Compute the complementarity between two molecules. More...
#include <IMP/multifit/ComplementarityRestraint.h>
Inheritance diagram for IMP::multifit::ComplementarityRestraint:Public Member Functions | |
| ComplementarityRestraint (const ParticlesTemp &a, const ParticlesTemp &b, std::string name="ComplementarityRestraint %1%") | |
| float | get_voxel_size () const |
| IMP_RESTRAINT (ComplementarityRestraint) | |
| void | set_boundary_coefficient (double bc) |
| void | set_complementarity_coefficient (double cc) |
| void | set_complementarity_thickness (double th) |
| void | set_complementarity_value (double th) |
| void | set_interior_layer_thickness (double th) |
| void | set_maximum_penetration (double d) |
| void | set_maximum_penetration_score (double s) |
| void | set_maximum_separation (double s) |
| void | set_penetration_coefficient (double pc) |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (Model *m, std::string name) | |
| void | add_score_and_derivatives (ScoreAccumulator sa) const |
| Restraint * | create_current_decomposition () const |
| Decompose this restraint into constituent terms for the current conf. More... | |
| Restraint * | create_decomposition () const |
| Decompose this restraint into constituent terms. More... | |
| virtual ScoringFunction * | create_scoring_function (double weight=1.0, double max=NO_MAX) const |
| ContainersTemp | get_input_containers () const |
| ParticlesTemp | get_input_particles () const |
| virtual double | get_last_score () const |
| double | get_score () const |
| bool | get_was_good () const |
| void | set_weight (Float weight) |
| Float | get_weight () const |
| double | get_maximum_score () const |
| void | set_maximum_score (double s) |
| Public Member Functions inherited from IMP::kernel::ModelObject | |
| ModelObject (Model *m, std::string name) | |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| virtual IMP::base::VersionInfo | get_version_info () const =0 |
| Get information about the module and version of the object. | |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More... | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::kernel::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| virtual void | do_update_dependencies () |
| Related Functions inherited from IMP::kernel::Restraint | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > > | RestraintsTemp |
Detailed Description
The score returned is infinity if the two molecules overlap by more than the value set for set_maximum_penetration_score() or if the two molecules are separated by more than set_maximum_separation().
Otherwise, the integral of the set_complementarity_value() value over a layer of thickness set_complementarity_thickness() around the molecule is returned.
- Note
- currently each of the particle lists must belong to exactly one rigid body. And, currently, each rigid body can only be associated with one list of particles (that is, there cannot be multiple restraints with different lists of particles that all belong to the same rigid body).
- The restraint does not support derivatives.
- The restraint pretty much only makes sense for use with Domino as it returns infinity for many cases. Monte Carlo might make sense with certain parameters.
Definition at line 40 of file ComplementarityRestraint.h.
Member Function Documentation
| void IMP::multifit::ComplementarityRestraint::set_complementarity_thickness | ( | double | th | ) |
Set the thickness to use for the external complementarity layer.
Definition at line 64 of file ComplementarityRestraint.h.
| void IMP::multifit::ComplementarityRestraint::set_complementarity_value | ( | double | th | ) |
Set the value to use for external complementarity voxels.
Definition at line 70 of file ComplementarityRestraint.h.
| void IMP::multifit::ComplementarityRestraint::set_interior_layer_thickness | ( | double | th | ) |
Set the thickness of the interior layers.
Definition at line 74 of file ComplementarityRestraint.h.
| void IMP::multifit::ComplementarityRestraint::set_maximum_penetration | ( | double | d | ) |
Alternatively, you can bound the maximum allowed penetration.
Definition at line 54 of file ComplementarityRestraint.h.
| void IMP::multifit::ComplementarityRestraint::set_maximum_penetration_score | ( | double | s | ) |
If the two molecules have a penetration score of more than this, infinity is returned as the score. This score is roughly the number of cubic angstroms that the two molecules overlap (assuming only one internal layer).
Definition at line 49 of file ComplementarityRestraint.h.
| void IMP::multifit::ComplementarityRestraint::set_maximum_separation | ( | double | s | ) |
If the two molecules' bounding sphere surfaces are separated by more than this distance, infinity is returned.
Definition at line 60 of file ComplementarityRestraint.h.
The documentation for this class was generated from the following file: