#include <AntibodyModeler.hh>

Inheritance diagram for protocols::antibody_legacy::AntibodyModeler:

[legend]

Public Member Functions
	AntibodyModeler ()

	~AntibodyModeler () override

void	set_default ()

void	init_from_options ()

void	apply (core::pose::Pose &pose_in) override
	Main Method. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

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 More...

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 More...

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 More...

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 ()

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

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

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

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...

virtual bool	reinitialize_for_each_job () const
	Inform 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
	Inform 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
	Generates a new Mover object freshly created with the default ctor. More...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Attributes
bool	model_h3_

bool	snugfit_

bool	native_present_

bool	graft_l1_

bool	graft_l2_

bool	graft_l3_

bool	graft_h1_

bool	graft_h2_

bool	graft_h3_

bool	camelid_

bool	camelid_constraints_

bool	benchmark_

bool	init_for_input_yet_

core::Real	cst_weight_

std::string	native_filename_

core::pose::Pose	start_pose_

core::pose::Pose	native_pose_

Antibody	antibody_in_

utility::vector1< core::fragment::FragData >	H3_base_library_

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

core::pack::task::TaskFactoryOP	tf_

core::pack::task::TaskFactoryOP	init_task_factory_

std::map< std::string, core::Real >	score_map_

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

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

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. 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...

Constructor & Destructor Documentation

◆ AntibodyModeler()

protocols::antibody_legacy::AntibodyModeler::AntibodyModeler ( )

References init_from_options(), set_default(), and protocols::moves::Mover::type().

◆ ~AntibodyModeler()

protocols::antibody_legacy::AntibodyModeler::~AntibodyModeler ( )

overridedefault

Member Function Documentation

◆ all_cdr_VL_VH_fold_tree()

void protocols::antibody_legacy::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

Parameters

[out]

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::delete_unordered_edge(), core::pose::Pose::fold_tree(), protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::pdb_info(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::residue_center_of_mass(), setup_simple_fold_tree(), and core::pose::Pose::size().

Referenced by apply().

◆ apply()

void protocols::antibody_legacy::AntibodyModeler::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::io::raw_data::ScoreMap::add_energies_data_from_scored_pose(), protocols::loops::add_single_cutpoint_variant(), protocols::antibody_legacy::Antibody::align_to_native(), protocols::antibody_legacy::Antibody::all_cdr_loops, all_cdr_VL_VH_fold_tree(), antibody_in_, core::scoring::atom_pair_constraint, benchmark_, camelid_, camelid_constraints_, protocols::antibody_legacy::Antibody::cdrh_, core::scoring::chainbreak, cst_weight_, core::pose::Pose::data(), display_constraint_residues(), protocols::antibody_legacy::Antibody::Fv, protocols::moves::Mover::get_native_pose(), core::scoring::get_score_function(), global_loop_rmsd(), graft_h1_, graft_h2_, graft_h3_, graft_l1_, graft_l2_, graft_l3_, H3_base_library_, init_for_input_yet_, init_on_new_input(), model_h3_, native_pose_, offset_frags_, core::scoring::overlap_chainbreak, relax_cdrs(), protocols::loops::remove_cutpoint_variants(), repulsive_ramp(), core::pose::datacache::CacheableDataType::SCORE_MAP, score_map_, core::pose::set_ss_from_phipsi(), protocols::antibody_legacy::simple_one_loop_fold_tree(), snugfit_, snugfit_mcm_protocol(), and start_pose_.

◆ clone()

protocols::moves::MoverOP protocols::antibody_legacy::AntibodyModeler::clone ( ) const

overridevirtual

Return a clone of the Mover object.

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.

◆ display_constraint_residues()

void protocols::antibody_legacy::AntibodyModeler::display_constraint_residues ( )

References antibody_in_, protocols::antibody_legacy::Antibody::cdrh_, protocols::antibody_legacy::Antibody::extended_, protocols::antibody_legacy::Antibody::Fv, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and protocols::TR().

Referenced by apply().

◆ get_name()

std::string protocols::antibody_legacy::AntibodyModeler::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ global_loop_rmsd()

Real protocols::antibody_legacy::AntibodyModeler::global_loop_rmsd	(	const core::pose::Pose &	pose_in,
		const core::pose::Pose &	native_pose,
		std::string	cdr_type
	)

References antibody_in_, protocols::antibody_legacy::Antibody::cdrh_, protocols::antibody_legacy::Antibody::cdrl_, protocols::antibody_legacy::Antibody::Fv, core::scoring::is_protein_CA(), core::scoring::rmsd_no_super_subset(), and core::pose::Pose::size().

Referenced by apply().

◆ init_from_options()

void protocols::antibody_legacy::AntibodyModeler::init_from_options ( )

References benchmark_, camelid_, camelid_constraints_, cst_weight_, graft_h1_, graft_h2_, graft_h3_, graft_l1_, graft_l2_, graft_l3_, model_h3_, native_filename_, native_present_, snugfit_, and protocols::TR().

Referenced by AntibodyModeler().

◆ init_on_new_input()

void protocols::antibody_legacy::AntibodyModeler::init_on_new_input ( )

virtual

References antibody_in_, camelid_, H3_base_library_, init_for_input_yet_, model_h3_, native_filename_, native_pose_, native_present_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), read_and_store_fragments(), protocols::antibody_legacy::read_H3_cter_fragment(), protocols::antibody_legacy::Antibody::set_Fv(), core::pose::set_ss_from_phipsi(), and start_pose_.

Referenced by apply().

◆ read_and_store_fragments()

void protocols::antibody_legacy::AntibodyModeler::read_and_store_fragments ( )

References antibody_in_, protocols::antibody_legacy::Antibody::cdrh_, protocols::antibody_legacy::Antibody::Fv, model_h3_, offset_frags_, protocols::loops::read_loop_fragments(), setup_simple_fold_tree(), and core::pose::Pose::size().

Referenced by init_on_new_input().

◆ relax_cdrs()

void protocols::antibody_legacy::AntibodyModeler::relax_cdrs ( )

relaxes all cdrs simultaneously

based on the all_cdrs loop definiton, minimizes only those regions. A standard dfpmin is utilized with the given score function 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]

References protocols::loops::add_cutpoint_variants(), protocols::antibody_legacy::Antibody::all_cdr_fold_tree(), protocols::antibody_legacy::Antibody::all_cdr_loops, antibody_in_, benchmark_, core::scoring::chainbreak, core::pose::Pose::fold_tree(), protocols::antibody_legacy::Antibody::Fv, core::scoring::get_score_function(), protocols::loops::Loops::num_loop(), core::scoring::overlap_chainbreak, protocols::antibody::design::repack, protocols::loops::select_loop_residues(), setup_packer_task(), core::pose::Pose::size(), tf_, and core::pose::Pose::update_residue_neighbors().

Referenced by apply().

◆ repulsive_ramp()

void protocols::antibody_legacy::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

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] input pose 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:

Author: Aroop 07/13/2010

References core::pose::add_variant_type_to_pose_residue(), antibody_in_, benchmark_, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::scoring::fa_rep, protocols::antibody_legacy::Antibody::Fv, core::scoring::get_score_function_legacy(), protocols::loops::Loops::num_loop(), core::scoring::overlap_chainbreak, core::scoring::PRE_TALARIS_2013_STANDARD_WTS, protocols::loops::remove_cutpoint_variants(), protocols::loops::select_loop_residues(), core::pose::Pose::size(), snugfit_MC_min(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply().

◆ set_default()

void protocols::antibody_legacy::AntibodyModeler::set_default ( )

References benchmark_, camelid_, camelid_constraints_, graft_h1_, graft_h2_, graft_h3_, graft_l1_, graft_l2_, graft_l3_, model_h3_, native_present_, snugfit_, and protocols::TR().

Referenced by AntibodyModeler().

◆ set_snugdock_foldtree()

void protocols::antibody_legacy::AntibodyModeler::set_snugdock_foldtree ( core::pose::Pose & pose_in )

References core::pose::Pose::fold_tree(), and protocols::TR().

◆ setup_packer_task()

void protocols::antibody_legacy::AntibodyModeler::setup_packer_task ( core::pose::Pose & pose_in )

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

Referenced by relax_cdrs(), snugfit_MC_min(), and snugfit_mcm_protocol().

◆ setup_simple_fold_tree()

void protocols::antibody_legacy::AntibodyModeler::setup_simple_fold_tree	(	core::Size	jumppoint1,
		core::Size	cutpoint,
		core::Size	jumppoint2,
		core::Size	nres,
		core::pose::Pose &	pose_in
	)

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::pose::Pose::fold_tree(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), and protocols::TR().

Referenced by all_cdr_VL_VH_fold_tree(), and read_and_store_fragments().

◆ snugfit_MC_min()

void protocols::antibody_legacy::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
	)