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IMP Reference Guide  develop.031dafb4d2,2024/05/21
The Integrative Modeling Platform
IMP::atom::CHARMMSegmentTopology Class Reference

The topology of a single CHARMM segment in a model. More...

#include <IMP/atom/charmm_segment_topology.h>

+ Inheritance diagram for IMP::atom::CHARMMSegmentTopology:

Detailed Description

The topology of a single CHARMM segment in a model.

CHARMM segments typically correspond to IMP::atom::Chain particles.

Definition at line 23 of file charmm_segment_topology.h.

Public Member Functions

 CHARMMSegmentTopology (std::string name="CHARMM segment topology %1%")
 
void apply_default_patches (const CHARMMParameters *ff)
 Apply patches to the first and last residue in the segment. More...
 
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...
 
- 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)
 

Residue topologies

The segment contains a chain of residue topologies, as CHARMMResidueTopology objects.

list residues
 A Python list of CHARMMResidueTopologies More...
 
void remove_residue (CHARMMResidueTopology *d)
 
void remove_residues (const CHARMMResidueTopologies &d)
 
void set_residues (const CHARMMResidueTopologies &ps)
 
void set_residues_order (const CHARMMResidueTopologies &objs)
 
unsigned int add_residue (CHARMMResidueTopology *obj)
 
void add_residues (const CHARMMResidueTopologies &objs)
 
void clear_residues ()
 
unsigned int get_number_of_residues () const
 
bool get_has_residues ()
 
CHARMMResidueTopologyget_residue (unsigned int i) const
 
CHARMMResidueTopologies get_residues () const
 
void erase_residue (unsigned int i)
 
void reserve_residues (unsigned int sz)
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Member Function Documentation

void IMP::atom::CHARMMSegmentTopology::apply_default_patches ( const CHARMMParameters ff)

Apply patches to the first and last residue in the segment.

Default patches are defined for each residue type in the topology file. For example, segments containing amino acids will by default apply the CTER and NTER patches to the C and N termini, respectively.

virtual ::IMP::VersionInfo IMP::atom::CHARMMSegmentTopology::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 35 of file charmm_segment_topology.h.

Member Data Documentation

list IMP::atom::CHARMMSegmentTopology::residues

A Python list of CHARMMResidueTopologies

Note
This class member is only available in Python.

Definition at line 32 of file charmm_segment_topology.h.


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