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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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The ideal topology of a single residue. More...
#include <IMP/atom/charmm_topology.h>
Inheritance diagram for IMP::atom::CHARMMIdealResidueTopology:The ideal topology of a single residue.
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()).
An ideal topology is intended to be created just once for each residue type. To actually use a topology, create a CHARMMResidueTopology object, which can be modified if necessary by adding/removing individual atoms, or applying patches to, for example, modify terminal residues or create disulfide bridges.
Definition at line 347 of file charmm_topology.h.
Public Member Functions | |
| CHARMMIdealResidueTopology (std::string type) | |
| CHARMMIdealResidueTopology (ResidueType type) | |
| std::string | get_default_first_patch () const |
| std::string | get_default_last_patch () const |
| virtual std::string | get_type_name () const override |
| virtual ::IMP::VersionInfo | get_version_info () const override |
| Get information about the module and version of the object. More... | |
| 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::Object | |
| virtual void | clear_caches () |
| CheckLevel | get_check_level () const |
| LogLevel | get_log_level () const |
| 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::atom::CHARMMResidueTopologyBase | |
| CHARMMResidueTopologyBase (std::string type) | |
| Protected Member Functions inherited from IMP::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| Protected Attributes inherited from IMP::atom::CHARMMResidueTopologyBase | |
| CHARMMAngles | angles_ |
| Vector< CHARMMAtomTopology > | atoms_ |
| CHARMMBonds | bonds_ |
| CHARMMDihedrals | dihedrals_ |
| CHARMMDihedrals | impropers_ |
| CHARMMInternalCoordinates | internal_coordinates_ |
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::atom::CHARMMResidueTopologyBase.
Reimplemented in IMP::atom::CHARMMResidueTopology.
Definition at line 370 of file charmm_topology.h.
| void IMP::atom::CHARMMIdealResidueTopology::remove_atom | ( | std::string | name | ) |
Remove the named atom.
Any bonds/angles that involve this atom are also removed.