PeptideStubMover.cc File Reference

The PeptideStubMover prepends, appends, or inserts residues into an existing pose, or builds a new polymeric chain. More...

#include <protocols/cyclic_peptide/PeptideStubMover.hh>
#include <protocols/cyclic_peptide/PeptideStubMoverCreator.hh>
#include <core/id/AtomID.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/AtomICoor.hh>
#include <core/chemical/types.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/variant_util.hh>
#include <core/select/residue_selector/util.hh>
#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <core/select/iterators.hh>
#include <numeric/conversions.hh>
#include <utility/tag/Tag.hh>
#include <basic/Tracer.hh>
#include <basic/citation_manager/CitationManager.hh>
#include <basic/citation_manager/CitationCollection.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/moves/mover_schemas.hh>
#include <algorithm>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::cyclic_peptide

Functions
static basic::Tracer	TR ("protocols.cyclic_peptide.PeptideStubMover")
void	protocols::cyclic_peptide::dump_debug_output (core::pose::Pose const &pose)
	if TR.Debug is visible, dump residue information to the console More...

Detailed Description

The PeptideStubMover prepends, appends, or inserts residues into an existing pose, or builds a new polymeric chain.

Author

Yifan Song @modified Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org): Added support for stripping N-acetylation and C-methylamidation when appending residues, preserving phi and the previous omega in the first case and psi and the following omega in the second. @modified Jack Maguire: breaking apply() into smaller methods

Function Documentation

TR()

static basic::Tracer TR ( "protocols.cyclic_peptide.PeptideStubMover"  )

static

Referenced by protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::cyclic_peptide::dump_debug_output(), protocols::cyclic_peptide::PeptideStubMover::get_connecting_id_for_append_by_bond(), protocols::cyclic_peptide::PeptideStubMover::handle_repeats_in_append_by_bond(), protocols::cyclic_peptide::PeptideStubMover::handle_termini_and_store_terminal_dihedrals(), and protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions().