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protocols::antibody_legacy::AntibodyModeler Class Reference

#include <AntibodyModeler.hh>

Inheritance diagram for protocols::antibody_legacy::AntibodyModeler:
Inheritance graph
[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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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::Realscore_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

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

Member Function Documentation

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]par Global Read:
Global Write:
Remarks
References:
Author
Aroop 07/13/2010

References core::pose::Pose::fold_tree(), protocols::mean_field::max(), protocols::mean_field::min(), core::pose::Pose::pdb_info(), protocols::make_rot_lib::PEPTIDE, core::pose::residue_center_of_mass(), setup_simple_fold_tree(), and core::pose::Pose::size().

Referenced by apply().

void protocols::antibody_legacy::AntibodyModeler::apply ( core::pose::Pose )
overridevirtual
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.

void protocols::antibody_legacy::AntibodyModeler::display_constraint_residues ( )
std::string protocols::antibody_legacy::AntibodyModeler::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

Real protocols::antibody_legacy::AntibodyModeler::global_loop_rmsd ( const core::pose::Pose pose_in,
const core::pose::Pose native_pose,
std::string  cdr_type 
)
void protocols::antibody_legacy::AntibodyModeler::init_from_options ( )
void protocols::antibody_legacy::AntibodyModeler::init_on_new_input ( )
virtual
void protocols::antibody_legacy::AntibodyModeler::read_and_store_fragments ( )
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]par Global Read:
Global Write:
Remarks
References:
Author
Aroop 02/15/2010

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().

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]inputpose 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().

void protocols::antibody_legacy::AntibodyModeler::set_default ( )
void protocols::antibody_legacy::AntibodyModeler::set_snugdock_foldtree ( core::pose::Pose pose_in)
void protocols::antibody_legacy::AntibodyModeler::setup_packer_task ( core::pose::Pose pose_in)
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 
)
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 
)
void protocols::antibody_legacy::AntibodyModeler::snugfit_mcm_protocol ( core::pose::Pose pose_in,
loops::Loops  loops_in 
)

Member Data Documentation

Antibody protocols::antibody_legacy::AntibodyModeler::antibody_in_
private
bool protocols::antibody_legacy::AntibodyModeler::benchmark_
private
bool protocols::antibody_legacy::AntibodyModeler::camelid_
private
bool protocols::antibody_legacy::AntibodyModeler::camelid_constraints_
private
core::Real protocols::antibody_legacy::AntibodyModeler::cst_weight_
private

Referenced by apply(), and init_from_options().

bool protocols::antibody_legacy::AntibodyModeler::graft_h1_
private
bool protocols::antibody_legacy::AntibodyModeler::graft_h2_
private
bool protocols::antibody_legacy::AntibodyModeler::graft_h3_
private
bool protocols::antibody_legacy::AntibodyModeler::graft_l1_
private
bool protocols::antibody_legacy::AntibodyModeler::graft_l2_
private
bool protocols::antibody_legacy::AntibodyModeler::graft_l3_
private
utility::vector1< core::fragment::FragData > protocols::antibody_legacy::AntibodyModeler::H3_base_library_
private

Referenced by apply(), and init_on_new_input().

bool protocols::antibody_legacy::AntibodyModeler::init_for_input_yet_
private

Referenced by apply(), and init_on_new_input().

core::pack::task::TaskFactoryOP protocols::antibody_legacy::AntibodyModeler::init_task_factory_
private

Referenced by setup_packer_task().

bool protocols::antibody_legacy::AntibodyModeler::model_h3_
private
std::string protocols::antibody_legacy::AntibodyModeler::native_filename_
private
core::pose::Pose protocols::antibody_legacy::AntibodyModeler::native_pose_
private

Referenced by apply(), and init_on_new_input().

bool protocols::antibody_legacy::AntibodyModeler::native_present_
private
utility::vector1< core::fragment::FragSetOP > protocols::antibody_legacy::AntibodyModeler::offset_frags_
private

Referenced by apply(), and read_and_store_fragments().

std::map< std::string, core::Real > protocols::antibody_legacy::AntibodyModeler::score_map_
private

Referenced by apply().

bool protocols::antibody_legacy::AntibodyModeler::snugfit_
private
core::pose::Pose protocols::antibody_legacy::AntibodyModeler::start_pose_
private

Referenced by apply(), and init_on_new_input().

core::pack::task::TaskFactoryOP protocols::antibody_legacy::AntibodyModeler::tf_
private

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