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protocols::grafting Namespace Reference

Namespaces

 simple_movers
 

Classes

class  AnchoredGraftMover
 Grafting class adapted from Steven Lewis' pose_into_pose algorithm. More...
 
class  AnchoredGraftMoverCreator
 
class  CCDEndsGraftMover
 General purpose Grafting class which: 1) superimposes the insert onto the scaffold using any overhang residues, 2) Inserts the pose piece into the scaffold pose, deleting any overhang residues or residues in the region the isertion will occur between. 3) Cycles of: a) SmallMover for sampling (Can be disabled)) b) CCDs both terminal ends of the scaffold using flexibility settings or movemap To close the graft. c) MinMover to help close the graft through chainbreak terms d) Closure check - will return if closed (Can be disabled) d) MonteCarlo Boltzmann criterion. More...
 
class  CCDEndsGraftMoverCreator
 
class  GraftMoverBase
 Fairly abstract base class for GraftMover classes. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< AnchoredGraftMover
AnchoredGraftMoverOP
 
typedef
utility::pointer::shared_ptr
< AnchoredGraftMover const > 
AnchoredGraftMoverCOP
 
typedef
utility::pointer::weak_ptr
< AnchoredGraftMover
AnchoredGraftMoverAP
 
typedef
utility::pointer::weak_ptr
< AnchoredGraftMover const > 
AnchoredGraftMoverCAP
 
typedef
utility::pointer::shared_ptr
< CCDEndsGraftMover
CCDEndsGraftMoverOP
 
typedef
utility::pointer::shared_ptr
< CCDEndsGraftMover const > 
CCDEndsGraftMoverCOP
 
typedef
utility::pointer::shared_ptr
< GraftMoverBase
GraftMoverBaseOP
 
typedef
utility::pointer::shared_ptr
< GraftMoverBase const > 
GraftMoverBaseCOP
 
typedef
utility::pointer::shared_ptr
< DeleteRegionMover > 
DeleteRegionMoverOP
 
typedef
utility::pointer::shared_ptr
< DeleteRegionMover const > 
DeleteRegionMoverCOP
 
typedef
utility::pointer::shared_ptr
< InsertPoseIntoPoseMover > 
InsertPoseIntoPoseMoverOP
 
typedef
utility::pointer::shared_ptr
< InsertPoseIntoPoseMover
const > 
InsertPoseIntoPoseMoverCOP
 
typedef
utility::pointer::shared_ptr
< ReplaceRegionMover > 
ReplaceRegionMoverOP
 
typedef
utility::pointer::shared_ptr
< ReplaceRegionMover const > 
ReplaceRegionMoverCOP
 

Functions

void delete_region (core::pose::Pose &pose, core::Size const start, core::Size const end)
 Deletes a region of the pose. Starting from and including 'start' and 'end' residue. More...
 
Pose return_region (core::pose::Pose &pose, core::Size const start, core::Size const end)
 Returns a region of the pose including start and end as a new pose. Has a simple foldtree. More...
 
Pose replace_region (core::pose::Pose const &from_pose, core::pose::Pose const &to_pose, core::Size const from_pose_start_residue, core::Size const to_pose_start_residue, core::Size const insertion_length, bool copy_pdbinfo=false)
 replaces residues from from_pose to to_pose into pose where insertion region is defined. Returns product as a new value. More...
 
Pose insert_pose_into_pose (core::pose::Pose const &scaffold_pose, core::pose::Pose const &insert_pose, core::Size const insert_point, bool copy_pdbinfo=false)
 inserts one pose into another pose, returning the product as a new value. More...
 
Pose insert_pose_into_pose (core::pose::Pose const &scaffold_pose, core::pose::Pose const &insert_pose, core::Size const insert_point, core::Size const insert_point_end, bool copy_pdbinfo=false)
 inserts one pose into another pose, returning the product as a new value. More...
 
void repack_connection_and_residues_in_movemap (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP fa_scorefxn, core::Size const start, core::Size const end, core::kinematics::MoveMapCOP movemap)
 convenience function for AFTER apply method. More...
 
void repack_connection_and_residues_in_movemap_and_piece (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP fa_scorefxn, core::Size const start, core::Size const end, core::kinematics::MoveMapCOP movemap)
 convenience function for AFTER apply method. More...
 
void repack_connection_and_residues_in_movemap_and_piece_and_neighbors (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP fa_scorefxn, core::Size const start, core::Size const end, core::kinematics::MoveMapCOP movemap, core::Real neighbor_dis=4.0)
 convenience function for AFTER apply method. More...
 
void superimpose_overhangs_heavy (core::pose::Pose const &pose, core::pose::Pose &piece, bool ca_only, core::Size start, core::Size end, core::Size Nter_overhang_len=2, core::Size Cter_overhang_length_len=2)
 uses rms_util to superimpose overhang residues of piece onto pose. More...
 
void delete_overhang_residues (core::pose::Pose &piece, core::Size Nter_overhang_len, core::Size Cter_overhang_length_len)
 deletes overhang residues of the pose piece. Recommended use is within apply method More...
 
MoveMapOP combine_movemaps_post_insertion (core::kinematics::MoveMapCOP scaffold_mm, core::kinematics::MoveMapCOP insert_mm, core::Size start, core::Size original_end, core::Size insertion_length, core::Size cter_overhang_start=0)
 combines the two main movemaps to use after the insertion. More...
 
core::Real perturb_backbone_for_test (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
 Uses a small mover at high KT to perturb residues in the movemap for testing. Returns bb_RMS_including_o. More...
 
void add_cutpoint_variants_for_ccd (core::pose::Pose &pose, protocols::loops::Loops const &loops)
 Adds cutpoint varients above and below cutpoint. More...
 
void remove_cutpoint_variants_for_ccd (core::pose::Pose &pose, protocols::loops::Loops const &loops)
 Removes cutpoint variants above and below cutpoint. More...
 
bool graft_closed (core::pose::Pose &pose, protocols::loops::Loops &loops)
 Uses has_severe_peptide_bond_issues with stringent geometry values to determine graft closure at cutpoint. More...
 
void idealize_combined_pose (core::pose::Pose &combined, core::kinematics::MoveMapOP movemap, core::Size start, core::Size insert_start, core::Size insert_end, core::Size Nter_loop_start, core::Size Cter_loop_end, bool idealize_insert=false)
 Idealize loop residues and residues in movemap. More...
 
void setup_single_loop_single_arm_remodeling_foldtree (Pose &pose, core::Size const Nter_loop_start, core::Size const Cter_loop_end, bool loop_modeling)
 ****Nter_loop_start-—>Piece-—> | Cter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is Cter_loop_end-1 More...
 
void setup_single_loop_double_arm_remodeling_foldtree (Pose &pose, core::Size const Nter_loop_start, core::Size const Cter_loop_end, core::Size end, bool loop_modeling)
 ****Nter_loop_start-—>Piece | <-—Nter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is end_-1 More...
 

Typedef Documentation

typedef utility::pointer::weak_ptr< AnchoredGraftMover > protocols::grafting::AnchoredGraftMoverAP
typedef utility::pointer::weak_ptr< AnchoredGraftMover const > protocols::grafting::AnchoredGraftMoverCAP
typedef utility::pointer::shared_ptr< AnchoredGraftMover const > protocols::grafting::AnchoredGraftMoverCOP
typedef utility::pointer::shared_ptr< AnchoredGraftMover > protocols::grafting::AnchoredGraftMoverOP
typedef utility::pointer::shared_ptr<CCDEndsGraftMover const> protocols::grafting::CCDEndsGraftMoverCOP
typedef utility::pointer::shared_ptr<CCDEndsGraftMover> protocols::grafting::CCDEndsGraftMoverOP
typedef utility::pointer::shared_ptr<DeleteRegionMover const> protocols::grafting::DeleteRegionMoverCOP
typedef utility::pointer::shared_ptr<DeleteRegionMover> protocols::grafting::DeleteRegionMoverOP
typedef utility::pointer::shared_ptr<GraftMoverBase const> protocols::grafting::GraftMoverBaseCOP
typedef utility::pointer::shared_ptr<GraftMoverBase> protocols::grafting::GraftMoverBaseOP
typedef utility::pointer::shared_ptr<InsertPoseIntoPoseMover const> protocols::grafting::InsertPoseIntoPoseMoverCOP
typedef utility::pointer::shared_ptr<InsertPoseIntoPoseMover> protocols::grafting::InsertPoseIntoPoseMoverOP
typedef utility::pointer::shared_ptr<ReplaceRegionMover const> protocols::grafting::ReplaceRegionMoverCOP
typedef utility::pointer::shared_ptr<ReplaceRegionMover> protocols::grafting::ReplaceRegionMoverOP

Function Documentation

void protocols::grafting::add_cutpoint_variants_for_ccd ( Pose pose,
Loops const &  loops 
)
core::kinematics::MoveMapOP protocols::grafting::combine_movemaps_post_insertion ( core::kinematics::MoveMapCOP  scaffold_mm,
core::kinematics::MoveMapCOP  insert_mm,
core::Size  start,
core::Size  original_end,
core::Size  insertion_length,
core::Size  cter_overhang_start = 0 
)

combines the two main movemaps to use after the insertion.

Start + End denote residue number before and after the insert. original_end denotes the end residue number before insertion occurred

References protocols::denovo_design::movers::new_id(), and protocols::TR().

Referenced by protocols::grafting::AnchoredGraftMover::setup_movemap_and_regions().

void protocols::grafting::delete_overhang_residues ( Pose piece,
core::Size  Nter_overhang,
core::Size  Cter_overhang 
)
void protocols::grafting::delete_region ( Pose pose,
core::Size const  start,
core::Size const  end 
)
bool protocols::grafting::graft_closed ( Pose pose,
Loops &  loops 
)
void protocols::grafting::idealize_combined_pose ( Pose combined,
MoveMapOP  movemap,
core::Size  start,
core::Size  insert_start,
core::Size  insert_end,
core::Size  Nter_loop_start,
core::Size  Cter_loop_end,
bool  idealize_insert 
)
core::pose::Pose protocols::grafting::insert_pose_into_pose ( core::pose::Pose const &  scaffold_pose,
core::pose::Pose const &  insert_pose,
core::Size const  insert_point,
bool  copy_pdbinfo = false 
)

inserts one pose into another pose, returning the product as a new value.

Nter->Cter. Coordinates and dihedrals of insert are unchanged.

Begins insertion AFTER insert point. insert_point_end is assumed to be insert_point+1.

Referenced by protocols::grafting::simple_movers::InsertPoseIntoPoseMover::apply(), protocols::antibody::design::insert_cdr_into_antibody(), and protocols::grafting::GraftMoverBase::insert_piece().

core::pose::Pose protocols::grafting::insert_pose_into_pose ( Pose const &  scaffold_pose,
Pose const &  insert_pose,
core::Size const  insert_point,
core::Size const  insert_point_end,
bool  copy_pdbinfo 
)

inserts one pose into another pose, returning the product as a new value.

Author
Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om

brief inserts one pose into another pose, returning the product as a new value. The insert pose will be added immediately after insert_point and before insert_point_end.

Author
Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om, Jared Adolf-Bryfogle

Nter->Cter. Coordinates and dihedrals of insert are unchanged.

Begins insertion AFTER insert point.

References core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::declare_chemical_bond(), core::conformation::disulfide_bonds(), core::pose::Pose::fold_tree(), core::pose::Pose::insert_residue_by_jump(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::Pose::pdb_info(), core::kinematics::Edge::PEPTIDE, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::set_reasonable_fold_tree(), core::pose::Pose::size(), protocols::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

core::Real protocols::grafting::perturb_backbone_for_test ( Pose pose,
MoveMapOP  mm 
)
void protocols::grafting::remove_cutpoint_variants_for_ccd ( Pose pose,
Loops const &  loops 
)
void protocols::grafting::repack_connection_and_residues_in_movemap ( core::pose::Pose pose,
core::scoring::ScoreFunctionCOP  fa_scorefxn,
core::Size const  start,
core::Size const  end,
core::kinematics::MoveMapCOP  movemap 
)

convenience function for AFTER apply method.

flexible Nter and Cter residues plus the first and last residue of the insert.

void protocols::grafting::repack_connection_and_residues_in_movemap_and_piece ( core::pose::Pose pose,
core::scoring::ScoreFunctionCOP  fa_scorefxn,
core::Size const  start,
core::Size const  end,
core::kinematics::MoveMapCOP  movemap 
)

convenience function for AFTER apply method.

flexible Nter and Cter residues plus the entire insert.

void protocols::grafting::repack_connection_and_residues_in_movemap_and_piece_and_neighbors ( core::pose::Pose pose,
core::scoring::ScoreFunctionCOP  fa_scorefxn,
core::Size const  start,
core::Size const  end,
core::kinematics::MoveMapCOP  movemap,
core::Real  neighbor_dis = 4.0 
)

convenience function for AFTER apply method.

flexible Nter and Cter residues plus the entire insert and neighbors.

Referenced by protocols::grafting::CCDEndsGraftMover::apply(), and protocols::grafting::AnchoredGraftMover::apply().

core::pose::Pose protocols::grafting::replace_region ( Pose const &  from_pose,
Pose const &  to_pose,
core::Size const  from_pose_start_residue,
core::Size const  to_pose_start_residue,
core::Size const  insertion_length,
bool  copy_pdbinfo 
)
core::pose::Pose protocols::grafting::return_region ( Pose pose,
core::Size const  start,
core::Size const  end 
)
void protocols::grafting::setup_single_loop_double_arm_remodeling_foldtree ( Pose pose,
core::Size const  Nter_loop_start,
core::Size const  Cter_loop_end,
core::Size  end,
bool  loop_modeling 
)

****Nter_loop_start-—>Piece | <-—Nter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is end_-1

References core::kinematics::FoldTree::clear(), core::pose::Pose::fold_tree(), core::kinematics::Edge::PEPTIDE, core::pose::Pose::size(), and protocols::TR().

void protocols::grafting::setup_single_loop_single_arm_remodeling_foldtree ( Pose pose,
core::Size const  Nter_loop_start,
core::Size const  Cter_loop_end,
bool  loop_modeling 
)

****Nter_loop_start-—>Piece-—> | Cter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is Cter_loop_end-1

****Nter_loop_start-—>Piece-—> | Cter_loop_end**** Default FoldTree used by AnchoredGraftMover. lower_cutpoint for CCD and loops is Cter_loop_end-1

FOLDTREE SETUP. options depending on how you want your graft algorithm to work! —Indicates Flexible regions, | indicates cutpoint. Arrows are direction of ARMs used to close the loop in conjunction with algorithm. (CCD, KIC)

References core::kinematics::FoldTree::clear(), core::pose::Pose::fold_tree(), core::kinematics::Edge::PEPTIDE, core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::grafting::AnchoredGraftMover::apply().

void protocols::grafting::superimpose_overhangs_heavy ( core::pose::Pose const &  pose,
core::pose::Pose piece,
bool  ca_only,
core::Size  start,
core::Size  end,
core::Size  Nter_overhang_len = 2,
core::Size  Cter_overhang_length_len = 2 
)

uses rms_util to superimpose overhang residues of piece onto pose.

Start + End denote residue number before and after the insert will be. For example, start = 10, end = 11 for a scaffold where the previous residues are already deleted or a scaffold where you are superposimposing a linker between two domains - one that ends at start and the other that begins at end

References core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::residue(), core::scoring::rms, core::pose::Pose::size(), core::scoring::superimpose_pose(), and protocols::TR().

Referenced by protocols::grafting::CCDEndsGraftMover::apply().