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IMP Reference Guide  develop.5de2a9ba5d,2024/02/25
The Integrative Modeling Platform
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:

Detailed Description

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 CHARMMAngleget_angle (unsigned int index) const
 
const CHARMMAtomTopologyget_atom (unsigned int i) const
 
const CHARMMAtomTopologyget_atom (AtomType type) const
 
const CHARMMAtomTopologyget_atom (std::string name) const
 
const CHARMMBondget_bond (unsigned int index) const
 
const CHARMMDihedralget_dihedral (unsigned int index) const
 
const CHARMMDihedralget_improper (unsigned int index) const
 
const CHARMMInternalCoordinateget_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< CHARMMAtomTopologyatoms_
 
CHARMMBonds bonds_
 
CHARMMDihedrals dihedrals_
 
CHARMMDihedrals impropers_
 
CHARMMInternalCoordinates internal_coordinates_
 

Member Function Documentation

virtual ::IMP::VersionInfo IMP::atom::CHARMMIdealResidueTopology::get_version_info ( ) const
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.


The documentation for this class was generated from the following file: