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protocols::simple_ddg::ddG Class Reference

#include <ddG.hh>

Inheritance diagram for protocols::simple_ddg::ddG:
Inheritance graph
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Public Types

typedef core::Real Real
 
typedef core::scoring::ScoreType ScoreType
 
typedef core::pose::Pose Pose
 
- 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
 

Public Member Functions

 ddG ()
 
 ddG (core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const jump=1)
 
 ddG (core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const jump, utility::vector1< core::Size > const &chain_ids)
 
void apply (Pose &pose) override
 Main Method. More...
 
void clean_pose (Pose &pose_copy)
 removed water and virtual residues from pose to hopefully make its size match that of an input native More...
 
void compute_rmsd_with_super (Pose const &pose, Real &input_rmsd_super, Real &input_rmsd)
 compute the rmsd of a pose to an input native with superposition More...
 
virtual void calculate (Pose const &pose_in)
 compute the energy of the repacked complex in the bound and unbound states More...
 
virtual void report_ddG (std::ostream &out) const
 
virtual Real sum_bound () const
 
virtual Real sum_unbound () const
 
virtual Real sum_ddG () const
 
core::Size rb_jump () const
 
void rb_jump (core::Size j)
 
core::Size repeats () const
 
void repeats (core::Size repeats)
 
core::Real translate_by () const
 
void translate_by (core::Real translate_by)
 
utility::vector1< core::Sizechain_ids () const
 Get the hard-set chain ids. Note these are not necessarily the only chains to be moved. More...
 
std::set< core::Sizeget_movable_jumps (core::pose::Pose const &pose) const
 
 ~ddG () override
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
protocols::moves::MoverOP relax_mover () const
 
void relax_mover (protocols::moves::MoverOP m)
 
protocols::filters::FilterOP filter () const
 
void filter (protocols::filters::FilterOP f)
 
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 
core::pack::task::TaskFactoryOP task_factory () const
 
void use_custom_task (bool uct)
 
bool use_custom_task () const
 
void repack_unbound (bool rpu)
 
bool repack_unbound () const
 
void repack_bound (bool rpb)
 
bool repack_bound () const
 
void relax_bound (bool rlb)
 
bool relax_bound () const
 
void relax_unbound (bool const rlu)
 
bool relax_unbound () const
 
void compute_rmsd (bool const crms)
 
bool compute_rmsd () const
 
virtual void scorefxn (core::scoring::ScoreFunctionCOP scorefxn_in)
 
void dump_pdbs (bool dp)
 
bool dump_pdbs () const
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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
utility::tag::XMLSchemaComplexTypeGeneratorOP 
define_ddG_schema ()
 
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

bool unbind (Pose &pose) const
 Helper method to appropriately form unbound complex. Returns false if monomer. More...
 
void setup_task (Pose const &pose)
 
void duplicate_waters_across_jump (Pose &pose, core::Size jumpnum) const
 
void setup_solvated_task (Pose const &pose, bool bound)
 
void do_minimize (Pose &pose) const
 
void fill_energy_vector (Pose const &pose, std::map< ScoreType, Real > &energy_map)
 
void fill_per_residue_energy_vector (Pose const &pose, std::map< core::Size, Real > &energy_map)
 

Private Attributes

std::map< ScoreType, Realbound_energies_
 
std::map< ScoreType, Realunbound_energies_
 
std::map< core::Size, Realbound_per_residue_energies_
 
std::map< core::Size, Realunbound_per_residue_energies_
 
core::Size repeats_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Size rb_jump_
 
utility::vector1< core::Sizechain_ids_
 
utility::vector1< std::string > chain_names_
 
bool per_residue_ddg_
 
bool repack_unbound_
 
protocols::moves::MoverOP relax_mover_
 
protocols::filters::FilterOP filter_
 
core::pack::task::TaskFactoryOP task_factory_
 
core::pack::task::PackerTaskOP task_
 
bool use_custom_task_
 
bool repack_bound_
 
bool relax_bound_
 
bool relax_unbound_
 
bool solvate_
 
bool solvate_unbound_
 
bool solvate_rbmin_
 
bool min_water_jump_
 
core::scoring::methods::PBLifetimeCacheOP pb_cached_data_
 info carrier for poisson-boltzmann potential energy computation More...
 
bool pb_enabled_
 true when PB potential is part of scorefxn More...
 
core::Real translate_by_
 distance in A to separate moledules More...
 
core::pose::PoseOP native_
 
core::Size bound_HOH_
 
core::Size bound_HOH_V_
 
core::Size unbound_HOH_
 
core::Size unbound_HOH_V_
 
bool compute_rmsd_
 
core::Real bound_rmsd_
 
core::Real bound_rmsd_super_
 
bool dump_pdbs_
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_ddg::ddG::ddG ( )
protocols::simple_ddg::ddG::ddG ( core::scoring::ScoreFunctionCOP  scorefxn_in,
core::Size const  jump = 1 
)
protocols::simple_ddg::ddG::ddG ( core::scoring::ScoreFunctionCOP  scorefxn_in,
core::Size const  jump,
utility::vector1< core::Size > const &  chain_ids 
)
protocols::simple_ddg::ddG::~ddG ( )
overridedefault

Member Function Documentation

void protocols::simple_ddg::ddG::apply ( Pose )
overridevirtual
void protocols::simple_ddg::ddG::calculate ( pose::Pose const &  pose_original)
virtual

compute the energy of the repacked complex in the bound and unbound states

Parameters
pose_inThe base pose.
Returns
Nothing, but the base pose's cache be augmented with extra cached data if the scorefunction contains non-zero PB_elec term.

References protocols::simple_moves::DumpPdb::apply(), protocols::simple_moves::ExplicitWaterMover::apply(), core::scoring::automorphic_rmsd(), bound_energies_, bound_HOH_, bound_HOH_V_, bound_per_residue_energies_, bound_rmsd_, bound_rmsd_super_, compute_rmsd(), compute_rmsd_with_super(), core::pack::task::TaskFactory::create_packer_task(), protocols::jd2::current_output_name(), do_minimize(), dump_pdbs_, fill_energy_vector(), fill_per_residue_energy_vector(), get_movable_jumps(), protocols::moves::Mover::name(), native_, core::pack::pack_rotamers(), pb_cached_data_, pb_enabled_, core::import_pose::PDB_file, per_residue_ddg_, core::scoring::pointwater, core::import_pose::pose_from_file(), relax_bound(), relax_mover(), relax_unbound(), repack_bound(), repack_bound_, repack_unbound_, scorefxn_, protocols::simple_moves::ExplicitWaterMover::set_gen_fixed(), protocols::simple_moves::ExplicitWaterMover::set_mode(), protocols::simple_moves::ExplicitWaterMover::set_taskop(), core::pose::setPoseExtraScore(), setup_solvated_task(), setup_task(), solvate_, solvate_unbound_, task_, protocols::simple_ddg::TR(), unbind(), unbound_energies_, unbound_HOH_, unbound_HOH_V_, unbound_per_residue_energies_, and core::pose::Pose::update_residue_neighbors().

Referenced by apply(), protocols::simple_ddg::DdgFilter::compute(), and protocols::protein_interface_design::ddG_cycles().

utility::vector1<core::Size> protocols::simple_ddg::ddG::chain_ids ( ) const
inline

Get the hard-set chain ids. Note these are not necessarily the only chains to be moved.

References chain_ids_.

Referenced by ddG(), and get_movable_jumps().

void protocols::simple_ddg::ddG::clean_pose ( pose::Pose pose_copy)
protocols::moves::MoverOP protocols::simple_ddg::ddG::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::simple_ddg::ddG::compute_rmsd ( bool const  crms)
inline

References compute_rmsd_.

bool protocols::simple_ddg::ddG::compute_rmsd ( ) const
inline

References compute_rmsd_.

Referenced by apply(), and calculate().

void protocols::simple_ddg::ddG::compute_rmsd_with_super ( pose::Pose const &  pose,
core::Real input_rmsd_super,
core::Real input_rmsd 
)
utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::simple_ddg::ddG::define_ddG_schema ( )
static
void protocols::simple_ddg::ddG::do_minimize ( Pose pose) const
private
void protocols::simple_ddg::ddG::dump_pdbs ( bool  dp)
inline
bool protocols::simple_ddg::ddG::dump_pdbs ( ) const
inline

References dump_pdbs_.

void protocols::simple_ddg::ddG::duplicate_waters_across_jump ( Pose pose,
core::Size  jumpnum 
) const
private
void protocols::simple_ddg::ddG::fill_energy_vector ( pose::Pose const &  pose,
std::map< ScoreType, Real > &  energy_map 
)
private
void protocols::simple_ddg::ddG::fill_per_residue_energy_vector ( pose::Pose const &  pose,
std::map< core::Size, Real > &  energy_map 
)
private
protocols::filters::FilterOP protocols::simple_ddg::ddG::filter ( ) const
void protocols::simple_ddg::ddG::filter ( protocols::filters::FilterOP  f)

References filter_.

protocols::moves::MoverOP protocols::simple_ddg::ddG::fresh_instance ( ) const
inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

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

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::simple_ddg::ddG::mover_name ( )
static
void protocols::simple_ddg::ddG::parse_my_tag ( utility::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 chain_ids_, chain_names_, compute_rmsd_, dump_pdbs_, filter(), min_water_jump_, protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), core::scoring::PB_elec, pb_enabled_, per_residue_ddg_, rb_jump_, relax_bound_, relax_mover(), relax_unbound_, repack_bound_, repack_unbound_, repeats_, scorefxn_, solvate_, solvate_rbmin_, solvate_unbound_, task_factory(), protocols::simple_ddg::TR(), translate_by_, and use_custom_task().

void protocols::simple_ddg::ddG::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Size protocols::simple_ddg::ddG::rb_jump ( ) const
inline

References rb_jump_.

Referenced by apply().

void protocols::simple_ddg::ddG::rb_jump ( core::Size  j)
inline

References rb_jump_.

void protocols::simple_ddg::ddG::relax_bound ( bool  rlb)
inline
bool protocols::simple_ddg::ddG::relax_bound ( ) const
inline

References relax_bound_.

Referenced by calculate().

protocols::moves::MoverOP protocols::simple_ddg::ddG::relax_mover ( ) const
inline
void protocols::simple_ddg::ddG::relax_mover ( protocols::moves::MoverOP  m)
inline

References relax_mover_.

void protocols::simple_ddg::ddG::relax_unbound ( bool const  rlu)
inline
bool protocols::simple_ddg::ddG::relax_unbound ( ) const
inline

References relax_unbound_.

Referenced by calculate().

void protocols::simple_ddg::ddG::repack_bound ( bool  rpb)
inline
bool protocols::simple_ddg::ddG::repack_bound ( ) const
inline

References repack_bound_.

Referenced by calculate().

void protocols::simple_ddg::ddG::repack_unbound ( bool  rpu)
inline

References repack_unbound_.

bool protocols::simple_ddg::ddG::repack_unbound ( ) const
inline

References repack_unbound_.

core::Size protocols::simple_ddg::ddG::repeats ( ) const
inline

References repeats_.

void protocols::simple_ddg::ddG::repeats ( core::Size  repeats)
inline

References repeats(), and repeats_.

Referenced by repeats().

void protocols::simple_ddg::ddG::report_ddG ( std::ostream &  out) const
virtual
void protocols::simple_ddg::ddG::scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn_in)
virtual

References scorefxn_.

void protocols::simple_ddg::ddG::setup_solvated_task ( Pose const &  pose,
bool  bound 
)
private
void protocols::simple_ddg::ddG::setup_task ( pose::Pose const &  pose)
private
Real protocols::simple_ddg::ddG::sum_bound ( ) const
virtual

returns energy sum of bound pose

References bound_energies_.

Referenced by report_ddG().

Real protocols::simple_ddg::ddG::sum_ddG ( ) const
virtual
Real protocols::simple_ddg::ddG::sum_unbound ( ) const
virtual

returns energy sum of unbound pose

References unbound_energies_.

Referenced by report_ddG().

void protocols::simple_ddg::ddG::task_factory ( core::pack::task::TaskFactoryOP  task_factory)
inline
core::pack::task::TaskFactoryOP protocols::simple_ddg::ddG::task_factory ( ) const
inline

References task_factory_.

Referenced by parse_my_tag().

core::Real protocols::simple_ddg::ddG::translate_by ( ) const
inline
void protocols::simple_ddg::ddG::translate_by ( core::Real  translate_by)
inline

References translate_by(), and translate_by_.

Referenced by translate_by().

bool protocols::simple_ddg::ddG::unbind ( pose::Pose pose) const
private
void protocols::simple_ddg::ddG::use_custom_task ( bool  uct)
inline
bool protocols::simple_ddg::ddG::use_custom_task ( ) const
inline

References use_custom_task_.

Referenced by parse_my_tag(), and setup_task().

Member Data Documentation

std::map< ScoreType, Real > protocols::simple_ddg::ddG::bound_energies_
private
core::Size protocols::simple_ddg::ddG::bound_HOH_
private

Referenced by apply(), and calculate().

core::Size protocols::simple_ddg::ddG::bound_HOH_V_
private

Referenced by apply(), and calculate().

std::map< core::Size, Real > protocols::simple_ddg::ddG::bound_per_residue_energies_
private

Referenced by apply(), calculate(), and ddG().

core::Real protocols::simple_ddg::ddG::bound_rmsd_
private

Referenced by apply(), and calculate().

core::Real protocols::simple_ddg::ddG::bound_rmsd_super_
private

Referenced by apply(), and calculate().

utility::vector1<core::Size> protocols::simple_ddg::ddG::chain_ids_
private
utility::vector1<std::string> protocols::simple_ddg::ddG::chain_names_
private
bool protocols::simple_ddg::ddG::compute_rmsd_
private

Referenced by compute_rmsd(), and parse_my_tag().

bool protocols::simple_ddg::ddG::dump_pdbs_
private

Referenced by calculate(), dump_pdbs(), and parse_my_tag().

protocols::filters::FilterOP protocols::simple_ddg::ddG::filter_
private
bool protocols::simple_ddg::ddG::min_water_jump_
private

Referenced by do_minimize(), and parse_my_tag().

core::pose::PoseOP protocols::simple_ddg::ddG::native_
private
core::scoring::methods::PBLifetimeCacheOP protocols::simple_ddg::ddG::pb_cached_data_
private

info carrier for poisson-boltzmann potential energy computation

Referenced by apply(), and calculate().

bool protocols::simple_ddg::ddG::pb_enabled_
private

true when PB potential is part of scorefxn

Referenced by calculate(), ddG(), and parse_my_tag().

bool protocols::simple_ddg::ddG::per_residue_ddg_
private

Referenced by apply(), calculate(), and parse_my_tag().

core::Size protocols::simple_ddg::ddG::rb_jump_
private
bool protocols::simple_ddg::ddG::relax_bound_
private

Referenced by parse_my_tag(), and relax_bound().

protocols::moves::MoverOP protocols::simple_ddg::ddG::relax_mover_
private

Referenced by relax_mover().

bool protocols::simple_ddg::ddG::relax_unbound_
private

Referenced by parse_my_tag(), and relax_unbound().

bool protocols::simple_ddg::ddG::repack_bound_
private
bool protocols::simple_ddg::ddG::repack_unbound_
private
core::Size protocols::simple_ddg::ddG::repeats_
private

Referenced by apply(), parse_my_tag(), and repeats().

core::scoring::ScoreFunctionOP protocols::simple_ddg::ddG::scorefxn_
private
bool protocols::simple_ddg::ddG::solvate_
private

Referenced by apply(), calculate(), parse_my_tag(), and unbind().

bool protocols::simple_ddg::ddG::solvate_rbmin_
private

Referenced by do_minimize(), and parse_my_tag().

bool protocols::simple_ddg::ddG::solvate_unbound_
private

Referenced by calculate(), and parse_my_tag().

core::pack::task::PackerTaskOP protocols::simple_ddg::ddG::task_
private
core::pack::task::TaskFactoryOP protocols::simple_ddg::ddG::task_factory_
private

Referenced by setup_task(), and task_factory().

core::Real protocols::simple_ddg::ddG::translate_by_
private

distance in A to separate moledules

Referenced by parse_my_tag(), translate_by(), and unbind().

std::map< ScoreType, Real > protocols::simple_ddg::ddG::unbound_energies_
private
core::Size protocols::simple_ddg::ddG::unbound_HOH_
private

Referenced by apply(), and calculate().

core::Size protocols::simple_ddg::ddG::unbound_HOH_V_
private

Referenced by apply(), and calculate().

std::map< core::Size, Real > protocols::simple_ddg::ddG::unbound_per_residue_energies_
private

Referenced by apply(), calculate(), and ddG().

bool protocols::simple_ddg::ddG::use_custom_task_
private

Referenced by use_custom_task().


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