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Rosetta Protocols
2015.22
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#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/chemical/AA.hh>
#include <core/types.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <core/scoring/constraints/NonResidueTypeConstraint.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/kinematics/FoldTree.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <protocols/protein_interface_design/design_utils.hh>
#include <protocols/simple_moves/ddG.hh>
#include <ObjexxFCL/format.hh>
#include <map>
#include <utility/vector0.hh>
#include <boost/lexical_cast.hpp>
Typedefs | |
typedef core::Real | Real |
typedef core::Size | Size |
typedef core::pose::Pose | Pose |
Functions | |
static thread_local basic::Tracer | TR ("protocols.protein_interface_design.design_utils") |
core::Real | ddG_cycles (pose::Pose const &pose, core::scoring::ScoreFunctionOP scorefxn, core::Size const cycles) |
void | point_mutation (pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const seqpos, core::Size const mutation) |
void | MinimizeInterface (pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, utility::vector1< bool > const min_bb, utility::vector1< bool > const min_sc, utility::vector1< bool > const min_rb, bool const optimize_foldtree, utility::vector1< core::Size > const target_residues, bool const simultaneous_minimization) |
utility function for minimizing sidechain in rigid-body dof, the interface sc, and bb in the entire protein. More... | |
void | SymMinimizeInterface (pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, utility::vector1< bool > const min_bb, utility::vector1< bool > const min_sc, utility::vector1< bool > const min_rb, bool const simultaneous_minimization) |
std::list< core::Size > | hbonded (Pose const &in_pose, core::Size const target_residue, std::set< core::Size > const &binders, bool const bb, bool const sc, core::Real const energy_thres, bool const bb_bb) |
utility function for finding hbonding partners among a list of potential binder residues to a specific target More... | |
std::list< core::Size > | hbonded_atom (Pose const &in_pose, core::Size const target_residue, std::string target_atom, std::set< core::Size > const &binders, bool const bb, bool const sc, core::Real const energy_thres, bool const bb_bb) |
utility function for finding hbonding partners among a list of potential binder residues to a specific target More... | |
typedef core::Real Real |
core::Real ddG_cycles | ( | pose::Pose const & | pose, |
core::scoring::ScoreFunctionOP | scorefxn, | ||
core::Size const | cycles | ||
) |
References protocols::simple_moves::ddG::calculate(), and protocols::simple_moves::ddG::sum_ddG().
Referenced by protocols::protein_interface_design::Revert::apply().
std::list< core::Size > hbonded | ( | Pose const & | in_pose, |
core::Size const | target_residue, | ||
std::set< core::Size > const & | binders, | ||
bool const | bb, | ||
bool const | sc, | ||
core::Real const | energy_thres, | ||
bool const | bb_bb | ||
) |
utility function for finding hbonding partners among a list of potential binder residues to a specific target
References distance(), F, get_hbond_energies(), core::scoring::get_score_function(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, I, identify_hbonds_1way(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), and core::scoring::TR().
Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), and protocols::protein_interface_design::filters::HbondsToResidueFilter::compute().
std::list< core::Size > hbonded_atom | ( | Pose const & | in_pose, |
core::Size const | target_residue, | ||
std::string | target_atom, | ||
std::set< core::Size > const & | binders, | ||
bool const | bb, | ||
bool const | sc, | ||
core::Real const | energy_thres, | ||
bool const | bb_bb | ||
) |
utility function for finding hbonding partners among a list of potential binder residues to a specific target
References core::conformation::Residue::atom_base(), core::conformation::Residue::atom_index(), distance(), F, get_hbond_energies(), core::scoring::get_score_function(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, I, identify_hbonds_1way(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), and core::scoring::TR().
Referenced by protocols::protein_interface_design::filters::HbondsToAtomFilter::compute().
void MinimizeInterface | ( | pose::Pose & | pose, |
core::scoring::ScoreFunctionCOP | scorefxn, | ||
utility::vector1< bool > const | min_bb, | ||
utility::vector1< bool > const | min_sc, | ||
utility::vector1< bool > const | min_rb, | ||
bool const | optimize_foldtree, | ||
utility::vector1< core::Size > const | target_residues, | ||
bool const | simultaneous_minimization | ||
) |
utility function for minimizing sidechain in rigid-body dof, the interface sc, and bb in the entire protein.
minimize the interface between two partners. If target_residues is defined the fold_tree for minimization is set up between the central residue in the target residues and the nearest residue on the partner. if simultaneous minimization is true, then all dofs are minimized at once.
References core::kinematics::FoldTree::add_edge(), begin, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), distance(), end, core::pose::Pose::fold_tree(), core::conformation::Residue::is_protein(), core::pose::Pose::num_jump(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), runtime_assert, core::kinematics::MoveMap::set_bb(), core::pose::Pose::total_residue(), core::scoring::TR(), core::pose::Pose::update_residue_neighbors(), and core::conformation::Residue::xyz().
Referenced by protocols::protein_interface_design::movers::PlacementMinimizationMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_no_bb(), protocols::protein_interface_design::movers::MapHotspot::MinimizeHotspots(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), and protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize().
void point_mutation | ( | pose::Pose & | pose, |
core::scoring::ScoreFunctionCOP | scorefxn, | ||
core::Size const | seqpos, | ||
core::Size const | mutation | ||
) |
void SymMinimizeInterface | ( | pose::Pose & | pose, |
core::scoring::ScoreFunctionCOP | scorefxn, | ||
utility::vector1< bool > const | min_bb, | ||
utility::vector1< bool > const | min_sc, | ||
utility::vector1< bool > const | min_rb, | ||
bool const | simultaneous_minimization | ||
) |
References core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::pose::Pose::residue(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), runtime_assert, core::kinematics::MoveMap::set_bb(), core::pose::Pose::total_residue(), core::scoring::TR(), and core::pose::Pose::update_residue_neighbors().
Referenced by protocols::protein_interface_design::movers::RepackMinimize::apply().
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