DockingInitialPerturbation.cc File Reference

initial position functions More...

#include <protocols/docking/DockingInitialPerturbation.hh>
#include <protocols/docking/DockingInitialPerturbationCreator.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/docking/RigidBodyInfo.hh>
#include <protocols/moves/DataMap.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <basic/options/option.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <ObjexxFCL/string.functions.hh>
#include <string>
#include <numeric/trig.functions.hh>
#include <numeric/xyzMatrix.fwd.hh>
#include <basic/Tracer.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/tag/Tag.hh>
#include <basic/options/keys/docking.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/vector1.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::docking

Constant Groups
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::docking

Functions
static basic::Tracer	TR ("protocols.docking.DockingInitialPerturbation")
static core::Size	trans (1)
static core::Size	rot (2)
std::ostream &	protocols::docking::operator<< (std::ostream &os, DockingSlideIntoContact const &mover)
std::ostream &	protocols::docking::operator<< (std::ostream &os, FaDockingSlideIntoContact const &fadock)

Detailed Description

initial position functions

Detailed:

This contains the functions that create initial positions for docking You can either randomize partner 1 or partner 2, spin partner 2, or perform a simple perturbation. Also contains docking mcm protocol

Author

Monica Berrondo

Detailed:

This contains the functions that create initial positions for docking

Author

Ingemar Andre

Function Documentation

static core::Size rot

(

2

)

Referenced by core::pack::dunbrack::RotamerConstraint::add_residue(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::docking::DockingInitialPerturbation::apply_body(), core::pack::rotamer_set::bb_independent_rotamers(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), core::pack::rotamer_set::build_dna_rotamers(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_random_dna_rotamers(), core::pack::rotamer_set::build_rna_chi_rotamers(), core::pack::rotamer_set::build_rna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(), protocols::simple_filters::RotamerBoltzmannWeight::compute_modified_ddG(), core::scoring::packstat::compute_sasa(), core::pack::rotamer_set::create_oriented_water_rotamer(), core::pack::rotamer_set::debug_dump_rotamers(), protocols::electron_density::dockPoseIntoMap(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_bbdep(), core::pack::dunbrack::SingleResidueDunbrackLibrary::hokey_template_workaround(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::init_rot_to_pack(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::initialize_bicubic_splines(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::initializeSymmOps(), core::scoring::electron_density::ElectronDensity::initializeSymmOps(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_set_to_symmetric_partner(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::orient_rotamer_set_to_symmetric_partner(), protocols::simple_filters::RotamerBoltzmannWeight::report(), protocols::multistate_design::restrict_to_canonical_aas(), core::pack::dunbrack::rotamer_from_chi(), protocols::comparative_modeling::rots_from_pose(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::rots_from_pose(), protocols::motifs::LigandMotifSearch::run(), protocols::motifs::MotifDnaPacker::run_motifs(), core::pack::dunbrack::DunbrackConstraint::score(), core::pack::dunbrack::RotamerConstraint::score(), protocols::rbsegment_relax::RBSegmentRelax::set_genericRBMoveStepsize(), protocols::rotamer_recovery::PerNativeRRReporterHuman::set_native(), protocols::sic_dock::SICFast::slide_into_contact(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::update_offset_data(), protocols::optimize_weights::PNatAAOptEPositionData::write_to_binary_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_file(), and protocols::optimize_weights::PNatAAOptEPositionData::write_to_file().

static basic::Tracer TR ( "protocols.docking.DockingInitialPerturbation"  )

static

static core::Size trans ( 1  )

static

Referenced by protocols::rbsegment_relax::HelicalGaussianMover::apply(), protocols::rbsegment_relax::GaussianRBSegmentMover::apply(), protocols::rbsegment_relax::StrandTwistingMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::docking::DockingInitialPerturbation::apply_body(), protocols::hybridization::InsertChunkMover::check_overlap(), core::scoring::electron_density::ElectronDensity::computeStats(), protocols::rbsegment_relax::RBSegmentMover::coordTransformFromThreePoints(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::initializeSymmOps(), core::scoring::electron_density::ElectronDensity::initializeSymmOps(), core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(), core::conformation::symmetry::recenter(), and protocols::rbsegment_relax::RBSegmentRelax::set_genericRBMoveStepsize().