Rosetta 3.4
Public Member Functions
protocols::antibody2::CDRH3Modeler2 Class Reference

Ab initio modeling of CDR H3 loop. More...

#include <CDRH3Modeler2.hh>

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List of all members.

Public Member Functions

 CDRH3Modeler2 ()
 default constructor
 CDRH3Modeler2 (bool apply_centroid_mode, bool apply_fullatom_mode, bool camelid, bool benchmark, Ab_InfoOP antibody_info)
 constructor with arguments
 ~CDRH3Modeler2 ()
 default destructor
void enable_benchmark_mode (bool setting)
 enable benchmark mode
void set_camelid (bool setting)
 enable camelid modeling mode
void set_centroid_loop_building (bool setting)
 set centroid mode loop building
void set_fullatom_loop_building (bool setting)
 set fullatom mode loop building
void set_default ()
virtual void apply (core::pose::Pose &pose_in)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void set_lowres_score_func (core::scoring::ScoreFunctionOP lowres_scorefxn)
 set scorefunction for low resolution of CDR H3 modeling
void set_highres_score_func (core::scoring::ScoreFunctionOP highres_scorefxn)
 set scorefunction for high resolution of CDR H3 modeling
void loop_centroid_relax (core::pose::Pose &pose_in, core::Size const loop_begin, core::Size const loop_end)
 actually relaxes the region specified

Detailed Description

Ab initio modeling of CDR H3 loop.


Constructor & Destructor Documentation

protocols::antibody2::CDRH3Modeler2::CDRH3Modeler2 ( )

default constructor

protocols::antibody2::CDRH3Modeler2::CDRH3Modeler2 ( bool  apply_centroid_mode,
bool  apply_fullatom_mode,
bool  camelid,
bool  benchmark,
Ab_InfoOP  antibody_info 
)

constructor with arguments

protocols::antibody2::CDRH3Modeler2::~CDRH3Modeler2 ( )

default destructor


Member Function Documentation

void protocols::antibody2::CDRH3Modeler2::apply ( core::pose::Pose pose_in) [virtual]
void protocols::antibody2::CDRH3Modeler2::enable_benchmark_mode ( bool  setting) [inline]

enable benchmark mode

std::string protocols::antibody2::CDRH3Modeler2::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

void protocols::antibody2::CDRH3Modeler2::loop_centroid_relax ( core::pose::Pose pose_in,
core::Size const  loop_begin,
core::Size const  loop_end 
)

actually relaxes the region specified

loop_centroid_relax

Detailed: This is all done in low resolution. Intention was to give
camelid CDR H1 a larger perturbation.
Parameters:
[in]pose,loopbegin position, loop end position
Global Read: none
Global Write: none
Remarks:
References:
Authors:
Aroop 05/07/2010
Last Modified: 05/07/2010

References core::pose::add_variant_type_to_pose_residue(), protocols::loops::loop_closure::ccd::ccd_moves(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), protocols::antibody2::simple_one_loop_fold_tree(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply().

void protocols::antibody2::CDRH3Modeler2::set_camelid ( bool  setting) [inline]

enable camelid modeling mode

void protocols::antibody2::CDRH3Modeler2::set_centroid_loop_building ( bool  setting) [inline]

set centroid mode loop building

void protocols::antibody2::CDRH3Modeler2::set_default ( )

References protocols::TR().

void protocols::antibody2::CDRH3Modeler2::set_fullatom_loop_building ( bool  setting) [inline]

set fullatom mode loop building

void protocols::antibody2::CDRH3Modeler2::set_highres_score_func ( core::scoring::ScoreFunctionOP  highres_scorefxn)

set scorefunction for high resolution of CDR H3 modeling

void protocols::antibody2::CDRH3Modeler2::set_lowres_score_func ( core::scoring::ScoreFunctionOP  lowres_scorefxn)

set scorefunction for low resolution of CDR H3 modeling


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