BALL::GeometricFit Class Reference
[Docking of
molecular structures]
GeometricFit
This class is derived from class DockingAlgorithm.
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#include <geometricFit.h>
Classes |
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| struct | Option |
| Symbolic names for option keys.
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| class | Peak_ |
| nested class
Peak_ This class is needed for an efficient handling of
all peaks corresponding to one orientation in a multiset
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|
| class | RotationAngles_ |
| nested class RotationAngles_
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|
Public Types |
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| enum | ProteinIndex { PROTEIN_A = 1, PROTEIN_B = 2 } |
| enum | SurfaceType { CONNOLLY = 1, VAN_DER_WAALS = 2, FTDOCK = 3 } |
Public Member Functions |
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| GeometricFit (System &system1, System &system2) | |
| Constructor. |
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| GeometricFit (Options &new_options) | |
| Constructor. |
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| GeometricFit (System &system1, System &system2, Options &new_options) | |
| Constructor. |
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| virtual void | setup (System &system1, System &system2, Options &new_options) |
| The setup routines. |
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| virtual void | setup (System &system1, System &system2) |
| Alternative setup. |
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| void | start () |
| Start the main loop of the
algorithm. |
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| float | getProgress () const |
| bool | hasFinished () const |
| Vector3 | getTranslation (Index con_num) const |
| Return the translation corresponding
to conformation con_num. |
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| Vector3 | getOrientation (Index con_num) const |
| Return the orientation corresponding
to conformation con_num. |
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| ConformationSet | getConformationSet (Index total_number=0) |
| Return the ranked
conformations. |
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Public Attributes |
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| Options | options |
| The options for the
algorithm. |
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Protected Member Functions |
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| void | destroy_ () |
| void | findInsidePoints_ (System &system, ProteinIndex pro_idx) |
| void | findConnollySurfacePoints_ (System &system, ProteinIndex pro_idx) |
| void | findVanDerWaalsSurfacePoints_ (System &system, ProteinIndex pro_idx) |
| void | findFTDockInsidePoints_ (System &system, ProteinIndex pro_idx) |
| void | findFTDockSurfacePoints_ (System &system, ProteinIndex pro_idx) |
| Vector3 | getMassCenter_ (System &system) |
| Compute the center of mass of
system. |
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| float | getRadius_ (System &system) |
| Compute the radius of the
circumsphere of all atoms in system. |
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| void | doPreTranslation_ (ProteinIndex pro_idx) |
| void | initGridSizes_ () |
| int | optimizeGridSize_ (int raw_size) |
| Optimize grid size for the FFTW.
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| void | initFFTGrid_ (ProteinIndex pro_idx) |
| Initialize the grid. |
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| void | makeFFTGrid_ (ProteinIndex pro_idx) |
| void | getGlobalPeak_ (Peak_ *peak_list) |
| void | changeProteinOrientation_ (System &system, Vector3 euler_ang) |
| void | calcConjugate_ (ProteinIndex pro_idx) |
| void | FFTGridMulti_ () |
| Vector3 | getTranslation_ (const Vector3 &mat_pos) |
| Vector3 | getSeparation_ (const Vector3 &mat_pos) |
Protected Attributes |
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| FFT3D * | FFT_grid_a_ |
| FFT3D * | FFT_grid_b_ |
| float | radius_a_ |
| float | radius_b_ |
| Vector3 | FFT_grid_lower_index_ |
| Vector3 | FFT_grid_upper_index_ |
| Vector3 | FFT_grid_lower_coord_ |
| Vector3 | FFT_grid_upper_coord_ |
| Vector3 | FFT_grid_size_index_ |
| Vector3 | pre_translation_a_ |
| Vector3 | pre_translation_b_ |
| Vector3 | FFT_grid_origin_ |
| int | current_round_ |
| int | total_round_ |
| std::multiset< Peak_ > | peak_set_ |
| System | system_backup_a_ |
| System | system_backup_b_ |
| vector< Vector3 > | translations_ |
| vector< Vector3 > | orientations_ |
Detailed Description
GeometricFit This class is derived from class DockingAlgorithm.Protein docking algorithm via geometric fit invented by Katchalski-Katzir, et at. (1992) is implemented in this class.
Constructor & Destructor Documentation
Constructor.
Creates an instance of Geometric Fit and calls setup(system1, system2). The options used are the default options.
| BALL::GeometricFit::GeometricFit | ( | Options & | new_options | ) |
Constructor.
Creates an instance of Geometric Fit and assigns the given options to the Geometric Fit object's options.
Constructor.
Creates an instance of FDPB and calls setup(system1, system2, new_options)
Member Function Documentation
| int BALL::GeometricFit::optimizeGridSize_ | ( | int | raw_size | ) | [protected] |
Optimize grid size for the FFTW.
Certain combinations of certain powers are optimal for the fft algorithm, and this function tries to determine the smallest optimal combination large enough to accomodate the original data.
Alternative setup.
Assigns systems 1 and two without changing the options for this DockingAlgorithm.
Reimplemented from BALL::DockingAlgorithm.
