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protocols::analysis::InterfaceAnalyzerMover Class Reference

#include <InterfaceAnalyzerMover.hh>

Inheritance diagram for protocols::analysis::InterfaceAnalyzerMover:
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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 Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 

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 More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 required in the context of the parser/scripting scheme More...
 
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. More...
 
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. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
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 More...
 
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 More...
 
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 More...
 
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 More...
 
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)
 setters for various computations - each of these are expensive, so you can turn them off if desired More...
 
void set_compute_interface_sc (bool const compute_interface_sc)
 
void set_compute_separated_sasa (bool const compute_separated_sasa)
 
void set_compute_interface_energy (bool const iface_en)
 
void set_calc_hbond_sasaE (bool const calc_hbond_sasaE)
 
void set_compute_interface_delta_hbond_unsat (bool const IDHU)
 
void set_pack_input (bool const pack_input)
 
void set_pack_separated (bool const pack_separated)
 
void set_interface_jump (core::Size const interface_jump)
 
void set_skip_reporting (bool const skip_reporting)
 
void set_tracer (bool const tracer)
 
void set_use_jobname (bool const use_jobname)
 
core::Real get_total_sasa ()
 getters for the various parameters used by the analyzer More...
 
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) More...
 
core::Real get_centroid_dG ()
 
core::Real get_total_Hbond_E ()
 the exposure/possible ratio avg for hbonds in the interface 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
 
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)
 
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
 this function informs 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
 this function informs 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
 

Private Member Functions

void register_calculators ()
 registers the posemetric calculators More...
 
void register_intergroup_calculator ()
 register calculator for multichain poses More...
 
void setup_task (core::pose::Pose &pose)
 sets up the packer task within the mover More...
 
void print_pymol_selection_of_interface_residues (core::pose::Pose const &pose, std::set< core::Size > const interface_set)
 
void print_pymol_selection_of_hbond_unsat (core::pose::Pose &pose, utility::vector1< core::id::AtomID > delta_unsat_hbond_atid_vector)
 
void print_pymol_selection_of_packing (core::pose::Pose const &pose, utility::vector1< core::Real > interface_pack_scores)
 
void calc_per_residue_energy (core::pose::Pose pose)
 calculate the average energy per residue in the interface More...
 
void mut_to_gly (core::pose::Pose complex_pose, core::pose::Pose separated_pose)
 mutate all residue in the interface to Gly and recalc the energy - not used right now More...
 
void calc_centroid_dG (core::pose::Pose complex_pose, core::pose::Pose separated_pose)
 report the dG of a centroid pose with score3 More...
 
void calc_hbond_sasaE (core::pose::Pose pose)
 fill in later More...
 
void compute_interface_sc (core::Size &interface_jump, core::pose::Pose const &complexed_pose)
 find the interface shape compementarity value between the chains More...
 

Private Attributes

core::Size interface_jump_
 jump to define which interface is interesting More...
 
std::set< intfixed_chains_
 
core::scoring::ScoreFunctionCOP sf_
 scorefunction More...
 
utility::file::FileName posename_
 
std::string posename_base_
 
core::Size chain1_
 
core::Size chain2_
 
std::string chain1_char_
 
std::string chain2_char_
 
std::set< core::Sizeupstream_chains_
 
std::set< core::Sizedownstream_chains_
 
bool tracer_
 output to tracer or PDB/silent file More...
 
bool calcs_ready_
 are calculators ready? More...
 
bool compute_packstat_
 bother with computing packstat More...
 
bool compute_interface_sc_
 bother with computing interface sc More...
 
bool compute_separated_sasa_
 skip this expensive calculation More...
 
bool compute_interface_energy_
 skip this expensive calculation More...
 
bool calc_hbond_sasaE_
 skip this expensive calculation More...
 
bool compute_interface_delta_hbond_unsat_
 skip this expensive calculation More...
 
bool skip_reporting_
 hush! be quiet! silence! More...
 
bool multichain_constructor_
 which constructor are we using More...
 
bool pack_input_
 pack the input pose More...
 
bool pack_separated_
 pack the separated poses default is false More...
 
bool use_jobname_
 just the jobname (true value) or the pose name (flase value) More...
 
bool use_resfile_
 use a resfile during the pack_input and pack_separated operations More...
 
bool use_centroid_
 skip the centroid_dG step, for incoming poses not centroid convertible More...
 
core::Real ddG_
 interface energy More...
 
core::Real total_sasa_
 
core::Real interface_delta_sasa_
 
core::Real interface_hsasa_
 
core::Real interface_polar_sasa_
 
core::Size n_interface_res_
 
core::Real per_residue_energy_
 
core::Real complex_energy_
 
core::Real separated_interface_energy_
 
core::Real crossterm_interface_energy_
 
core::Real separated_interface_energy_ratio_
 
core::Real crossterm_interface_energy_ratio_
 
core::Real interface_packstat_
 
core::Real gly_dG_
 Energy of a all Gly interface. More...
 
core::Real centroid_dG_
 centroid_dG of interface More...
 
core::Size delta_unsat_hbond_counter_
 number of unsat hbonds in complex More...
 
std::string pymol_sel_interface_
 pymol style selections More...
 
std::string pymol_sel_hbond_unsat_
 
std::string pymol_sel_packing_
 
core::Real side1_score_
 
core::Real side2_score_
 
core::Size nres_
 
core::Size side1_nres_
 
core::Size side2_nres_
 
core::Real total_hb_E_
 avg hbond exposure ratio More...
 
core::Real sc_value_
 shape complementarity values More...
 
std::set< core::Sizeinterface_set_
 set of residues at the interface in question More...
 
group_set chain_groups_
 group of residue ids of fixed chains and mobile chains (see typedef) More...
 
core::pack::task::PackerTaskOP task_
 packer task used to repack pulled apart chains More...
 
std::string Sasa_
 Sasa calculator name string. More...
 
std::string InterfaceNeighborDefinition_
 InterfaceNeighborDefinition calculator name string. More...
 
std::string InterfaceSasaDefinition_
 InterfaceSasaDefinition calculator name string. More...
 
std::string InterfaceDeltaEnergetics_
 InterfaceDeltaEnergetics calculator name string. More...
 
std::string NumberHBonds_
 NumberHBonds calculator name string. More...
 
std::string BuriedUnsatisfiedPolars_
 BuriedUnsatisfiedPolars calculator name string. More...
 
std::string InterGroupNeighborsCalculator_
 InterGroupNeighborsCalculator calculator name string. More...
 

Additional Inherited Members

- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...
 

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 
)
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
void protocols::analysis::InterfaceAnalyzerMover::calc_centroid_dG ( core::pose::Pose  complex_pose,
core::pose::Pose  separated_pose 
)
private
void protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE ( core::pose::Pose  pose)
private
void protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_energy ( core::pose::Pose  pose)
private
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
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
void protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc ( core::Size interface_jump,
core::pose::Pose const &  complexed_pose 
)
private
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(), interface_delta_sasa_, interface_hsasa_, interface_polar_sasa_, core::pose::Pose::metric(), Sasa_, core::pose::Pose::total_residue(), and total_sasa_.

Referenced by apply(), and set_compute_separated_sasa().

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 ( )

References centroid_dG_.

InterfaceAnalyzerMover::group_set protocols::analysis::InterfaceAnalyzerMover::get_chain_groups ( )

References chain_groups_.

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

References 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 ( )

References 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)

References gly_dG_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_interface_ddG ( ) const

References ddG_.

core::Size protocols::analysis::InterfaceAnalyzerMover::get_interface_delta_hbond_unsat ( )
core::Real protocols::analysis::InterfaceAnalyzerMover::get_interface_delta_sasa ( )

References interface_delta_sasa_.

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

References interface_packstat_.

std::set< core::Size > protocols::analysis::InterfaceAnalyzerMover::get_interface_set ( )

References 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 ( )

References n_interface_res_.

bool protocols::analysis::InterfaceAnalyzerMover::get_pack_input ( )

References pack_input_.

core::pack::task::PackerTaskOP protocols::analysis::InterfaceAnalyzerMover::get_packer_task ( )

References task_.

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

References per_residue_energy_.

std::string protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_hbond_unsat ( )
std::string protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_interface ( )

References pymol_sel_interface_.

std::string protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_packing ( )

References 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

References side1_nres_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_side1_score ( )
inline

References side1_score_.

core::Size protocols::analysis::InterfaceAnalyzerMover::get_side2_nres ( )
inline

References side2_nres_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_side2_score ( )
inline

References side2_score_.

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

the exposure/possible ratio avg for hbonds in the interface

total hbond energy for pose

References total_hb_E_.

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

getters for the various parameters used by the analyzer

getters

References total_sasa_.

bool protocols::analysis::InterfaceAnalyzerMover::get_use_centroid_dG ( ) const

References use_centroid_.

bool protocols::analysis::InterfaceAnalyzerMover::get_use_resfile ( ) const

References use_resfile_.

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
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(), interface_jump_, sf_, protocols::TR(), and protocols::swa::translate().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::mut_to_gly ( core::pose::Pose  complex_pose,
core::pose::Pose  separated_pose 
)
private

mutate all residue in the interface to Gly and recalc the energy - not used right now

Mutate all residues to GlY rescore complex energy and separated energy

References core::chemical::aa_from_oneletter_code(), core::pack::task::TaskFactory::create_packer_task(), core::sequence::end, gly_dG_, interface_set_, core::chemical::num_canonical_aas, sf_, core::pose::Pose::total_residue(), and protocols::TR().

void protocols::analysis::InterfaceAnalyzerMover::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap datamap,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &  pose 
)
virtual
void protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat ( core::pose::Pose pose,
utility::vector1< core::id::AtomID delta_unsat_hbond_atid_vector 
)
private

This function reports a few things: a pymol sytle selection of the unstat atoms and reports to the tracer or job what these atoms are. The app InterfaceAnalyzer gets the multi-line string to write a file or print the selection. Unsat hbonds to be shown as Spheres

References core::conformation::Residue::atom_name(), protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), core::pose::Pose::pdb_info(), posename_base_, pymol_sel_hbond_unsat_, core::pose::Pose::residue(), core::pack::interaction_graph::T(), tracer_, TRhbonds(), and protocols::analysis::which_ostream().

Referenced by compute_interface_delta_hbond_unsat().

void protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_interface_residues ( core::pose::Pose const &  pose,
std::set< core::Size > const  interface_set 
)
private

prints tracer output of pymol selction of interface residues, also builds a pymol selection that can be used from a file.

References compute_packstat_, protocols::nonlocal::current_job(), core::sequence::end, protocols::jd2::JobDistributor::get_instance(), core::pose::Pose::pdb_info(), posename_base_, pymol_sel_interface_, tracer_, TRinterface(), and protocols::analysis::which_ostream().

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_packing ( core::pose::Pose const &  pose,
utility::vector1< core::Real interface_pack_scores 
)
private

This function doesn't do the printing itself. The app InterfaceAnalyzer gets the multi-line string to write a file or print the selection

From best packing to worse packing, colors go as Blue, Purple, Pink, Red

References core::pose::Pose::pdb_info(), posename_base_, pymol_sel_packing_, and core::pose::Pose::total_residue().

Referenced by compute_interface_packstat().

void protocols::analysis::InterfaceAnalyzerMover::register_calculators ( )
private

registers the posemetric calculators

Only want to register the calculators once, thus the 'if' statement in apply

References BuriedUnsatisfiedPolars_, chain1_, chain2_, interface_jump_, InterfaceDeltaEnergetics_, InterfaceNeighborDefinition_, InterfaceSasaDefinition_, NumberHBonds_, and Sasa_.

Referenced by apply().

void protocols::analysis::InterfaceAnalyzerMover::register_intergroup_calculator ( )
private

register calculator for multichain poses

References chain_groups_, InterGroupNeighborsCalculator_, and posename_base_.

Referenced by make_multichain_interface_set().

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
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

References complex_energy_, ddG_, pack_input_, pack_separated_, separated_interface_energy_, sf_, and task_.

Referenced by compute_interface_energy().

void protocols::analysis::InterfaceAnalyzerMover::set_calc_hbond_sasaE ( bool const  calc_hbond_sasaE)
inline
void protocols::analysis::InterfaceAnalyzerMover::set_compute_interface_delta_hbond_unsat ( bool const  IDHU)
inline
void protocols::analysis::InterfaceAnalyzerMover::set_compute_interface_energy ( bool const  iface_en)
inline
void protocols::analysis::InterfaceAnalyzerMover::set_compute_interface_sc ( bool const  compute_interface_sc)
inline
void protocols::analysis::InterfaceAnalyzerMover::set_compute_packstat ( bool const  compute_packstat)

setters for various computations - each of these are expensive, so you can turn them off if desired

References compute_packstat_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_compute_separated_sasa ( bool const  compute_separated_sasa)
inline
void protocols::analysis::InterfaceAnalyzerMover::set_interface_jump ( core::Size const  interface_jump)

References interface_jump_.

Referenced by parse_my_tag().

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

References pack_input_.

Referenced by parse_my_tag().

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

References pack_separated_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_pose_info ( core::pose::Pose const &  pose)
void protocols::analysis::InterfaceAnalyzerMover::set_skip_reporting ( bool const  skip_reporting)
inline

References skip_reporting_.

void protocols::analysis::InterfaceAnalyzerMover::set_tracer ( bool const  tracer)

References protocols::frag_picker::tracer(), and tracer_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_use_centroid_dG ( bool const  use_centroid)

References use_centroid_.

void protocols::analysis::InterfaceAnalyzerMover::set_use_jobname ( bool const  use_jobname)

References 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

References use_resfile_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::setup_task ( core::pose::Pose pose)
private

sets up the packer task within the mover

sets up the packer task for the interface

References InterfaceNeighborDefinition_, InterGroupNeighborsCalculator_, multichain_constructor_, task_, and use_resfile_.

Referenced by apply().

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

Member Data Documentation

std::string protocols::analysis::InterfaceAnalyzerMover::BuriedUnsatisfiedPolars_
private

BuriedUnsatisfiedPolars calculator name string.

Referenced by compute_interface_delta_hbond_unsat(), and register_calculators().

bool protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE_
private

skip this expensive calculation

Referenced by apply(), and set_calc_hbond_sasaE().

bool protocols::analysis::InterfaceAnalyzerMover::calcs_ready_
private

are calculators ready?

Referenced by apply().

core::Real protocols::analysis::InterfaceAnalyzerMover::centroid_dG_
private

centroid_dG of interface

Referenced by calc_centroid_dG(), get_centroid_dG(), and report_data().

core::Size protocols::analysis::InterfaceAnalyzerMover::chain1_
private
std::string protocols::analysis::InterfaceAnalyzerMover::chain1_char_
private

Referenced by set_pose_info().

core::Size protocols::analysis::InterfaceAnalyzerMover::chain2_
private
std::string protocols::analysis::InterfaceAnalyzerMover::chain2_char_
private

Referenced by set_pose_info().

group_set protocols::analysis::InterfaceAnalyzerMover::chain_groups_
private

group of residue ids of fixed chains and mobile chains (see typedef)

Referenced by get_chain_groups(), make_multichain_interface_set(), and register_intergroup_calculator().

core::Real protocols::analysis::InterfaceAnalyzerMover::complex_energy_
private
bool protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat_
private

skip this expensive calculation

Referenced by apply(), and set_compute_interface_delta_hbond_unsat().

bool protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy_
private

skip this expensive calculation

Referenced by apply(), and set_compute_interface_energy().

bool protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc_
private

bother with computing interface sc

Referenced by apply(), report_data(), and set_compute_interface_sc().

bool protocols::analysis::InterfaceAnalyzerMover::compute_packstat_
private

bother with computing packstat

Referenced by apply(), print_pymol_selection_of_interface_residues(), report_data(), and set_compute_packstat().

bool protocols::analysis::InterfaceAnalyzerMover::compute_separated_sasa_
private

skip this expensive calculation

Referenced by apply(), and set_compute_separated_sasa().

core::Real protocols::analysis::InterfaceAnalyzerMover::crossterm_interface_energy_
private
core::Real protocols::analysis::InterfaceAnalyzerMover::crossterm_interface_energy_ratio_
private
core::Real protocols::analysis::InterfaceAnalyzerMover::ddG_
private

interface energy

Referenced by get_interface_ddG(), and score_separated_chains().

core::Size protocols::analysis::InterfaceAnalyzerMover::delta_unsat_hbond_counter_
private

number of unsat hbonds in complex

Referenced by compute_interface_delta_hbond_unsat(), get_interface_delta_hbond_unsat(), and report_data().

std::set<core::Size> protocols::analysis::InterfaceAnalyzerMover::downstream_chains_
private
std::set<int> protocols::analysis::InterfaceAnalyzerMover::fixed_chains_
private
core::Real protocols::analysis::InterfaceAnalyzerMover::gly_dG_
private

Energy of a all Gly interface.

Referenced by get_gly_interface_energy(), and mut_to_gly().

core::Real protocols::analysis::InterfaceAnalyzerMover::interface_delta_sasa_
private
core::Real protocols::analysis::InterfaceAnalyzerMover::interface_hsasa_
private
core::Size protocols::analysis::InterfaceAnalyzerMover::interface_jump_
private

jump to define which interface is interesting

Referenced by apply(), make_separated_pose(), register_calculators(), set_interface_jump(), and set_pose_info().

core::Real protocols::analysis::InterfaceAnalyzerMover::interface_packstat_
private
core::Real protocols::analysis::InterfaceAnalyzerMover::interface_polar_sasa_
private
std::set< core::Size > protocols::analysis::InterfaceAnalyzerMover::interface_set_
private
std::string protocols::analysis::InterfaceAnalyzerMover::InterfaceDeltaEnergetics_
private

InterfaceDeltaEnergetics calculator name string.

Referenced by compute_interface_energy(), and register_calculators().

std::string protocols::analysis::InterfaceAnalyzerMover::InterfaceNeighborDefinition_
private

InterfaceNeighborDefinition calculator name string.

Referenced by compute_interface_energy(), make_interface_set(), register_calculators(), and setup_task().

std::string protocols::analysis::InterfaceAnalyzerMover::InterfaceSasaDefinition_
private

InterfaceSasaDefinition calculator name string.

Referenced by register_calculators().

std::string protocols::analysis::InterfaceAnalyzerMover::InterGroupNeighborsCalculator_
private

InterGroupNeighborsCalculator calculator name string.

Referenced by make_multichain_interface_set(), register_intergroup_calculator(), and setup_task().

bool protocols::analysis::InterfaceAnalyzerMover::multichain_constructor_
private
core::Size protocols::analysis::InterfaceAnalyzerMover::n_interface_res_
private
core::Size protocols::analysis::InterfaceAnalyzerMover::nres_
private
std::string protocols::analysis::InterfaceAnalyzerMover::NumberHBonds_
private

NumberHBonds calculator name string.

Referenced by register_calculators().

bool protocols::analysis::InterfaceAnalyzerMover::pack_input_
private

pack the input pose

Referenced by get_pack_input(), score_separated_chains(), and set_pack_input().

bool protocols::analysis::InterfaceAnalyzerMover::pack_separated_
private

pack the separated poses default is false

Referenced by score_separated_chains(), and set_pack_separated().

core::Real protocols::analysis::InterfaceAnalyzerMover::per_residue_energy_
private
utility::file::FileName protocols::analysis::InterfaceAnalyzerMover::posename_
private

Referenced by set_pose_info().

std::string protocols::analysis::InterfaceAnalyzerMover::posename_base_
private
std::string protocols::analysis::InterfaceAnalyzerMover::pymol_sel_hbond_unsat_
private
std::string protocols::analysis::InterfaceAnalyzerMover::pymol_sel_interface_
private
std::string protocols::analysis::InterfaceAnalyzerMover::pymol_sel_packing_
private
std::string protocols::analysis::InterfaceAnalyzerMover::Sasa_
private

Sasa calculator name string.

Referenced by compute_separated_sasa(), and register_calculators().

core::Real protocols::analysis::InterfaceAnalyzerMover::sc_value_
private

shape complementarity values

Referenced by compute_interface_sc(), and report_data().

core::Real protocols::analysis::InterfaceAnalyzerMover::separated_interface_energy_
private
core::Real protocols::analysis::InterfaceAnalyzerMover::separated_interface_energy_ratio_
private
core::scoring::ScoreFunctionCOP protocols::analysis::InterfaceAnalyzerMover::sf_
private
core::Size protocols::analysis::InterfaceAnalyzerMover::side1_nres_
private
core::Real protocols::analysis::InterfaceAnalyzerMover::side1_score_
private
core::Size protocols::analysis::InterfaceAnalyzerMover::side2_nres_
private
core::Real protocols::analysis::InterfaceAnalyzerMover::side2_score_
private
bool protocols::analysis::InterfaceAnalyzerMover::skip_reporting_
private

hush! be quiet! silence!

Referenced by apply(), and set_skip_reporting().

core::pack::task::PackerTaskOP protocols::analysis::InterfaceAnalyzerMover::task_
private

packer task used to repack pulled apart chains

Referenced by get_packer_task(), score_separated_chains(), and setup_task().

core::Real protocols::analysis::InterfaceAnalyzerMover::total_hb_E_
private

avg hbond exposure ratio

total energy of interface Hbonds

Referenced by calc_hbond_sasaE(), get_total_Hbond_E(), and report_data().

core::Real protocols::analysis::InterfaceAnalyzerMover::total_sasa_
private
bool protocols::analysis::InterfaceAnalyzerMover::tracer_
private
std::set<core::Size> protocols::analysis::InterfaceAnalyzerMover::upstream_chains_
private
bool protocols::analysis::InterfaceAnalyzerMover::use_centroid_
private

skip the centroid_dG step, for incoming poses not centroid convertible

Referenced by apply(), calc_centroid_dG(), get_use_centroid_dG(), report_data(), and set_use_centroid_dG().

bool protocols::analysis::InterfaceAnalyzerMover::use_jobname_
private

just the jobname (true value) or the pose name (flase value)

Referenced by set_pose_info(), and set_use_jobname().

bool protocols::analysis::InterfaceAnalyzerMover::use_resfile_
private

use a resfile during the pack_input and pack_separated operations

Referenced by get_use_resfile(), set_use_resfile(), and setup_task().


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