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protocols::toolbox::pose_manipulation Namespace Reference

Functions

static basic::Tracer TR ("protocols.toolbox.pose_manipulation")
 
static basic::Tracer TR_DI ("protocols.toolbox.pose_manipulation.insert_pose_into_pose")
 
void 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 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 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 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 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 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 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 remove_non_protein_residues (core::pose::Pose &pose)
 deletes all nonprotein residues from a pose More...
 
void add_chainbreaks_according_to_jumps (core::pose::Pose &pose)
 adds chainbreak residue types depending on fold tree jumps More...
 
void add_chainbreaks_according_to_jumps (core::pose::Pose &pose, utility::vector1< core::Size > const &no_cutpoint_residues)
 
void remove_chainbreaks_according_to_jumps (core::pose::Pose &pose)
 removes chainbreak residue types depending on fold tree jumps More...
 
core::Real 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 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 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 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 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 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 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...
 

Function Documentation

void protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps ( core::pose::Pose pose)
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::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 
)
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.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References construct_poly_uniq_restype_pose(), and core::chemical::FA_STANDARD.

Referenced by protocols::denovo_design::construct_poly_ala_pose().

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

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References construct_poly_uniq_restype_pose(), and core::chemical::FA_STANDARD.

Referenced by protocols::denovo_design::construct_poly_ala_pose().

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

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References construct_poly_uniq_restype_pose(), and core::chemical::FA_STANDARD.

Referenced by protocols::denovo_design::construct_poly_ala_pose().

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 
)
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 
)
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 
)
void protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps ( core::pose::Pose pose)
void protocols::toolbox::pose_manipulation::remove_non_protein_residues ( core::pose::Pose pose)
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.

Author
Brian Coventry (bcov@.nosp@m.uw.e.nosp@m.du)

References core::select::get_residue_selector_from_subset(), and protocols::antibody::design::repack.

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.

Author
Brian Coventry (bcov@.nosp@m.uw.e.nosp@m.du)

References protocols::antibody::design::repack, and core::id::to_string().

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 
)

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.

Referenced by protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::compute(), and rigid_body_move().

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 
)

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.

References rigid_body_move(), and protocols::toolbox::rigid_body::translate().

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 
)

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.

References core::pose::center_of_mass(), core::select::get_residues_from_subset(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::set_xyz().

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 
)

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.

References rigid_body_move(), and protocols::toolbox::rigid_body::translate().

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

Author
Florian Richter( flori.nosp@m.c@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu) , sep 08 with the offset specified

References core::conformation::Residue::atom_index(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID::set(), and core::scoring::superimpose_pose().

static basic::Tracer protocols::toolbox::pose_manipulation::TR ( "protocols.toolbox.pose_manipulation"  )
static
static basic::Tracer protocols::toolbox::pose_manipulation::TR_DI ( "protocols.toolbox.pose_manipulation.insert_pose_into_pose"  )
static