Rosetta 3.4
Public Member Functions | Static Public Member Functions | Friends
protocols::antibody2::Ab_ModelCDRH3 Class Reference

#include <Ab_ModelCDRH3.hh>

Inheritance diagram for protocols::antibody2::Ab_ModelCDRH3:
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Collaboration diagram for protocols::antibody2::Ab_ModelCDRH3:
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List of all members.

Public Member Functions

 Ab_ModelCDRH3 ()
 ~Ab_ModelCDRH3 ()
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
void set_default ()
 Assigns default values to primitive members.
void sync_objects_with_flags ()
 Instantiates non-primitive members based on the value of the primitive members.
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void set_snugfit (bool snugfit)
void set_camelid (bool camelid)
void set_camelid_constraints (bool camelid_constraints)
void set_benchmark (bool benchmark)
void relax_cdrs (core::pose::Pose &pose)
 relaxes all cdrs simultaneously
void all_cdr_VL_VH_fold_tree (core::pose::Pose &pose_in, const loops::Loops &loops)
 change to all CDR and VL-VH dock fold tree
core::Real global_loop_rmsd (const core::pose::Pose &pose_in, const core::pose::Pose &native_pose, std::string cdr_type)
void display_constraint_residues (core::pose::Pose &pose)
void show (std::ostream &out=std::cout)

Static Public Member Functions

static void register_options ()
 Associates relevant options with the AntibodyModeler class.

Friends

std::ostream & operator<< (std::ostream &out, const Ab_ModelCDRH3 &ab_m_2)

Constructor & Destructor Documentation

protocols::antibody2::Ab_ModelCDRH3::Ab_ModelCDRH3 ( )

Referenced by clone().

protocols::antibody2::Ab_ModelCDRH3::~Ab_ModelCDRH3 ( )

Member Function Documentation

void protocols::antibody2::Ab_ModelCDRH3::all_cdr_VL_VH_fold_tree ( core::pose::Pose pose_in,
const loops::Loops loops_in 
)

change to all CDR and VL-VH dock fold tree

all_cdr_VL_VH_fold_tree

Detailed:
Parameters:
[out]
Global Read:
Global Write:
Remarks:
References:
Authors:
Aroop 07/13/2010
Last Modified: 07/13/2010

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), make_table_of_pilot_apps::f, core::pose::Pose::fold_tree(), core::pose::Pose::pdb_info(), protocols::geometry::residue_center_of_mass(), protocols::antibody2::setup_simple_fold_tree(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::antibody2::Ab_ModelCDRH3::apply ( core::pose::Pose pose) [virtual]
protocols::moves::MoverOP protocols::antibody2::Ab_ModelCDRH3::clone ( ) const [virtual]

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References Ab_ModelCDRH3().

void protocols::antibody2::Ab_ModelCDRH3::display_constraint_residues ( core::pose::Pose pose)
std::string protocols::antibody2::Ab_ModelCDRH3::get_name ( ) const [virtual]

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Real protocols::antibody2::Ab_ModelCDRH3::global_loop_rmsd ( const core::pose::Pose pose_in,
const core::pose::Pose native_pose,
std::string  cdr_type 
)
void protocols::antibody2::Ab_ModelCDRH3::register_options ( ) [static]

Associates relevant options with the AntibodyModeler class.

Reimplemented from protocols::moves::Mover.

void protocols::antibody2::Ab_ModelCDRH3::relax_cdrs ( core::pose::Pose pose)

relaxes all cdrs simultaneously

relax_cdrs

Detailed: based on the all_cdrs loop definiton, minimizes only those
regions. A standard dfpmin is utilized with score12 and chain -break and chain-overlap set. The allow_bb/chi arrays are changed accordingly but then are reset to their initial states before exiting the routine. Similarly the fold tree and jump movements are restored to their initial states
Parameters:
[out]
Global Read:
Global Write:
Remarks:
References:
Authors:
Aroop 02/15/2010
Last Modified: 02/15/2010

References core::util::add_cutpoint_variants(), core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::fold_tree(), core::scoring::overlap_chainbreak, protocols::loops::select_loop_residues(), protocols::antibody2::setup_packer_task(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::antibody2::Ab_ModelCDRH3::set_benchmark ( bool  benchmark) [inline]
void protocols::antibody2::Ab_ModelCDRH3::set_camelid ( bool  camelid) [inline]
void protocols::antibody2::Ab_ModelCDRH3::set_camelid_constraints ( bool  camelid_constraints) [inline]
void protocols::antibody2::Ab_ModelCDRH3::set_default ( )

Assigns default values to primitive members.

References protocols::TR().

void protocols::antibody2::Ab_ModelCDRH3::set_snugfit ( bool  snugfit) [inline]
void protocols::antibody2::Ab_ModelCDRH3::show ( std::ostream &  out = std::cout)

Show the complete setup of the antibody modeler protocol

References sync_objects_with_flags().

void protocols::antibody2::Ab_ModelCDRH3::sync_objects_with_flags ( )

Instantiates non-primitive members based on the value of the primitive members.

Referenced by apply(), and show().


Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const Ab_ModelCDRH3 ab_m_2 
) [friend]

The documentation for this class was generated from the following files:
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