IMP::atom::CHARMMStereochemistryRestraint Class Reference
Enforce CHARMM stereochemistry on the given Hierarchy. More...
#include <IMP/atom/CHARMMStereochemistryRestraint.h>
Inheritance diagram for IMP::atom::CHARMMStereochemistryRestraint:Public Member Functions | |
| CHARMMStereochemistryRestraint (Hierarchy h, CHARMMTopology *topology) | |
| virtual void | do_show (std::ostream &out) const |
| StereochemistryPairFilter * | get_pair_filter () |
| Get a PairFilter that excludes all stereochemical pairs. More... | |
| 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
It is assumed that the Hierarchy has already had CHARMM atom types assigned and conforms with the CHARMM topology information (for example, by calling CHARMMTopology::setup_hierarchy() first).
- Note
- This is a convenient high-level wrapper; the bonds, angles, dihedrals and impropers can also be created manually and evaluated using standard IMP building blocks - for example, angles can be created using CHARMMParameters::create_angles() and then evaluated using an AngleSingletonScore in combination with a container::SingletonsRestraint.
Definition at line 37 of file CHARMMStereochemistryRestraint.h.
Member Function Documentation
| StereochemistryPairFilter* IMP::atom::CHARMMStereochemistryRestraint::get_pair_filter | ( | ) |
- Returns
- a StereochemistryPairFilter that excludes all 1-2 (bond), 1-3 (angle) and 1-4 (dihedral) pairs.
The documentation for this class was generated from the following file: