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pose_manipulation.hh File Reference

some general functions to manipulate poses. feel free to add your own More...

#include <core/types.hh>
#include <utility/vector1.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <numeric/xyzVector.hh>
#include <utility/vector1.hh>

Namespaces

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

Functions

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::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 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 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...
 

Detailed Description

some general functions to manipulate poses. feel free to add your own

if you add your own, please mention your name:)

Author
Florian Richter, flori.nosp@m.c@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu
Steven Lewis, smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om (insert_pose_into_pose) domain insertion code