Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::docking::membrane::MPFindInterfaceMover Class Reference

#include <MPFindInterfaceMover.hh>

Inheritance diagram for protocols::docking::membrane::MPFindInterfaceMover:
Inheritance graph

Public Member Functions

 MPFindInterfaceMover ()
 Constructors ///. More...
 MPFindInterfaceMover (MPFindInterfaceMover const &src)
 Copy Constructor. More...
 ~MPFindInterfaceMover () override
 Destructor. More...
protocols::moves::MoverOP clone () const override
 Rosetta Scripts Methods ///. More...
protocols::moves::MoverOP fresh_instance () const override
 Create a Fresh Instance of this Mover. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Pase Rosetta Scripts Options for this Mover. More...
std::string get_name () const override
 Mover Methods ///. More...
void apply (core::pose::Pose &pose) override
 Sampling protein-protein interface in the membrane. 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...

Private Member Functions

void register_options ()
 Setup Methods ///. More...
void init_from_cmd ()
 Initialize Mover options from the commandline. More...
void finalize_setup (core::pose::Pose &pose)
 Finalize setup. More...
void superimpose_upstream_partner (core::pose::Pose &pose)
 Superimpose upstream partner. More...
core::Real calculate_interface_SASA (core::pose::Pose &pose, protocols::scoring::Interface &interface)
 Calculate interface SASA. More...
std::pair< core::Real, core::Realfractions_small_residues (core::pose::Pose &pose, protocols::scoring::Interface &interface)
 Calculate fraction of small residues in interface details See Andrew Bordner, 2009, BMC Bioinformatics. More...

Private Attributes

bool mode_lowres_
 Centroid mode? More...
Pose native_
 Native pose. More...
std::string partners_
 docking partners More...
int jump_
 jumps More...
utility::vector1< int > jumps_
core::conformation::membrane::SpanningTopologyOP topo_
 SpanningTopology objects. More...
core::conformation::membrane::SpanningTopologyOP topo_up_
core::conformation::membrane::SpanningTopologyOP topo_down_
core::scoring::ScoreFunctionOP sfxn_lowres_
 scorefunction More...
core::scoring::ScoreFunctionOP sfxn_hires_
core::scoring::ScoreFunctionOP sfxn_pack_
bool flips_
 allow flips in the membrane? More...
bool flexible_bb_
 Run quick relax before and after protocol. More...
bool flexible_sc_
 Sidechain repacking. 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...

Constructor & Destructor Documentation

◆ MPFindInterfaceMover() [1/2]

protocols::docking::membrane::MPFindInterfaceMover::MPFindInterfaceMover ( )

Constructors ///.

Default Constructor

Takes topology from MembraneInfo, gets the jump from docking partners

◆ MPFindInterfaceMover() [2/2]

protocols::docking::membrane::MPFindInterfaceMover::MPFindInterfaceMover ( MPFindInterfaceMover const &  src)

Copy Constructor.

◆ ~MPFindInterfaceMover()

protocols::docking::membrane::MPFindInterfaceMover::~MPFindInterfaceMover ( )


Member Function Documentation

◆ apply()

void protocols::docking::membrane::MPFindInterfaceMover::apply ( core::pose::Pose pose)

Sampling protein-protein interface in the membrane.

Implements protocols::moves::Mover.

References protocols::jd2::add_string_real_pair_to_current_job(), core::scoring::all_atom_rmsd_nosuper(), protocols::docking::calc_Fnat(), protocols::docking::calc_Fnonnat(), protocols::docking::calc_intf_score(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Lrmsd(), protocols::docking::calc_P1rmsd(), protocols::docking::calc_P2rmsd(), core::scoring::sc::ShapeComplementarityCalculator::CalcSc(), protocols::scoring::Interface::calculate(), protocols::membrane::geometry::EmbeddingDef::center(), core::pose::chain_end_res(), core::pose::Pose::conformation(), core::pose::Pose::dump_pdb(), core::pose::Pose::dump_scored_pdb(), core::sequence::end, core::pose::Pose::energies(), core::scoring::fa_rep, finalize_setup(), flexible_bb_, flexible_sc_, flips_, core::pose::Pose::fold_tree(), fractions_small_residues(), core::pose::get_chain_id_from_chain(), core::scoring::sc::MolecularSurfaceCalculator::Init(), init_from_cmd(), core::pose::Pose::is_centroid(), protocols::membrane::is_membrane_fixed(), jump_, jumps_, protocols::mean_field::max(), protocols::membrane::membrane_axis(), core::pose::Pose::membrane_info(), mode_lowres_, protocols::docking::move_apart(), protocols::docking::move_together(), native_, protocols::membrane::geometry::EmbeddingDef::normal(), core::pose::nres_protein(), core::pack::pack_rotamers(), partners_, register_options(), protocols::antibody::design::relax, protocols::antibody::design::repack, core::pose::Pose::residue(), sfxn_hires_, sfxn_lowres_, sfxn_pack_, core::kinematics::FoldTree::show(), core::pose::Pose::size(), protocols::loops::start, superimpose_upstream_partner(), core::scoring::Energies::total_energies(), core::scoring::Energies::total_energy(), protocols::docking::TR(), protocols::membrane::update_partner_embeddings(), and protocols::kinmatch::xyz().

◆ calculate_interface_SASA()

core::Real protocols::docking::membrane::MPFindInterfaceMover::calculate_interface_SASA ( core::pose::Pose pose,
protocols::scoring::Interface interface 

Calculate interface SASA.

Calculate SASA buried in the interface

References core::scoring::sasa::SasaCalc::get_residue_sasa(), protocols::scoring::Interface::is_interface(), and core::pose::nres_protein().

◆ clone()

protocols::moves::MoverOP protocols::docking::membrane::MPFindInterfaceMover::clone ( ) const

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

◆ finalize_setup()

void protocols::docking::membrane::MPFindInterfaceMover::finalize_setup ( core::pose::Pose pose)

◆ fractions_small_residues()

std::pair< core::Real, core::Real > protocols::docking::membrane::MPFindInterfaceMover::fractions_small_residues ( core::pose::Pose pose,
protocols::scoring::Interface interface 

Calculate fraction of small residues in interface details See Andrew Bordner, 2009, BMC Bioinformatics.

References protocols::scoring::Interface::is_interface(), core::conformation::Residue::name3(), core::pose::nres_protein(), core::pose::Pose::residue(), and protocols::docking::TR().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::docking::membrane::MPFindInterfaceMover::fresh_instance ( ) const

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::docking::membrane::MPFindInterfaceMover::get_name ( ) const

Mover Methods ///.

Get the name of this Mover (MPFindInterfaceMover)

Implements protocols::moves::Mover.

◆ init_from_cmd()

void protocols::docking::membrane::MPFindInterfaceMover::init_from_cmd ( )

Initialize Mover options from the commandline.

Initialize Mover options from the comandline.

References flexible_bb_, flexible_sc_, flips_, mode_lowres_, native_, partners_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::docking::TR().

Referenced by apply().

◆ parse_my_tag()

void protocols::docking::membrane::MPFindInterfaceMover::parse_my_tag ( utility::tag::TagCOP  tag,

Pase Rosetta Scripts Options for this Mover.

Parse Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

References partners_.

◆ register_options()

void protocols::docking::membrane::MPFindInterfaceMover::register_options ( )

Setup Methods ///.

Register Options with JD2

Referenced by apply().

◆ superimpose_upstream_partner()

void protocols::docking::membrane::MPFindInterfaceMover::superimpose_upstream_partner ( core::pose::Pose pose)

Superimpose upstream partner.

Superimpose upstream partner of the pose with the native

References core::sequence::end, native_, partners_, core::pose::Pose::pdb_info(), core::pose::Pose::size(), protocols::sparta::split(), protocols::loops::start, core::id::to_string(), and protocols::docking::TR().

Referenced by apply().

Member Data Documentation

◆ flexible_bb_

bool protocols::docking::membrane::MPFindInterfaceMover::flexible_bb_

Run quick relax before and after protocol.

Kind of like flexible backbone and sidechain docking

Referenced by apply(), and init_from_cmd().

◆ flexible_sc_

bool protocols::docking::membrane::MPFindInterfaceMover::flexible_sc_

Sidechain repacking.

Referenced by apply(), and init_from_cmd().

◆ flips_

bool protocols::docking::membrane::MPFindInterfaceMover::flips_

allow flips in the membrane?

Referenced by apply(), and init_from_cmd().

◆ jump_

int protocols::docking::membrane::MPFindInterfaceMover::jump_


Referenced by apply(), and finalize_setup().

◆ jumps_

utility::vector1< int > protocols::docking::membrane::MPFindInterfaceMover::jumps_

Referenced by apply(), and finalize_setup().

◆ mode_lowres_

bool protocols::docking::membrane::MPFindInterfaceMover::mode_lowres_

Centroid mode?

Referenced by apply(), and init_from_cmd().

◆ native_

Pose protocols::docking::membrane::MPFindInterfaceMover::native_

◆ partners_

std::string protocols::docking::membrane::MPFindInterfaceMover::partners_

◆ sfxn_hires_

core::scoring::ScoreFunctionOP protocols::docking::membrane::MPFindInterfaceMover::sfxn_hires_

Referenced by apply(), and finalize_setup().

◆ sfxn_lowres_

core::scoring::ScoreFunctionOP protocols::docking::membrane::MPFindInterfaceMover::sfxn_lowres_


Referenced by apply(), and finalize_setup().

◆ sfxn_pack_

core::scoring::ScoreFunctionOP protocols::docking::membrane::MPFindInterfaceMover::sfxn_pack_

Referenced by apply(), and finalize_setup().

◆ topo_

core::conformation::membrane::SpanningTopologyOP protocols::docking::membrane::MPFindInterfaceMover::topo_

SpanningTopology objects.

Referenced by finalize_setup().

◆ topo_down_

core::conformation::membrane::SpanningTopologyOP protocols::docking::membrane::MPFindInterfaceMover::topo_down_

Referenced by finalize_setup().

◆ topo_up_

core::conformation::membrane::SpanningTopologyOP protocols::docking::membrane::MPFindInterfaceMover::topo_up_

Referenced by finalize_setup().

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