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

#include <CyclizationMover.hh>

Inheritance diagram for protocols::simple_moves::CyclizationMover:
Inheritance graph

Public Member Functions

 CyclizationMover (core::Size chain_to_cyclize, bool add_constraints, bool minimize, core::Size minimization_rebuild_rounds)
 Default constructor. More...
 CyclizationMover (core::Size chain_to_cyclize, bool add_constraints, bool minimize, core::Size minimization_rebuild_rounds, core::scoring::ScoreFunctionOP score_fxn, core::kinematics::MoveMapOP move_map)
 ~CyclizationMover () override=default
void apply (core::pose::Pose &pose) override
 Sets up inter residue cyclic connections and potentially adds constraints, and minimizes the pose. 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 MoverOP clone () const
 Return a clone of the Mover object. 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
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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...

Private Member Functions

void setup_connections (core::pose::Pose &pose)
 Modifes terminal ResidueTypes to cyclized variants and then uses connformation::detect_bonds() to create a residue connection. More...
void setup_constraints (core::pose::Pose &pose)
 Creates constraints to maintain the proper conformation and adds it to the pose. More...
void setup_scorefunction ()
 Setup the score function with the appropriate weights on the constraints. If user has provided a score function the and set the weights to a specific value, that value is kept. If weight is not set, prints a warning. More...
void setup_minimizer (core::pose::Pose &pose)
void minimize_rebuild (core::pose::Pose &pose)
 Minimize the pose using the score function, and constraints we setup. More...

Private Attributes

core::Size chain_to_cyclize_
core::Size nterm_rsd_num_
core::Size cterm_rsd_num_
bool add_constraints_
bool minimize_
core::Size minimization_rebuild_rounds_
core::scoring::ScoreFunctionOP score_fxn_
core::kinematics::MoveMapOP move_map_
core::scoring::mm::MMTorsionLibrary const & mm_torsion_library_
 MMTorsionLibrary for looking up torsion parameters. 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 std::list< std::string > Strings
- 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

This mover performas a variaty of functions related to cyclizing a chain in a pose.

Constructor & Destructor Documentation

◆ CyclizationMover() [1/2]

protocols::simple_moves::CyclizationMover::CyclizationMover ( core::Size  chain_to_cyclize,
bool  add_constraints = true,
bool  minimize = true,
core::Size  minimization_rebuild_rounds = 3 

Default constructor.

◆ CyclizationMover() [2/2]

protocols::simple_moves::CyclizationMover::CyclizationMover ( core::Size  chain_to_cyclize,
bool  add_constraints,
bool  minimize,
core::Size  minimization_rebuild_rounds,
core::scoring::ScoreFunctionOP  score_fxn,
core::kinematics::MoveMapOP  move_map 

◆ ~CyclizationMover()

protocols::simple_moves::CyclizationMover::~CyclizationMover ( )

Member Function Documentation

◆ apply()

void protocols::simple_moves::CyclizationMover::apply ( core::pose::Pose pose)

◆ get_name()

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

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

Implements protocols::moves::Mover.

◆ minimize_rebuild()

void protocols::simple_moves::CyclizationMover::minimize_rebuild ( core::pose::Pose pose)

Minimize the pose using the score function, and constraints we setup.

References core::pose::Pose::conformation(), cterm_rsd_num_, move_map_, nterm_rsd_num_, core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), and score_fxn_.

Referenced by apply().

◆ setup_connections()

void protocols::simple_moves::CyclizationMover::setup_connections ( core::pose::Pose pose)

◆ setup_constraints()

void protocols::simple_moves::CyclizationMover::setup_constraints ( core::pose::Pose pose)

Creates constraints to maintain the proper conformation and adds it to the pose.

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::atom_name(), core::chemical::ICoorAtomID::atomno(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection(), core::chemical::ResidueType::atoms_within_two_bonds_of_a_residue_connection(), core::conformation::Residue::connections_to_residue(), cterm_rsd_num_, core::chemical::AtomICoor::d(), core::chemical::FULL_ATOM_t, core::chemical::ResidueConnection::icoor(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueTypeBase::is_protein(), core::scoring::mm::MMTorsionLibrary::lookup(), core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::mm_name(), mm_torsion_library_, core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name3(), nterm_rsd_num_, core::scoring::pair, core::chemical::AtomICoor::phi(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::pose::Pose::residue_type_set_for_pose(), core::conformation::Residue::seqpos(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::stub_atom3(), core::chemical::AtomICoor::theta(), protocols::simple_moves::TR(), core::conformation::Residue::type(), core::chemical::ResidueType::upper_connect(), and core::chemical::ResidueType::upper_connect_id().

Referenced by apply().

◆ setup_minimizer()

void protocols::simple_moves::CyclizationMover::setup_minimizer ( core::pose::Pose pose)

◆ setup_scorefunction()

void protocols::simple_moves::CyclizationMover::setup_scorefunction ( )

Setup the score function with the appropriate weights on the constraints. If user has provided a score function the and set the weights to a specific value, that value is kept. If weight is not set, prints a warning.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::dihedral_constraint, core::scoring::get_score_function(), score_fxn_, and protocols::simple_moves::TR().

Referenced by apply().

Member Data Documentation

◆ add_constraints_

bool protocols::simple_moves::CyclizationMover::add_constraints_

Referenced by apply().

◆ chain_to_cyclize_

core::Size protocols::simple_moves::CyclizationMover::chain_to_cyclize_

Referenced by apply(), and setup_minimizer().

◆ cterm_rsd_num_

core::Size protocols::simple_moves::CyclizationMover::cterm_rsd_num_

◆ minimization_rebuild_rounds_

core::Size protocols::simple_moves::CyclizationMover::minimization_rebuild_rounds_

Referenced by apply().

◆ minimize_

bool protocols::simple_moves::CyclizationMover::minimize_

Referenced by apply().

◆ mm_torsion_library_

core::scoring::mm::MMTorsionLibrary const& protocols::simple_moves::CyclizationMover::mm_torsion_library_

MMTorsionLibrary for looking up torsion parameters.

Referenced by setup_constraints().

◆ move_map_

core::kinematics::MoveMapOP protocols::simple_moves::CyclizationMover::move_map_

◆ nterm_rsd_num_

core::Size protocols::simple_moves::CyclizationMover::nterm_rsd_num_

◆ score_fxn_

core::scoring::ScoreFunctionOP protocols::simple_moves::CyclizationMover::score_fxn_

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