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protocols::analysis::InterfaceAnalyzerMover Class Reference

Class for analyzing interfaces of a pose. Many metrics are calculated and accessible after the apply method. More...

#include <InterfaceAnalyzerMover.hh>

Inheritance diagram for protocols::analysis::InterfaceAnalyzerMover:
Inheritance graph
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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::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 InterfaceAnalyzerMover (core::Size interface_jump=1, bool const tracer=false, core::scoring::ScoreFunctionCOP sf=nullptr, bool compute_packstat=false, bool pack_input=false, bool pack_separated=false, bool use_jobname=true)
 Constructor for 2 chain poses, separates them by jump number. More...
 
 InterfaceAnalyzerMover (std::set< int > const &fixed_chains, bool const tracer=false, core::scoring::ScoreFunctionCOP sf=nullptr, bool compute_packstat=false, bool pack_input=false, bool pack_separated=false, bool use_jobname=true)
 Constructor for poses with >= 1 jump, keeps defined chains together. More...
 
 InterfaceAnalyzerMover (std::string dock_chains, bool const tracer=false, core::scoring::ScoreFunctionCOP sf=nullptr, bool compute_packstat=false, bool pack_input=false, bool pack_separated=false, bool use_jobname=true)
 Constructor for any interface in a pose. Uses string designation (ex LH_A) to keep the left chain/chains fixed ALA docking. More...
 
 ~InterfaceAnalyzerMover () override
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
void init_on_new_input (const core::pose::Pose &pose)
 Explicitly initialize settings on apply - not at the constructor, since this can hold state, and some protocols use apply multiple times. More...
 
void parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void apply (core::pose::Pose &pose) override
 apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects). It will add data to the pose for output into a scorefile. More...
 
virtual void apply_const (core::pose::Pose const &pose)
 Apply method for const pose. Used by InterfaceFeatures reporter. More...
 
virtual void report_data ()
 Print data to tracer or scorefile if tracer is not set (default). More...
 
void add_score_info_to_pose (core::pose::Pose &pose)
 Add all the scoring data normally output via job to the pose instead. Can't add this to method due to const apply. Use after you have used the apply for the class. More...
 
bool reinitialize_for_each_job () const override
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
bool reinitialize_for_new_input () const override
 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...
 
void set_defaults ()
 
void set_scorefunction (core::scoring::ScoreFunctionCOP sf)
 
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_compute_interface_sc (bool const compute_interface_sc)
 Compute the Lawrence and Coleman Shape Complementarity score? More...
 
void set_compute_separated_sasa (bool const compute_separated_sasa)
 
void set_calc_dSASA (bool calc_dSASA)
 
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)
 Repack the interface of the complex before separation. More...
 
void set_pack_separated (bool const pack_separated)
 Repack the interface of the complex after separation. More...
 
void set_pack_rounds (core::Size pack_rounds)
 If pack separated or together is set, this controls how many rounds of packing we do. Default is 1, but that certainly may not be enough... More...
 
void set_interface_jump (core::Size const interface_jump)
 Repack any interface between ignored chains and others. Used by dock_chains constructor if the dock_chains interface is less than the total number of pose chains. More...
 
void set_interface (std::string const &interface)
 
void set_skip_reporting (bool const skip_reporting)
 
void set_use_tracer (bool const tracer)
 
void set_use_jobname (bool const use_jobname)
 
void set_scorefile_reporting_prefix (std::string const &prefix)
 
void set_use_resfile (bool const use_resfile)
 
InterfaceData get_all_data ()
 Get all interface data. More...
 
PerResidueInterfaceData get_all_per_residue_data ()
 Get all per residue interface data. More...
 
core::Size get_num_interface_residues ()
 
core::Real get_complexed_sasa ()
 
core::Real get_interface_delta_sasa ()
 
core::Real get_complex_energy ()
 
core::Real get_per_residue_energy ()
 return the average per residue interface energy More...
 
core::Real get_total_Hbond_E ()
 
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_gly_interface_energy ()
 Return the interface energy of an all glycine interface (like bb-bb energies) More...
 
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_dG () const
 
bool get_multichain_constructor ()
 Return boolean if a multichain (fixedchain) constructor was used. More...
 
std::set< int > get_fixed_chains ()
 
std::set< core::Sizeget_interface_set ()
 Get the residues at the interface in question. More...
 
group_set get_chain_groups ()
 
bool get_pack_input ()
 
core::Real get_centroid_dG ()
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
std::string get_scorefile_reporting_prefix () const
 
- 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...
 
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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Member Functions

void register_calculators ()
 the exposure/possible ratio avg for hbonds in the interface More...
 
core::pack::task::PackerTaskOP setup_task (core::pose::Pose &pose)
 sets up the packer task. Used for both sep and tog pose More...
 
virtual void make_multichain_interface_set (core::pose::Pose &Pose, std::set< int > &fixed_chains)
 functions to make interface sets needed More...
 
virtual void make_interface_set (core::pose::Pose &pose)
 makes the interface sets for either constructor and sets up any other basic interface info. (chains, upstream chains, etc.) More...
 
virtual core::pose::Pose make_separated_pose (core::pose::Pose &pose, core::Size interface_jump, core::Size step_size=1000)
 Creates a single pose that is separated structurally at the interface. More...
 
virtual core::pose::Pose make_separated_pose (core::pose::Pose &pose, std::set< core::Size > const &moving_chains, core::Size step_size=1000)
 Creates a single pose that is separated structurally at the interface. 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...
 
void compute_interface_sc (core::Size &interface_jump, core::pose::Pose const &complexed_pose)
 find the interface shape compementarity value between the chains using old fortran SC score. 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)
 
void calc_per_residue_and_regional_data (core::pose::Pose &complexed_pose, core::pose::Pose &separated_pose)
 Calculate the average energy per residue in the interface as well as other data. More...
 
utility::vector1< core::Realcalc_per_residue_dSASA (const core::pose::Pose &complexed_pose, const utility::vector1< core::Real > &separated_sasa, const utility::vector1< core::Real > &complexed_sasa)
 calculates dSASA for each residue More...
 
core::Real calc_per_residue_dSASA_general (const core::Size resnum, const core::pose::Pose &complexed_pose, const core::Real separated_sasa, const core::Real complexed_sasa, utility::vector1< core::Real > &regional)
 
utility::vector1< core::Realcalc_per_residue_dG (core::pose::Pose &complexed_pose, const utility::vector1< core::Real > &separated_energy, const utility::vector1< core::Real > &complexed_energy)
 
void calc_hbond_sasaE (core::pose::Pose &pose)
 
void calc_centroid_dG (core::pose::Pose const &complex_pose, core::pose::Pose const &separated_pose)
 report the dG of a centroid pose with score3 More...
 
void calc_interface_to_surface_fraction (core::pose::Pose const &separated_pose, const utility::vector1< core::Real > &separated_sasa)
 Calculate the number of residues in the interface vs the surface based on SASA cutoff (40A^2 as per LayerDesign and selection operations). 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 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 set_pose_info (core::pose::Pose const &pose)
 sets up the pose information such as the name and chain ids More...
 
void init_per_residue_data (core::pose::Pose const &pose)
 Initialize the per residue data structure. More...
 
void init_data (const core::pose::Pose &pose)
 Initialize the data structure. More...
 
void setup_scorefxn ()
 Setup the scorefunction to include hbond energies in the EnergyGraph. Yay forums and Rocco for this bug fix! More...
 
void setup_for_dock_chains (core::pose::Pose &pose, std::string dock_chains)
 Setup for the dock_chains constructor. More...
 
std::string scorefile_column_name (std::string const &base_name) const
 
void setup_score_data ()
 

Private Attributes

core::Size interface_jump_
 jump to define which interface is interesting More...
 
utility::vector1< std::string > fixed_chain_strings_
 what chains are fixed in an interface More...
 
std::set< int > fixed_chains_
 
std::string ligand_chain_
 the ligand chain that will be moved in an interface In this scheme, everything else is fixed More...
 
core::scoring::ScoreFunctionOP sf_
 scorefunction More...
 
utility::file::FileName posename_
 
std::string posename_base_
 
core::Size chain1_ = 1
 
core::Size chain2_ = 2
 
std::string dock_chains_
 
std::set< core::Sizeupstream_chains_
 
std::set< core::Sizedownstream_chains_
 
std::set< core::Sizeignored_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 explicit_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...
 
InterfaceData data_
 
PerResidueInterfaceData per_residue_data_
 
core::Size included_nres_
 avg hbond exposure ratio More...
 
std::set< core::Sizeinterface_set_
 set of residues at the interface in question More...
 
utility::vector1< boolinclude_residue_
 
group_set chain_groups_
 group of residue ids of fixed chains and mobile chains (see typedef) More...
 
std::string Sasa_
 Sasa calculator name string. More...
 
std::string InterfaceNeighborDefinition_
 InterfaceNeighborDefinition 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::map< std::string, core::Realscore_data_
 
std::string scorefile_reporting_prefix_
 
core::Size pack_rounds_ = 1
 

Additional Inherited Members

- 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

Class for analyzing interfaces of a pose. Many metrics are calculated and accessible after the apply method.

Member Typedef Documentation

Constructor & Destructor Documentation

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

Constructor for 2 chain poses, separates them by jump number.

pack_separated and pack_input only pack the detected interface residues.

References set_defaults(), sf_, and protocols::moves::Mover::type().

protocols::analysis::InterfaceAnalyzerMover::InterfaceAnalyzerMover ( std::set< int > const &  fixed_chains,
bool const  tracer = false,
core::scoring::ScoreFunctionCOP  sf = nullptr,
bool  compute_packstat = false,
bool  pack_input = false,
bool  pack_separated = false,
bool  use_jobname = true 
)

Constructor for poses with >= 1 jump, keeps defined chains together.

pack_separated and pack_input only pack the detected interface residues.

References set_defaults(), sf_, and protocols::moves::Mover::type().

protocols::analysis::InterfaceAnalyzerMover::InterfaceAnalyzerMover ( std::string  dock_chains,
bool const  tracer = false,
core::scoring::ScoreFunctionCOP  sf = nullptr,
bool  compute_packstat = false,
bool  pack_input = false,
bool  pack_separated = false,
bool  use_jobname = true 
)

Constructor for any interface in a pose. Uses string designation (ex LH_A) to keep the left chain/chains fixed ALA docking.

Can be used for subsets of interfaces, for example L_H in a LHA pose. pack_separated and pack_input only pack the detected interface residues.

References dock_chains_, set_defaults(), sf_, and protocols::moves::Mover::type().

protocols::analysis::InterfaceAnalyzerMover::~InterfaceAnalyzerMover ( )
overridedefault

Member Function Documentation

void protocols::analysis::InterfaceAnalyzerMover::add_score_info_to_pose ( core::pose::Pose pose)

Add all the scoring data normally output via job to the pose instead. Can't add this to method due to const apply. Use after you have used the apply for the class.

References score_data_, scorefile_column_name(), core::pose::setPoseExtraScore(), and protocols::TR().

Referenced by apply(), and protocols::antibody::design::AntibodyDesignMover::finalize_pose().

void protocols::analysis::InterfaceAnalyzerMover::apply ( core::pose::Pose pose)
overridevirtual

apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects). It will add data to the pose for output into a scorefile.

InterfaceAnalyzerMover computes various interface statistics and makes them available through getters

Implements protocols::moves::Mover.

References add_score_info_to_pose(), and apply_const().

Referenced by protocols::antibody::AntibodyModelerProtocol::apply(), protocols::antibody::snugdock::SnugDockProtocol::apply(), and protocols::antibody::design::AntibodyDesignMover::finalize_pose().

void protocols::analysis::InterfaceAnalyzerMover::apply_const ( core::pose::Pose const &  pose)
virtual
void protocols::analysis::InterfaceAnalyzerMover::calc_centroid_dG ( core::pose::Pose const &  complex_pose,
core::pose::Pose const &  separated_pose 
)
private
void protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE ( core::pose::Pose pose)
private
void protocols::analysis::InterfaceAnalyzerMover::calc_interface_to_surface_fraction ( core::pose::Pose const &  separated_pose,
const utility::vector1< core::Real > &  separated_sasa 
)
private

Calculate the number of residues in the interface vs the surface based on SASA cutoff (40A^2 as per LayerDesign and selection operations).

Correct way to calculate this though is through % maximal SASA buried, but calculations will need to be done later to find these values.

References core::pose::Pose::chain(), data_, include_residue_, protocols::analysis::InterfaceData::interface_nres, protocols::analysis::InterfaceData::interface_to_surface_fraction, protocols::analysis::side1, protocols::analysis::side2, protocols::analysis::total, and upstream_chains_.

Referenced by compute_separated_sasa().

void protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data ( core::pose::Pose complexed_pose,
core::pose::Pose separated_pose 
)
private

Calculate the average energy per residue in the interface as well as other data.

calculate the average energy per residue in the interface as well as other data

References protocols::analysis::InterfaceData::aromatic_dG_fraction, protocols::analysis::InterfaceData::aromatic_dSASA_fraction, protocols::analysis::InterfaceData::aromatic_nres, calc_per_residue_dG(), core::conformation::Residue::chain(), protocols::analysis::PerResidueInterfaceData::complexed_energy, protocols::analysis::InterfaceData::complexed_interface_score, data_, protocols::analysis::PerResidueInterfaceData::dG, protocols::analysis::InterfaceData::dG, protocols::analysis::PerResidueInterfaceData::dhSASA, protocols::analysis::InterfaceData::dhSASA, protocols::analysis::PerResidueInterfaceData::dhSASA_rel_by_charge, protocols::analysis::InterfaceData::dhSASA_rel_by_charge, protocols::analysis::PerResidueInterfaceData::dSASA, protocols::analysis::InterfaceData::dSASA, protocols::simple_filters::dssp(), core::pose::Pose::energies(), core::scoring::dssp::Dssp::get_dssp_secstruct(), protocols::analysis::InterfaceData::interface_nres, interface_set_, core::conformation::Residue::is_aromatic(), core::conformation::Residue::is_protein(), per_residue_data_, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_energy_int, core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), protocols::analysis::PerResidueInterfaceData::separated_energy, protocols::analysis::InterfaceData::separated_interface_score, protocols::analysis::side1, protocols::analysis::side2, protocols::analysis::InterfaceData::ss_helix_nres, protocols::analysis::InterfaceData::ss_loop_nres, protocols::analysis::InterfaceData::ss_sheet_nres, protocols::analysis::total, core::scoring::total_score, protocols::TR(), and upstream_chains_.

Referenced by compute_interface_energy().

vector1< core::Real > protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_dG ( core::pose::Pose complexed_pose,
const utility::vector1< core::Real > &  separated_energy,
const utility::vector1< core::Real > &  complexed_energy 
)
private
vector1< core::Real > protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_dSASA ( const core::pose::Pose complexed_pose,
const utility::vector1< core::Real > &  separated_sasa,
const utility::vector1< core::Real > &  complexed_sasa 
)
private
Real protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_dSASA_general ( const core::Size  resnum,
const core::pose::Pose complexed_pose,
const core::Real  separated_sasa,
const core::Real  complexed_sasa,
utility::vector1< core::Real > &  regional 
)
private
protocols::moves::MoverOP protocols::analysis::InterfaceAnalyzerMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

void protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat ( core::pose::Pose complexed_pose,
core::pose::Pose separated_pose 
)
privatevirtual
void protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy ( core::pose::Pose complexed_pose,
core::pose::Pose separated_pose 
)
privatevirtual
void protocols::analysis::InterfaceAnalyzerMover::compute_interface_packstat ( core::pose::Pose pose)
privatevirtual
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 
)
privatevirtual
protocols::moves::MoverOP protocols::analysis::InterfaceAnalyzerMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

InterfaceData protocols::analysis::InterfaceAnalyzerMover::get_all_data ( )
inline

Get all interface data.

References data_.

PerResidueInterfaceData protocols::analysis::InterfaceAnalyzerMover::get_all_per_residue_data ( )
inline

Get all per residue interface data.

References per_residue_data_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_centroid_dG ( )
InterfaceAnalyzerMover::group_set protocols::analysis::InterfaceAnalyzerMover::get_chain_groups ( )

References chain_groups_.

core::Real protocols::analysis::InterfaceAnalyzerMover::get_complex_energy ( )
core::Real protocols::analysis::InterfaceAnalyzerMover::get_complexed_sasa ( )
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_.

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

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

References data_, and protocols::analysis::InterfaceData::gly_dG.

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_dG ( ) const
core::Real protocols::analysis::InterfaceAnalyzerMover::get_interface_packstat ( )
std::set< core::Size > protocols::analysis::InterfaceAnalyzerMover::get_interface_set ( )

Get the residues at the interface in question.

References interface_set_.

bool protocols::analysis::InterfaceAnalyzerMover::get_multichain_constructor ( )

Return boolean if a multichain (fixedchain) constructor was used.

References explicit_constructor_.

std::string protocols::analysis::InterfaceAnalyzerMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Size protocols::analysis::InterfaceAnalyzerMover::get_num_interface_residues ( )
bool protocols::analysis::InterfaceAnalyzerMover::get_pack_input ( )

References pack_input_.

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 ( )
std::string protocols::analysis::InterfaceAnalyzerMover::get_scorefile_reporting_prefix ( ) const
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 ( )
bool protocols::analysis::InterfaceAnalyzerMover::get_use_centroid_dG ( ) const

References use_centroid_.

void protocols::analysis::InterfaceAnalyzerMover::init_data ( const core::pose::Pose pose)
private

Initialize the data structure.

References protocols::analysis::InterfaceData::aromatic_dG_fraction, protocols::analysis::InterfaceData::aromatic_dSASA_fraction, protocols::analysis::InterfaceData::aromatic_nres, protocols::analysis::InterfaceData::centroid_dG, protocols::analysis::InterfaceData::complex_total_energy, protocols::analysis::InterfaceData::complexed_interface_score, protocols::analysis::InterfaceData::complexed_SASA, protocols::analysis::InterfaceData::crossterm_interface_energy, protocols::analysis::InterfaceData::crossterm_interface_energy_dSASA_ratio, data_, protocols::analysis::InterfaceData::delta_unsat_hbonds, protocols::analysis::InterfaceData::dG, protocols::analysis::InterfaceData::dG_dSASA_ratio, protocols::analysis::InterfaceData::dhSASA, protocols::analysis::InterfaceData::dhSASA_rel_by_charge, protocols::analysis::InterfaceData::dhSASA_sc, protocols::analysis::InterfaceData::dSASA, protocols::analysis::InterfaceData::dSASA_sc, protocols::analysis::InterfaceData::gly_dG, protocols::analysis::InterfaceData::interface_hbonds, protocols::analysis::InterfaceData::interface_nres, protocols::analysis::InterfaceData::interface_residues, protocols::analysis::InterfaceData::interface_to_surface_fraction, protocols::analysis::InterfaceData::packstat, protocols::analysis::InterfaceData::sc_value, protocols::analysis::InterfaceData::separated_interface_score, protocols::analysis::InterfaceData::separated_SASA, protocols::analysis::InterfaceData::separated_total_energy, core::pose::Pose::size(), protocols::analysis::InterfaceData::ss_helix_nres, protocols::analysis::InterfaceData::ss_loop_nres, protocols::analysis::InterfaceData::ss_sheet_nres, and protocols::analysis::InterfaceData::total_hb_E.

Referenced by init_on_new_input().

void protocols::analysis::InterfaceAnalyzerMover::init_on_new_input ( const core::pose::Pose pose)
void protocols::analysis::InterfaceAnalyzerMover::init_per_residue_data ( core::pose::Pose const &  pose)
private
void protocols::analysis::InterfaceAnalyzerMover::make_interface_set ( core::pose::Pose pose)
privatevirtual
void protocols::analysis::InterfaceAnalyzerMover::make_multichain_interface_set ( core::pose::Pose Pose,
std::set< int > &  fixed_chains 
)
privatevirtual
core::pose::Pose protocols::analysis::InterfaceAnalyzerMover::make_separated_pose ( core::pose::Pose pose,
core::Size  interface_jump,
core::Size  step_size = 1000 
)
privatevirtual

Creates a single pose that is separated structurally at the interface.

Uses the jump number to find downstream residues and move them in the Z axis in cartesian space according to step_size (A)

References core::pose::Pose::fold_tree(), core::kinematics::residues_downstream_of_jump(), and protocols::toolbox::rigid_body::translate().

Referenced by apply_const(), and setup_for_dock_chains().

core::pose::Pose protocols::analysis::InterfaceAnalyzerMover::make_separated_pose ( core::pose::Pose pose,
std::set< core::Size > const &  chain_nums,
core::Size  step_size = 1000 
)
privatevirtual

Creates a single pose that is separated structurally at the interface.

Moves the moving_chains in cartesian space a distance according to step_size (A) in the Z axis

References core::conformation::Residue::chain(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::toolbox::rigid_body::translate().

std::string protocols::analysis::InterfaceAnalyzerMover::mover_name ( )
static
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(), data_, protocols::analysis::InterfaceData::gly_dG, interface_set_, core::chemical::num_canonical_aas, sf_, core::pose::Pose::size(), and protocols::TR().

void protocols::analysis::InterfaceAnalyzerMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual

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 dock_chains_, explicit_constructor_, fixed_chain_strings_, ligand_chain_, core::scoring::parse_score_function(), set_compute_interface_sc(), set_compute_packstat(), set_interface_jump(), set_pack_input(), set_pack_separated(), set_scorefile_reporting_prefix(), set_use_jobname(), set_use_resfile(), set_use_tracer(), sf_, and protocols::TR().

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 protocols::jd2::add_string_to_current_job(), core::conformation::Residue::atom_name(), data_, core::pose::Pose::pdb_info(), posename_base_, protocols::analysis::InterfaceData::pymol_sel_hbond_unsat, core::pose::Pose::residue(), 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 protocols::jd2::add_string_to_current_job(), compute_packstat_, data_, core::pose::Pose::pdb_info(), posename_base_, protocols::analysis::InterfaceData::pymol_sel_interface, tracer_, TRinterface(), and protocols::analysis::which_ostream().

Referenced by apply_const().

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 data_, include_residue_, core::pose::Pose::pdb_info(), posename_base_, protocols::analysis::InterfaceData::pymol_sel_packing, core::pose::Pose::size(), and protocols::TR().

Referenced by compute_interface_packstat().

void protocols::analysis::InterfaceAnalyzerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::analysis::InterfaceAnalyzerMover::register_calculators ( )
private

the exposure/possible ratio avg for hbonds in the interface

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

total hbond energy for pose registers the posemetric calculators

References BuriedUnsatisfiedPolars_, chain1_, chain2_, interface_jump_, InterfaceDeltaEnergetics_, InterfaceNeighborDefinition_, NumberHBonds_, Sasa_, and protocols::TR().

Referenced by apply_const().

bool protocols::analysis::InterfaceAnalyzerMover::reinitialize_for_each_job ( ) const
inlineoverridevirtual

Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

bool protocols::analysis::InterfaceAnalyzerMover::reinitialize_for_new_input ( ) const
inlineoverridevirtual

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).

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

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

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(), core::pose::get_chain_id_from_chain(), core::pose::get_jump_id_from_chain_id(), ligand_chain_, core::conformation::Conformation::num_chains(), and protocols::make_rot_lib::PEPTIDE.

void protocols::analysis::InterfaceAnalyzerMover::report_data ( )
virtual
void protocols::analysis::InterfaceAnalyzerMover::score_separated_chains ( core::pose::Pose complexed_pose,
core::pose::Pose separated_pose 
)
privatevirtual
std::string protocols::analysis::InterfaceAnalyzerMover::scorefile_column_name ( std::string const &  base_name) const
private
void protocols::analysis::InterfaceAnalyzerMover::set_calc_dSASA ( bool  calc_dSASA)
inline
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

Compute the Lawrence and Coleman Shape Complementarity score?

References compute_interface_sc(), and compute_interface_sc_.

Referenced by parse_my_tag().

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

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_defaults ( )
void protocols::analysis::InterfaceAnalyzerMover::set_interface ( std::string const &  interface)
void protocols::analysis::InterfaceAnalyzerMover::set_interface_jump ( core::Size const  interface_jump)

Repack any interface between ignored chains and others. Used by dock_chains constructor if the dock_chains interface is less than the total number of pose chains.

Ex: LHA pose, pass L_H dock_chains to get the interface between L and H. A will be translated away from the L H interface to do the calculation. If this option is set - it will repack any SC that would make an LH_A interface after separation

References explicit_constructor_, and interface_jump_.

Referenced by parse_my_tag().

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

Repack the interface of the complex before separation.

References pack_input_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_pack_rounds ( core::Size  pack_rounds)
inline

If pack separated or together is set, this controls how many rounds of packing we do. Default is 1, but that certainly may not be enough...

References pack_rounds_.

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

Repack the interface of the complex after separation.

References pack_separated_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_pose_info ( core::pose::Pose const &  pose)
private
void protocols::analysis::InterfaceAnalyzerMover::set_scorefile_reporting_prefix ( std::string const &  prefix)

References scorefile_reporting_prefix_.

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::set_scorefunction ( core::scoring::ScoreFunctionCOP  sf)

References sf_.

void protocols::analysis::InterfaceAnalyzerMover::set_skip_reporting ( bool const  skip_reporting)
inline

References skip_reporting_.

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

References use_resfile_.

Referenced by parse_my_tag().

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

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

Referenced by parse_my_tag().

void protocols::analysis::InterfaceAnalyzerMover::setup_for_dock_chains ( core::pose::Pose pose,
std::string  dock_chains 
)
private
void protocols::analysis::InterfaceAnalyzerMover::setup_score_data ( )
private
void protocols::analysis::InterfaceAnalyzerMover::setup_scorefxn ( )
private

Setup the scorefunction to include hbond energies in the EnergyGraph. Yay forums and Rocco for this bug fix!

References core::scoring::get_score_function(), sf_, and protocols::TR().

Referenced by apply_const().

core::pack::task::PackerTaskOP protocols::analysis::InterfaceAnalyzerMover::setup_task ( core::pose::Pose pose)
private

sets up the packer task. Used for both sep and tog pose

sets up the packer task for the interface

References data_, protocols::analysis::InterfaceData::interface_residues, protocols::analysis::total, and use_resfile_.

Referenced by score_separated_chains().

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_const(), set_calc_hbond_sasaE(), and set_defaults().

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

are calculators ready?

Referenced by apply_const(), and set_defaults().

core::Size protocols::analysis::InterfaceAnalyzerMover::chain1_ = 1
private
core::Size protocols::analysis::InterfaceAnalyzerMover::chain2_ = 2
private
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(), and make_multichain_interface_set().

bool protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat_
private

skip this expensive calculation

Referenced by apply_const(), set_compute_interface_delta_hbond_unsat(), and set_defaults().

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

skip this expensive calculation

Referenced by apply_const(), set_compute_interface_energy(), and set_defaults().

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

bother with computing interface sc

Referenced by apply_const(), report_data(), set_compute_interface_sc(), and set_defaults().

bool protocols::analysis::InterfaceAnalyzerMover::compute_packstat_
private
bool protocols::analysis::InterfaceAnalyzerMover::compute_separated_sasa_
private
InterfaceData protocols::analysis::InterfaceAnalyzerMover::data_
private
std::string protocols::analysis::InterfaceAnalyzerMover::dock_chains_
private
std::set<core::Size> protocols::analysis::InterfaceAnalyzerMover::downstream_chains_
private
bool protocols::analysis::InterfaceAnalyzerMover::explicit_constructor_
private
utility::vector1< std::string > protocols::analysis::InterfaceAnalyzerMover::fixed_chain_strings_
private

what chains are fixed in an interface

Referenced by init_on_new_input(), parse_my_tag(), and setup_for_dock_chains().

std::set<int> protocols::analysis::InterfaceAnalyzerMover::fixed_chains_
private
std::set<core::Size> protocols::analysis::InterfaceAnalyzerMover::ignored_chains_
private
utility::vector1< bool > protocols::analysis::InterfaceAnalyzerMover::include_residue_
private
core::Size protocols::analysis::InterfaceAnalyzerMover::included_nres_
private

avg hbond exposure ratio

Referenced by init_on_new_input(), score_separated_chains(), and setup_score_data().

core::Size protocols::analysis::InterfaceAnalyzerMover::interface_jump_
private

jump to define which interface is interesting

Referenced by apply_const(), register_calculators(), set_interface_jump(), and set_pose_info().

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 make_interface_set(), and register_calculators().

std::string protocols::analysis::InterfaceAnalyzerMover::ligand_chain_
private

the ligand chain that will be moved in an interface In this scheme, everything else is fixed

Referenced by apply_const(), parse_my_tag(), and reorder_foldtree_find_jump().

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().

core::Size protocols::analysis::InterfaceAnalyzerMover::pack_rounds_ = 1
private
bool protocols::analysis::InterfaceAnalyzerMover::pack_separated_
private

pack the separated poses default is false

Referenced by score_separated_chains(), and set_pack_separated().

PerResidueInterfaceData protocols::analysis::InterfaceAnalyzerMover::per_residue_data_
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::Sasa_
private

Sasa calculator name string.

Referenced by compute_separated_sasa(), and register_calculators().

std::map< std::string, core::Real > protocols::analysis::InterfaceAnalyzerMover::score_data_
private
std::string protocols::analysis::InterfaceAnalyzerMover::scorefile_reporting_prefix_
private
core::scoring::ScoreFunctionOP protocols::analysis::InterfaceAnalyzerMover::sf_
private
bool protocols::analysis::InterfaceAnalyzerMover::skip_reporting_
private

hush! be quiet! silence!

Referenced by apply_const(), set_defaults(), and set_skip_reporting().

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_const(), calc_centroid_dG(), get_use_centroid_dG(), report_data(), set_defaults(), set_use_centroid_dG(), and setup_score_data().

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 set_defaults(), set_use_resfile(), and setup_task().


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