pose_manipulation.cc File Reference

#include <protocols/toolbox/pose_manipulation/pose_manipulation.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueProperties.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pack/task/operation/OperateOnResidueSubset.hh>
#include <core/pack/task/operation/ResLvlTaskOperations.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/select/util.hh>
#include <core/select/residue_selector/ResidueIndexSelector.hh>
#include <core/id/AtomID_Map.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <basic/Tracer.hh>
#include <core/types.hh>
#include <core/chemical/VariantType.hh>
#include <core/pose/variant_util.hh>
#include <utility/vector1.hh>
#include <core/pose/init_id_map.hh>
#include <core/pack/task/TaskFactory.hh>

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

Functions
static basic::Tracer	protocols::toolbox::pose_manipulation::TR ("protocols.toolbox.pose_manipulation")
static basic::Tracer	protocols::toolbox::pose_manipulation::TR_DI ("protocols.toolbox.pose_manipulation.insert_pose_into_pose")
void	protocols::toolbox::pose_manipulation::construct_poly_ala_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool const keep_pro, bool const keep_gly, bool const keep_disulfide_cys)
	puts in ala residues at the positions specified in the 'positions' input array More...
void	protocols::toolbox::pose_manipulation::construct_poly_d_ala_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool const keep_pro, bool const keep_gly, bool const keep_disulfide_cys)
	puts in D-ala residues at the positions specified in the 'positions' input array More...
void	protocols::toolbox::pose_manipulation::construct_poly_beta_ala_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool const keep_pro, bool const keep_gly, bool const keep_disulfide_cys)
	puts in beta-3-ala residues at the positions specified in the 'positions' input array. More...
void	protocols::toolbox::pose_manipulation::construct_poly_d_beta_ala_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool const keep_pro, bool const keep_gly, bool const keep_disulfide_cys)
	puts in D-beta-3-ala residues at the positions specified in the 'positions' input array More...
void	protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, core::chemical::ResidueType const &restype, bool const keep_pro, bool const keep_gly, bool const keep_disulfide_cys)
	allows construction of a polymer of any residue type More...
void	protocols::toolbox::pose_manipulation::construct_poly_XXX_pose (std::string const &aa, core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool keep_pro, bool keep_gly, bool keep_disulfide_cys)
	puts in XXX residues at the positions specified in the 'positions' input array More...
void	protocols::toolbox::pose_manipulation::construct_poly_XXX_pose (std::string const &aa, core::pose::Pose &pose, utility::vector1< core::Size > const &positions, core::chemical::ResidueTypeSetCOP restype_set, bool keep_pro, bool keep_gly, bool keep_disulfide_cys)
	puts in XXX residues at the positions from the given residue typeset specified in the 'positions' input array More...
void	protocols::toolbox::pose_manipulation::remove_non_protein_residues (core::pose::Pose &pose)
	deletes all nonprotein residues from a pose More...
void	protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps (core::pose::Pose &pose)
	adds chainbreak residue types depending on fold tree jumps More...
void	protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps (core::pose::Pose &pose, utility::vector1< core::Size > const &no_cutpoint_residues)
void	protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps (core::pose::Pose &pose)
	removes chainbreak residue types depending on fold tree jumps More...
core::Real	protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA (core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< core::Size > const &positions, int const offset=0)
	superimposes one pose onto the other at the positions specified and More...
void	protocols::toolbox::pose_manipulation::repack_this_residue (core::Size seq_pos, core::pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, bool include_current=true, std::string name1s_if_design="")
	Repack a single residue @detail Repacks a single residue using the command-line flags A list of amino acid name1s may be provided if one wishes to design. Leaving this "" or default implies no design. More...
void	protocols::toolbox::pose_manipulation::repack_these_residues (core::select::residue_selector::ResidueSubset const &subset, core::pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, bool include_current=true, std::string name1s_if_design="")
	Repack a subset of residues @detail Repacks a multiple residues using the command-line flags A list of amino acid name1s may be provided if one wishes to design. Leaving this "" or default implies no design. More...
void	protocols::toolbox::pose_manipulation::rigid_body_move (numeric::xyzVector< core::Real > const &rotation_unit_vector, core::Real angle_deg, numeric::xyzVector< core::Real > const &translation_vector, core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &subset, numeric::xyzVector< core::Real > center_of_rotation=numeric::xyzVector< core::Real >(std::numeric_limits< core::Real >::quiet_NaN(), 0, 0))
	Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation. More...
void	protocols::toolbox::pose_manipulation::rigid_body_move (numeric::xyzVector< core::Real > const &rotation_unit_vector, core::Real angle_deg, numeric::xyzVector< core::Real > const &translation_vector, core::Real translation_scalar, core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &subset, numeric::xyzVector< core::Real > center_of_rotation=numeric::xyzVector< core::Real >(std::numeric_limits< core::Real >::quiet_NaN(), 0, 0))
	Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation. More...
void	protocols::toolbox::pose_manipulation::rigid_body_move (numeric::xyzMatrix< core::Real > rotation, numeric::xyzVector< core::Real > const &translation_vector, core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &subset, numeric::xyzVector< core::Real > center_of_rotation=numeric::xyzVector< core::Real >(std::numeric_limits< core::Real >::quiet_NaN(), 0, 0))
	Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation. More...
void	protocols::toolbox::pose_manipulation::rigid_body_move (numeric::xyzMatrix< core::Real > rotation, numeric::xyzVector< core::Real > const &translation_vector, core::Real translation_scalar, core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &subset, numeric::xyzVector< core::Real > center_of_rotation=numeric::xyzVector< core::Real >(std::numeric_limits< core::Real >::quiet_NaN(), 0, 0))
	Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation. More...