Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::simple_moves::ConstrainToIdealMover Class Reference

#include <ConstrainToIdealMover.hh>

Public Member Functions

 ConstrainToIdealMover ()
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
 ConstrainToIdealMover (ConstrainToIdealMover const &rhs)
 
ConstrainToIdealMoveroperator= (ConstrainToIdealMover const &rhs)
 
virtual ~ConstrainToIdealMover ()
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
virtual moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
void set_movemap (core::kinematics::MoveMapOP movemap)
 supply a MoveMap to be further modified by this mover; otherwise it will modify a blank one More...
 
core::kinematics::MoveMapOP get_movemap () const
 get the MoveMap last created during apply() More...
 
void set_AllowInsert (protocols::toolbox::AllowInsertOP allow_insert)
 setter for AllowInsert; makes a shallow copy More...
 
protocols::toolbox::AllowInsertOP get_AllowInsert () const
 getter for AllowInsert More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
void set_type (std::string const &setting)
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_type () const
 
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...
 
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 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Member Functions

void vary_bond_geometry (core::pose::Pose &pose, core::pose::Pose const &pose_reference)
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
virtual void create_pose_reference (core::pose::Pose const &pose, core::pose::Pose &pose_reference)
 this function generates a "reference pose" for the input pose that has the same chemistry (as best as possible), but has ideal angles and bond lengths. These are then used to generate the constraints later. Virtual in case you want to make the reference in a different fashion. More...
 
virtual bool i_want_this_atom_to_move (core::pose::Pose const &pose, core::id::AtomID const &atom_id)
 maps to other version of function; should this type of atom be moved during idealization? More...
 
virtual bool i_want_this_atom_to_move (core::conformation::Residue const &residue2, core::Size const &k)
 returns whether or not this atom should move during idealiation categorically; mostly boils down to "don't move the sidechains". Virtual in case you want to deny using a different metric. More...
 
bool check_if_really_connected (core::pose::Pose const &pose, core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2)
 
bool check_in_bonded_list (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &bonded_atom_list)
 
bool check_in_bond_angle_list (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::id::AtomID const &atom_id3, utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &bond_angle_list)
 
void add_bond_angle_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::id::AtomID const &atom_id3, utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &bond_angle_list, core::pose::Pose const &pose, core::pose::Pose const &pose_reference, core::scoring::constraints::ConstraintSetOP &cst_set)
 
void add_bond_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &bonded_atom_list, core::pose::Pose const &pose, core::pose::Pose const &pose_reference, core::scoring::constraints::ConstraintSetOP &cst_set)
 

Private Attributes

protocols::toolbox::AllowInsertOP allow_insert_
 sort of like a MoveMap? Allowed to maintain use w/Rhiju's RNA code. More...
 
core::kinematics::MoveMapOP mm_
 MoveMap used to allow bond and angle torsions. More...
 
bool supplied_movemap_
 does the mm_ variable contain a movemap filled by apply(), or a movemap supplied to be modified? Necessary to know if a self-generated movemap needs to be tossed out at the beginning of apply() More...
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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...
 

Detailed Description

Idealization is generally performed by adding constraints to the Pose that keep bond lengths and angles within the appropriate ranges; then freeing those DOFs and performing minimization or sampling. This protocols::moves::Mover creates bond and angle constraints compatible with idealization; it does not modify the input Pose other than by adding constraints. If your pose is already ideal, this is likely to unidealize it. Also, it will add a LOT of degrees of freedom to your minimization, which may lead to significant slowdowns!

Constructor & Destructor Documentation

protocols::simple_moves::ConstrainToIdealMover::ConstrainToIdealMover ( )

parse XML (specifically in the context of the parser/scripting scheme)

Referenced by clone(), and fresh_instance().

protocols::simple_moves::ConstrainToIdealMover::ConstrainToIdealMover ( ConstrainToIdealMover const &  rhs)
protocols::simple_moves::ConstrainToIdealMover::~ConstrainToIdealMover ( )
virtual

Member Function Documentation

void protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint ( core::id::AtomID const &  atom_id1,
core::id::AtomID const &  atom_id2,
core::id::AtomID const &  atom_id3,
utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &  bond_angle_list,
core::pose::Pose const &  pose,
core::pose::Pose const &  pose_reference,
core::scoring::constraints::ConstraintSetOP cst_set 
)
private
void protocols::simple_moves::ConstrainToIdealMover::add_bond_constraint ( core::id::AtomID const &  atom_id1,
core::id::AtomID const &  atom_id2,
utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &  bonded_atom_list,
core::pose::Pose const &  pose,
core::pose::Pose const &  pose_reference,
core::scoring::constraints::ConstraintSetOP cst_set 
)
private
void protocols::simple_moves::ConstrainToIdealMover::apply ( core::pose::Pose pose)
virtual

This code will modify your input pose by adding constraints which will trend bond lengths and angles towards ideal. If you input a movemap via set_movemap, that movemap will be modified to free the same set of bond lengths and angles (needs some testing) and will be available from get_movemap.

Implements protocols::moves::Mover.

References allow_insert_, create_pose_reference(), mm_, supplied_movemap_, and vary_bond_geometry().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::apply(), and protocols::farna::RNA_Minimizer::setup_movemap().

bool protocols::simple_moves::ConstrainToIdealMover::check_if_really_connected ( core::pose::Pose const &  pose,
core::id::AtomID const &  atom_id1,
core::id::AtomID const &  atom_id2 
)
private
bool protocols::simple_moves::ConstrainToIdealMover::check_in_bond_angle_list ( core::id::AtomID const &  atom_id1,
core::id::AtomID const &  atom_id2,
core::id::AtomID const &  atom_id3,
utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &  bond_angle_list 
)
private
bool protocols::simple_moves::ConstrainToIdealMover::check_in_bonded_list ( core::id::AtomID const &  atom_id1,
core::id::AtomID const &  atom_id2,
utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &  bonded_atom_list 
)
private

Referenced by add_bond_constraint().

protocols::moves::MoverOP protocols::simple_moves::ConstrainToIdealMover::clone ( ) const
virtual

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.

References ConstrainToIdealMover().

void protocols::simple_moves::ConstrainToIdealMover::create_pose_reference ( core::pose::Pose const &  pose,
core::pose::Pose pose_reference 
)
privatevirtual

this function generates a "reference pose" for the input pose that has the same chemistry (as best as possible), but has ideal angles and bond lengths. These are then used to generate the constraints later. Virtual in case you want to make the reference in a different fashion.

References protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker(), core::chemical::ChemicalManager::get_instance(), make_pose_from_sequence(), core::chemical::ChemicalManager::residue_type_set(), and core::pose::Pose::sequence().

Referenced by apply().

protocols::moves::MoverOP protocols::simple_moves::ConstrainToIdealMover::fresh_instance ( ) const
virtual

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.

References ConstrainToIdealMover().

protocols::toolbox::AllowInsertOP protocols::simple_moves::ConstrainToIdealMover::get_AllowInsert ( ) const

getter for AllowInsert

References allow_insert_.

Referenced by operator=().

core::kinematics::MoveMapOP protocols::simple_moves::ConstrainToIdealMover::get_movemap ( ) const

get the MoveMap last created during apply()

get the MoveMap last created during apply(); it has the bond and angles free for minimization

References mm_.

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::apply(), operator=(), and protocols::farna::RNA_Minimizer::setup_movemap().

std::string protocols::simple_moves::ConstrainToIdealMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

bool protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move ( core::pose::Pose const &  pose,
core::id::AtomID const &  atom_id 
)
privatevirtual

maps to other version of function; should this type of atom be moved during idealization?

References core::id::AtomID::atomno(), core::pose::Pose::residue(), residue, and core::id::AtomID::rsd().

Referenced by vary_bond_geometry().

bool protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move ( core::conformation::Residue const &  residue2,
core::Size const &  k 
)
privatevirtual

returns whether or not this atom should move during idealiation categorically; mostly boils down to "don't move the sidechains". Virtual in case you want to deny using a different metric.

References allow_insert_, core::chemical::rna::first_base_atom_index(), core::conformation::Residue::first_sidechain_atom(), utility::pointer::owning_ptr< T >::get(), core::conformation::Residue::is_virtual(), and core::conformation::Residue::seqpos().

ConstrainToIdealMover & protocols::simple_moves::ConstrainToIdealMover::operator= ( ConstrainToIdealMover const &  rhs)
void protocols::simple_moves::ConstrainToIdealMover::set_AllowInsert ( protocols::toolbox::AllowInsertOP  allow_insert)

setter for AllowInsert; makes a shallow copy

setter for AllowInsert; shallow copy

References allow_insert_.

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::apply(), and protocols::farna::RNA_Minimizer::setup_movemap().

void protocols::simple_moves::ConstrainToIdealMover::set_movemap ( core::kinematics::MoveMapOP  movemap)

supply a MoveMap to be further modified by this mover; otherwise it will modify a blank one

supply a MoveMap to be further modified by this mover; otherwise it will modify a blank one; notice it sets a boolean flag to mark the source of the movemap

References mm_, and supplied_movemap_.

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::apply(), and protocols::farna::RNA_Minimizer::setup_movemap().

void protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry ( core::pose::Pose pose,
core::pose::Pose const &  pose_reference 
)
private

Member Data Documentation

protocols::toolbox::AllowInsertOP protocols::simple_moves::ConstrainToIdealMover::allow_insert_
private

sort of like a MoveMap? Allowed to maintain use w/Rhiju's RNA code.

Referenced by apply(), get_AllowInsert(), i_want_this_atom_to_move(), operator=(), set_AllowInsert(), and vary_bond_geometry().

core::kinematics::MoveMapOP protocols::simple_moves::ConstrainToIdealMover::mm_
private

MoveMap used to allow bond and angle torsions.

Referenced by apply(), get_movemap(), operator=(), set_movemap(), and vary_bond_geometry().

bool protocols::simple_moves::ConstrainToIdealMover::supplied_movemap_
private

does the mm_ variable contain a movemap filled by apply(), or a movemap supplied to be modified? Necessary to know if a self-generated movemap needs to be tossed out at the beginning of apply()

Referenced by apply(), operator=(), and set_movemap().


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