Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::simple_moves::PeriodicBoxMover Class Reference

#include <PeriodicBoxMover.hh>

Inheritance diagram for protocols::simple_moves::PeriodicBoxMover:
Inheritance graph

Public Member Functions

 PeriodicBoxMover ()
void apply (Pose &pose) override
 Main Method. More...
void setup_pose (Pose &pose, core::Real &, core::Size &)
void change_volume_move (Pose &pose, core::Size, bool &)
void perturb_molecule_move (Pose &pose, core::Size, bool &)
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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::conformation::ResidueOP make_vrt (core::Vector O, core::Vector X, core::Vector Y)
void report_thermodynamics (Pose &pose, core::Size lattice_jump)
void recenter_pose (Pose &pose, core::Real const lattice, core::Real const new_lattice) const
void dump_ASU (Pose &pose, core::Size &lattice_jump, std::string filename)
void add_thermodynamic_data_to_silent (core::io::silent::SilentStructOP ss) const
void check_virial_pressure (Pose &pose, core::Real L) const
void setup_LJcorrection (core::pose::Pose const &pose)
 correction to energy that accounts for missing vdw interaction from cut-off to infinity More...

Private Attributes

core::scoring::ScoreFunctionOP sf_
core::Real nmol_side_
core::Real initial_density_
core::Real origin_
core::Real temp_
core::Real vol_step_
core::Real trans_step_
core::Real rot_step_
core::Real tor_step_
core::Size resize_vol_every_
core::Real probability_rigid_
core::Size nsteps_equilibrate_
core::Size nsteps_sim_
core::Size istart_
core::Size dump_every_
core::Size report_every_
core::Size report_thermodynamics_
std::string rg_atom1_
std::string rg_atom2_
std::string report_silent_
std::string report_scorefile_
ThermodynamicData thermodynamic_data_
core::Real ljcorrection_factor_
bool correct_LJtruncation_
core::Real P0_
core::Size central_resno_
std::string central_molecule_pdb_

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...

Constructor & Destructor Documentation

◆ PeriodicBoxMover()

protocols::simple_moves::PeriodicBoxMover::PeriodicBoxMover ( )

Member Function Documentation

◆ add_thermodynamic_data_to_silent()

void protocols::simple_moves::PeriodicBoxMover::add_thermodynamic_data_to_silent ( core::io::silent::SilentStructOP  ss) const

◆ apply()

void protocols::simple_moves::PeriodicBoxMover::apply ( Pose )

◆ change_volume_move()

void protocols::simple_moves::PeriodicBoxMover::change_volume_move ( Pose pose,
core::Size  lattice_jump,
bool &  accept 

◆ check_virial_pressure()

void protocols::simple_moves::PeriodicBoxMover::check_virial_pressure ( Pose pose,
core::Real  L 
) const

◆ clone()

protocols::moves::MoverOP protocols::simple_moves::PeriodicBoxMover::clone ( ) const

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.

◆ dump_ASU()

void protocols::simple_moves::PeriodicBoxMover::dump_ASU ( Pose pose,
core::Size lattice_jump,
std::string  filename 

◆ fresh_instance()

protocols::moves::MoverOP protocols::simple_moves::PeriodicBoxMover::fresh_instance ( ) const

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.

◆ get_name()

std::string protocols::simple_moves::PeriodicBoxMover::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

◆ make_vrt()

core::conformation::ResidueOP protocols::simple_moves::PeriodicBoxMover::make_vrt ( core::Vector  O,
core::Vector  X,
core::Vector  Y 

◆ mover_name()

std::string protocols::simple_moves::PeriodicBoxMover::mover_name ( )

◆ parse_my_tag()

void protocols::simple_moves::PeriodicBoxMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

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 central_molecule_pdb_, correct_LJtruncation_, dump_every_, initial_density_, istart_, nmol_side_, nsteps_equilibrate_, nsteps_sim_, P0_, core::scoring::parse_score_function(), probability_rigid_, report_every_, report_scorefile_, report_silent_, report_thermodynamics_, resize_vol_every_, rg_atom1_, rg_atom2_, rot_step_, sf_, temp_, tor_step_, trans_step_, and vol_step_.

◆ perturb_molecule_move()

void protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move ( Pose pose,
core::Size  lattice_jump,
bool &  accept 

◆ provide_xml_schema()

void protocols::simple_moves::PeriodicBoxMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ recenter_pose()

void protocols::simple_moves::PeriodicBoxMover::recenter_pose ( Pose pose,
core::Real const  lattice,
core::Real const  new_lattice 
) const

◆ report_thermodynamics()

void protocols::simple_moves::PeriodicBoxMover::report_thermodynamics ( Pose pose,
core::Size  lattice_jump 

◆ setup_LJcorrection()

void protocols::simple_moves::PeriodicBoxMover::setup_LJcorrection ( core::pose::Pose const &  pose)

◆ setup_pose()

void protocols::simple_moves::PeriodicBoxMover::setup_pose ( Pose pose,
core::Real mweight,
core::Size lattice_jump 

References core::io::CrystInfo::A(), core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::symmetry::SymmetryInfo::add_bb_clone(), core::conformation::symmetry::SymmetryInfo::add_chi_clone(), core::conformation::symmetry::SymmetryInfo::add_jump_clone(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::apply_transform_Rx_plus_v(), core::conformation::Residue::atom_type(), core::io::CrystInfo::B(), core::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::io::CrystInfo::C(), core::conformation::membrane::center, central_molecule_pdb_, central_resno_, protocols::membrane::com(), core::pose::Pose::dump_pdb(), core::chemical::AtomType::element(), core::pose::Pose::fold_tree(), initial_density_, core::pose::Pose::insert_residue_by_jump(), core::pose::Pose::jump(), core::pose::symmetry::make_symmetric_pose(), make_vrt(), core::conformation::Residue::natoms(), nmol_side_, core::pose::nres_protein(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::num_jump(), core::conformation::symmetry::SymmetryInfo::num_virtuals(), core::chemical::element::O, origin_, core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), core::pose::Pose::residue(), core::conformation::symmetry::SymmetryInfo::set_dofs(), core::conformation::symmetry::SymmetryInfo::set_flat_score_multiply(), core::pose::Pose::set_jump(), core::conformation::symmetry::SymmetryInfo::set_jump_name(), core::conformation::symmetry::SymmetryInfo::set_nres_subunit(), core::conformation::symmetry::SymmetryInfo::set_score_multiply(), core::conformation::symmetry::SymmetryInfo::set_use_symmetry(), core::conformation::Residue::set_xyz(), core::pose::Pose::size(), core::id::to_string(), protocols::simple_moves::TR(), core::conformation::symmetry::SymmetryInfo::update_score_multiply_factor(), and core::conformation::Residue::xyz().

Referenced by apply().

Member Data Documentation

◆ central_molecule_pdb_

std::string protocols::simple_moves::PeriodicBoxMover::central_molecule_pdb_

◆ central_resno_

core::Size protocols::simple_moves::PeriodicBoxMover::central_resno_

◆ correct_LJtruncation_

bool protocols::simple_moves::PeriodicBoxMover::correct_LJtruncation_

◆ dump_every_

core::Size protocols::simple_moves::PeriodicBoxMover::dump_every_

◆ initial_density_

core::Real protocols::simple_moves::PeriodicBoxMover::initial_density_

◆ istart_

core::Size protocols::simple_moves::PeriodicBoxMover::istart_

◆ ljcorrection_factor_

core::Real protocols::simple_moves::PeriodicBoxMover::ljcorrection_factor_

◆ nmol_side_

core::Real protocols::simple_moves::PeriodicBoxMover::nmol_side_

◆ nsteps_equilibrate_

core::Size protocols::simple_moves::PeriodicBoxMover::nsteps_equilibrate_

◆ nsteps_sim_

core::Size protocols::simple_moves::PeriodicBoxMover::nsteps_sim_

◆ origin_

core::Real protocols::simple_moves::PeriodicBoxMover::origin_

◆ P0_

core::Real protocols::simple_moves::PeriodicBoxMover::P0_

◆ probability_rigid_

core::Real protocols::simple_moves::PeriodicBoxMover::probability_rigid_

◆ report_every_

core::Size protocols::simple_moves::PeriodicBoxMover::report_every_

◆ report_scorefile_

std::string protocols::simple_moves::PeriodicBoxMover::report_scorefile_

◆ report_silent_

std::string protocols::simple_moves::PeriodicBoxMover::report_silent_

◆ report_thermodynamics_

core::Size protocols::simple_moves::PeriodicBoxMover::report_thermodynamics_

Referenced by apply(), and parse_my_tag().

◆ resize_vol_every_

core::Size protocols::simple_moves::PeriodicBoxMover::resize_vol_every_

◆ rg_atom1_

std::string protocols::simple_moves::PeriodicBoxMover::rg_atom1_

◆ rg_atom2_

std::string protocols::simple_moves::PeriodicBoxMover::rg_atom2_

◆ rot_step_

core::Real protocols::simple_moves::PeriodicBoxMover::rot_step_

◆ sf_

core::scoring::ScoreFunctionOP protocols::simple_moves::PeriodicBoxMover::sf_

◆ temp_

core::Real protocols::simple_moves::PeriodicBoxMover::temp_

◆ thermodynamic_data_

ThermodynamicData protocols::simple_moves::PeriodicBoxMover::thermodynamic_data_

◆ tor_step_

core::Real protocols::simple_moves::PeriodicBoxMover::tor_step_

◆ trans_step_

core::Real protocols::simple_moves::PeriodicBoxMover::trans_step_

◆ vol_step_

core::Real protocols::simple_moves::PeriodicBoxMover::vol_step_

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