | psi | ||
| ) |
Initialize a rotation from Euler angles.
| [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 |
| Rotation3D IMP::algebra::get_rotation_from_fixed_zyz | ( | double | Rot, |
| double | Tilt, | ||
| double | Psi | ||
| ) |
Generate a rotation object from Euler Angles.
| [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 IMP::algebra::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 IMP::algebra::get_rotation_from_matrix | ( | Eigen::Matrix3d | m | ) |
Generate a Rotation3D object from a rotation matrix.
| Rotation3D IMP::algebra::get_rotation_from_vector4d | ( | const VectorD< 4 > & | v | ) |
Compute a rotation from an unnormalized quaternion.
Definition at line 441 of file Rotation3D.h.
| 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 axes must be perpendicular unit vectors.
| Rotation3D IMP::algebra::get_rotation_taking_first_to_second | ( | const Vector3D & | v1, |
| const Vector3D & | v2 | ||
| ) |
Create a rotation from the first vector to the second one.
| Rotation2D IMP::algebra::get_rotation_to_x_axis | ( | const Vector2D & | v | ) |
Build the rotation that transforms the vector X of the origin of coordinates into the given vector
Definition at line 100 of file Rotation2D.h.
| int IMP::algebra::get_rounded | ( | const T & | x | ) |
Rounds a number to next integer.
The result is of type integer but the argument can be of any type. Some examples:
Definition at line 43 of file algebra/utility.h.
| algebra::Segment3D IMP::algebra::get_segment_connecting_first_to_second | ( | const Line3D & | a, |
| const Line3D & | b | ||
| ) |
Get shortest possible segment from the first line to the second.
| Segment3D IMP::algebra::get_shortest_segment | ( | const Segment3D & | s, |
| const Vector3D & | p | ||
| ) |
| Segment3D IMP::algebra::get_shortest_segment | ( | const Segment3D & | sa, |
| const Segment3D & | sb | ||
| ) |
| int IMP::algebra::get_sign | ( | const T & | x | ) |
Sign of a number. 1 if the number is higher or equal to 0 and -1 otherwise.
Definition at line 25 of file algebra/utility.h.
| Sphere3Ds IMP::algebra::get_simplified_from_volume | ( | Sphere3Ds | in, |
| double | maximum_allowed_error_angstroms | ||
| ) |
Get a set of balls that approximates the surface of the passed set.
Any point in the old surface will be within roughly maximum_allowed_error_angstroms of a point in the new surface and any point outside the old volume will be within roughly maximum_allowed_error_angstroms of a point outside the new volume.
| double IMP::algebra::get_squared_distance | ( | const VectorD< D > & | v1, |
| const VectorD< D > & | v2 | ||
| ) |
| double IMP::algebra::get_surface_area | ( | const Geometry & | ) |
Compute the surface area of any volumetric object.
| FloatPair IMP::algebra::get_surface_area_and_volume | ( | const algebra::Sphere3Ds & | ss | ) |
Get surface area & 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 | ) |
Build a 3D transformation from a 2D one.
| IMP::algebra::Transformation3D IMP::algebra::get_transformation_aligning_first_to_second | ( | const Vector3DsOrXYZs0 & | source, |
| const Vector3DsOrXYZs1 & | target | ||
| ) |
Compute the rigid transform bringing the first point set to the second.
The points are assumed to be corresponding (that is, from[0] is aligned to to[0] etc.). The alignment computed is that which minimizes the sum of squared distances between corresponding points. This uses the Kabsch algorithm.
\[ \textit{argmin}_T \sum \left|T\left(f\left[i\right]\right)-t[i]\right|^2 \]
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 generic geometry for more information.
Definition at line 45 of file geometric_alignment.h.
Here is the call graph for this function:| Transformation3D IMP::algebra::get_transformation_aligning_first_to_second | ( | Vector3Ds | a, |
| Vector3Ds | b | ||
| ) |
Equivalent to
| 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
| Transformation3D IMP::algebra::get_transformation_from_first_triangle_to_second | ( | Triangle3D | first_tri, |
| Triangle3D | second_tri | ||
| ) |
Return a transformation between two triangles.
| BoundingBoxD<3> IMP::algebra::get_transformed | ( | const BoundingBoxD< 3 > & | bb, |
| const Transformation3D & | tr | ||
| ) |
Return a bounding box containing the transformed box.
Definition at line 154 of file Transformation3D.h.
Here is the call graph for this function:| const Storage::Value IMP::algebra::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.
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().
Definition at line 36 of file grid_utility.h.
Here is the call graph for this function:| Rotation3Ds IMP::algebra::get_uniform_cover_rotations_3d | ( | unsigned int | num_points | ) |
Cover the space of rotations evenly.
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.
| Vector<VectorD<D> > IMP::algebra::get_uniform_surface_cover | ( | const SphereD< D > & | s, |
| unsigned int | n | ||
| ) |
Generate a set of vectors which covers a sphere uniformly.
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.
Definition at line 116 of file vector_generators.h.
| Vector3Ds IMP::algebra::get_uniform_surface_cover | ( | const Cylinder3D & | cyl, |
| int | number_of_points | ||
| ) |
Generate a set of 3d points that uniformly cover a cylinder.
| Vector3Ds IMP::algebra::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.
| Vector3Ds IMP::algebra::get_uniform_surface_cover | ( | const Cone3D & | cone, |
| unsigned int | number_of_points | ||
| ) |
| Vector3Ds IMP::algebra::get_uniform_surface_cover | ( | const Sphere3Ds & | in, |
| double | points_per_square_angstrom | ||
| ) |
Return a cover of the surface of the volume defined by a union of balls bounded by the spheres.
This is effectively a sampling of the solvent exposed surface of a set of spheres. The density of points has approximately the passed value.
This method is much faster than get_connolly_surface().
| Vector<VectorD<D> > IMP::algebra::get_uniform_upper_hemisphere_cover | ( | const SphereD< D > & | s, |
| unsigned int | n | ||
| ) |
Generate a set of 3D points that uniformly cover a hemisphere.
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 134 of file vector_generators.h.
| algebra::Rotation3Ds IMP::algebra::get_uniformly_sampled_rotations | ( | double | delta | ) |
Generates a nondegenerate set of Euler angles with a delta resolution.
| [in] | delta | sample every delta angles in radians. |
| BoundingBoxD<D> IMP::algebra::get_union | ( | BoundingBoxD< D > | a, |
| const BoundingBoxD< D > & | b | ||
| ) |
Return the union bounding box.
This is the same as doing a+b.
Definition at line 254 of file BoundingBoxD.h.
| BoundingBoxD<D> IMP::algebra::get_unit_bounding_box_d | ( | ) |
| BoundingBoxD<-1> IMP::algebra::get_unit_bounding_box_kd | ( | unsigned int | d | ) |
Box with radius one.
Definition at line 187 of file BoundingBoxD.h.
Here is the call graph for this function:| VT IMP::algebra::get_unit_vector | ( | VT | vt | ) |
Returns a unit vector pointing at the same direction as this vector.
Definition at line 229 of file VectorBaseD.h.
| const VectorD<C::DIMENSION>& IMP::algebra::get_vector_geometry | ( | const C & | g | ) |
| Vector3D IMP::algebra::get_vector_product | ( | const Vector3D & | p1, |
| const Vector3D & | p2 | ||
| ) |
Return the vector product (cross product) of two vectors.
Definition at line 31 of file Vector3D.h.
Return a list of the 2^D bounding points for the bounding box.
Definition at line 274 of file BoundingBoxD.h.
Here is the call graph for this function:| double IMP::algebra::get_volume | ( | const BoundingBoxD< D > & | bb | ) |
See BoundingBoxD.
Definition at line 163 of file BoundingBoxD.h.
Here is the call graph for this function:| double IMP::algebra::get_volume | ( | const Geometry & | ) |
Compute the volume of any volumetric object.
| double IMP::algebra::get_weighted_rmsd | ( | const Vector3DsOrXYZs0 & | m1, |
| const Vector3DsOrXYZs1 & | m2, | ||
| const Floats & | weights | ||
| ) |
See get_weighted_rmsd_transforming_first().
Definition at line 83 of file algebra/distance.h.
Here is the call graph for this function:| VectorD<D> IMP::algebra::get_zero_vector_d | ( | ) |
| VectorD<-1 > IMP::algebra::get_zero_vector_kd | ( | int | Di | ) |
| VectorD<D> IMP::algebra::operator* | ( | double | s, |
| VectorD< D > | o | ||
| ) |
| Vector3Ds IMP::algebra::read_pts | ( | TextInput | input | ) |
| Sphere3Ds IMP::algebra::read_spheres | ( | TextInput | input | ) |
| void IMP::algebra::reversed_read | ( | void * | dest, |
| size_t | size, | ||
| size_t | nitems, | ||
| std::ifstream & | f, | ||
| bool | reverse | ||
| ) |
Reads from file in normal or reverse order.
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 |
||
| ) |
Writes to a file in normal or reversed order.
This function is the same as fwrite from C, but at the end there is a flag saying if data should be written in reverse order or not.
If the reverse parameter is true, the data will be written in reverse order.
| void IMP::algebra::set_vector_geometry | ( | C & | g, |
| const E & | v | ||
| ) |
| void IMP::algebra::write_pts | ( | const Vector3Ds & | vs, |
| TextOutput | out | ||
| ) |
| void IMP::algebra::write_spheres | ( | const Sphere3Ds & | vs, |
| TextOutput | out | ||
| ) |
|
static |
the constant pi
Definition at line 21 of file algebra/constants.h.