Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Module computing the shelling order forests of particles in a binding patch. Module computing the shelling order forests of particles in a binding patch. More...
#include "Union_of_balls_boundary_patch_shelling_3_module.hpp"
Static Public Member Functions | |
static boost::program_options::options_description *& | get_options (void) |
Access to the options' description of the module. More... | |
Traits Requirements | |
typedef ModuleTraits::Union_of_balls_boundary_3 | Union_of_balls_boundary_3 |
Representation of the boundary of the union of balls. More... | |
typedef ModuleTraits::Is_in_patch | Is_in_patch |
Predicate checking that an input face of the boundary has its ball on a given patch. More... | |
Other Types | |
typedef SBL::GT::T_Union_of_balls_boundary_patch_shelling_3< Union_of_balls_boundary_3, Is_in_patch > | Union_of_balls_boundary_patch_shelling_3 |
Shelling diagram of a patch on the boundary of the union of 3D balls. More... | |
typedef Union_of_balls_boundary_patch_shelling_3::Face_shelling_forest | Face_shelling_forest |
Shelling forest of the faces (i.e. spherical caps) of the spheres involved in a patch (see Cell_complex_shelling_diagram). More... | |
typedef Union_of_balls_boundary_patch_shelling_3::Ball_shelling_forest | Ball_shelling_forest |
Shelling forest of the vertices of the alpha-complex involved in a patch (see Cell_complex_shelling_diagram). More... | |
Input Accessors | |
Union_of_balls_boundary_3 *& | get_boundary (void) |
Reference to a pointer over the input boundary. More... | |
Is_in_patch *& | get_is_in_patch (void) |
Reference to a pointer over the predicate representing the input patch. More... | |
Output Accessors | |
const Face_shelling_forest & | get_face_shelling_forest (void) const |
Const reference to the output Face Shelling Forest. More... | |
Face_shelling_forest & | get_face_shelling_forest (void) |
Reference to the output Face Shelling Forest. More... | |
const Ball_shelling_forest & | get_ball_shelling_forest (void) const |
Const reference to the output Ball Shelling Forest. More... | |
Ball_shelling_forest & | get_ball_shelling_forest (void) |
Reference to the output Ball Shelling Forest. More... | |
Mandatory Requirements | |
void | run (unsigned verbose, std::ostream &out) override |
Runs the module following the input options. More... | |
bool | is_runnable (void) const override |
Checks that all the input options were set. More... | |
void | statistics (std::ostream &out) override |
Reports high-level statistics on the module. More... | |
std::string | get_name (void) const override |
Returns the name of the package. More... | |
Optional Requirements | |
boost::program_options::options_description | add_options (void) override |
Virtual method for adding options to the module. More... | |
bool | check_options (std::string &message) const override |
Checks that the input options' values are coherent. More... | |
std::string | get_output_prefix (void) const override |
Returns a prefix that concatains the input line options used when running the module. More... | |
void | report (const std::string &prefix) override |
Reports the output and statistics in output files. More... | |
Modules Management | |
void | set_module_instance_name (const std::string &module_instance_name) |
Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules. More... | |
const std::string & | get_module_instance_name (void) const |
Get the name of this instance of this module. More... | |
void | set_report_mode (std::ios_base::openmode report_mode) |
Set a report mode, that is open or append modes. More... | |
void | set_report_mode (std::ios_base::openmode &report_mode) |
Set a report mode, that is open or append modes. More... | |
const std::ios_base::openmode | get_report_mode (void) const |
Get the report mode to be used when reporting. More... | |
Optional Requirements | |
void | check_filesystem_directory_exists (const std::string &output_prefix) |
To avoid later crash: check filesystem / existence of directory / directory exists. More... | |
Others | |
template<class Self_ > | |
Self_ * | clone (const Self_ *s) const |
Clones the object using the copy constructor. More... | |
virtual bool | is_logical_module (void) const |
Checks that this module defines a logical operator. More... | |
virtual bool | is_condition_module (void) const |
Checks that this module defines a condition operator. More... | |
virtual bool | operator() (void) |
Only for condition modules, for returning the predicate value. More... | |
virtual bool | is_modules_collection (void) const |
Checks that this module defines a collection of modules. More... | |
Module computing the shelling order forests of particles in a binding patch. Module computing the shelling order forests of particles in a binding patch.
Remind that the the shelling order forest of the input balls in a patch requires to compute the boundary of the union of all the input balls. This boundary is represented using the class SBL::GT::T_Union_of_balls_boundary_3_data_structure that follows the concept HalfEdgeDataStructure of the CGAL library. As fully explained in the user manual Union_of_balls_boundary_patch_shelling_3, the computation is done on five steps:
The input boundary of the union of all the input balls be set using the method SBL::Modules::T_Union_of_balls_boundary_patch_shelling_3_module::get_boundary, that returns a reference to a pointer over the input boundary.
The definition of the patch is given using a functor of type SBL::Modules::T_Union_of_balls_boundary_patch_shelling_3_module::Is_in_patch, that takes a face of the boundary as input, and returns true iff its associated ball is in the patch. This functor can be set using the method SBL::Modules::T_Union_of_balls_boundary_patch_shelling_3_module::get_is_in_patch, that returns a reference to a pointer over the input functor.
The output Ball Shelling Forest is accessible using the method SBL::Modules::T_Union_of_balls_boundary_patch_shelling_3_module::get_ball_shelling_forest.
Note that the Face Shelling Forest is also accessible using the method SBL::Modules::T_Union_of_balls_boundary_patch_shelling_3_module::get_face_shelling_forest.
ModuleTraits | Traits class defining the types SBL::Modules::T_Union_of_balls_boundary_patch_shelling_3_module::Union_of_balls_boundary_3 and SBL::Modules::T_Union_of_balls_boundary_patch_shelling_3_module::Is_in_patch. |
OutputArchive | Archive concept from the Boost library, allowing to switch between a full serialization of the output data with for example the class boost::archive::xml_oarchive, or a multiple archives serialization with the class SBL::IO::T_Multiple_archives_serialization_xml_oarchive. |
Shelling forest of the vertices of the alpha-complex involved in a patch (see Cell_complex_shelling_diagram).
Shelling forest of the faces (i.e. spherical caps) of the spheres involved in a patch (see Cell_complex_shelling_diagram).
typedef ModuleTraits::Is_in_patch Is_in_patch |
Predicate checking that an input face of the boundary has its ball on a given patch.
typedef ModuleTraits::Union_of_balls_boundary_3 Union_of_balls_boundary_3 |
Representation of the boundary of the union of balls.
Representation of the boundary of the union of balls.
WeightedAlphaComplex3 | A Model of the 3D Weighted -complex of the CGAL Library. |
IS_CCW | Tag allowing to orientate in CW or CCW the sense of the half-edges. |
HalfedgeDSBase | Base data structure for the boundary of union of balls. |
typedef SBL::GT::T_Union_of_balls_boundary_patch_shelling_3<Union_of_balls_boundary_3, Is_in_patch> Union_of_balls_boundary_patch_shelling_3 |
Shelling diagram of a patch on the boundary of the union of 3D balls.
Shelling diagram of a patch on the boundary of the union of 3D balls.
UnionOfBallsBoundary3 | Representation of the boundary of a union of 3D balls. |
IsInPatch | Simple predicate checking that a face or a halfedge of the boundary is in a patch. |
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inlineoverridevirtual |
Virtual method for adding options to the module.
Reimplemented from T_Module_option_description< Dummy >.
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inlineinherited |
To avoid later crash: check filesystem / existence of directory / directory exists.
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inlineoverridevirtual |
Checks that the input options' values are coherent.
Reimplemented from T_Module_option_description< Dummy >.
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inlineinherited |
Clones the object using the copy constructor.
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inline |
Reference to the output Ball Shelling Forest.
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inline |
Const reference to the output Ball Shelling Forest.
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inline |
Reference to a pointer over the input boundary.
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inline |
Reference to the output Face Shelling Forest.
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inline |
Const reference to the output Face Shelling Forest.
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inline |
Reference to a pointer over the predicate representing the input patch.
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inlineinherited |
Get the name of this instance of this module.
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inlineoverridevirtual |
Returns the name of the package.
Reimplemented from Module_base.
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inlinestaticinherited |
Access to the options' description of the module.
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inlineoverridevirtual |
Returns a prefix that concatains the input line options used when running the module.
Reimplemented from T_Module_option_description< Dummy >.
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inlineinherited |
Get the report mode to be used when reporting.
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inlineprotectedvirtualinherited |
Checks that this module defines a condition operator.
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inlineprotectedvirtualinherited |
Checks that this module defines a logical operator.
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inlineprotectedvirtualinherited |
Checks that this module defines a collection of modules.
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inlineoverridevirtual |
Checks that all the input options were set.
Reimplemented from Module_base.
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inlineprotectedvirtualinherited |
Only for condition modules, for returning the predicate value.
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inlineoverridevirtual |
Reports the output and statistics in output files.
Reimplemented from Module_base.
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inlineoverridevirtual |
Runs the module following the input options.
Implements Module_base.
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inlineinherited |
Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules.
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inlineinherited |
Set a report mode, that is open or append modes.
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inlineinherited |
Set a report mode, that is open or append modes.
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inlineoverridevirtual |
Reports high-level statistics on the module.
Reimplemented from Module_base.