Rosetta 3.4
Public Types | Public Member Functions
protocols::analysis::InterfaceAnalyzerMover Class Reference

#include <InterfaceAnalyzerMover.hh>

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List of all members.

Public Types

typedef std::set< core::Sizeone_group
typedef std::pair< one_group,
one_group
group_pair
typedef utility::vector1
< group_pair
group_set

Public Member Functions

 InterfaceAnalyzerMover (core::Size interface_jump=1, bool const tracer=false, core::scoring::ScoreFunctionCOP sf=NULL, bool compute_packstat=false, bool pack_input=false, bool pack_separated=false, bool use_jobname=true)
 InterfaceAnalyzerMover (std::set< int > fixed_chains, bool const tracer=false, core::scoring::ScoreFunctionCOP sf=NULL, bool compute_packstat=false, bool pack_input=false, bool pack_separated=false, bool use_jobname=true)
virtual ~InterfaceAnalyzerMover ()
virtual protocols::moves::MoverOP clone () const
 required in the context of the parser/scripting scheme
virtual protocols::moves::MoverOP fresh_instance () const
 required in the context of the parser/scripting scheme
virtual void parse_my_tag (utility::tag::TagPtr const, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
virtual void apply (core::pose::Pose &pose)
 apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects) although it may toss data into the DataCache or a Job object.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void set_pose_info (core::pose::Pose const &pose)
void use_tracer (bool const tracer)
virtual void make_multichain_interface_set (core::pose::Pose &Pose, std::set< int > &fixed_chains)
 funtions to make interface sets needed
virtual void make_interface_set (core::pose::Pose &pose)
virtual core::pose::Pose make_separated_pose (core::pose::Pose &pose)
 assigns the complexed and separated poses for the entire mover
virtual core::Size reorder_foldtree_find_jump (core::pose::Pose &pose, std::set< int > &fixed_chains)
 reorder the fold tree to allow multichain interfaces to be evaluated returns the jump number to use to define the interface
virtual void compute_separated_sasa (core::pose::Pose &complexed_pose, core::pose::Pose &separated_pose)
virtual void compute_interface_energy (core::pose::Pose &complexed_pose, core::pose::Pose &separated_pose)
virtual void compute_interface_packstat (core::pose::Pose &pose)
virtual void compute_interface_delta_hbond_unsat (core::pose::Pose &complexed_pose, core::pose::Pose &separated_pose)
virtual void score_separated_chains (core::pose::Pose &complexed_pose, core::pose::Pose &separated_pose)
virtual void report_data ()
void set_use_resfile (bool const use_resfile)
 setters for the various parameters used by the analyze
bool get_use_resfile () const
void set_use_centroid_dG (bool const use_centroid)
bool get_use_centroid_dG () const
void set_compute_packstat (bool const compute_packstat)
void set_pack_input (bool const pack_input)
void set_interface_jump (core::Size const interface_jump)
void set_tracer (bool const tracer)
void set_calcs_ready (bool const calcs_ready)
void set_use_jobname (bool const use_jobname)
void set_pack_separated (bool const pack_separated)
core::Real get_total_sasa ()
 getters for the various parameters used by the analyzer
core::Real get_interface_delta_sasa ()
core::Size get_num_interface_residues ()
core::Real get_complex_energy ()
core::Real get_per_residue_energy ()
core::Real get_separated_interface_energy ()
core::Real get_crossterm_interface_energy ()
core::Real get_separated_interface_energy_ratio ()
core::Real get_crossterm_interface_energy_ratio ()
core::Real get_interface_packstat ()
core::Size get_interface_delta_hbond_unsat ()
core::Real get_side1_score ()
core::Real get_side2_score ()
core::Size get_side1_nres ()
core::Size get_side2_nres ()
std::string get_pymol_sel_interface ()
std::string get_pymol_sel_hbond_unsat ()
std::string get_pymol_sel_packing ()
core::Real get_interface_ddG () const
bool get_multichain_constructor ()
std::set< intget_fixed_chains ()
std::set< core::Sizeget_interface_set ()
group_set get_chain_groups ()
bool get_pack_input ()
core::pack::task::PackerTaskOP get_packer_task ()
core::Real get_gly_interface_energy ()
 return the interface energy of an all glycine interface (like bb-bb energies)
core::Real get_centroid_dG ()
core::Real get_total_Hbond_E ()
 the exposure/possible ratio avg for hbonds in the interface

Member Typedef Documentation


Constructor & Destructor Documentation

protocols::analysis::InterfaceAnalyzerMover::InterfaceAnalyzerMover ( core::Size  interface_jump = 1,
bool const  tracer = false,
core::scoring::ScoreFunctionCOP  sf = NULL,
bool  compute_packstat = false,
bool  pack_input = false,
bool  pack_separated = false,
bool  use_jobname = true 
)

References protocols::moves::Mover::type().

Referenced by clone(), and fresh_instance().

protocols::analysis::InterfaceAnalyzerMover::InterfaceAnalyzerMover ( std::set< int fixed_chains,
bool const  tracer = false,
core::scoring::ScoreFunctionCOP  sf = NULL,
bool  compute_packstat = false,
bool  pack_input = false,
bool  pack_separated = false,
bool  use_jobname = true 
)
protocols::analysis::InterfaceAnalyzerMover::~InterfaceAnalyzerMover ( ) [virtual]

Member Function Documentation

void protocols::analysis::InterfaceAnalyzerMover::apply ( core::pose::Pose pose) [virtual]

apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects) although it may toss data into the DataCache or a Job object.

InterfaceAnalyzerMover computes various interface statistics and makes them available through getters

Implements protocols::moves::Mover.

References compute_interface_delta_hbond_unsat(), compute_interface_energy(), compute_interface_packstat(), compute_separated_sasa(), core::pose::Pose::conformation(), get_fixed_chains(), make_interface_set(), make_separated_pose(), core::conformation::Conformation::num_chains(), reorder_foldtree_find_jump(), report_data(), set_pose_info(), and protocols::TR().

protocols::moves::MoverOP protocols::analysis::InterfaceAnalyzerMover::clone ( ) const [virtual]

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

References InterfaceAnalyzerMover().

void protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat ( core::pose::Pose complexed_pose,
core::pose::Pose separated_pose 
) [virtual]

If a polar atom at the interface is also "buried unsat" in the monomer, we don't count this one

References core::sequence::end, make_interface_set(), core::pose::Pose::metric(), core::pose::Pose::residue_type(), and protocols::TR().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy ( core::pose::Pose complexed_pose,
core::pose::Pose separated_pose 
) [virtual]
void protocols::analysis::InterfaceAnalyzerMover::compute_interface_packstat ( core::pose::Pose pose) [virtual]

Averaged packstat of interface residues only

References core::scoring::packstat::compute_residue_packing_scores(), core::sequence::end, make_interface_set(), and protocols::TR().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::compute_separated_sasa ( core::pose::Pose complexed_pose,
core::pose::Pose separated_pose 
) [virtual]

computes the SASA by finding difference between complex and separated SASA also does the same thing for hydrophobic/polar SASA

References core::scoring::calc_per_res_hydrophobic_sasa(), core::pose::Pose::metric(), and core::pose::Pose::total_residue().

Referenced by apply().

protocols::moves::MoverOP protocols::analysis::InterfaceAnalyzerMover::fresh_instance ( ) const [virtual]

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

References InterfaceAnalyzerMover().

core::Real protocols::analysis::InterfaceAnalyzerMover::get_centroid_dG ( )
InterfaceAnalyzerMover::group_set protocols::analysis::InterfaceAnalyzerMover::get_chain_groups ( )
core::Real protocols::analysis::InterfaceAnalyzerMover::get_complex_energy ( )
core::Real protocols::analysis::InterfaceAnalyzerMover::get_crossterm_interface_energy ( )
core::Real protocols::analysis::InterfaceAnalyzerMover::get_crossterm_interface_energy_ratio ( )
std::set< int > protocols::analysis::InterfaceAnalyzerMover::get_fixed_chains ( )

Referenced by apply().

core::Real protocols::analysis::InterfaceAnalyzerMover::get_gly_interface_energy ( )

return the interface energy of an all glycine interface (like bb-bb energies)

core::Real protocols::analysis::InterfaceAnalyzerMover::get_interface_ddG ( ) const
core::Size protocols::analysis::InterfaceAnalyzerMover::get_interface_delta_hbond_unsat ( )
core::Real protocols::analysis::InterfaceAnalyzerMover::get_interface_delta_sasa ( )
core::Real protocols::analysis::InterfaceAnalyzerMover::get_interface_packstat ( )
std::set< core::Size > protocols::analysis::InterfaceAnalyzerMover::get_interface_set ( )
bool protocols::analysis::InterfaceAnalyzerMover::get_multichain_constructor ( )
std::string protocols::analysis::InterfaceAnalyzerMover::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

core::Size protocols::analysis::InterfaceAnalyzerMover::get_num_interface_residues ( )
bool protocols::analysis::InterfaceAnalyzerMover::get_pack_input ( )
core::pack::task::PackerTaskOP protocols::analysis::InterfaceAnalyzerMover::get_packer_task ( )
core::Real protocols::analysis::InterfaceAnalyzerMover::get_per_residue_energy ( )
std::string protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_hbond_unsat ( )
std::string protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_interface ( )
std::string protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_packing ( )
core::Real protocols::analysis::InterfaceAnalyzerMover::get_separated_interface_energy ( )
core::Real protocols::analysis::InterfaceAnalyzerMover::get_separated_interface_energy_ratio ( )
core::Size protocols::analysis::InterfaceAnalyzerMover::get_side1_nres ( ) [inline]
core::Real protocols::analysis::InterfaceAnalyzerMover::get_side1_score ( ) [inline]
core::Size protocols::analysis::InterfaceAnalyzerMover::get_side2_nres ( ) [inline]
core::Real protocols::analysis::InterfaceAnalyzerMover::get_side2_score ( ) [inline]
core::Real protocols::analysis::InterfaceAnalyzerMover::get_total_Hbond_E ( )

the exposure/possible ratio avg for hbonds in the interface

total hbond energy for pose

core::Real protocols::analysis::InterfaceAnalyzerMover::get_total_sasa ( )

getters for the various parameters used by the analyzer

getters

bool protocols::analysis::InterfaceAnalyzerMover::get_use_centroid_dG ( ) const
bool protocols::analysis::InterfaceAnalyzerMover::get_use_resfile ( ) const
void protocols::analysis::InterfaceAnalyzerMover::make_interface_set ( core::pose::Pose pose) [virtual]
void protocols::analysis::InterfaceAnalyzerMover::make_multichain_interface_set ( core::pose::Pose Pose,
std::set< int > &  fixed_chains 
) [virtual]

funtions to make interface sets needed

References core::pose::Pose::chain(), core::pose::Pose::metric(), and core::pose::Pose::total_residue().

Referenced by make_interface_set().

core::pose::Pose protocols::analysis::InterfaceAnalyzerMover::make_separated_pose ( core::pose::Pose pose) [virtual]

assigns the complexed and separated poses for the entire mover

makes the complexed and separated poses for the mover

References core::scoring::getScoreFunction(), protocols::TR(), and protocols::swa::translate().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap datamap,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
) [virtual]

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

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

Reimplemented from protocols::moves::Mover.

References protocols::rosetta_scripts::parse_score_function(), set_compute_packstat(), set_interface_jump(), set_pack_input(), set_pack_separated(), set_tracer(), set_use_jobname(), and set_use_resfile().

core::Size protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump ( core::pose::Pose pose,
std::set< int > &  fixed_chains 
) [virtual]

reorder the fold tree to allow multichain interfaces to be evaluated returns the jump number to use to define the interface

reorder the fold tree to allow multichain interfaces to be evaluated returns the new chain for the jump

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), and core::conformation::Conformation::num_chains().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::report_data ( ) [virtual]

reports all the cool stuff we calculate to tracer output OR puts it into the job object.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), and core::pack::interaction_graph::T().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::score_separated_chains ( core::pose::Pose complexed_pose,
core::pose::Pose separated_pose 
) [virtual]

actual function to separate the chains based on the chosen jump and score

Referenced by compute_interface_energy().

void protocols::analysis::InterfaceAnalyzerMover::set_calcs_ready ( bool const  calcs_ready)
void protocols::analysis::InterfaceAnalyzerMover::set_compute_packstat ( bool const  compute_packstat)

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_interface_jump ( core::Size const  interface_jump)

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_pack_input ( bool const  pack_input)

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_pack_separated ( bool const  pack_separated)

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_pose_info ( core::pose::Pose const &  pose)
void protocols::analysis::InterfaceAnalyzerMover::set_tracer ( bool const  tracer)
void protocols::analysis::InterfaceAnalyzerMover::set_use_centroid_dG ( bool const  use_centroid)
void protocols::analysis::InterfaceAnalyzerMover::set_use_jobname ( bool const  use_jobname)

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_use_resfile ( bool const  use_resfile)

setters for the various parameters used by the analyze

setters

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::use_tracer ( bool const  tracer) [inline]

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