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protocols::features::InterfaceDdGMover Class Reference

Calculates ddG of binding. More...

#include <InterfaceDdGMover.hh>

Inheritance diagram for protocols::features::InterfaceDdGMover:
Inheritance graph
[legend]

Public Member Functions

 InterfaceDdGMover ()
 
 ~InterfaceDdGMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void const_pose_apply (core::pose::Pose const &pose)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML tag (to use this Mover in Rosetta Scripts) More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
void unbind (core::pose::Pose &pose) const
 "unbinds" a pose based on degrees of freedom previously defined More...
 
std::set< core::Sizeget_movable_jumps (core::pose::Pose const &pose) const
 
void add_chain_id (core::Size chain_id, core::pose::Pose const &pose)
 appends chain_id More...
 
void add_chain_id (core::Size chain_id)
 
void add_chain_name (std::string const &chain_name, core::pose::Pose const &pose)
 converts chain_name to a chain_id, and then appends More...
 
void add_chain_name (std::string const &chain_name)
 
void add_jump_id (core::Size jump, core::pose::Pose const &pose)
 gets chain_id from jump id, and then appends More...
 
void add_jump_id (core::Size jump)
 
void set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
 Sets the scorefunction. More...
 
void set_wt_pose (core::pose::Pose const &pose)
 Stores the wildtype pose. More...
 
void set_mut_pose (core::pose::Pose const &pose)
 Stores the mutant pose. More...
 
void set_wt_pose (core::pose::PoseOP pose)
 Stores the wildtype pose. More...
 
void set_mut_pose (core::pose::PoseOP pose)
 Stores the mutant pose. More...
 
void set_db_reporter (protocols::features::ReportToDBOP db_reporter)
 Clones db_reporter into all member variable database reporters, and sets batch names accordingly. More...
 
core::pose::PoseCOP get_unbound_wt_pose () const
 
core::pose::PoseCOP get_bound_wt_pose () const
 
core::pose::PoseCOP get_unbound_mut_pose () const
 
core::pose::PoseCOP get_bound_mut_pose () const
 
utility::vector1< std::pair
< std::string, core::Real > > 
get_all_scores () const
 
utility::vector1< std::tuple
< std::string, core::Size,
std::string > > 
mutation_list () const
 Determines which residues, if any, are different between bound_wt_pose_ and bound_mut_pose_. 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...
 
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_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...
 

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

core::Real compute ()
 Scores the cached poses, caches the scores. More...
 

Private Attributes

utility::vector1< core::Sizechain_ids_
 
utility::vector1< std::string > chain_names_
 
utility::vector1< core::Sizejump_ids_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Real translate_by_
 distance in angstroms to separate moledules More...
 
core::pose::PoseOP unbound_wt_pose_
 unbound wildtype pose state; stored for later use More...
 
core::pose::PoseOP bound_wt_pose_
 bound wildtype pose state; stored for later use More...
 
core::pose::PoseOP unbound_mut_pose_
 unbound mutant pose state; stored for later use More...
 
core::pose::PoseOP bound_mut_pose_
 bound mutant pose state; stored for later use More...
 
core::Real unbound_wt_score_
 
core::Real bound_wt_score_
 
core::Real unbound_mut_score_
 
core::Real bound_mut_score_
 
core::Real ddG_score_
 
bool apply_pose_is_mutant_
 Keeps track of whether the pose passed to the apply function will be considered to be the wildtype of mutant structure. More...
 
protocols::rosetta_scripts::SavePoseMoverOP wt_save_pose_mover_
 Used in Rosetta scripts context to save a reference pose of the wildtype pose state. More...
 
protocols::rosetta_scripts::SavePoseMoverOP mut_save_pose_mover_
 Used in Rosetta scripts context to save a reference pose of the mutant pose state. More...
 
protocols::features::ReportToDBOP bound_wt_db_reporter_
 
protocols::features::ReportToDBOP unbound_wt_db_reporter_
 
protocols::features::ReportToDBOP bound_mut_db_reporter_
 
protocols::features::ReportToDBOP unbound_mut_db_reporter_
 
bool report_to_db_
 

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

Calculates ddG of binding.

Constructor & Destructor Documentation

protocols::features::InterfaceDdGMover::InterfaceDdGMover ( )
protocols::features::InterfaceDdGMover::~InterfaceDdGMover ( )
overridedefault

Member Function Documentation

void protocols::features::InterfaceDdGMover::add_chain_id ( core::Size  chain_id,
core::pose::Pose const &  pose 
)

appends chain_id

appends chain_id to chain_ids_

takes pose in as an argument for input checking

References chain_ids_, core::pose::has_chain(), and core::id::to_string().

Referenced by parse_my_tag().

void protocols::features::InterfaceDdGMover::add_chain_id ( core::Size  chain_id)

References chain_ids_.

void protocols::features::InterfaceDdGMover::add_chain_name ( std::string const &  chain_name,
core::pose::Pose const &  pose 
)

converts chain_name to a chain_id, and then appends

converts chain_name to a chain_id and then appends

takes pose in as an argument for input checking

References chain_names_, and core::pose::has_chain().

Referenced by parse_my_tag().

void protocols::features::InterfaceDdGMover::add_chain_name ( std::string const &  chain_name)

References chain_names_.

void protocols::features::InterfaceDdGMover::add_jump_id ( core::Size  jump,
core::pose::Pose const &  pose 
)

gets chain_id from jump id, and then appends

converts jump to a chain_id and then appends

takes pose in as an argument for input checking

References jump_ids_, core::pose::Pose::num_jump(), and core::id::to_string().

Referenced by parse_my_tag().

void protocols::features::InterfaceDdGMover::add_jump_id ( core::Size  jump)

References jump_ids_.

void protocols::features::InterfaceDdGMover::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References const_pose_apply().

protocols::moves::MoverOP protocols::features::InterfaceDdGMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::Real protocols::features::InterfaceDdGMover::compute ( )
private
void protocols::features::InterfaceDdGMover::const_pose_apply ( core::pose::Pose const &  pose)
protocols::moves::MoverOP protocols::features::InterfaceDdGMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

utility::vector1< std::pair< std::string, core::Real > > protocols::features::InterfaceDdGMover::get_all_scores ( ) const
core::pose::PoseCOP protocols::features::InterfaceDdGMover::get_bound_mut_pose ( ) const

References bound_mut_pose_.

core::pose::PoseCOP protocols::features::InterfaceDdGMover::get_bound_wt_pose ( ) const

References bound_wt_pose_.

std::set< core::Size > protocols::features::InterfaceDdGMover::get_movable_jumps ( core::pose::Pose const &  pose) const
std::string protocols::features::InterfaceDdGMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References protocols::features::InterfaceDdGMoverCreator::mover_name().

core::pose::PoseCOP protocols::features::InterfaceDdGMover::get_unbound_mut_pose ( ) const

References unbound_mut_pose_.

core::pose::PoseCOP protocols::features::InterfaceDdGMover::get_unbound_wt_pose ( ) const

References unbound_wt_pose_.

std::string protocols::features::InterfaceDdGMover::mover_name ( )
static
utility::vector1< std::tuple< std::string, core::Size, std::string > > protocols::features::InterfaceDdGMover::mutation_list ( ) const

Determines which residues, if any, are different between bound_wt_pose_ and bound_mut_pose_.

References bound_mut_pose_, bound_wt_pose_, and protocols::features::TR().

Referenced by compute().

void protocols::features::InterfaceDdGMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::features::InterfaceDdGMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::features::InterfaceDdGMover::set_db_reporter ( protocols::features::ReportToDBOP  db_reporter)

Clones db_reporter into all member variable database reporters, and sets batch names accordingly.

References bound_mut_db_reporter_, bound_wt_db_reporter_, report_to_db_, unbound_mut_db_reporter_, and unbound_wt_db_reporter_.

Referenced by parse_my_tag().

void protocols::features::InterfaceDdGMover::set_mut_pose ( core::pose::Pose const &  pose)

Stores the mutant pose.

References bound_mut_pose_, core::pose::Pose::clone(), unbind(), and unbound_mut_pose_.

Referenced by compute(), and const_pose_apply().

void protocols::features::InterfaceDdGMover::set_mut_pose ( core::pose::PoseOP  pose)

Stores the mutant pose.

References bound_mut_pose_, unbind(), and unbound_mut_pose_.

void protocols::features::InterfaceDdGMover::set_scorefxn ( core::scoring::ScoreFunctionCOP  sfxn_in)

Sets the scorefunction.

References scorefxn_.

Referenced by parse_my_tag().

void protocols::features::InterfaceDdGMover::set_wt_pose ( core::pose::Pose const &  pose)

Stores the wildtype pose.

References bound_wt_pose_, core::pose::Pose::clone(), unbind(), and unbound_wt_pose_.

Referenced by compute(), and const_pose_apply().

void protocols::features::InterfaceDdGMover::set_wt_pose ( core::pose::PoseOP  pose)

Stores the wildtype pose.

References bound_wt_pose_, unbind(), and unbound_wt_pose_.

void protocols::features::InterfaceDdGMover::unbind ( core::pose::Pose pose) const

Member Data Documentation

bool protocols::features::InterfaceDdGMover::apply_pose_is_mutant_
private

Keeps track of whether the pose passed to the apply function will be considered to be the wildtype of mutant structure.

Referenced by const_pose_apply(), and parse_my_tag().

protocols::features::ReportToDBOP protocols::features::InterfaceDdGMover::bound_mut_db_reporter_
private
core::pose::PoseOP protocols::features::InterfaceDdGMover::bound_mut_pose_
private

bound mutant pose state; stored for later use

Referenced by compute(), const_pose_apply(), get_bound_mut_pose(), mutation_list(), and set_mut_pose().

core::Real protocols::features::InterfaceDdGMover::bound_mut_score_
private

Referenced by compute(), and get_all_scores().

protocols::features::ReportToDBOP protocols::features::InterfaceDdGMover::bound_wt_db_reporter_
private
core::pose::PoseOP protocols::features::InterfaceDdGMover::bound_wt_pose_
private

bound wildtype pose state; stored for later use

Referenced by compute(), const_pose_apply(), get_bound_wt_pose(), mutation_list(), and set_wt_pose().

core::Real protocols::features::InterfaceDdGMover::bound_wt_score_
private

Referenced by compute(), and get_all_scores().

utility::vector1<core::Size> protocols::features::InterfaceDdGMover::chain_ids_
private
utility::vector1<std::string> protocols::features::InterfaceDdGMover::chain_names_
private
core::Real protocols::features::InterfaceDdGMover::ddG_score_
private

Referenced by compute(), and get_all_scores().

utility::vector1<core::Size> protocols::features::InterfaceDdGMover::jump_ids_
private
protocols::rosetta_scripts::SavePoseMoverOP protocols::features::InterfaceDdGMover::mut_save_pose_mover_
private

Used in Rosetta scripts context to save a reference pose of the mutant pose state.

Referenced by compute(), and parse_my_tag().

bool protocols::features::InterfaceDdGMover::report_to_db_
private
core::scoring::ScoreFunctionOP protocols::features::InterfaceDdGMover::scorefxn_
private

Referenced by set_scorefxn().

core::Real protocols::features::InterfaceDdGMover::translate_by_
private

distance in angstroms to separate moledules

Referenced by unbind().

protocols::features::ReportToDBOP protocols::features::InterfaceDdGMover::unbound_mut_db_reporter_
private
core::pose::PoseOP protocols::features::InterfaceDdGMover::unbound_mut_pose_
private

unbound mutant pose state; stored for later use

Referenced by compute(), const_pose_apply(), get_unbound_mut_pose(), and set_mut_pose().

core::Real protocols::features::InterfaceDdGMover::unbound_mut_score_
private

Referenced by compute(), and get_all_scores().

protocols::features::ReportToDBOP protocols::features::InterfaceDdGMover::unbound_wt_db_reporter_
private
core::pose::PoseOP protocols::features::InterfaceDdGMover::unbound_wt_pose_
private

unbound wildtype pose state; stored for later use

Referenced by compute(), const_pose_apply(), get_unbound_wt_pose(), and set_wt_pose().

core::Real protocols::features::InterfaceDdGMover::unbound_wt_score_
private

Referenced by compute(), and get_all_scores().

protocols::rosetta_scripts::SavePoseMoverOP protocols::features::InterfaceDdGMover::wt_save_pose_mover_
private

Used in Rosetta scripts context to save a reference pose of the wildtype pose state.

Referenced by compute(), and parse_my_tag().


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