IMP Reference Guide
2.20.0
The Integrative Modeling Platform
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The topology of a single CHARMM segment in a model. More...
#include <IMP/atom/charmm_segment_topology.h>
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 () |
CHARMMResidueTopology * | get_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 () |
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.
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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.
list IMP::atom::CHARMMSegmentTopology::residues |
A Python list of CHARMMResidueTopologies
Definition at line 32 of file charmm_segment_topology.h.