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The topology of a single CHARMM segment in a model.
CHARMM segments typically correspond to IMP::atom::Chain particles.
Inheritance diagram for IMP::atom::CHARMMSegmentTopology: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. | |
| Public Member Functions inherited from IMP::base::Object | |
| std::size_t | __hash__ () const |
| virtual std::string | get_type_name () const =0 |
| Return a string identifying the type of the object. | |
| virtual IMP::base::VersionInfo | get_version_info () const =0 |
| Get information about the module and version of the object. | |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. | |
| 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) |
Static Public Member Functions | |
| static CHARMMSegmentTopology * | get_from (IMP::base::Object *o) |
Residues | |
| void | remove_residue (CHARMMResidueTopology *d) |
| template<class F > | |
| void | remove_residues_if (const F &f) |
| template<class List > | |
| void | remove_residues (List d) |
| template<class List > | |
| void | set_residues (List ps) |
| template<class List > | |
| void | set_residues_order (List ps) |
| unsigned int | add_residue (CHARMMResidueTopology *obj) |
| template<class List > | |
| void | add_residues (List objs) |
| void | clear_residues () |
| unsigned int | get_number_of_residues () const |
| bool | get_has_residues () const |
| CHARMMResidueTopology * | get_residue (unsigned int i) const |
| CHARMMResidueTopologies | get_residues () const |
| void | reserve_residues (unsigned int sz) |
| CHARMMResidueTopologyIterator | residues_begin () |
| CHARMMResidueTopologyIterator | residues_end () |
| CHARMMResidueTopologyConstIterator | residues_begin () const |
| CHARMMResidueTopologyConstIterator | residues_end () const |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| 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.
