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IMP Reference Guide
develop.63b38c487d,2024/12/21
The Integrative Modeling Platform
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The topology of a single residue in a model. More...
#include <IMP/atom/charmm_topology.h>
Inheritance diagram for IMP::atom::CHARMMResidueTopology:The topology of a single residue in a model.
Each CHARMMResidueTopology object can represent an 'unknown' residue (containing no atoms or bonds) or is a copy of an existing CHARMMIdealResidueTopology. Optionally, patches can be applied to residues (see CHARMMPatch::apply()) to add N- or C-termini, disulfide bridges, sidechain modifications, etc.
Definition at line 437 of file charmm_topology.h.
Public Member Functions | |
| CHARMMResidueTopology (ResidueType type) | |
| Create an empty topology, containing no atoms or bonds. More... | |
| CHARMMResidueTopology (CHARMMIdealResidueTopology *ideal) | |
| Construct residue topology as a copy of an existing topology. More... | |
| bool | get_patched () 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 | set_patched (bool patched) |
| Public Member Functions inherited from IMP::atom::CHARMMIdealResidueTopology | |
| CHARMMIdealResidueTopology (std::string type) | |
| CHARMMIdealResidueTopology (ResidueType type) | |
| 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::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_ |
| IMP::atom::CHARMMResidueTopology::CHARMMResidueTopology | ( | ResidueType | type | ) |
Create an empty topology, containing no atoms or bonds.
Definition at line 442 of file charmm_topology.h.
| IMP::atom::CHARMMResidueTopology::CHARMMResidueTopology | ( | CHARMMIdealResidueTopology * | ideal | ) |
Construct residue topology as a copy of an existing topology.
Definition at line 446 of file charmm_topology.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::atom::CHARMMIdealResidueTopology.
Definition at line 477 of file charmm_topology.h.