#include <AntibodyModeler.hh>

Inheritance diagram for protocols::antibody::AntibodyModeler:

Collaboration diagram for protocols::antibody::AntibodyModeler:

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. More...

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. 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	~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 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

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	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::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

Definition at line 42 of file AntibodyModeler.hh.

Constructor & Destructor Documentation

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

Definition at line 112 of file AntibodyModeler.cc.

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

Referenced by clone().

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

Definition at line 121 of file AntibodyModeler.cc.

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] @par Global Read:

Global Write:

Remarks

References:

Authors: Aroop 07/13/2010

Last Modified: 07/13/2010

Definition at line 583 of file AntibodyModeler.cc.

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), 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

Implements protocols::moves::Mover.

Definition at line 210 of file AntibodyModeler.cc.

References protocols::loops::add_single_cutpoint_variant(), protocols::antibody::Antibody::align_to_native(), protocols::antibody::Antibody::all_cdr_loops, all_cdr_VL_VH_fold_tree(), antibody_in_, core::scoring::atom_pair_constraint, benchmark_, camelid_, camelid_constraints_, protocols::antibody::Antibody::cdrh_, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), cst_weight_, core::pose::Pose::data(), display_constraint_residues(), protocols::antibody::Antibody::Fv, protocols::moves::Mover::get_native_pose(), 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_, protocols::jd2::ScoreMap::nonzero_energies(), 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::simple_one_loop_fold_tree(), snugfit_, snugfit_mcm_protocol(), and start_pose_.

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.

Definition at line 124 of file AntibodyModeler.cc.

References AntibodyModeler().

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

Definition at line 1050 of file AntibodyModeler.cc.

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

Definition at line 375 of file AntibodyModeler.cc.

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

Definition at line 1007 of file AntibodyModeler.cc.

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

Referenced by apply().

void protocols::antibody::AntibodyModeler::init_from_options ( )

Definition at line 145 of file AntibodyModeler.cc.

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().

void protocols::antibody::AntibodyModeler::init_on_new_input ( )

virtual

Definition at line 183 of file AntibodyModeler.cc.

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

Referenced by apply().

void protocols::antibody::AntibodyModeler::read_and_store_fragments ( )

Definition at line 380 of file AntibodyModeler.cc.

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

Referenced by init_on_new_input().

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] @par Global Read:

Global Write:

Remarks

References:

Authors: Aroop 02/15/2010

Last Modified: 02/15/2010

Definition at line 490 of file AntibodyModeler.cc.

References protocols::loops::add_cutpoint_variants(), protocols::antibody::Antibody::all_cdr_fold_tree(), protocols::antibody::Antibody::all_cdr_loops, antibody_in_, benchmark_, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::fold_tree(), protocols::antibody::Antibody::Fv, protocols::loops::Loops::num_loop(), core::scoring::overlap_chainbreak, protocols::loops::select_loop_residues(), setup_packer_task(), tf_, and core::pose::Pose::total_residue().

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] 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:

Authors: Aroop 07/13/2010

Last Modified: 07/13/2010

Definition at line 692 of file AntibodyModeler.cc.

References core::pose::add_variant_type_to_pose_residue(), protocols::loops::Loops::begin(), benchmark_, 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, protocols::loops::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 ( )

Definition at line 128 of file AntibodyModeler.cc.

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().

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

Definition at line 176 of file AntibodyModeler.cc.

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

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

Definition at line 967 of file AntibodyModeler.cc.

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

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

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
	)

Definition at line 436 of file AntibodyModeler.cc.

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

Referenced by all_cdr_VL_VH_fold_tree(), and read_and_store_fragments().

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
	)