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

#include <CDRH3Modeler.hh>

Inheritance diagram for protocols::antibody::CDRH3Modeler:

Collaboration diagram for protocols::antibody::CDRH3Modeler:

Public Member Functions
	CDRH3Modeler (utility::vector1< core::fragment::FragSetOP > cdr_h3_frags)
	default constructor More...

	~CDRH3Modeler ()
	default destructor More...

void	model_h3 (bool setting)
	enable CDR H3 loop building More...

void	enable_benchmark_mode (bool setting)
	enable benchmark mode More...

void	set_camelid (bool setting)
	enable camelid modeling mode More...

void	set_centroid_loop_building (bool setting)
	set centroid mode loop building More...

void	set_fullatom_loop_building (bool setting)
	set fullatom mode loop building More...

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. More...

void	build_centroid_loop ()
	Build centroid mode CDR H3 loop. More...

void	build_fullatom_loop ()
	Build fullatom mode CDR H3 loop. More...

void	set_lowres_score_func (core::scoring::ScoreFunctionOP lowres_scorefxn)
	set scorefunction for low resolution of CDR H3 modeling More...

void	set_highres_score_func (core::scoring::ScoreFunctionOP highres_scorefxn)
	set scorefunction for high resolution of CDR H3 modeling More...

void	antibody_modeling_insert_ter ()
	insert C-terminal fragments More...

void	store_H3_cter_fragment (utility::vector1< core::fragment::FragData > &base_library_in)
	store CDR H3 C-terminal fragments More...

bool	cutpoints_separation ()
	return false if any cdr cutpoint is broken More...

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. More...

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 More...

void	loop_fa_relax (core::pose::Pose &pose_in, core::Size const loop_begin, core::Size const loop_end)
	actually relaxes the region specified More...

void	loop_centroid_relax (core::pose::Pose &pose_in, core::Size const loop_begin, core::Size const loop_end)
	actually relaxes the region specified More...

void	setup_packer_task (core::pose::Pose &pose_in)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Public Attributes
utility::vector1 < core::fragment::FragData >	H3_base_library

Private Attributes
core::pose::Pose	template_pose_

core::pose::Pose	start_pose_

core::Size	base_
	Number of ADDITIONAL residues modeled from H3_CTERM These residues range from H:n-2,n-1,n,n+1 of H3. More...

core::Size	c_ter_stem_

core::Real	cen_cst_

core::Real	high_cst_

bool	do_h3_modeling_

core::scoring::ScoreFunctionOP	fa_scorefxn_

utility::vector1 < core::fragment::FragSetOP >	cdr_h3_frags_

core::scoring::ScoreFunctionOP	lowres_scorefxn_

core::scoring::ScoreFunctionOP	highres_scorefxn_

bool	benchmark_
	benchmark flag More...

bool	apply_centroid_mode_
	Centroid mode loop building. More...

bool	apply_fullatom_mode_
	Fullatom mode loop building. More...

bool	current_loop_is_H3_
	flag indicating that current loop being modeled is CDR H3 More...

bool	H3_filter_
	actually enables H3 filter for H3 operations More...

bool	antibody_build_
	build H3 only More...

bool	antibody_refine_
	refine H3 only More...

bool	min_base_relax_
	lower amplitude during base relaxation More...

bool	h3_random_cut_
	use random cutpoints for h3 modeling More...

Size	decoy_loop_cutpoint_
	cutpoint whose separation is computed in scorefile More...

bool	snug_fit_
	enable docking local refine of LH chains & simultaneous H3 min More...

bool	loops_flag_
	loop_building in docking More...

bool	docking_local_refine_

bool	dle_flag_
	insert fragment in docking More...

bool	refine_input_loop_
	just refine input loop More...

core::Size	h3_flank_
	number of flanking residues:default 5 More...

bool	flank_relax_
	relax flanking regions of h3 More...

bool	freeze_h3_
	freeze h3 during all cdr relax and local refine More...

bool	is_camelid_
	is camelid antibody without light chain More...

core::Size	cutoff_9_
	size of loop above which 9mer frags are used More...

core::Size	cutoff_3_
	size of loop above which 3mer frags are used More...

Antibody	antibody_in_

core::pack::task::TaskFactoryOP	tf_

core::pack::task::TaskFactoryOP	init_task_factory_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

Ab initio modeling of CDR H3 loop.

Definition at line 56 of file CDRH3Modeler.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 86 of file CDRH3Modeler.cc.

References cdr_h3_frags_, and set_default().

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

default destructor

Definition at line 95 of file CDRH3Modeler.cc.

Member Function Documentation

void protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter ( )

insert C-terminal fragments

Definition at line 574 of file CDRH3Modeler.cc.

References antibody_in_, core::fragment::FragData::apply(), protocols::antibody::Antibody::cdrh_, core::pose::Pose::fold_tree(), protocols::antibody::Antibody::Fv, H3_base_library, is_camelid_, protocols::RG(), protocols::antibody::simple_one_loop_fold_tree(), and protocols::TR().

Referenced by build_centroid_loop().

void protocols::antibody::CDRH3Modeler::apply ( core::pose::Pose & pose_in)

virtual

Implements protocols::moves::Mover.

Definition at line 163 of file CDRH3Modeler.cc.

References antibody_in_, antibody_refine_, protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), apply_centroid_mode_, apply_fullatom_mode_, benchmark_, build_centroid_loop(), build_fullatom_loop(), c_ter_stem_, protocols::antibody::Antibody::cdrh_, core::chemical::CENTROID, current_loop_is_H3_, cutpoints_separation(), do_h3_modeling_, protocols::antibody::Antibody::extended_, core::chemical::FA_STANDARD, protocols::antibody::Antibody::Fv, H3_filter_, highres_scorefxn_, is_camelid_, protocols::antibody::Antibody::kinked_, loop_centroid_relax(), loop_fa_relax(), protocols::antibody::Antibody::set_Fv(), setup_packer_task(), protocols::antibody::simple_one_loop_fold_tree(), snug_fit_, start_pose_, tf_, protocols::medal::to_centroid(), core::pose::Pose::total_residue(), and protocols::TR().

void protocols::antibody::CDRH3Modeler::build_centroid_loop ( )

Build centroid mode CDR H3 loop.

Definition at line 271 of file CDRH3Modeler.cc.

References antibody_in_, antibody_modeling_insert_ter(), apply_centroid_mode_, c_ter_stem_, protocols::antibody::Antibody::cdrh_, protocols::antibody::Antibody::current_start, cutoff_9_, cutpoints_separation(), protocols::antibody::Antibody::Fv, core::pose::Pose::omega(), core::import_pose::pose_from_pdb(), core::pose::Pose::psi(), scored_frag_close(), core::pose::Pose::set_omega(), core::pose::Pose::set_psi(), protocols::antibody::simple_one_loop_fold_tree(), protocols::loops::Loop::size(), template_pose_, and protocols::TR().

Referenced by apply().

void protocols::antibody::CDRH3Modeler::build_fullatom_loop ( )

Build fullatom mode CDR H3 loop.

Definition at line 338 of file CDRH3Modeler.cc.

References antibody_in_, apply_fullatom_mode_, base_, protocols::antibody::Antibody::cdrh_, cutpoints_separation(), protocols::antibody::Antibody::Fv, 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

Definition at line 893 of file CDRH3Modeler.cc.

References protocols::frag_picker::CA, H3_filter_, is_camelid_, 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
	)

Definition at line 638 of file CDRH3Modeler.cc.

References protocols::forge::build::SegmentInsertConnectionScheme::C, protocols::forge::build::SegmentInsertConnectionScheme::N, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by cutpoints_separation().

bool protocols::antibody::CDRH3Modeler::cutpoints_separation ( )

return false if any cdr cutpoint is broken

Definition at line 619 of file CDRH3Modeler.cc.

References protocols::antibody::Antibody::all_cdr_loops, antibody_in_, protocols::loops::Loops::begin(), cutpoint_separation(), protocols::loops::Loops::end(), and protocols::antibody::Antibody::Fv.

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

void protocols::antibody::CDRH3Modeler::enable_benchmark_mode ( bool setting)

inline

enable benchmark mode

Definition at line 70 of file CDRH3Modeler.hh.

References benchmark_.

std::string protocols::antibody::CDRH3Modeler::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 266 of file CDRH3Modeler.cc.

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,loop begin position, loop end position

Global Read: none

Global Write: none

Remarks

References:

Authors: Aroop 05/07/2010

Last Modified: 05/07/2010

Definition at line 1401 of file CDRH3Modeler.cc.

References core::pose::add_variant_type_to_pose_residue(), antibody_refine_, benchmark_, 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(), lowres_scorefxn_, refine_input_loop_, core::pose::Pose::residue(), protocols::antibody::simple_one_loop_fold_tree(), snug_fit_, 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,loop begin position, loop end position

Global Read: none

Global Write: none

Remarks

References:

Authors: Aroop 02/04/2010

Last Modified: 02/04/2010

Definition at line 1070 of file CDRH3Modeler.cc.

References core::pose::add_variant_type_to_pose_residue(), antibody_build_, antibody_in_, antibody_refine_, protocols::moves::ChangeFoldTreeMover::apply(), benchmark_, protocols::loops::loop_closure::ccd::ccd_moves(), CDR_H3_filter(), protocols::antibody::Antibody::cdrh_, current_loop_is_H3_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, decoy_loop_cutpoint_, flank_relax_, core::pose::Pose::fold_tree(), freeze_h3_, H3_filter_, h3_flank_, h3_random_cut_, core::conformation::Residue::has_variant_type(), highres_scorefxn_, core::pose::Pose::is_fullatom(), core::conformation::Residue::is_upper_terminus(), min_base_relax_, refine_input_loop_, core::pose::Pose::residue(), protocols::loops::select_loop_residues(), setup_packer_task(), protocols::antibody::simple_fold_tree(), snug_fit_, start_pose_, tf_, 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

Definition at line 65 of file CDRH3Modeler.hh.

References do_h3_modeling_.

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

Definition at line 686 of file CDRH3Modeler.cc.

References core::pose::add_variant_type_to_pose_residue(), antibody_in_, protocols::loops::loop_closure::ccd::ccd_moves(), CDR_H3_filter(), cdr_h3_frags_, protocols::antibody::Antibody::cdrh_, current_loop_is_H3_, protocols::loops::Loop::cut(), cutoff_9_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, protocols::antibody::Antibody::extended_, core::pose::Pose::fold_tree(), H3_filter_, is_camelid_, lowres_scorefxn_, 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

Definition at line 75 of file CDRH3Modeler.hh.

References docking_local_refine_, H3_filter_, is_camelid_, and snug_fit_.

void protocols::antibody::CDRH3Modeler::set_centroid_loop_building ( bool setting)

inline

set centroid mode loop building

Definition at line 86 of file CDRH3Modeler.hh.

References apply_centroid_mode_.

void protocols::antibody::CDRH3Modeler::set_default ( )

void protocols::antibody::CDRH3Modeler::set_fullatom_loop_building ( bool setting)

inline

set fullatom mode loop building

Definition at line 91 of file CDRH3Modeler.hh.

References apply_fullatom_mode_.

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

set scorefunction for high resolution of CDR H3 modeling

Definition at line 156 of file CDRH3Modeler.cc.

References highres_scorefxn_.

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

set scorefunction for low resolution of CDR H3 modeling

Definition at line 149 of file CDRH3Modeler.cc.

References lowres_scorefxn_.

void protocols::antibody::CDRH3Modeler::setup_packer_task ( core::pose::Pose & pose_in)

Definition at line 1543 of file CDRH3Modeler.cc.

References init_task_factory_, core::pack::dunbrack::load_unboundrot(), tf_, and protocols::TR().

Referenced by apply(), and loop_fa_relax().

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

store CDR H3 C-terminal fragments

Definition at line 364 of file CDRH3Modeler.cc.

References H3_base_library.

Member Data Documentation

bool protocols::antibody::CDRH3Modeler::antibody_build_

private

build H3 only

Definition at line 196 of file CDRH3Modeler.hh.

Referenced by loop_fa_relax(), and set_default().

Antibody protocols::antibody::CDRH3Modeler::antibody_in_

private

Definition at line 227 of file CDRH3Modeler.hh.

Referenced by antibody_modeling_insert_ter(), apply(), build_centroid_loop(), build_fullatom_loop(), cutpoints_separation(), loop_fa_relax(), and scored_frag_close().

bool protocols::antibody::CDRH3Modeler::antibody_refine_

private

refine H3 only

Definition at line 198 of file CDRH3Modeler.hh.

Referenced by apply(), loop_centroid_relax(), loop_fa_relax(), and set_default().

bool protocols::antibody::CDRH3Modeler::apply_centroid_mode_

private

Centroid mode loop building.

Definition at line 188 of file CDRH3Modeler.hh.

Referenced by apply(), build_centroid_loop(), set_centroid_loop_building(), and set_default().

bool protocols::antibody::CDRH3Modeler::apply_fullatom_mode_

private

Fullatom mode loop building.

Definition at line 190 of file CDRH3Modeler.hh.

Referenced by apply(), build_fullatom_loop(), set_default(), and set_fullatom_loop_building().

core::Size protocols::antibody::CDRH3Modeler::base_

private

Number of ADDITIONAL residues modeled from H3_CTERM These residues range from H:n-2,n-1,n,n+1 of H3.

Definition at line 169 of file CDRH3Modeler.hh.

Referenced by build_fullatom_loop(), and set_default().

bool protocols::antibody::CDRH3Modeler::benchmark_

private

benchmark flag

Definition at line 186 of file CDRH3Modeler.hh.

Referenced by apply(), enable_benchmark_mode(), loop_centroid_relax(), loop_fa_relax(), and set_default().

core::Size protocols::antibody::CDRH3Modeler::c_ter_stem_

private

Definition at line 170 of file CDRH3Modeler.hh.

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

utility::vector1< core::fragment::FragSetOP > protocols::antibody::CDRH3Modeler::cdr_h3_frags_

private

Definition at line 179 of file CDRH3Modeler.hh.

Referenced by CDRH3Modeler(), and scored_frag_close().

core::Real protocols::antibody::CDRH3Modeler::cen_cst_

private

Definition at line 172 of file CDRH3Modeler.hh.

Referenced by set_default().

bool protocols::antibody::CDRH3Modeler::current_loop_is_H3_

private

flag indicating that current loop being modeled is CDR H3

Definition at line 192 of file CDRH3Modeler.hh.

Referenced by apply(), loop_fa_relax(), scored_frag_close(), and set_default().

core::Size protocols::antibody::CDRH3Modeler::cutoff_3_

private

size of loop above which 3mer frags are used

Definition at line 225 of file CDRH3Modeler.hh.

Referenced by set_default().

core::Size protocols::antibody::CDRH3Modeler::cutoff_9_

private

size of loop above which 9mer frags are used

Definition at line 223 of file CDRH3Modeler.hh.

Referenced by build_centroid_loop(), scored_frag_close(), and set_default().

Size protocols::antibody::CDRH3Modeler::decoy_loop_cutpoint_

private

cutpoint whose separation is computed in scorefile

Definition at line 204 of file CDRH3Modeler.hh.

Referenced by loop_fa_relax(), and set_default().

bool protocols::antibody::CDRH3Modeler::dle_flag_

private

insert fragment in docking

Definition at line 211 of file CDRH3Modeler.hh.

Referenced by set_default().

bool protocols::antibody::CDRH3Modeler::do_h3_modeling_

private

Definition at line 176 of file CDRH3Modeler.hh.

Referenced by apply(), model_h3(), and set_default().

bool protocols::antibody::CDRH3Modeler::docking_local_refine_

private

Definition at line 209 of file CDRH3Modeler.hh.

Referenced by set_camelid(), and set_default().

core::scoring::ScoreFunctionOP protocols::antibody::CDRH3Modeler::fa_scorefxn_

private

Definition at line 177 of file CDRH3Modeler.hh.

bool protocols::antibody::CDRH3Modeler::flank_relax_

private

relax flanking regions of h3

Definition at line 217 of file CDRH3Modeler.hh.

Referenced by loop_fa_relax(), and set_default().

bool protocols::antibody::CDRH3Modeler::freeze_h3_

private

freeze h3 during all cdr relax and local refine

Definition at line 219 of file CDRH3Modeler.hh.

Referenced by loop_fa_relax(), and set_default().

utility::vector1< core::fragment::FragData > protocols::antibody::CDRH3Modeler::H3_base_library

Definition at line 162 of file CDRH3Modeler.hh.

Referenced by antibody_modeling_insert_ter(), and store_H3_cter_fragment().

bool protocols::antibody::CDRH3Modeler::H3_filter_

private

actually enables H3 filter for H3 operations

Definition at line 194 of file CDRH3Modeler.hh.

Referenced by apply(), CDR_H3_filter(), loop_fa_relax(), scored_frag_close(), set_camelid(), and set_default().

core::Size protocols::antibody::CDRH3Modeler::h3_flank_

private

number of flanking residues:default 5

Definition at line 215 of file CDRH3Modeler.hh.

Referenced by loop_fa_relax(), and set_default().

bool protocols::antibody::CDRH3Modeler::h3_random_cut_

private

use random cutpoints for h3 modeling

Definition at line 202 of file CDRH3Modeler.hh.

Referenced by loop_fa_relax(), and set_default().

core::Real protocols::antibody::CDRH3Modeler::high_cst_

private

Definition at line 173 of file CDRH3Modeler.hh.

Referenced by set_default().

core::scoring::ScoreFunctionOP protocols::antibody::CDRH3Modeler::highres_scorefxn_

private

Definition at line 183 of file CDRH3Modeler.hh.

Referenced by apply(), loop_fa_relax(), set_default(), and set_highres_score_func().

core::pack::task::TaskFactoryOP protocols::antibody::CDRH3Modeler::init_task_factory_

private

Definition at line 231 of file CDRH3Modeler.hh.

Referenced by setup_packer_task().

bool protocols::antibody::CDRH3Modeler::is_camelid_

private

is camelid antibody without light chain

Definition at line 221 of file CDRH3Modeler.hh.

Referenced by antibody_modeling_insert_ter(), apply(), CDR_H3_filter(), scored_frag_close(), set_camelid(), and set_default().

bool protocols::antibody::CDRH3Modeler::loops_flag_

private

loop_building in docking

Definition at line 208 of file CDRH3Modeler.hh.

Referenced by set_default().

core::scoring::ScoreFunctionOP protocols::antibody::CDRH3Modeler::lowres_scorefxn_

private

Definition at line 182 of file CDRH3Modeler.hh.

Referenced by loop_centroid_relax(), scored_frag_close(), set_default(), and set_lowres_score_func().

bool protocols::antibody::CDRH3Modeler::min_base_relax_

private

lower amplitude during base relaxation

Definition at line 200 of file CDRH3Modeler.hh.

Referenced by loop_fa_relax(), and set_default().

bool protocols::antibody::CDRH3Modeler::refine_input_loop_

private

just refine input loop

Definition at line 213 of file CDRH3Modeler.hh.

Referenced by loop_centroid_relax(), loop_fa_relax(), and set_default().

bool protocols::antibody::CDRH3Modeler::snug_fit_

private

enable docking local refine of LH chains & simultaneous H3 min

Definition at line 206 of file CDRH3Modeler.hh.

Referenced by apply(), loop_centroid_relax(), loop_fa_relax(), set_camelid(), and set_default().

core::pose::Pose protocols::antibody::CDRH3Modeler::start_pose_

private

Definition at line 166 of file CDRH3Modeler.hh.

Referenced by apply(), and loop_fa_relax().

core::pose::Pose protocols::antibody::CDRH3Modeler::template_pose_

private

Definition at line 165 of file CDRH3Modeler.hh.

Referenced by build_centroid_loop().

core::pack::task::TaskFactoryOP protocols::antibody::CDRH3Modeler::tf_

private

Definition at line 230 of file CDRH3Modeler.hh.

Referenced by apply(), loop_fa_relax(), and setup_packer_task().

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

src/protocols/antibody/CDRH3Modeler.hh
src/protocols/antibody/CDRH3Modeler.cc

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