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protocols::protein_interface_design Namespace Reference

Namespaces

 filters
 
 movers
 

Classes

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

Typedefs

typedef
utility::pointer::owning_ptr
< DockDesignFilterFactory
DockDesignFilterFactoryOP
 
typedef
utility::pointer::owning_ptr
< DockDesignFilterFactory
const > 
DockDesignFilterFactoryCOP
 
typedef
utility::pointer::owning_ptr
< ParserJobInputter
PatchdockJobInputterOP
 
typedef
utility::pointer::owning_ptr
< ParserJobInputter const > 
PatchdockJobInputterCOP
 

Functions

core::Real sum_total_residue_energy (core::pose::Pose const &pose, core::Size const resid)
 
void transform_pose (core::pose::Pose &pose, core::Size const chain, Transformation const &t)
 
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

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

Detailed: 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.

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 core::scoring::dssp::Dssp::insert_ss_into_pose(), core::pose::Pose::secstruct(), and core::pose::Pose::total_residue().

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)
core::kinematics::FoldTree protocols::protein_interface_design::make_hotspot_foldtree ( core::pose::Pose const &  pose)
std::string protocols::protein_interface_design::optimal_connection_point ( std::string const  residue_type)
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(), core::sequence::end, and core::pose::Pose::remove_constraints().

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design(), 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 ( core::pose::Pose const &  pose,
core::Size const  resid 
)
void protocols::protein_interface_design::transform_pose ( core::pose::Pose pose,
core::Size const  chain,
Transformation const &  t 
)