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protocols::generalized_kinematic_closure Namespace Reference

Namespaces

 filter
 
 perturber
 
 selector
 

Classes

class  GeneralizedKIC
 
class  GeneralizedKICCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< GeneralizedKIC
GeneralizedKICOP
 
typedef
utility::pointer::shared_ptr
< GeneralizedKIC const > 
GeneralizedKICCOP
 
typedef utility::vector1
< GeneralizedKICOP
GeneralizedKICOPs
 
typedef utility::vector1
< GeneralizedKICCOP
GeneralizedKICCOPs
 

Functions

static basic::Tracer TR ("protocols.generalized_kinematic_closure.GeneralizedKIC")
 
std::string gen_kic_subelement_mangler (std::string const &element_name)
 
std::string gen_kic_sample_cis_subelement_mangler (std::string const &element_name)
 
std::string gen_kic_add_pert_subelement_mangler (std::string const &element_name)
 
std::string gen_kic_add_filter_subelement_mangler (std::string const &element_name)
 
static basic::Tracer TR ("protocols.generalized_kinematic_closure.util")
 
bool is_in_list (core::Size const val, utility::vector1< core::Size > const &list)
 Function to determine whether a value is in a list. More...
 
bool original_pose_residue_is_in_residue_map (core::Size const residue_index, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
 function to determine whether a residue index from the original pose is in the residue_map list. More...
 
void set_loop_pose (core::pose::Pose &pose, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &t_ang, utility::vector1< core::Real > const &b_ang, utility::vector1< core::Real > const &b_len)
 Set the loop pose conformation based on a set of results from kinematic closure. More...
 
void set_loop_pose (core::pose::Pose &pose, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &t_ang)
 Set the loop pose conformation based on a set of results from kinematic closure. More...
 
void copy_loop_pose_to_original (core::pose::Pose &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map)
 Copy the atom positions of the residues in the loop pose to the original pose. More...
 
void correct_polymer_dependent_atoms_in_pose_segment (core::pose::Pose &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
 Update the polymer bond-dependent atom positions for every residue in the residue map. More...
 
void general_set_phi (core::pose::Pose &pose, core::Size const residue_index, core::Real const &phi_value)
 Sets phi for an L-alpha amino acid, even if the nitrogen has a nonstandard connection. More...
 
void general_set_psi (core::pose::Pose &pose, core::Size const residue_index, core::Real const &psi_value)
 Sets psi for an L-alpha amino acid, even if the carbonyl carbon has a nonstandard connection. More...
 
core::Size get_original_pose_rsd (core::Size const perturbedloop_rsd, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
 Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >, and a residue index in the perturbed loop, return the corresponding residue index in the original pose. More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< GeneralizedKIC const > protocols::generalized_kinematic_closure::GeneralizedKICCOP

Function Documentation

void protocols::generalized_kinematic_closure::copy_loop_pose_to_original ( core::pose::Pose original_pose,
core::pose::Pose const &  loop_pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map,
utility::vector1< std::pair< core::Size, core::Size > > const &  tail_residue_map 
)
void protocols::generalized_kinematic_closure::correct_polymer_dependent_atoms_in_pose_segment ( core::pose::Pose original_pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map 
)
std::string protocols::generalized_kinematic_closure::gen_kic_add_filter_subelement_mangler ( std::string const &  element_name)
std::string protocols::generalized_kinematic_closure::gen_kic_add_pert_subelement_mangler ( std::string const &  element_name)
std::string protocols::generalized_kinematic_closure::gen_kic_sample_cis_subelement_mangler ( std::string const &  element_name)
std::string protocols::generalized_kinematic_closure::gen_kic_subelement_mangler ( std::string const &  element_name)
void protocols::generalized_kinematic_closure::general_set_phi ( core::pose::Pose pose,
core::Size const  residue_index,
core::Real const &  phi_value 
)
void protocols::generalized_kinematic_closure::general_set_psi ( core::pose::Pose pose,
core::Size const  residue_index,
core::Real const &  psi_value 
)
core::Size protocols::generalized_kinematic_closure::get_original_pose_rsd ( core::Size const  perturbedloop_rsd,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map 
)

Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >, and a residue index in the perturbed loop, return the corresponding residue index in the original pose.

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), and protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots().

bool protocols::generalized_kinematic_closure::is_in_list ( core::Size const  val,
utility::vector1< core::Size > const &  list 
)

Function to determine whether a value is in a list.

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs().

bool protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map ( core::Size const  residue_index,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_map 
)

function to determine whether a residue index from the original pose is in the residue_map list.

Returns true if the residue index in the original pose has been mapped to a residue in the loop, false otherwise.

Parameters
[in]residue_index- The index of a residue in the original pose.
[in]residue_map- A vector of pairs of indices. Each pair is (index in loop, index in original pose).

Referenced by protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_backbone_bin(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), and protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check().

void protocols::generalized_kinematic_closure::set_loop_pose ( core::pose::Pose pose,
utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &  atomlist,
utility::vector1< core::Real > const &  t_ang,
utility::vector1< core::Real > const &  b_ang,
utility::vector1< core::Real > const &  b_len 
)

Set the loop pose conformation based on a set of results from kinematic closure.

Parameters
[in,out]poseA pose consisting of the loop to be closed only.
[in]atomlistA list of AtomIDs and corresponding xyz coordinates (though we don't use the latter) of the chain of atoms closed by KIC. Note that the residue indices refer to the loop pose, not the original pose.
[in]t_ang– The torsion angles values to set.
[in]b_ang– The bond angle values to set.
[in]b_len– The bond length values to set.
[in,out]poseA pose consisting of the loop to be closed only.
[in]atomlistA list of AtomIDs and corresponding xyz coordinates (though we don't use the latter) of the chain of atoms closed by KIC. Note that the residue indices refer to the loop pose, not the original pose.
[in]torsions– The torsion angles values to set.
[in]bondangles– The bond angle values to set.
[in]bondlengths– The bond length values to set.

References core::pose::Pose::conformation(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::conformation::Conformation::set_torsion_angle(), TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_backbone_bin(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_lowest_rmsd_selector(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), protocols::generalized_kinematic_closure::GeneralizedKIC::doKIC(), and protocols::generalized_kinematic_closure::GeneralizedKIC::set_final_solution().

void protocols::generalized_kinematic_closure::set_loop_pose ( core::pose::Pose pose,
utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &  atomlist,
utility::vector1< core::Real > const &  t_ang 
)

Set the loop pose conformation based on a set of results from kinematic closure.

This version ONLY sets mainchain torsions, and does no rebuilding of mainchain O or H atoms.

Parameters
[in,out]poseA pose consisting of the loop to be closed only.
[in]atomlistA list of AtomIDs and corresponding xyz coordinates (though we don't use the latter) of the chain of atoms closed by KIC. Note that the residue indices refer to the loop pose, not the original pose.
[in]torsions– The torsion angles values to set.

References core::pose::Pose::conformation(), core::conformation::Conformation::set_torsion_angle(), and core::pose::Pose::update_residue_neighbors().

static basic::Tracer protocols::generalized_kinematic_closure::TR ( "protocols.generalized_kinematic_closure.util"  )
static
static basic::Tracer protocols::generalized_kinematic_closure::TR ( "protocols.generalized_kinematic_closure.GeneralizedKIC"  )
static