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protocols::protein_interface_design Namespace Reference

Namespaces

 filters
 
 movers
 

Classes

class  FavorNativeResidue
 
class  FavorNonNativeResidue
 
class  ParserJobInputter
 
class  ParserJobInputterCreator
 
class  PatchdockReader
 
class  ReportPSSMDifferences
 
class  ReportSequenceDifferences
 
class  Revert
 
struct  Transformation
 

Typedefs

using Real = core::Real
 
using Pose = core::pose::Pose
 
typedef
utility::pointer::shared_ptr
< ParserJobInputter
PatchdockJobInputterOP
 
typedef
utility::pointer::shared_ptr
< ParserJobInputter const > 
PatchdockJobInputterCOP
 
typedef
utility::pointer::shared_ptr
< PatchdockReader
PatchdockReaderOP
 
typedef
utility::pointer::shared_ptr
< PatchdockReader const > 
PatchdockReaderCOP
 

Functions

static basic::Tracer TR ("protocols.protein_interface_design.design_utils")
 
core::Real sum_total_residue_energy (pose::Pose const &pose, core::Size const resid)
 
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 (core::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=false)
 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 (core::pose::Pose const &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=false, core::scoring::ScoreFunctionOP sfxn=nullptr)
 utility function for finding hbonding partners among a list of potential binder residues to a specific target More...
 
std::list< core::Sizehbonded_atom (core::pose::Pose const &pose, core::Size const target_residue, std::string const &target_atom, std::set< core::Size > const &binders, bool const bb, bool const sc, core::Real const energy_thres, bool const bb_bb=false, core::scoring::ScoreFunctionOP sfxn=nullptr)
 utility function for finding hbonding partners among a list of potential binder residues to a specific target More...
 
core::kinematics::FoldTree star_fold_tree (core::pose::Pose &pose)
 generate a star fold tree (originating at residue 1) More...
 
std::string optimal_connection_point (std::string const &residue_type)
 what is the optimal connection point for an atom tree, given a residue type (puts the connection point at the beginning of a functional group More...
 
core::kinematics::FoldTree make_hotspot_foldtree (core::pose::Pose const &pose)
 
core::scoring::constraints::ConstraintCOPs get_bbcsts (core::pose::Pose const &pose)
 
utility::vector1< core::Sizebest_bbcst_residues (core::pose::Pose const &pose, core::Size const chain, core::Size const n_return)
 evaluate backbone_stub_constraints for each residue in a chain and return a vector with the top n_return residue numbers by cst score note that this function is NOT guaranteed to return n_return residues! It will return the best n<=n_return More...
 
void find_lowest_constraint_energy_residue (core::pose::Pose const &pose, core::Size const chain, core::Size &resi, core::Real &lowest_energy)
 
core::scoring::constraints::ConstraintCOPs remove_coordinate_constraints_from_pose (core::pose::Pose &pose)
 removes ALL coordinate constraints from a pose. returns the constraints that were removed More...
 
core::Size best_cutpoint (core::pose::Pose &pose, core::Size const prev_u, core::Size const prev_d, core::Size const u, core::Size const d)
 utility function for stub_based_atom_tree. tries to find an optimal cutpoint in a pose given two different boundaries. More...
 
core::Size find_nearest_residue (core::pose::Pose const &pose, core::Size const target_chain, core::Size const res, std::string const &atom="CA")
 find nearest residue on target_chain to res More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< PatchdockReader const > protocols::protein_interface_design::PatchdockReaderCOP

Function Documentation

utility::vector1< core::Size > protocols::protein_interface_design::best_bbcst_residues ( core::pose::Pose const &  pose,
core::Size const  chain,
core::Size const  n_return 
)

evaluate backbone_stub_constraints for each residue in a chain and return a vector with the top n_return residue numbers by cst score note that this function is NOT guaranteed to return n_return residues! It will return the best n<=n_return

a utility function to evaluate backbone_stub_constraints for each residue in a chain and return a vector with the top n_return residue numbers by cst score note that this function is NOT guaranteed to return n_return residues! It will return the best n<=n_return

References core::scoring::backbone_stub_constraint, and protocols::hybridization::score.

Referenced by protocols::protein_interface_design::movers::BestHotspotCstMover::apply().

core::Size protocols::protein_interface_design::best_cutpoint ( core::pose::Pose pose,
core::Size const  prev_u,
core::Size const  prev_d,
core::Size const  u,
core::Size const  d 
)

utility function for stub_based_atom_tree. tries to find an optimal cutpoint in a pose given two different boundaries.

utility function for stub_based_atom_tree. tries to find an optimal cutpoint in a pose given two different boundaries. First looks for a 3-res loop stretch on the downstream partner and returns the middle residue. Then, does the same for the upstream chain. Then, becomes desperate and tries to find any loop residue on downstream chain, and then on upstream chain. Finally, if no success, returns 0 which means that no break was found

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::insert_ss_into_pose(), core::pose::Pose::secstruct(), and core::pose::Pose::size().

core::Real protocols::protein_interface_design::ddG_cycles ( pose::Pose const &  pose,
core::scoring::ScoreFunctionOP  scorefxn,
core::Size const  cycles 
)
void protocols::protein_interface_design::find_lowest_constraint_energy_residue ( core::pose::Pose const &  pose,
core::Size const  chain,
core::Size resi,
core::Real lowest_energy 
)
core::Size protocols::protein_interface_design::find_nearest_residue ( core::pose::Pose const &  pose,
core::Size const  target_chain,
core::Size const  res,
std::string const &  atom 
)
core::scoring::constraints::ConstraintCOPs protocols::protein_interface_design::get_bbcsts ( core::pose::Pose const &  pose)
std::list< core::Size > protocols::protein_interface_design::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,
core::scoring::ScoreFunctionOP  sfxn 
)
std::list< core::Size > protocols::protein_interface_design::hbonded_atom ( Pose const &  in_pose,
core::Size const  target_residue,
std::string const &  target_atom,
std::set< core::Size > const &  binders,
bool const  bb,
bool const  sc,
core::Real const  energy_thres,
bool const  bb_bb,
core::scoring::ScoreFunctionOP  sfxn 
)
core::kinematics::FoldTree protocols::protein_interface_design::make_hotspot_foldtree ( core::pose::Pose const &  pose)
void protocols::protein_interface_design::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(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::kinematics::distance(), core::sequence::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(), core::kinematics::MoveMap::set_bb(), core::pose::Pose::size(), 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().

std::string protocols::protein_interface_design::optimal_connection_point ( std::string const &  residue_type)

what is the optimal connection point for an atom tree, given a residue type (puts the connection point at the beginning of a functional group

References protocols::protein_interface_design::movers::connect_to(), and TR().

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::splice::Splice::fold_tree(), and make_hotspot_foldtree().

void protocols::protein_interface_design::point_mutation ( pose::Pose pose,
core::scoring::ScoreFunctionCOP  scorefxn,
core::Size const  seqpos,
core::Size const  mutation 
)
core::scoring::constraints::ConstraintCOPs protocols::protein_interface_design::remove_coordinate_constraints_from_pose ( core::pose::Pose pose)

removes ALL coordinate constraints from a pose. returns the constraints that were removed

a utility function for removing ALL coordinate constraints from a pose. returns the constraints that were removed

References core::pose::Pose::constraint_set(), and core::pose::Pose::remove_constraints().

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), and protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints().

core::kinematics::FoldTree protocols::protein_interface_design::star_fold_tree ( core::pose::Pose pose)
core::Real protocols::protein_interface_design::sum_total_residue_energy ( pose::Pose const &  pose,
core::Size const  resid 
)
void protocols::protein_interface_design::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 
)
static basic::Tracer protocols::protein_interface_design::TR ( "protocols.protein_interface_design.design_utils"  )
static