#include <MPFindInterfaceMover.hh>
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 Strings & | info () |
| 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::Real > | 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. 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]
|
default |
Copy Constructor.
◆ ~MPFindInterfaceMover()
|
overridedefault |
Destructor.
Member Function Documentation
◆ apply()
|
overridevirtual |
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()
|
private |
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()
|
overridevirtual |
Rosetta Scripts Methods ///.
Create a Clone of this mover
Reimplemented from protocols::moves::Mover.
◆ finalize_setup()
|
private |
Finalize setup.
References protocols::membrane::create_membrane_docking_foldtree_from_partners(), core::scoring::ScoreFunctionFactory::create_score_function(), jump_, jumps_, core::pose::Pose::membrane_info(), native_, partners_, sfxn_hires_, sfxn_lowres_, sfxn_pack_, protocols::membrane::split_topology_by_jump_noshift(), topo_, topo_down_, topo_up_, and protocols::docking::TR().
Referenced by apply().
◆ fractions_small_residues()
|
private |
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()
|
overridevirtual |
Create a Fresh Instance of this Mover.
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
Mover Methods ///.
Get the name of this Mover (MPFindInterfaceMover)
Implements protocols::moves::Mover.
◆ init_from_cmd()
|
private |
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()
|
overridevirtual |
Pase Rosetta Scripts Options for this Mover.
Parse Rosetta Scripts Options for this Mover.
Reimplemented from protocols::moves::Mover.
References partners_.
◆ register_options()
|
private |
◆ superimpose_upstream_partner()
|
private |
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_
|
private |
Run quick relax before and after protocol.
Kind of like flexible backbone and sidechain docking
Referenced by apply(), and init_from_cmd().
◆ flexible_sc_
|
private |
Sidechain repacking.
Referenced by apply(), and init_from_cmd().
◆ flips_
|
private |
allow flips in the membrane?
Referenced by apply(), and init_from_cmd().
◆ jump_
|
private |
jumps
Referenced by apply(), and finalize_setup().
◆ jumps_
|
private |
Referenced by apply(), and finalize_setup().
◆ mode_lowres_
|
private |
Centroid mode?
Referenced by apply(), and init_from_cmd().
◆ native_
|
private |
Native pose.
Referenced by apply(), finalize_setup(), init_from_cmd(), and superimpose_upstream_partner().
◆ partners_
|
private |
docking partners
Referenced by apply(), finalize_setup(), init_from_cmd(), parse_my_tag(), and superimpose_upstream_partner().
◆ sfxn_hires_
|
private |
Referenced by apply(), and finalize_setup().
◆ sfxn_lowres_
|
private |
scorefunction
Referenced by apply(), and finalize_setup().
◆ sfxn_pack_
|
private |
Referenced by apply(), and finalize_setup().
◆ topo_
|
private |
SpanningTopology objects.
Referenced by finalize_setup().
◆ topo_down_
|
private |
Referenced by finalize_setup().
◆ topo_up_
|
private |
Referenced by finalize_setup().
The documentation for this class was generated from the following files:
- src/protocols/docking/membrane/MPFindInterfaceMover.hh
- src/protocols/docking/membrane/MPFindInterfaceMover.cc
