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Clipper
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Namespaces | |
| namespace | datatypes |
| namespace | data32 |
| namespace | data64 |
Classes | |
| class | AtomShapeFn |
| Atomic shape function object. More... | |
| class | AtomSF |
| Atomic scattering factor object. More... | |
| class | Metric_tensor |
| Metric tensor. More... | |
| class | Cell_descr |
| cell description (automatically converts to radians) More... | |
| class | Cell |
| Cell object. More... | |
| class | ClipperInstance |
| class | ClipperInstantiator |
| class | Property_base |
| Base class for properties of arbitrary types. More... | |
| class | Property |
| Template for a property holding an arbitrary type. More... | |
| class | PropertyManager |
| Class for holding a list of labelled properties of arbitrary types. More... | |
| class | ObjectCache |
| Object Cache manager. More... | |
| class | Message |
| Message handler class. More... | |
| class | Message_base |
| Base type for messages. More... | |
| class | Message_generic |
| Generic message. More... | |
| class | Message_fatal |
| Fatal message (level = 9) More... | |
| class | Message_warn |
| Warning message (level = 5) More... | |
| class | Message_info |
| Info message (level = 1) More... | |
| class | Message_ctor |
| Constructor message (level = 2) More... | |
| class | Message_dtor |
| Destructor message (level = 2) More... | |
| class | Range |
| Range - upper and lower bounds of some type. More... | |
| class | Range_sampling |
| Range sampling: discrete sampling of a real range. More... | |
| class | Histogram |
| General histogram class. More... | |
| class | Generic_ordinal |
| Generic ordinal gernerator. More... | |
| class | Test_base |
| Base class for clipper self-test classes. More... | |
| class | Mutex |
| Mutex class: used for locking and unlocking shared resources. More... | |
| class | Thread_base |
| Thread base class: Override this to create new threads. More... | |
| class | String |
| String extension with simple parsing methods. More... | |
| class | Vec3 |
| 3-vector class More... | |
| class | Mat33 |
| 3x3-matrix class More... | |
| class | Mat33sym |
| Compressed form for 3x3 symmetric matrix class. More... | |
| class | RTop |
| Rotation-translation operator. More... | |
| class | Array2d |
| Simple 2-d array class. More... | |
| class | Matrix |
| General matrix class: like Array2d but with numerical methods. More... | |
| class | Util |
| Utility class. More... | |
| class | Container |
| Definition for a generic container Object. More... | |
| class | CHKL_info |
| HKL list and indexing object container. More... | |
| class | CHKL_data |
| Reflection data list container. More... | |
| class | CXmap |
| Crystallographic map container. More... | |
| class | CNXmap |
| Non-Crystallographic map container. More... | |
| class | CNXmap_operator |
| Non-Crystallographic map operator container. More... | |
| class | CResolution |
| Resolution container. More... | |
| class | CSpacegroup |
| Spacegroup container. More... | |
| class | CCell |
| CCell container. More... | |
| class | CGrid_sampling |
| CGrid_sampling container. More... | |
| class | Resolution |
| Resolution in angstroms. More... | |
| class | HKL_class |
| reflection class More... | |
| class | RTop_orth |
| Orthogonal operator class. More... | |
| class | HKL |
| reflection 'Miller' index More... | |
| class | Coord_reci_orth |
| orthogonal reciprocal coordinate (length of which is invresolsq) More... | |
| class | Coord_reci_frac |
| fractional reciprocal coordinate (i.e. non-integer hkl) More... | |
| class | Coord_grid |
| Grid coordinate. More... | |
| class | Coord_orth |
| orthogonal (Angstrom) coordinates More... | |
| class | Coord_frac |
| fractional (cell) coordinates More... | |
| class | Coord_map |
| map coordinate: this is like Coord_grid, but non-integer More... | |
| class | U_aniso_orth |
| Anisotropic orthogonal atomic displacement parameters. More... | |
| class | U_aniso_frac |
| Anisotropic fractional atomic displacement parameters. More... | |
| class | Grid |
| generic grid More... | |
| class | Grid_sampling |
| Grid sampling of a unit cell. More... | |
| class | HKL_sampling |
| HKL sampling of reciprocal space. More... | |
| class | Grid_range |
| Grid range class: defines array limits for a grid. More... | |
| class | Atom |
| Atom class. More... | |
| class | Atom_list |
| Atom list class. More... | |
| class | Grad_orth |
| orthogonal (Angstom) gradient, with respect to orthogonal x,y,z More... | |
| class | Grad_frac |
| fractional (cell) gradient, with respect to fractional u,v,w More... | |
| class | Grad_map |
| map coordinate gradient, with respect to grid u,v,w More... | |
| class | Curv_orth |
| orthogonal (Angstom) curvatures, with respect to orthogonal x,y,z More... | |
| class | Curv_frac |
| fractional (cell) curvatures, with respect to fractional u,v,w More... | |
| class | Curv_map |
| map coordinate curvatures, with respect to grid u,v,w More... | |
| class | FFTmap_base |
| class | FFTmap_p1 |
| FFTmap_p1: low level P1 map used for calculating FFTs. More... | |
| class | FFTmap |
| FFTmap: P1 map with symmetry used for calculating FFTs. More... | |
| class | FFTmap_sparse_p1_base |
| base type for sparse P1 fft maps More... | |
| class | FFTmap_sparse_p1_hx |
| FFTmap_sparse_p1_hx: low level sparse P1 map used for calculating FFTs. More... | |
| class | FFTmap_sparse_p1_xh |
| FFTmap_sparse_p1_xh: low level sparse P1 map used for calculating FFTs. More... | |
| class | HKL_data_cacheobj |
| class | Datatype_base |
| Reflection data type objects. More... | |
| class | HKL_data_base |
| HKL_data_base. More... | |
| class | HKL_data |
| HKL_data<> More... | |
| class | HKL_info |
| HKL list container and tree root. More... | |
| class | HKL_lookup |
| Fast reflection lookup object. More... | |
| class | LogPhaseProb |
| Log phase probability distribution object. More... | |
| class | Interp_nearest |
| Wrapper class for zeroth-order (nearest neighbour) interpolation fns. More... | |
| class | Interp_linear |
| Wrapper class for first-order (linear) interpolation fns. More... | |
| class | Interp_cubic |
| Wrapper class for third-order (cubic) interpolation fns. More... | |
| class | Map_stats |
| Generic map statistics class. More... | |
| class | Map_index_sort |
| Generic map sorting class. More... | |
| class | NXmap_base |
| NXmap_base: base for non-crystallographic map class. More... | |
| class | NXmap |
| NXmap<T>: actual non-crystallographic map class. More... | |
| class | NX_operator |
| NX_operator: non-crystal map operator. More... | |
| class | NXmap_operator |
| NXmap_operator: non-crystal map operator referencing a particular NXmap. More... | |
| class | Prob_phi_2d |
| 2-d angular probability distibution class More... | |
| class | Ramachandran |
| Ramachandran plot class. More... | |
| class | Resolution_ordinal |
| Resolution ordinal gernerator. More... | |
| class | BasisFn_binner |
| simple binning basis function More... | |
| class | BasisFn_linear |
| simple linear basis function More... | |
| class | BasisFn_spline |
| simple smooth basis function More... | |
| class | BasisFn_gaussian |
| simple Gaussian basis function More... | |
| class | BasisFn_aniso_gaussian |
| simple anisotropic Gaussian basis function More... | |
| class | BasisFn_log_gaussian |
| simple log Gaussian basis function More... | |
| class | BasisFn_log_aniso_gaussian |
| simple anisotropic Gaussian basis function More... | |
| class | BasisFn_expcubic |
| simple Expcubic basis function More... | |
| class | BasisFn_base |
| abstract base class for resolution function basis functions More... | |
| class | TargetFn_base |
| abstract base class for least-squares resolution function target functions More... | |
| class | ResolutionFn |
| 2nd order resolution function evaluator More... | |
| class | ResolutionFn_nonlinear |
| 2nd order resolution function evaluator More... | |
| class | TargetFn_meanFnth |
| simple mean |F|n target More... | |
| class | TargetFn_meanEnth |
| simple mean |E|n target More... | |
| class | TargetFn_scaleF1F2 |
| |F|2 scaling target More... | |
| class | TargetFn_scaleLogF1F2 |
| log |F|2 scaling target More... | |
| class | TargetFn_scaleI1I2 |
| class | TargetFn_scaleLogI1I2 |
| log |I| scaling target More... | |
| class | TargetFn_scaleEsq |
| |E|2 scaling target More... | |
| class | TargetFn_sigmaa_omegaa |
| class | TargetFn_sigmaa |
| class | Euler |
| Euler angle class. More... | |
| class | Euler_ccp4 |
| Euler_ccp4 angle class. More... | |
| class | Polar_ccp4 |
| Polar_ccp4 angle class. More... | |
| class | Rotation |
| Rotation class. More... | |
| struct | Compare_grid |
| class | Spgr_descr |
| spacegroup description More... | |
| class | Spgr_cacheobj |
| class | Spacegroup |
| Spacegroup object. More... | |
| class | RTop_frac |
| Fractional operator class. More... | |
| class | Symop |
| Crystallographic symmetry operator. More... | |
| class | Isymop |
| Integerised symmetry matrix. More... | |
| class | Symop_code |
| Compressed encoded symmetry operator. More... | |
| class | Test_core |
| class | Xmap_cacheobj |
| class | Xmap_base |
| Xmap_base: base for crystallographic map class. More... | |
| class | Xmap |
| Xmap<T>: actual crystallographic map class. More... | |
Typedefs | |
| typedef ftype64 | ftype |
| ftype definition for floating point representation | |
| typedef ftype64 | xtype |
| xtype definition for import/export of data | |
| typedef float | ftype32 |
| typedef double | ftype64 |
| typedef int | itype32 |
| typedef unsigned int | uitype32 |
| typedef long long | itype64 |
| typedef unsigned long long | uitype64 |
| typedef Grid_range | Grid_map |
| Obsolete form for Grid_range. | |
| typedef float | ffttype |
Functions | |
| template<class T > | |
| int | operator== (const Vec3< T > &v1, const Vec3< T > &v2) |
| template<class T > | |
| int | operator!= (const Vec3< T > &v1, const Vec3< T > &v2) |
| template<class T > | |
| Vec3< T > | operator- (const Vec3< T > &v) |
| template<class T > | |
| Vec3< T > | operator+ (const Vec3< T > &v1, const Vec3< T > &v2) |
| template<class T > | |
| Vec3< T > | operator- (const Vec3< T > &v1, const Vec3< T > &v2) |
| template<class T > | |
| Vec3< T > | operator* (const T &s, const Vec3< T > &v1) |
| template<class T > | |
| Vec3< T > | operator* (const Vec3< T > &v1, const T &s) |
| template<class T > | |
| T | operator* (const Vec3< T > &v1, const Vec3< T > &v2) |
| template<class T > | |
| Vec3< T > | operator* (const Mat33< T > &m, const Vec3< T > &v) |
| template<class T > | |
| Vec3< T > | operator* (const Vec3< T > &v, const Mat33< T > &m) |
| template<class T > | |
| Mat33< T > | operator* (const Mat33< T > &m1, const Mat33< T > &m2) |
| template<class T > | |
| Mat33< T > | operator+ (const Mat33< T > &m1, const Mat33< T > &m2) |
| template<class T > | |
| Mat33< T > | operator- (const Mat33< T > &m) |
| template<class T > | |
| Vec3< T > | operator* (const Mat33sym< T > &m, const Vec3< T > &v) |
| template<class T > | |
| Mat33sym< T > | operator+ (const Mat33sym< T > &m1, const Mat33sym< T > &m2) |
| template<class T > | |
| Mat33sym< T > | operator- (const Mat33sym< T > &m) |
| template<class T > | |
| Vec3< T > | operator* (const RTop< T > &r, const Vec3< T > &v) |
| template<class T > | |
| RTop< T > | operator* (const RTop< T > &r1, const RTop< T > &r2) |
| template<class T > | |
| std::vector< T > | operator* (const Matrix< T > &m, const std::vector< T > &v) |
| Rotation | operator* (const Rotation &r1, const Rotation &r2) |
| bool | reci_asu (const Spgr_descr::Symop_codes &ops, data::ASUfn asufn) |
| Vec3 | real_asu (const Spgr_descr::Symop_codes &ops) |
Variables | |
| Message | message |
| Message_fatal | message_parent_of_root ("Container: attempt to access parent of root") |
| Message_fatal | message_child_out_of_range ("Container: child index out of range") |
| Message_fatal | message_duplicate_path ("Container: attempt to create duplicate path") |
| const HKL_info | NullHKL_info |
| const Resolution | NullResolution |
| const Spacegroup | NullSpacegroup |
| const Cell | NullCell |
| const Grid_sampling | NullGrid_sampling |
| Message_fatal | message_fftmap_get_real_space_error ("FFTmap: get_real_data in reciprocal space") |
| Message_fatal | message_fftmap_set_real_space_error ("FFTmap: set_real_data in reciprocal space") |
| Message_fatal | message_fftmap_get_reci_space_error ("FFTmap: get_recip_data in real space") |
| Message_fatal | message_fftmap_set_reci_space_error ("FFTmap: set_recip_data in real space") |
| Message_ctor | message_ctor_fftmap (" [FFTmap: constructed]") |
| Message_ctor | message_ctor_hkl_data (" [HKL_data: constructed]") |
| Message_fatal | message_recip_asu_error ("HKL_info: find_sym reciprocal space ASU error") |
| Message_ctor | message_ctor_hkl_info (" [HKL_info: constructed]") |
| Message_ctor | message_ctor_nxmap (" [NXmap: constructed]") |
| Message_ctor | message_ctor_xmap (" [Xmap: constructed]") |
All normal clipper objects except data objects are defined in this namespace.
| typedef ftype64 clipper::ftype |
ftype definition for floating point representation
This type is used for all floating point values except data. The whole package could be templatised on ftype. However for now it is typedef'ed
| Vec3<T> clipper::operator* | ( | const Mat33< T > & | m, |
| const Vec3< T > & | v | ||
| ) | [inline] |
Assumes a column vector
| Vec3<T> clipper::operator* | ( | const Vec3< T > & | v, |
| const Mat33< T > & | m | ||
| ) | [inline] |
Assumes a row vector, i.e. equivalent to the matrix-vector product with the matrix trasposed
| std::vector<T> clipper::operator* | ( | const Matrix< T > & | m, |
| const std::vector< T > & | v | ||
| ) |
Assumes a column vector
References clipper::Array2d< T >::cols(), clipper::Message::message(), and clipper::Array2d< T >::rows().
| Rotation clipper::operator* | ( | const Rotation & | r1, |
| const Rotation & | r2 | ||
| ) |
Note: This multiplication operator combines rotations in left-to-right order, rather than the right-to-left order used for matrices. Thus, the rotation which arises from applying rotation r1 followed by rotation r2 is given by r1*r2. Similarly, the rotation which arises from applying rotation r1 followed by rotation r2 and rotation r3 is given by (r1*r2)*r3.
1.7.4