Rosetta 3.4
Functions
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 keep_pro, bool keep_gly, bool keep_disulfide_cys)
 puts in ala residues at the positions specified in the 'positions' input array
void construct_poly_uniq_restype_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, core::chemical::ResidueType const &restype, bool keep_pro, bool keep_gly, bool keep_disulfide_cys)
 allows construction of a polymer of any residue type
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
void remove_non_protein_residues (core::pose::Pose &pose)
 deletes all nonprotein residues from a pose
void add_chainbreaks_according_to_jumps (core::pose::Pose &pose)
 adds chainbreak residue types depending on fold tree jumps
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
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
core::pose::Pose insert_pose_into_pose (core::pose::Pose const &scaffold_pose, core::pose::Pose const &insert_pose, core::Size const insert_loop_start, core::Size const insert_point, core::Size &insert_loop_end, core::Size const cycles=1500)
 inserts one pose into another pose, returning the product as a new value. This is basically a seed for a domain insertion application. The three core::Size arguments define a flexible surface loop on the scaffold, the insert pose will be added immediately after insert_point. The insert will be left unchanged in internal-coordinate space except for the phi on the first residue, and the psi/omega on the last residue, and atoms whose bonding partners change as a result of the insertion. Note that insert_loop_end is pass-by-reference: this field will be updated to reflect its numbering in the result pose (post-insertion).

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  keep_pro,
bool  keep_gly,
bool  keep_disulfide_cys 
)
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  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,
bool  keep_pro,
bool  keep_gly,
bool  keep_disulfide_cys 
)
core::pose::Pose protocols::toolbox::pose_manipulation::insert_pose_into_pose ( core::pose::Pose const &  scaffold_pose,
core::pose::Pose const &  insert_pose,
core::Size const  insert_loop_start,
core::Size const  insert_point,
core::Size insert_loop_end,
core::Size const  cycles 
)

inserts one pose into another pose, returning the product as a new value. This is basically a seed for a domain insertion application. The three core::Size arguments define a flexible surface loop on the scaffold, the insert pose will be added immediately after insert_point. The insert will be left unchanged in internal-coordinate space except for the phi on the first residue, and the psi/omega on the last residue, and atoms whose bonding partners change as a result of the insertion. Note that insert_loop_end is pass-by-reference: this field will be updated to reflect its numbering in the result pose (post-insertion).

Author:
Steven Lewis smlewi@gmail.com

brief inserts one pose into another pose, returning the product as a new value. This is basically a seed for a domain insertion application. The three core::Size arguments define a flexible surface loop on the scaffold, the insert pose will be added immediately after insert_point. The insert will be left unchanged in internal-coordinate space except for the phi on the first residue, and the psi/omega on the last residue, and atoms whose bonding partners change as a result of the insertion. Note that insert_loop_end is pass-by-reference: this field will be updated to reflect its numbering in the result pose (post-insertion). Internally, this function performs the insertion, idealizes the loop residues (omegas to 180, peptide bonds idealized) and the newly made polymer connections at the insert point, and then attempts to close the loop (chainbreak is next to the end of the loop). It is intended, but not guarunteed, to produce a loop with good rama, omega, and chainbreak/peptide_bond scores. If there is a bad chainbreak, it will be at the return value in (insert_loop_end-1). It does NOT attempt to give a loop with good sidechains (it does not repack at all) or worry overmuch about van der Waals.

Author:
Steven Lewis smlewi@gmail.com

References protocols::loops::Loops::add_loop(), core::pose::add_variant_type_to_pose_residue(), protocols::simple_moves::BackboneMover::angle_max(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::MinMover::apply(), protocols::loops::loop_closure::ccd::CcdLoopClosureMover::apply(), protocols::simple_moves::BackboneMover::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::id::BB, protocols::loops::Loops::begin(), core::scoring::cbeta, core::scoring::cenpack, core::chemical::CENTROID, core::scoring::chainbreak, core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, protocols::simple_moves::insert, core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::pose::Pose::insert_residue_by_jump(), core::chemical::LOWER_TERMINUS, core::scoring::omega, core::scoring::pair, core::id::phi_torsion(), core::id::psi_torsion(), core::scoring::rama, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::scoring::ScoreFunction::set_weight(), core::pose::Pose::total_residue(), core::chemical::UPPER_TERMINUS, and core::scoring::vdw.

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)
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( floric@u.washington.edu) , sep 08 with the offset specified

References core::conformation::Residue::atom_index(), core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), core::pose::Pose::residue(), 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]
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