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Namespaces | Functions
DockingInitialPerturbation.cc File Reference

initial position functions More...

#include <protocols/docking/DockingInitialPerturbation.hh>
#include <protocols/docking/DockingInitialPerturbationCreator.hh>
#include <protocols/docking/DockingSlideIntoContactCreator.hh>
#include <protocols/docking/metrics.hh>
#include <core/conformation/membrane/SpanningTopology.hh>
#include <core/conformation/membrane/MembraneInfo.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/membrane/geometry/EmbeddingDef.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/docking/RigidBodyInfo.hh>
#include <protocols/docking/EllipsoidalRandomizationMover.hh>
#include <protocols/scoring/Interface.hh>
#include <basic/datacache/DataMap.hh>
#include <core/pose/selection.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/subpose_manipulation_util.hh>
#include <core/conformation/Conformation.hh>
#include <core/kinematics/FoldTree.hh>
#include <basic/options/option.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/energy_methods/RG_Energy_Fast.hh>
#include <basic/options/keys/mp.OptionKeys.gen.hh>
#include <ObjexxFCL/string.functions.hh>
#include <string>
#include <numeric/trig.functions.hh>
#include <numeric/xyzMatrix.fwd.hh>
#include <basic/Tracer.hh>
#include <utility>
#include <utility/tools/make_vector1.hh>
#include <utility/tag/Tag.hh>
#include <protocols/membrane/util.hh>
#include <basic/options/keys/docking.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/vector1.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/moves/mover_schemas.hh>

Namespaces

 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)
 
void protocols::docking::move_apart (core::pose::Pose &pose, int jump, core::Vector const &axis)
 
void protocols::docking::move_together (core::pose::Pose &pose, int jump, core::scoring::ScoreFunctionOP sfxn)
 

Detailed Description

initial position functions

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

This contains the functions that create initial positions for docking

Author
Ingemar Andre

Function Documentation

static core::Size rot ( )

Referenced by core::pack::dunbrack::RotamerConstraint::add_residue(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), protocols::hbnet::HBNet::append_to_network_vector(), protocols::rigid::UniformRigidBodyMover::apply(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::minimization_packing::BoltzmannRotamerMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::docking::DockingInitialPerturbation::apply_body(), protocols::electron_density::DensitySymmInfo::autocorrelate(), core::pack::rotamer_set::bb_independent_rotamers(), core::pack::dunbrack::DunbrackConstraint::bin_matches(), 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::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_proton_chi_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(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_sew_waters_to_donor(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(), protocols::mean_field::FlexBBMeanField::calc_bb_boltz_probs(), protocols::mean_field::FlexBBMeanField::calc_exp_value_rot_matrix(), protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG(), core::scoring::packstat::compute_sasa(), protocols::mean_field::MeanField::converge(), protocols::mean_field::MeanField::convert_energies_to_alt_rm(), core::pack::rotamer_set::create_oriented_water_rotamer(), core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(), core::pack::rotamer_set::debug_dump_rotamers(), protocols::electron_density::DockIntoDensityMover::density_grid_search(), core::pack::hbonds::determine_atom_level_node_info(), core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(), core::pack::interaction_graph::estimate_n_2body_calcs_for_linmem_ig(), protocols::splice::RotLibdb::fill_rotamer_matrix_from_db_file(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::fill_rotamer_matrix_from_db_file(), core::pack::hbonds::HBondGraphInitializerIG::find_symmetric_hbonds(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_probability_for_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_bbdep(), protocols::mean_field::MeanField::has_converged(), protocols::hbnet::hbnet_symm_one_body_energies(), core::pack::dunbrack::SingleResidueDunbrackLibrary::hokey_template_workaround(), protocols::mean_field::AAMatrix::init(), protocols::mean_field::RotMatrix::init(), core::pack::hbonds::init_node_info(), protocols::pose_metric_calculators::RotamerBoltzCalculator::init_rot_to_pack(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::initialize_bicubic_splines(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::initializeSymmOps(), core::pack::dunbrack::interpolate_rotamers(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue(), protocols::electron_density::DockIntoDensityMover::map_from_spectrum(), core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_set_to_symmetric_partner(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::orient_rotamer_set_to_symmetric_partner(), core::scoring::lkball::LK_BallEnergy::prepare_rotamers_for_packing(), core::chemical::read_topology_file(), protocols::mean_field::FlexBBMeanField::renumber_rotamers(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::report(), protocols::multistate_design::restrict_to_canonical_aas(), core::pack::dunbrack::rotamer_from_chi(), protocols::comparative_modeling::rots_from_pose(), protocols::pose_metric_calculators::RotamerRecovery::rots_from_pose(), protocols::motifs::LigandMotifSearch::run(), protocols::motifs::MotifDnaPacker::run_motifs(), core::pack::dunbrack::RotamerConstraint::score(), protocols::electron_density::DockIntoDensityMover::select_points(), protocols::minimization_packing::BoltzmannRotamerMover::select_rotamer(), protocols::rbsegment_relax::RBSegmentRelax::set_genericRBMoveStepsize(), protocols::rotamer_recovery::PerNativeRRReporterHuman::set_native(), core::pack::rotamer_set::RotamerSubset::show(), core::pack::rotamer_set::RotamerSet_::show(), core::conformation::UltraLightResidue::slide(), protocols::sic_dock::SICFast::slide_into_contact(), core::pack::rotamer_set::sort_new_rotamers_into_rotset_vector(), core::conformation::UltraLightResidue::transform(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::update_offset_data(), core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(), 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 ( )
static