Rosetta 3.4
Public Member Functions | Public Attributes
protocols::antibody::CDRH3Modeler Class Reference

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

#include <CDRH3Modeler.hh>

Inheritance diagram for protocols::antibody::CDRH3Modeler:
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List of all members.

Public Member Functions

 CDRH3Modeler (utility::vector1< core::fragment::FragSetOP > cdr_h3_frags)
 default constructor
 ~CDRH3Modeler ()
 default destructor
void model_h3 (bool setting)
 enable CDR H3 loop building
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 build_centroid_loop ()
 Build centroid mode CDR H3 loop.
void build_fullatom_loop ()
 Build fullatom mode CDR H3 loop.
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 antibody_modeling_insert_ter ()
 insert C-terminal fragments
void store_H3_cter_fragment (utility::vector1< core::fragment::FragData > &base_library_in)
 store CDR H3 C-terminal fragments
bool cutpoints_separation ()
 return false if any cdr cutpoint is broken
core::Real cutpoint_separation (core::pose::Pose &pose_in, Size cutpoint)
void scored_frag_close (core::pose::Pose &pose_in, loops::Loop const trimmed_cdr_h3)
 builds a loop from fragments file.
bool CDR_H3_filter (const core::pose::Pose &pose_in, core::Size const loop_begin, core::Size const size, char const light_chain= 'L')
 tests if a loop has H3 like base charachteristics
void loop_fa_relax (core::pose::Pose &pose_in, core::Size const loop_begin, core::Size const loop_end)
 actually relaxes the region specified
void loop_centroid_relax (core::pose::Pose &pose_in, core::Size const loop_begin, core::Size const loop_end)
 actually relaxes the region specified
void setup_packer_task (core::pose::Pose &pose_in)

Public Attributes

utility::vector1
< core::fragment::FragData
H3_base_library

Detailed Description

Ab initio modeling of CDR H3 loop.


Constructor & Destructor Documentation

protocols::antibody::CDRH3Modeler::CDRH3Modeler ( utility::vector1< core::fragment::FragSetOP cdr_h3_frags)

default constructor

References set_default().

protocols::antibody::CDRH3Modeler::~CDRH3Modeler ( )

default destructor


Member Function Documentation

void protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter ( )
void protocols::antibody::CDRH3Modeler::apply ( core::pose::Pose pose_in) [virtual]
void protocols::antibody::CDRH3Modeler::build_centroid_loop ( )
void protocols::antibody::CDRH3Modeler::build_fullatom_loop ( )

Build fullatom mode CDR H3 loop.

References cutpoints_separation(), loop_fa_relax(), and protocols::TR().

Referenced by apply().

bool protocols::antibody::CDRH3Modeler::CDR_H3_filter ( const core::pose::Pose pose_in,
core::Size const  loop_begin,
core::Size const  size,
char const  light_chain = 'L' 
)

tests if a loop has H3 like base charachteristics

CDR_H3_filter

Detailed: Uses the Shirai rules to find out if the dihedral angle
formed by CA atoms of residues n-2,n-1,n and n+1 conform to a kinked/extended structure in accordance with the sequence. If there is a match, a true value is returned
Parameters:
[in]pose,:full actual protein loop_begin: seq numbered loop begin corresponding to pose size: size of loop to compute loop_end
Global Read: reads -command line flag -base stored in dle_ns
to determine to do the complete H3 filter check or just do a prediction of the H3 base type based on the aforementioned dihedral angle
Global Write:
Remarks:
References: Structural classification of CDR-H3 in antibodies
Hiroki Shirai, Akinori Kidera, Haruki Nakamura FEBS Letters 399 (1996) 1-8
Authors:
Aroop 02/04/2010
Last Modified: 02/04/2010

References protocols::frag_picker::CA, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::TR(), and protocols::kinmatch::xyz().

Referenced by loop_fa_relax(), and scored_frag_close().

Real protocols::antibody::CDRH3Modeler::cutpoint_separation ( core::pose::Pose pose_in,
Size  cutpoint 
)
bool protocols::antibody::CDRH3Modeler::cutpoints_separation ( )

return false if any cdr cutpoint is broken

References cutpoint_separation().

Referenced by apply(), build_centroid_loop(), and build_fullatom_loop().

void protocols::antibody::CDRH3Modeler::enable_benchmark_mode ( bool  setting) [inline]

enable benchmark mode

std::string protocols::antibody::CDRH3Modeler::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

void protocols::antibody::CDRH3Modeler::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::antibody::simple_one_loop_fold_tree(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply().

void protocols::antibody::CDRH3Modeler::loop_fa_relax ( core::pose::Pose pose_in,
core::Size const  loop_begin,
core::Size const  loop_end 
)

actually relaxes the region specified

loop_fa_relax

Detailed: This is all done in high resolution.Hence there are no rigid
body moves relative to the docking partners. Only small moves are carried out here to see if there are better fits. Repacking is carried out extensively after each move.
Parameters:
[in]pose,loopbegin position, loop end position
Global Read: none
Global Write: none
Remarks:
References:
Authors:
Aroop 02/04/2010
Last Modified: 02/04/2010

References core::pose::add_variant_type_to_pose_residue(), protocols::moves::ChangeFoldTreeMover::apply(), protocols::loops::loop_closure::ccd::ccd_moves(), CDR_H3_filter(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::pose::Pose::is_fullatom(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), protocols::loops::select_loop_residues(), setup_packer_task(), protocols::antibody::simple_fold_tree(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply(), and build_fullatom_loop().

void protocols::antibody::CDRH3Modeler::model_h3 ( bool  setting) [inline]

enable CDR H3 loop building

void protocols::antibody::CDRH3Modeler::scored_frag_close ( core::pose::Pose pose_in,
loops::Loop const  trimmed_cdr_h3 
)

builds a loop from fragments file.

scored_frag_close

Detailed: Loop is built by a monte carlo simulation using fragments
from a fragment files. CCD moves are used to close loops with gaps at cutpoint.H3_check is enforced if H3_filter flag is set in command line. Loop building results in many files containing differnt conformations of the same loop in phi-psi-omega angles. Parallel processing is utilized.
Parameters:
[in]weight_map,:in this case its a centroid weight pose_in: loop to be built on this template provided loop_begin/loop_end: loop termini definition frag_size: 3-mer or 9-mer frag_offset:agreement in frag file numbering & pose numberng cycles1: max cycles to be spent building loops cycles2: # of fragment swaps for each loop(depends on size) do_ccd_moves: should ccd moves be used to close gaps
Global Read: benchmark_
Global Write:
Remarks:
References:
Authors:
Aroop 02/04/2010
Last Modified: 02/04/2010

References core::pose::add_variant_type_to_pose_residue(), protocols::loops::loop_closure::ccd::ccd_moves(), CDR_H3_filter(), protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::pose::Pose::residue(), protocols::RG(), protocols::antibody::simple_one_loop_fold_tree(), protocols::loops::Loop::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::TR().

Referenced by build_centroid_loop().

void protocols::antibody::CDRH3Modeler::set_camelid ( bool  setting) [inline]

enable camelid modeling mode

void protocols::antibody::CDRH3Modeler::set_centroid_loop_building ( bool  setting) [inline]

set centroid mode loop building

void protocols::antibody::CDRH3Modeler::set_default ( )
void protocols::antibody::CDRH3Modeler::set_fullatom_loop_building ( bool  setting) [inline]

set fullatom mode loop building

void protocols::antibody::CDRH3Modeler::set_highres_score_func ( core::scoring::ScoreFunctionOP  highres_scorefxn)

set scorefunction for high resolution of CDR H3 modeling

void protocols::antibody::CDRH3Modeler::set_lowres_score_func ( core::scoring::ScoreFunctionOP  lowres_scorefxn)

set scorefunction for low resolution of CDR H3 modeling

void protocols::antibody::CDRH3Modeler::setup_packer_task ( core::pose::Pose pose_in)
void protocols::antibody::CDRH3Modeler::store_H3_cter_fragment ( utility::vector1< core::fragment::FragData > &  base_library_in)

store CDR H3 C-terminal fragments

References H3_base_library.


Member Data Documentation


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