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protocols::antibody::constraints::ParatopeSiteConstraintMover Class Reference

Adds and removes ambiguous site constraints for the Antibody Paratope to antigen, defined for simplicity as the CDRs, however a set of paratope residues can be given to the class to use instead. More...

#include <ParatopeSiteConstraintMover.hh>

Inheritance diagram for protocols::antibody::constraints::ParatopeSiteConstraintMover:
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Public Member Functions

 ParatopeSiteConstraintMover ()
 
 ParatopeSiteConstraintMover (AntibodyInfoCOP ab_info)
 
 ~ParatopeSiteConstraintMover () override
 
 ParatopeSiteConstraintMover (ParatopeSiteConstraintMover const &src)
 
protocols::moves::MoverOP clone () const override
 Copy this object and return a pointer to the copy. More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void apply (core::pose::Pose &pose) override
 Add AmbiguousSiteConstraints to specified paratope residues, or each CDR set. Default is all of them. If there are already exits AmbiguousSiteConstraints from the antigen to the residue, add them. If they are missing, such as after a graft, add them. More...
 
void remove (core::pose::Pose &pose, bool reset_paratope_residues=false)
 Remove constraints from each paratope residue and antigen chain set. If reset_paratope_residues is true, then it will update the set of paratope residues it has. This is used after pose length changes such as CDR insertion or deletion. More...
 
void constrain_to_paratope_cdrs (utility::vector1< CDRNameEnum > const &paratope_cdrs)
 Optionally use only these CDRs as the paratope. Useful for constraining to Light or Heavy chain CDRs. More...
 
void constrain_to_paratope_cdrs (utility::vector1< bool > const &paratope_cdrs)
 
void constrain_to_paratope_residues (utility::vector1< bool > const &paratope_residues)
 Optionally constrain to a set of pre-determined paratope residues. More...
 
void constrain_to_antigen_chains (utility::vector1< std::string > const &antigen_chains)
 Optionally constrain to a set of antigen chains instead of all of them. More...
 
void set_constraint_func (core::scoring::func::FuncOP constraint_func)
 Optionally set the Func that will be used for the constraint. Default is the Flat_Harmonic at 0, 1, 5. More...
 
void set_interface_distance (core::Real interface_distance)
 Set the interface distance that will be only be used as the tolerance for the linear harmonic constraint if no constraint func is set. More...
 
void set_defaults ()
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provides citation info for the residue selector used by this mover, if that residue selector is unpublished and non-null. More...
 
- 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
 
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_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...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Member Functions

utility::vector1< boolparatope_residues_from_cdrs (core::pose::Pose const &pose)
 
core::scoring::constraints::SiteConstraintOP setup_constraints (core::pose::Pose const &pose, core::Size resnum, std::string chain)
 

Private Attributes

AntibodyInfoCOP ab_info_
 
utility::vector1< boolcdrs_to_apply_
 
core::select::residue_selector::ResidueSelectorOP paratope_residues_
 
utility::vector1< std::string > antigen_chains_
 
core::Real interface_distance_
 
core::scoring::func::FuncOP current_func_
 

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
 
- 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

Adds and removes ambiguous site constraints for the Antibody Paratope to antigen, defined for simplicity as the CDRs, however a set of paratope residues can be given to the class to use instead.

Constructor & Destructor Documentation

protocols::antibody::constraints::ParatopeSiteConstraintMover::ParatopeSiteConstraintMover ( )

References set_defaults().

protocols::antibody::constraints::ParatopeSiteConstraintMover::ParatopeSiteConstraintMover ( AntibodyInfoCOP  ab_info)

References ab_info_, and set_defaults().

protocols::antibody::constraints::ParatopeSiteConstraintMover::~ParatopeSiteConstraintMover ( )
overridedefault
protocols::antibody::constraints::ParatopeSiteConstraintMover::ParatopeSiteConstraintMover ( ParatopeSiteConstraintMover const &  src)

References ab_info_, and current_func_.

Member Function Documentation

void protocols::antibody::constraints::ParatopeSiteConstraintMover::apply ( core::pose::Pose pose)
overridevirtual

Add AmbiguousSiteConstraints to specified paratope residues, or each CDR set. Default is all of them. If there are already exits AmbiguousSiteConstraints from the antigen to the residue, add them. If they are missing, such as after a graft, add them.

Implements protocols::moves::Mover.

References ab_info_, core::pose::Pose::add_constraint(), antigen_chains_, cdrs_to_apply_, core::pose::Pose::constraint_set(), current_func_, protocols::moves::FAIL_BAD_INPUT, interface_distance_, protocols::antibody::l1, protocols::antibody::l2, protocols::antibody::l3, paratope_residues_, paratope_residues_from_cdrs(), protocols::moves::Mover::set_last_move_status(), setup_constraints(), core::pose::Pose::size(), and protocols::antibody::TR().

protocols::moves::MoverOP protocols::antibody::constraints::ParatopeSiteConstraintMover::clone ( ) const
overridevirtual

Copy this object and return a pointer to the copy.

Reimplemented from protocols::moves::Mover.

void protocols::antibody::constraints::ParatopeSiteConstraintMover::constrain_to_antigen_chains ( utility::vector1< std::string > const &  antigen_chains)

Optionally constrain to a set of antigen chains instead of all of them.

References antigen_chains_.

void protocols::antibody::constraints::ParatopeSiteConstraintMover::constrain_to_paratope_cdrs ( utility::vector1< CDRNameEnum > const &  paratope_cdrs)

Optionally use only these CDRs as the paratope. Useful for constraining to Light or Heavy chain CDRs.

References cdrs_to_apply_.

void protocols::antibody::constraints::ParatopeSiteConstraintMover::constrain_to_paratope_cdrs ( utility::vector1< bool > const &  paratope_cdrs)

References cdrs_to_apply_.

void protocols::antibody::constraints::ParatopeSiteConstraintMover::constrain_to_paratope_residues ( utility::vector1< bool > const &  paratope_residues)

Optionally constrain to a set of pre-determined paratope residues.

References paratope_residues_.

std::string protocols::antibody::constraints::ParatopeSiteConstraintMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::antibody::constraints::ParatopeSiteConstraintMover::mover_name ( )
static
bool protocols::antibody::constraints::ParatopeSiteConstraintMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns true.

Reimplemented from protocols::moves::Mover.

utility::vector1< bool > protocols::antibody::constraints::ParatopeSiteConstraintMover::paratope_residues_from_cdrs ( core::pose::Pose const &  pose)
private
void protocols::antibody::constraints::ParatopeSiteConstraintMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References antigen_chains_, cdrs_to_apply_, protocols::antibody::get_cdr_bool_from_tag(), interface_distance_, paratope_residues_, and protocols::antibody::TR().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::antibody::constraints::ParatopeSiteConstraintMover::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provides citation info for the residue selector used by this mover, if that residue selector is unpublished and non-null.

Reimplemented from protocols::moves::Mover.

References paratope_residues_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::antibody::constraints::ParatopeSiteConstraintMover::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

Reimplemented from protocols::moves::Mover.

References paratope_residues_.

void protocols::antibody::constraints::ParatopeSiteConstraintMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::antibody::constraints::ParatopeSiteConstraintMover::remove ( core::pose::Pose pose,
bool  reset_paratope_residues = false 
)

Remove constraints from each paratope residue and antigen chain set. If reset_paratope_residues is true, then it will update the set of paratope residues it has. This is used after pose length changes such as CDR insertion or deletion.

References ab_info_, antigen_chains_, paratope_residues_, paratope_residues_from_cdrs(), core::pose::Pose::remove_constraints(), setup_constraints(), and core::pose::Pose::size().

void protocols::antibody::constraints::ParatopeSiteConstraintMover::set_constraint_func ( core::scoring::func::FuncOP  constraint_func)

Optionally set the Func that will be used for the constraint. Default is the Flat_Harmonic at 0, 1, 5.

References current_func_.

void protocols::antibody::constraints::ParatopeSiteConstraintMover::set_defaults ( )
void protocols::antibody::constraints::ParatopeSiteConstraintMover::set_interface_distance ( core::Real  interface_distance)

Set the interface distance that will be only be used as the tolerance for the linear harmonic constraint if no constraint func is set.

References interface_distance_.

core::scoring::constraints::SiteConstraintOP protocols::antibody::constraints::ParatopeSiteConstraintMover::setup_constraints ( core::pose::Pose const &  pose,
core::Size  resnum,
std::string  chain 
)
private

References current_func_.

Referenced by apply(), and remove().

Member Data Documentation

AntibodyInfoCOP protocols::antibody::constraints::ParatopeSiteConstraintMover::ab_info_
private
utility::vector1<std::string> protocols::antibody::constraints::ParatopeSiteConstraintMover::antigen_chains_
private
utility::vector1<bool> protocols::antibody::constraints::ParatopeSiteConstraintMover::cdrs_to_apply_
private
core::scoring::func::FuncOP protocols::antibody::constraints::ParatopeSiteConstraintMover::current_func_
private
core::Real protocols::antibody::constraints::ParatopeSiteConstraintMover::interface_distance_
private
core::select::residue_selector::ResidueSelectorOP protocols::antibody::constraints::ParatopeSiteConstraintMover::paratope_residues_
private

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