Rosetta 3.4
Public Member Functions
protocols::antibody::AntibodyModeler Class Reference

#include <AntibodyModeler.hh>

Inheritance diagram for protocols::antibody::AntibodyModeler:
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List of all members.

Public Member Functions

 AntibodyModeler ()
 ~AntibodyModeler ()
void set_default ()
void init_from_options ()
virtual void apply (core::pose::Pose &pose_in)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
virtual void init_on_new_input ()
void set_snugdock_foldtree (core::pose::Pose &pose_in)
void setup_simple_fold_tree (core::Size jumppoint1, core::Size cutpoint, core::Size jumppoint2, core::Size nres, core::pose::Pose &pose_in)
void relax_cdrs ()
 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
void repulsive_ramp (core::pose::Pose &pose_in, loops::Loops loops_in)
 ramping up the fullatom repulsive weight slowly to allow the partners to relieve clashes and make way for each other
void snugfit_MC_min (core::pose::Pose &pose_in, core::kinematics::MoveMapOP cdr_dock_map, core::Size cycles, core::Real minimization_threshold, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP pack_scorefxn, utility::vector1< bool > is_flexible)
void snugfit_mcm_protocol (core::pose::Pose &pose_in, loops::Loops loops_in)
void setup_packer_task (core::pose::Pose &pose_in)
core::Real global_loop_rmsd (const core::pose::Pose &pose_in, const core::pose::Pose &native_pose, std::string cdr_type)
void read_and_store_fragments ()
void display_constraint_residues ()

Constructor & Destructor Documentation

protocols::antibody::AntibodyModeler::AntibodyModeler ( )
protocols::antibody::AntibodyModeler::~AntibodyModeler ( )

Member Function Documentation

void protocols::antibody::AntibodyModeler::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(), setup_simple_fold_tree(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::antibody::AntibodyModeler::apply ( core::pose::Pose pose_in) [virtual]
protocols::moves::MoverOP protocols::antibody::AntibodyModeler::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 AntibodyModeler().

void protocols::antibody::AntibodyModeler::display_constraint_residues ( )

References protocols::TR().

Referenced by apply().

std::string protocols::antibody::AntibodyModeler::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

Real protocols::antibody::AntibodyModeler::global_loop_rmsd ( const core::pose::Pose pose_in,
const core::pose::Pose native_pose,
std::string  cdr_type 
)
void protocols::antibody::AntibodyModeler::init_from_options ( )

References protocols::TR().

Referenced by AntibodyModeler().

void protocols::antibody::AntibodyModeler::init_on_new_input ( ) [virtual]
void protocols::antibody::AntibodyModeler::read_and_store_fragments ( )
void protocols::antibody::AntibodyModeler::relax_cdrs ( )

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::scoring::overlap_chainbreak, protocols::loops::select_loop_residues(), and setup_packer_task().

Referenced by apply().

void protocols::antibody::AntibodyModeler::repulsive_ramp ( core::pose::Pose pose_in,
loops::Loops  loops_in 
)

ramping up the fullatom repulsive weight slowly to allow the partners to relieve clashes and make way for each other

repulsive_ramp

Detailed: This routine is specially targetted to the coupled
optimization of docking partners and the loop region. The loop modelling & all previous steps involve mainly centroid mode .On switching on fullatom mode, one is bound to end up with clashes.To relieve the clashes, it is essential to slowly dial up the repulsive weight instead of turning it on to the maximum value in one single step
Parameters:
[in]inputpose which is assumed to have a docking fold tree
Global Read: fa_rep : fullatom repulsive weight
Global Write: fa_rep ( It is reset to the original value at the end )
Remarks:
A particular portion is commented out,which can be uncommented if one uses a low resolution homology model. Check details in the beginning of the commented out region
References:
Authors:
Aroop 07/13/2010
Last Modified: 07/13/2010

References core::pose::add_variant_type_to_pose_residue(), protocols::loops::Loops::begin(), core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, protocols::loops::Loops::end(), core::scoring::fa_rep, protocols::loops::Loops::num_loop(), core::scoring::overlap_chainbreak, core::util::remove_cutpoint_variants(), protocols::loops::select_loop_residues(), snugfit_MC_min(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::antibody::AntibodyModeler::set_default ( )

References protocols::TR().

Referenced by AntibodyModeler().

void protocols::antibody::AntibodyModeler::set_snugdock_foldtree ( core::pose::Pose pose_in)
void protocols::antibody::AntibodyModeler::setup_packer_task ( core::pose::Pose pose_in)
void protocols::antibody::AntibodyModeler::setup_simple_fold_tree ( core::Size  jumppoint1,
core::Size  cutpoint,
core::Size  jumppoint2,
core::Size  nres,
core::pose::Pose pose_in 
)
void protocols::antibody::AntibodyModeler::snugfit_MC_min ( core::pose::Pose pose_in,
core::kinematics::MoveMapOP  cdr_dock_map,
core::Size  cycles,
core::Real  minimization_threshold,
core::scoring::ScoreFunctionOP  scorefxn,
core::scoring::ScoreFunctionOP  pack_scorefxn,
utility::vector1< bool is_flexible 
)
void protocols::antibody::AntibodyModeler::snugfit_mcm_protocol ( core::pose::Pose pose_in,
loops::Loops  loops_in 
)

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