IMP::atom::CHARMMIdealResidueTopology Class Reference
The ideal topology of a single residue. More...
#include <IMP/atom/charmm_topology.h>
Inheritance diagram for IMP::atom::CHARMMIdealResidueTopology:Public Member Functions | |
| CHARMMIdealResidueTopology (std::string type) | |
| CHARMMIdealResidueTopology (ResidueType type) | |
| virtual void | do_show (std::ostream &out) const |
| std::string | get_default_first_patch () const |
| std::string | get_default_last_patch () const |
| void | remove_atom (std::string name) |
| Remove the named atom. More... | |
| void | set_default_first_patch (std::string patch) |
| void | set_default_last_patch (std::string patch) |
| Public Member Functions inherited from IMP::atom::CHARMMResidueTopologyBase | |
| void | add_angle (const CHARMMAngle &bond) |
| void | add_atom (const CHARMMAtomTopology &atom) |
| void | add_bond (const CHARMMBond &bond) |
| void | add_dihedral (const CHARMMDihedral &bond) |
| void | add_improper (const CHARMMDihedral &bond) |
| void | add_internal_coordinate (const CHARMMInternalCoordinate &ic) |
| const CHARMMAngle & | get_angle (unsigned int index) const |
| const CHARMMAtomTopology & | get_atom (unsigned int i) const |
| const CHARMMAtomTopology & | get_atom (AtomType type) const |
| const CHARMMAtomTopology & | get_atom (std::string name) const |
| const CHARMMBond & | get_bond (unsigned int index) const |
| const CHARMMDihedral & | get_dihedral (unsigned int index) const |
| const CHARMMDihedral & | get_improper (unsigned int index) const |
| const CHARMMInternalCoordinate & | get_internal_coordinate (unsigned int index) const |
| unsigned int | get_number_of_angles () const |
| unsigned int | get_number_of_atoms () const |
| unsigned int | get_number_of_bonds () const |
| unsigned int | get_number_of_dihedrals () const |
| unsigned int | get_number_of_impropers () const |
| unsigned int | get_number_of_internal_coordinates () const |
| std::string | get_type () 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) |
Related Functions | |
(Note that these are not member functions.) | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < CHARMMIdealResidueTopology > > | CHARMMIdealResidueTopologiesTemp |
| Related Functions inherited from IMP::atom::CHARMMResidueTopologyBase | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < CHARMMResidueTopologyBase > > | CHARMMResidueTopologyBasesTemp |
| Related Functions inherited from IMP::base::Object | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Object > > | ObjectsTemp |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::atom::CHARMMResidueTopologyBase | |
| CHARMMResidueTopologyBase (std::string type) | |
| Protected Attributes inherited from IMP::atom::CHARMMResidueTopologyBase | |
| CHARMMAngles | angles_ |
| base::Vector< CHARMMAtomTopology > | atoms_ |
| CHARMMBonds | bonds_ |
| CHARMMDihedrals | dihedrals_ |
| CHARMMDihedrals | impropers_ |
| CHARMMInternalCoordinates | internal_coordinates_ |
Detailed Description
These residue topologies can be constructed manually (by adding CHARMMAtomTopology objects with add_atom()). However, they are more commonly populated automatically by reading a CHARMM topology file (CHARMMParameters::get_residue_topology()).
Definition at line 334 of file charmm_topology.h.
Member Function Documentation
| void IMP::atom::CHARMMIdealResidueTopology::remove_atom | ( | std::string | name | ) |
Any bonds/angles that involve this atom are also removed.
Friends And Related Function Documentation
|
related |
Pass a set of objects.
Definition at line 359 of file charmm_topology.h.
The documentation for this class was generated from the following file: