Rosetta Protocols  2014.35
Typedefs | Functions | Variables
design_utils.cc File Reference

various utilities for interface design. More...

#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

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::Sizehbonded (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::Sizehbonded_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...
 

Variables

static basic::Tracer TR ("protocols.protein_interface_design.design_utils")
 

Detailed Description

various utilities for interface design.

Author
Sarel Fleishman (sarel.nosp@m.f@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)

Typedef Documentation

Function Documentation

core::Real ddG_cycles ( pose::Pose const &  pose,
core::scoring::ScoreFunctionOP  scorefxn,
core::Size const  cycles 
)
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 
)
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 
)
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.

Detailed: 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(), nres, core::pose::Pose::num_jump(), optimization, 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 
)

Variable Documentation

basic::Tracer TR("protocols.protein_interface_design.design_utils")
static