Rosetta
Public Member Functions | Private Types | Private Attributes | List of all members
UBQ_E2Mover Class Reference
Inheritance diagram for UBQ_E2Mover:
Inheritance graph
[legend]

Public Member Functions

 UBQ_E2Mover ()
 
virtual void init_on_new_input ()
 init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply(). More...
 
virtual ~UBQ_E2Mover ()
 
virtual void apply (core::pose::Pose &pose)
 
void analyze_and_filter (core::pose::Pose &pose)
 
virtual protocols::moves::MoverOP fresh_instance () const
 
virtual bool reinitialize_for_each_job () const
 
virtual bool reinitialize_for_new_input () const
 
virtual std::string get_name () const
 
 UBQ_E2Mover ()
 
virtual void init_on_new_input ()
 init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply(). More...
 
 ~UBQ_E2Mover () override=default
 
void apply (core::pose::Pose &pose) override
 
void analyze_and_filter (core::pose::Pose &pose)
 
protocols::moves::MoverOP fresh_instance () const override
 
bool reinitialize_for_each_job () const override
 
bool reinitialize_for_new_input () const override
 
std::string get_name () const override
 

Private Types

enum  atomID {
  CYS_C = 1 , CYS_CA = 2 , CYS_CB = 3 , CYS_SG = 4 ,
  GLY_C = 5 , GLY_CA = 6 , GLY_N = 7 , GLY2_C = 8 ,
  LYS_2HZ = 9 , LYS_NZ = 10 , LYS_CE = 11 , LYS_CD = 12 ,
  atomID_tot = LYS_CD , CYS_C = 1 , CYS_CA = 2 , CYS_CB = 3 ,
  CYS_SG = 4 , GLY_C = 5 , GLY_CA = 6 , GLY_N = 7 ,
  GLY2_C = 8 , LYS_2HZ = 9 , LYS_NZ = 10 , LYS_CE = 11 ,
  LYS_CD = 12 , atomID_tot = LYS_CD
}
 
enum  atomID {
  CYS_C = 1 , CYS_CA = 2 , CYS_CB = 3 , CYS_SG = 4 ,
  GLY_C = 5 , GLY_CA = 6 , GLY_N = 7 , GLY2_C = 8 ,
  LYS_2HZ = 9 , LYS_NZ = 10 , LYS_CE = 11 , LYS_CD = 12 ,
  atomID_tot = LYS_CD , CYS_C = 1 , CYS_CA = 2 , CYS_CB = 3 ,
  CYS_SG = 4 , GLY_C = 5 , GLY_CA = 6 , GLY_N = 7 ,
  GLY2_C = 8 , LYS_2HZ = 9 , LYS_NZ = 10 , LYS_CE = 11 ,
  LYS_CD = 12 , atomID_tot = LYS_CD
}
 

Private Attributes

bool init_for_input_yet_ {false}
 
core::scoring::ScoreFunctionOP fullatom_scorefunction_
 
core::pack::task::TaskFactoryOP task_factory_
 
core::kinematics::MoveMapOP thioester_mm_
 
protocols::loops::Loop loop_
 
utility::vector1< core::id::AtomID > atomIDs
 vector contains atomIDs for thioester bond and atoms before/after bond to determine various torsions More...
 
core::pose::Pose starting_pose_
 
std::string const InterfaceSasaDefinition_
 
protocols::analysis::InterfaceAnalyzerMoverOP IAM_
 
bool two_ubiquitins_ = false
 used for two-ubiquitins mode More...
 
utility::vector1< core::Size > extra_bodies_chains_
 used to track which chains are "extra" nonmoving bodies in extra bodies mode More...
 
core::Size ubq2_lys_pos_in_complex_ = 0
 the lysine attachment position for the second ubiquitin (the second moving chain), in the whole complex numbering More...
 

Member Enumeration Documentation

◆ atomID [1/2]

enum UBQ_E2Mover::atomID
private
Enumerator
CYS_C 
CYS_CA 
CYS_CB 
CYS_SG 
GLY_C 
GLY_CA 
GLY_N 
GLY2_C 
LYS_2HZ 
LYS_NZ 
LYS_CE 
LYS_CD 
atomID_tot 
CYS_C 
CYS_CA 
CYS_CB 
CYS_SG 
GLY_C 
GLY_CA 
GLY_N 
GLY2_C 
LYS_2HZ 
LYS_NZ 
LYS_CE 
LYS_CD 
atomID_tot 

◆ atomID [2/2]

enum UBQ_E2Mover::atomID
private
Enumerator
CYS_C 
CYS_CA 
CYS_CB 
CYS_SG 
GLY_C 
GLY_CA 
GLY_N 
GLY2_C 
LYS_2HZ 
LYS_NZ 
LYS_CE 
LYS_CD 
atomID_tot 
CYS_C 
CYS_CA 
CYS_CB 
CYS_SG 
GLY_C 
GLY_CA 
GLY_N 
GLY2_C 
LYS_2HZ 
LYS_NZ 
LYS_CE 
LYS_CD 
atomID_tot 

Constructor & Destructor Documentation

◆ UBQ_E2Mover() [1/2]

UBQ_E2Mover::UBQ_E2Mover ( )
inline

References fullatom_scorefunction_, IAM_, InterfaceSasaDefinition_, loop_, basic::options::OptionKeys::loops::loop_file, basic::options::OptionKeys::cluster::loops, basic::options::option, basic::options::OptionKeys::frags::scoring::scoring, TR, basic::options::OptionKeys::inout::dbms::user, and value.

Referenced by fresh_instance().

◆ ~UBQ_E2Mover() [1/2]

virtual UBQ_E2Mover::~UBQ_E2Mover ( )
inlinevirtual

◆ UBQ_E2Mover() [2/2]

UBQ_E2Mover::UBQ_E2Mover ( )
inline

References fullatom_scorefunction_, IAM_, InterfaceSasaDefinition_, basic::options::option, basic::options::OptionKeys::frags::scoring::scoring, TR, basic::options::OptionKeys::chemically_conjugated_docking::two_ubiquitins, and two_ubiquitins_.

◆ ~UBQ_E2Mover() [2/2]

UBQ_E2Mover::~UBQ_E2Mover ( )
overridedefault

Member Function Documentation

◆ analyze_and_filter() [1/2]

void UBQ_E2Mover::analyze_and_filter ( core::pose::Pose &  pose)
inline

References atomIDs, erraser_util::copy(), numeric::conversions::degrees(), fullatom_scorefunction_, IAM_, InterfaceSasaDefinition_, basic::options::option, beta_nonlocal::pose, SASAfilter, create_a3b_hbs::score, scorefilter, TR, basic::MetricValue< T >::value(), and value.

Referenced by apply().

◆ analyze_and_filter() [2/2]

void UBQ_E2Mover::analyze_and_filter ( core::pose::Pose &  pose)
inline

References atomIDs, erraser_util::copy(), numeric::conversions::degrees(), basic::options::OptionKeys::chemically_conjugated_docking::extra_bodies, fullatom_scorefunction_, IAM_, InterfaceSasaDefinition_, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::chemically_conjugated_docking::publication, basic::options::OptionKeys::chemically_conjugated_docking::SASAfilter, create_a3b_hbs::score, basic::options::OptionKeys::chemically_conjugated_docking::scorefilter, TR, two_ubiquitins_, basic::options::OptionKeys::inout::dbms::user, basic::MetricValue< T >::value(), and value.

◆ apply() [1/2]

virtual void UBQ_E2Mover::apply ( core::pose::Pose &  pose)
inlinevirtual

References analyze_and_filter(), atomIDs, basic::options::OptionKeys::coupled_moves::backbone_mover, fullatom_scorefunction_, create_a3b_hbs::i, init_for_input_yet_, init_on_new_input(), loop_, LYS_2HZ, LYS_CD, LYS_CE, LYS_NZ, mc, vancomycin::min_mover, basic::options::OptionKeys::run::min_type, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::option, option, test.Workshop6test::pack_mover, beta_nonlocal::pose, basic::options::OptionKeys::AnchoredDesign::refine_cycles, basic::options::OptionKeys::AnchoredDesign::refine_repack_cycles, basic::options::OptionKeys::AnchoredDesign::refine_temp, basic::options::OptionKeys::repack_cycles, test.Workshop5test::shear_mover, test.Workshop5test::small_mover, starting_pose_, vancomycin::task, task_factory_, thioester_mm_, TR, and value.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ apply() [2/2]

void UBQ_E2Mover::apply ( core::pose::Pose &  pose)
inlineoverride

References analyze_and_filter(), atomIDs, basic::options::OptionKeys::coupled_moves::backbone_mover, fullatom_scorefunction_, create_a3b_hbs::i, init_for_input_yet_, init_on_new_input(), loop_, LYS_2HZ, LYS_CD, LYS_CE, LYS_NZ, mc, vancomycin::min_mover, basic::options::OptionKeys::run::min_type, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::option, option, test.Workshop6test::pack_mover, beta_nonlocal::pose, basic::options::OptionKeys::AnchoredDesign::refine_cycles, basic::options::OptionKeys::AnchoredDesign::refine_repack_cycles, basic::options::OptionKeys::AnchoredDesign::refine_temp, basic::options::OptionKeys::repack_cycles, test.Workshop5test::shear_mover, test.Workshop5test::small_mover, starting_pose_, vancomycin::task, task_factory_, thioester_mm_, TR, two_ubiquitins_, and value.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ fresh_instance() [1/2]

virtual protocols::moves::MoverOP UBQ_E2Mover::fresh_instance ( ) const
inlinevirtual

References UBQ_E2Mover().

◆ fresh_instance() [2/2]

protocols::moves::MoverOP UBQ_E2Mover::fresh_instance ( ) const
inlineoverride

◆ get_name() [1/2]

virtual std::string UBQ_E2Mover::get_name ( ) const
inlinevirtual

◆ get_name() [2/2]

std::string UBQ_E2Mover::get_name ( ) const
inlineoverride

◆ init_on_new_input() [1/2]

virtual void UBQ_E2Mover::init_on_new_input ( )
inlinevirtual

init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply().

References atomIDs, E2_residue, E2pdb, end, pyrosetta.toolbox.load_ligand::fa_standard, create_a3b_hbs::i, init_for_input_yet_, create_a3b_hbs::j, loop_, basic::options::OptionKeys::loops::loop_file, LYS_2HZ, LYS_CD, LYS_CE, LYS_NZ, basic::options::option, pyrosetta.distributed.io::pose_from_file, numeric::conversions::radians(), basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::in::file::residue_type_set, runtime_assert, starting_pose_, vancomycin::task, task_factory_, thioester_mm_, TR, UBQpdb, basic::options::OptionKeys::inout::dbms::user, and value.

Referenced by apply().

◆ init_on_new_input() [2/2]

virtual void UBQ_E2Mover::init_on_new_input ( )
inlinevirtual

init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply().

References apps::public1::scenarios::chemically_conjugated_docking::add_extra_bodies(), atomIDs, basic::options::OptionKeys::chemically_conjugated_docking::dont_minimize_omega, basic::options::OptionKeys::chemically_conjugated_docking::E2_residue, basic::options::OptionKeys::chemically_conjugated_docking::E2pdb, basic::options::OptionKeys::score::empty, end, basic::Tracer::Error, basic::options::OptionKeys::chemically_conjugated_docking::extra_bodies, extra_bodies_chains_, pyrosetta.toolbox.load_ligand::fa_standard, create_a3b_hbs::first, fullatom_scorefunction_, create_a3b_hbs::i, init_for_input_yet_, create_a3b_hbs::j, loop_, basic::options::OptionKeys::loops::loop_file, basic::options::OptionKeys::chemically_conjugated_docking::n_tail_res, basic::options::option, apps::public1::scenarios::chemically_conjugated_docking::pack_extra_bodies(), pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::chemically_conjugated_docking::publication, numeric::conversions::radians(), test.G101_Functions_Output::regions, basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::in::file::residue_type_set, runtime_assert, starting_pose_, vancomycin::task, task_factory_, thioester_mm_, TR, two_ubiquitins_, basic::options::OptionKeys::chemically_conjugated_docking::UBQ2_lys, ubq2_lys_pos_in_complex_, basic::options::OptionKeys::chemically_conjugated_docking::UBQ2_pdb, basic::options::OptionKeys::chemically_conjugated_docking::UBQpdb, basic::options::OptionKeys::inout::dbms::user, and value.

◆ reinitialize_for_each_job() [1/2]

virtual bool UBQ_E2Mover::reinitialize_for_each_job ( ) const
inlinevirtual

◆ reinitialize_for_each_job() [2/2]

bool UBQ_E2Mover::reinitialize_for_each_job ( ) const
inlineoverride

◆ reinitialize_for_new_input() [1/2]

virtual bool UBQ_E2Mover::reinitialize_for_new_input ( ) const
inlinevirtual

◆ reinitialize_for_new_input() [2/2]

bool UBQ_E2Mover::reinitialize_for_new_input ( ) const
inlineoverride

Member Data Documentation

◆ atomIDs

utility::vector1< core::id::AtomID > UBQ_E2Mover::atomIDs
private

vector contains atomIDs for thioester bond and atoms before/after bond to determine various torsions

Referenced by analyze_and_filter(), apply(), and init_on_new_input().

◆ extra_bodies_chains_

utility::vector1< core::Size > UBQ_E2Mover::extra_bodies_chains_
private

used to track which chains are "extra" nonmoving bodies in extra bodies mode

Referenced by init_on_new_input().

◆ fullatom_scorefunction_

core::scoring::ScoreFunctionOP UBQ_E2Mover::fullatom_scorefunction_
private

Referenced by analyze_and_filter(), apply(), init_on_new_input(), and UBQ_E2Mover().

◆ IAM_

protocols::analysis::InterfaceAnalyzerMoverOP UBQ_E2Mover::IAM_
private

Referenced by analyze_and_filter(), and UBQ_E2Mover().

◆ init_for_input_yet_

bool UBQ_E2Mover::init_for_input_yet_ {false}
private

Referenced by apply(), and init_on_new_input().

◆ InterfaceSasaDefinition_

std::string const UBQ_E2Mover::InterfaceSasaDefinition_
private

Referenced by analyze_and_filter(), and UBQ_E2Mover().

◆ loop_

protocols::loops::Loop UBQ_E2Mover::loop_
private

Referenced by apply(), init_on_new_input(), and UBQ_E2Mover().

◆ starting_pose_

core::pose::Pose UBQ_E2Mover::starting_pose_
private

Referenced by apply(), and init_on_new_input().

◆ task_factory_

core::pack::task::TaskFactoryOP UBQ_E2Mover::task_factory_
private

Referenced by apply(), and init_on_new_input().

◆ thioester_mm_

core::kinematics::MoveMapOP UBQ_E2Mover::thioester_mm_
private

Referenced by apply(), and init_on_new_input().

◆ two_ubiquitins_

bool UBQ_E2Mover::two_ubiquitins_ = false
private

used for two-ubiquitins mode

Referenced by analyze_and_filter(), apply(), init_on_new_input(), and UBQ_E2Mover().

◆ ubq2_lys_pos_in_complex_

core::Size UBQ_E2Mover::ubq2_lys_pos_in_complex_ = 0
private

the lysine attachment position for the second ubiquitin (the second moving chain), in the whole complex numbering

Referenced by init_on_new_input().

The documentation for this class was generated from the following files:
Generated on Sat Mar 2 2024 15:18:11 for Rosetta by doxygen 1.9.1