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protocols::sic_dock Namespace Reference

Namespaces

 scores
 

Classes

struct  AtomIDHashFunction
 
class  BuriedPolarScore
 
class  CBScore
 
struct  CBScoreVisitor
 
class  ConstraintSetScore
 
struct  CorrectionVisitor
 
class  EdgeStandScore
 
class  HelixScore
 
class  JointScore
 
class  LinkerScore
 
class  NoPoseXYX_Func
 
class  RigidScore
 
class  Rose
 
class  SICFast
 
struct  Vec3
 
struct  XfoxmScore
 
class  xyzStripeHashPoseWithMeta
 

Typedefs

using Vec = numeric::xyzVector< platform::Real >
 
using Mat = numeric::xyzMatrix< platform::Real >
 
using Real = core::Real
 
using Pose = core::pose::Pose
 
using Xform = Xform
 
using Vecs = utility::vector1< Vec >
 
using Reals = utility::vector1< Real >
 
using Sizes = utility::vector1< core::Size >
 
using Xforms = numeric::Xforms
 
using Scores = utility::vector1< RigidScoreCOP >
 
typedef
utility::pointer::shared_ptr
< RigidScore
RigidScoreOP
 
typedef
utility::pointer::shared_ptr
< RigidScore const > 
RigidScoreCOP
 
typedef
utility::pointer::shared_ptr
< CBScore
CBScoreOP
 
typedef
utility::pointer::shared_ptr
< CBScore const > 
CBScoreCOP
 
typedef
utility::pointer::shared_ptr
< LinkerScore
LinkerScoreOP
 
typedef
utility::pointer::shared_ptr
< LinkerScore const > 
LinkerScoreCOP
 
typedef
utility::pointer::shared_ptr
< ConstraintSetScore
ConstraintSetScoreOP
 
typedef
utility::pointer::shared_ptr
< ConstraintSetScore const > 
ConstraintSetScoreCOP
 
typedef
utility::pointer::shared_ptr
< JointScore
JointScoreOP
 
typedef
utility::pointer::shared_ptr
< JointScore const > 
JointScoreCOP
 
typedef
utility::pointer::shared_ptr
< SICFast
SICFastOP
 
typedef
utility::pointer::shared_ptr
< SICFast const > 
SICFastCOP
 
typedef utility::vector1
< std::pair< platform::Size,
Vec3 > > 
TermInfo
 
typedef utility::vector1< MatMats
 
typedef
utility::pointer::shared_ptr
< xyzStripeHashPoseWithMeta
xyzStripeHashPoseWithMetaOP
 
typedef
utility::pointer::shared_ptr
< xyzStripeHashPoseWithMeta
const > 
xyzStripeHashPoseWithMetaCOP
 

Functions

void get_xform_stats (Xform const &sir, Xform const &sjr, Real &dx, Real &dy, Real &dz, Real &ex, Real &ey, Real &ez)
 
Vec3 get_leap_lower_stub (core::pose::Pose const &pose, core::Size ir)
 
Vec3 get_leap_upper_stub (core::pose::Pose const &pose, core::Size ir)
 
Xform vec3_to_stub (Vec3 const &v3)
 
Xform vec3_to_stub (Xform const &xform, Vec3 const &v3)
 
void get_termini_from_pose (core::pose::Pose const &pose, core::Size ir, TermInfo &lowers, TermInfo &uppers)
 
void get_termini_from_pose (core::pose::Pose const &pose, TermInfo &lowers, TermInfo &uppers)
 
numeric::geometry::hashing::Real6 get_leap_6dof (Xform const &lower, Xform const &upper)
 
core::Size count_linkers (Xform const &lower, Xform const &upper, protocols::loophash::LoopHashLibraryCOP loop_hash_library, Sizes const &loopsizes, core::Size radius)
 
core::Size dump_loophash_linkers (Xform const &lower, Xform const &upper, protocols::loophash::LoopHashLibraryCOP loop_hash_library, Sizes const &loopsizes, core::Size radius, std::string const &outtag)
 
Real linker_count2score (core::Size count)
 
platform::Size count_linkers (Xform const &lower, Xform const &upper, protocols::loophash::LoopHashLibraryCOP loop_hash_library, utility::vector1< platform::Size > const &loopsizes, platform::Size radius=0)
 
platform::Size dump_loophash_linkers (Xform const &lower, Xform const &upper, protocols::loophash::LoopHashLibraryCOP loop_hash_library, utility::vector1< platform::Size > const &loopsizes, platform::Size radius=0, std::string const &outtag="")
 
bool read_biounit (string const &fname, Pose &pose, int max_res, bool debug)
 
bool read_biounit (string const &fname, Pose &pose, utility::vector1< Real > &bfactors, utility::vector1< Real > &occupancy, int max_res, bool debug)
 
bool read_biounit (string const &fname, Pose &pose, vector1< Real > &bfactors, vector1< Real > &occupancy, vector1< int > &pdbres, std::map< int, char > &pdbchain, int &nresmodel1, int max_res, bool debug)
 
bool read_biounit (std::string const &fname, core::pose::Pose &pose, utility::vector1< core::Real > &bfactors, utility::vector1< core::Real > &occupancy, int max_res=9999999, bool debug=false)
 
bool read_biounit (std::string const &fname, core::pose::Pose &pose, utility::vector1< core::Real > &bfactors, utility::vector1< core::Real > &occupancy, utility::vector1< int > &pdbres, std::map< int, char > &pdbchain, int &nresmodel1, int max_res=9999999, bool debug=false)
 
static basic::Tracer TR ("protocols.sic_dock.RigidScore")
 
std::ostream & operator<< (std::ostream &out, Vec3 v)
 
template<typename T >
CBScore_dist_score (T const &sqdist, T const &start, T const &stop)
 
core::Real dist_score (core::Real const &sqdist, core::Real const &start, core::Real const &stop)
 
bool get_bounds_intersection (vector1< Vec > const &pb, vector1< Vec > const &pa, core::Real &xmx, core::Real &xmn, core::Real &ymx, core::Real &ymn)
 
void fill_plane_hash (vector1< Vec > const &pb, vector1< Vec > const &pa, core::Real const &xmx, core::Real const &xmn, core::Real const &ymx, core::Real const &ymn, core::Real const &BIN, ObjexxFCL::FArray2D< Vec > &ha, ObjexxFCL::FArray2D< Vec > &hb, int &xlb, int &ylb, int &xub, int &yub)
 
core::Real get_mindis_with_plane_hashes (int const &xlb, int const &ylb, int const &xub, int const &yub, ObjexxFCL::FArray2D< Vec > const &ha, ObjexxFCL::FArray2D< Vec > const &hb, core::Real const &clashdis2)
 
core::Real refine_mindis_with_xyzHash (xyzStripeHashPose *xh, Xform const &xform_to_struct2_start, vector1< Vec > const &pa, vector1< Real > const &radii, Vec const &ori, core::Real const &clash_dis_sq, core::Real const &mindis_approx)
 
static basic::Tracer TR ("protocols.sic_dock.util")
 
Real get_rg (core::pose::Pose const &pose)
 
int neighbor_count (core::pose::Pose const &pose, int ires, core::Real distance_threshold)
 
Real cb_weight (core::pose::Pose const &pose, core::Size ires, Real distance_threshold)
 
void make_Cx (core::pose::Pose &pose, int N, numeric::xyzVector< core::Real > axis)
 
core::Real slide_into_contact_and_score (protocols::sic_dock::SICFast const &sic, protocols::sic_dock::RigidScore const &sfxn, Xform &xa, Xform const &xb, numeric::xyzVector< core::Real > const &ori, core::Real &score)
 
core::Real slide_into_contact_and_score_DEPRICATED (protocols::sic_dock::SICFast const &sic, protocols::sic_dock::RigidScore const &sfxn, core::kinematics::Stub &xa, core::kinematics::Stub const &xb, numeric::xyzVector< core::Real > const &ori, core::Real &score)
 
core::id::AtomID_Map< core::Realcb_weight_map_from_pose (core::pose::Pose const &pose)
 
core::Size count_CBs (core::pose::Pose const &pose)
 
core::pose::Pose const & pose_with_most_CBs (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
 
bool pose1_has_most_CBs (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
 
vector1< numeric::xyzVector
< core::Real > > 
get_CB_Vecs_from_pose (core::pose::Pose const &pose)
 
vector1< numeric::xyzVector
< core::Real > > 
get_CB_Vecs_from_map (core::pose::Pose const &pose, core::id::AtomID_Map< core::Real > const &map)
 
vector1< core::Realcb_weights_from_pose (core::pose::Pose const &pose)
 
vector1< core::Realcb_weights_from_map (core::pose::Pose const &pose, core::id::AtomID_Map< core::Real > const &map)
 
vector1< core::Sizerange (core::Size beg, core::Size end)
 
int flood_fill3D (int i, int j, int k, ObjexxFCL::FArray3D< core::Real > &grid, core::Real t)
 
bool residue_is_floppy (core::pose::Pose const &pose, core::Size const ir, Real const ttrim_cut, core::Size const nfold)
 
void auto_trim_floppy_termini (core::pose::Pose &pose, Real const ttrim_cut, core::Size const nfold)
 
void dump_points_pdb (vector1< Vec > const &p, std::string fn)
 
void dump_points_pdb (vector1< Vec > const &p, Vec t, std::string fn)
 
void trans_pose (Pose &pose, Vec const &trans, core::Size start, core::Size end)
 
void rot_pose (Pose &pose, Mat const &rot, core::Size start, core::Size end)
 
void rot_pose (Pose &pose, Mat const &rot, Vec const &cen, core::Size start, core::Size end)
 
void rot_pose (Pose &pose, Vec const &axis, Real const &ang, core::Size start, core::Size end)
 
void rot_pose (Pose &pose, Vec const &axis, Real const &ang, Vec const &cen, core::Size start, core::Size end)
 
void alignaxis (Pose &pose, Vec newaxis, Vec oldaxis, Vec cen)
 
numeric::xyzTransform< core::Realalignaxis_xform (numeric::xyzVector< core::Real > newaxis, numeric::xyzVector< core::Real > oldaxis, numeric::xyzVector< core::Real > cen)
 
void xform_pose (core::pose::Pose &pose, core::kinematics::Stub const &s, core::Size sres, core::Size eres)
 
void xform_pose_rev (core::pose::Pose &pose, core::kinematics::Stub const &s)
 
void xform_pose (core::pose::Pose &pose, numeric::xyzTransform< core::Real > const &s, core::Size sres, core::Size eres)
 
void xform_pose_rev (core::pose::Pose &pose, numeric::xyzTransform< core::Real > const &s)
 
Vec center_of_geom (core::pose::Pose const &pose, core::Size str, core::Size end)
 
core::kinematics::Stub getxform (core::conformation::Residue const &move_resi, core::conformation::Residue const &fixd_resi)
 
Real brute_mindis (vector1< Vec > const &pa, vector1< Vec > const &pb, Vec const &ofst=Vec(0, 0, 0))
 
std::string KMGT (core::Real const &x, int const &w, int const &d)
 
Xform multstubs (Xform const &a, Xform const &b)
 
Xform invstub (Xform const &a)
 
void dump_points_pdb (utility::vector1< numeric::xyzVector< core::Real > > const &p, std::string fn)
 
void dump_points_pdb (utility::vector1< numeric::xyzVector< core::Real > > const &p, numeric::xyzVector< core::Real > t, std::string fn)
 
void trans_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &trans, core::Size start=1, core::Size end=0)
 
void rot_pose (core::pose::Pose &pose, numeric::xyzMatrix< core::Real > const &rot, core::Size start=1, core::Size end=0)
 
void rot_pose (core::pose::Pose &pose, numeric::xyzMatrix< core::Real > const &rot, numeric::xyzVector< core::Real > const &cen, core::Size start=1, core::Size end=0)
 
void rot_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &axis, core::Real const &ang, core::Size start=1, core::Size end=0)
 
void rot_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &axis, core::Real const &ang, numeric::xyzVector< core::Real > const &cen, core::Size start=1, core::Size end=0)
 
void alignaxis (core::pose::Pose &pose, numeric::xyzVector< core::Real > newaxis, numeric::xyzVector< core::Real > oldaxis, numeric::xyzVector< core::Real > cen=numeric::xyzVector< core::Real >(0, 0, 0))
 
numeric::xyzVector< core::Realprojperp (numeric::xyzVector< core::Real > const &u, numeric::xyzVector< core::Real > const &v)
 
template<typename T >
sqr (T x)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< CBScore const > protocols::sic_dock::CBScoreCOP
typedef utility::pointer::shared_ptr< CBScore > protocols::sic_dock::CBScoreOP
typedef utility::pointer::shared_ptr< ConstraintSetScore const > protocols::sic_dock::ConstraintSetScoreCOP
typedef utility::pointer::shared_ptr< ConstraintSetScore > protocols::sic_dock::ConstraintSetScoreOP
typedef utility::pointer::shared_ptr< JointScore const > protocols::sic_dock::JointScoreCOP
typedef utility::pointer::shared_ptr< JointScore > protocols::sic_dock::JointScoreOP
typedef utility::pointer::shared_ptr< LinkerScore const > protocols::sic_dock::LinkerScoreCOP
typedef utility::pointer::shared_ptr< LinkerScore > protocols::sic_dock::LinkerScoreOP
typedef numeric::xyzMatrix< Real > protocols::sic_dock::Mat
typedef utility::vector1<Mat> protocols::sic_dock::Mats
typedef vector1< Real > protocols::sic_dock::Reals
typedef utility::pointer::shared_ptr< RigidScore const > protocols::sic_dock::RigidScoreCOP
typedef utility::pointer::shared_ptr< RigidScore > protocols::sic_dock::RigidScoreOP
typedef utility::pointer::shared_ptr< SICFast const > protocols::sic_dock::SICFastCOP
typedef utility::pointer::shared_ptr< SICFast > protocols::sic_dock::SICFastOP
typedef utility::vector1<std::pair<platform::Size,Vec3> > protocols::sic_dock::TermInfo
typedef numeric::xyzVector< Real > protocols::sic_dock::Vec
typedef vector1< Vec > protocols::sic_dock::Vecs
typedef numeric::Xforms protocols::sic_dock::Xforms

Function Documentation

void protocols::sic_dock::alignaxis ( core::pose::Pose pose,
numeric::xyzVector< core::Real newaxis,
numeric::xyzVector< core::Real oldaxis,
numeric::xyzVector< core::Real cen = numeric::xyzVector< core::Real >(0, 0, 0) 
)
void protocols::sic_dock::alignaxis ( Pose pose,
Vec  newaxis,
Vec  oldaxis,
Vec  cen 
)
numeric::xyzTransform< core::Real > protocols::sic_dock::alignaxis_xform ( numeric::xyzVector< core::Real newaxis,
numeric::xyzVector< core::Real oldaxis,
numeric::xyzVector< core::Real cen 
)
void protocols::sic_dock::auto_trim_floppy_termini ( core::pose::Pose pose,
Real const  ttrim_cut,
core::Size const  nfold 
)
Real protocols::sic_dock::brute_mindis ( vector1< Vec > const &  pa,
vector1< Vec > const &  pb,
Vec const &  ofst = Vec(0,0,0) 
)
core::Real protocols::sic_dock::cb_weight ( core::pose::Pose const &  pose,
core::Size  ires,
Real  distance_threshold 
)
core::id::AtomID_Map< core::Real > protocols::sic_dock::cb_weight_map_from_pose ( core::pose::Pose const &  pose)
utility::vector1< core::Real > protocols::sic_dock::cb_weights_from_map ( core::pose::Pose const &  pose,
core::id::AtomID_Map< core::Real > const &  map 
)
utility::vector1< core::Real > protocols::sic_dock::cb_weights_from_pose ( core::pose::Pose const &  pose)
template<typename T >
T protocols::sic_dock::CBScore_dist_score ( T const &  sqdist,
T const &  start,
T const &  stop 
)
inline
numeric::xyzVector< core::Real > protocols::sic_dock::center_of_geom ( core::pose::Pose const &  pose,
core::Size  str,
core::Size  end 
)
core::Size protocols::sic_dock::count_CBs ( core::pose::Pose const &  pose)
platform::Size protocols::sic_dock::count_linkers ( Xform const &  lower,
Xform const &  upper,
protocols::loophash::LoopHashLibraryCOP  loop_hash_library,
utility::vector1< platform::Size > const &  loopsizes,
platform::Size  radius = 0 
)
core::Size protocols::sic_dock::count_linkers ( Xform const &  lower,
Xform const &  upper,
protocols::loophash::LoopHashLibraryCOP  loop_hash_library,
Sizes const &  loopsizes,
core::Size  radius 
)
core::Real protocols::sic_dock::dist_score ( core::Real const &  sqdist,
core::Real const &  start,
core::Real const &  stop 
)
inline
platform::Size protocols::sic_dock::dump_loophash_linkers ( Xform const &  lower,
Xform const &  upper,
protocols::loophash::LoopHashLibraryCOP  loop_hash_library,
utility::vector1< platform::Size > const &  loopsizes,
platform::Size  radius = 0,
std::string const &  outtag = "" 
)
core::Size protocols::sic_dock::dump_loophash_linkers ( Xform const &  lower,
Xform const &  upper,
protocols::loophash::LoopHashLibraryCOP  loop_hash_library,
Sizes const &  loopsizes,
core::Size  radius,
std::string const &  outtag 
)
void protocols::sic_dock::dump_points_pdb ( utility::vector1< numeric::xyzVector< core::Real > > const &  p,
std::string  fn 
)
void protocols::sic_dock::dump_points_pdb ( utility::vector1< numeric::xyzVector< core::Real > > const &  p,
numeric::xyzVector< core::Real t,
std::string  fn 
)
void protocols::sic_dock::dump_points_pdb ( vector1< Vec > const &  p,
std::string  fn 
)
void protocols::sic_dock::dump_points_pdb ( vector1< Vec > const &  p,
Vec  t,
std::string  fn 
)
void protocols::sic_dock::fill_plane_hash ( vector1< Vec > const &  pb,
vector1< Vec > const &  pa,
core::Real const &  xmx,
core::Real const &  xmn,
core::Real const &  ymx,
core::Real const &  ymn,
core::Real const &  BIN,
ObjexxFCL::FArray2D< Vec > &  ha,
ObjexxFCL::FArray2D< Vec > &  hb,
int &  xlb,
int &  ylb,
int &  xub,
int &  yub 
)
inline
int protocols::sic_dock::flood_fill3D ( int  i,
int  j,
int  k,
ObjexxFCL::FArray3D< core::Real > &  grid,
core::Real  t 
)
bool protocols::sic_dock::get_bounds_intersection ( vector1< Vec > const &  pb,
vector1< Vec > const &  pa,
core::Real xmx,
core::Real xmn,
core::Real ymx,
core::Real ymn 
)
inline
utility::vector1< numeric::xyzVector< core::Real > > protocols::sic_dock::get_CB_Vecs_from_map ( core::pose::Pose const &  pose,
core::id::AtomID_Map< core::Real > const &  map 
)
utility::vector1< numeric::xyzVector< core::Real > > protocols::sic_dock::get_CB_Vecs_from_pose ( core::pose::Pose const &  pose)
numeric::geometry::hashing::Real6 protocols::sic_dock::get_leap_6dof ( Xform const &  lower,
Xform const &  upper 
)
Vec3 protocols::sic_dock::get_leap_lower_stub ( core::pose::Pose const &  pose,
core::Size  ir 
)
Vec3 protocols::sic_dock::get_leap_upper_stub ( core::pose::Pose const &  pose,
core::Size  ir 
)
core::Real protocols::sic_dock::get_mindis_with_plane_hashes ( int const &  xlb,
int const &  ylb,
int const &  xub,
int const &  yub,
ObjexxFCL::FArray2D< Vec > const &  ha,
ObjexxFCL::FArray2D< Vec > const &  hb,
core::Real const &  clashdis2 
)
inline
core::Real protocols::sic_dock::get_rg ( core::pose::Pose const &  pose)
void protocols::sic_dock::get_termini_from_pose ( core::pose::Pose const &  pose,
core::Size  ir,
TermInfo &  lowers,
TermInfo &  uppers 
)
void protocols::sic_dock::get_termini_from_pose ( core::pose::Pose const &  pose,
TermInfo &  lowers,
TermInfo &  uppers 
)
void protocols::sic_dock::get_xform_stats ( Xform const &  sir,
Xform const &  sjr,
Real &  dx,
Real &  dy,
Real &  dz,
Real &  ex,
Real &  ey,
Real &  ez 
)
core::kinematics::Stub protocols::sic_dock::getxform ( core::conformation::Residue const &  move_resi,
core::conformation::Residue const &  fixd_resi 
)
Xform protocols::sic_dock::invstub ( Xform const &  a)
inline
std::string protocols::sic_dock::KMGT ( core::Real const &  x,
int const &  w,
int const &  d 
)
platform::Real protocols::sic_dock::linker_count2score ( core::Size  count)
void protocols::sic_dock::make_Cx ( core::pose::Pose pose,
int  N,
numeric::xyzVector< core::Real axis 
)
Xform protocols::sic_dock::multstubs ( Xform const &  a,
Xform const &  b 
)
inline
int protocols::sic_dock::neighbor_count ( core::pose::Pose const &  pose,
int  ires,
core::Real  distance_threshold 
)
std::ostream& protocols::sic_dock::operator<< ( std::ostream &  out,
Vec3  v 
)
bool protocols::sic_dock::pose1_has_most_CBs ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
)

References count_CBs().

core::pose::Pose const & protocols::sic_dock::pose_with_most_CBs ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
)

References count_CBs().

numeric::xyzVector<core::Real> protocols::sic_dock::projperp ( numeric::xyzVector< core::Real > const &  u,
numeric::xyzVector< core::Real > const &  v 
)
inline
utility::vector1< core::Size > protocols::sic_dock::range ( core::Size  beg,
core::Size  end 
)

References core::sequence::end.

Referenced by core::select::residue_selector::SecondaryStructureSelector::add_overlap(), protocols::helical_bundle::BackboneGridSampler::add_torsion_to_sample(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::apply(), core::scoring::PolymerBondedEnergyContainer::const_neighbor_iterator_begin(), core::scoring::PolymerBondedEnergyContainer::const_upper_neighbor_iterator_begin(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::environment::claims::CutBiasClaim::CutBiasClaim(), core::scoring::methods::LK_SigmoidalFunc::dfunc(), core::fragment::picking_old::vall::eval::ABEGOEval::eval_impl(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), core::scoring::motif::MotifHash::find_motifs(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::fix_ranges(), core::scoring::methods::LK_SigmoidalFunc::func(), update_ResidueType_enum_files::generate_enum_header_file(), protocols::jobdist::BaseJobDistributor::get_next_random_range(), protocols::fold_from_loops::utils::Nub::get_nub_pieces(), protocols::indexed_structure_store::StructureStore::get_residues(), protocols::canonical_sampling::TemperingBase::init_from_options(), protocols::match::OccupiedSpaceHash::initialize(), protocols::match::Matcher::initialize_from_file(), core::scoring::PolymerBondedEnergyContainer::is_valid(), protocols::loophash::LoopHashMap::lookup(), protocols::loophash::LoopHashMap::lookup_withkey(), protocols::fold_from_loops::NubInitioMover::make_template_ranges(), protocols::loophash::LoopHashLibrary::merge(), core::scoring::PolymerBondedEnergyContainer::neighbor_iterator_begin(), protocols::fldsgn::MatchResidues::parse_my_tag(), core::select::residue_selector::GlycanPositionSelector::parse_my_tag(), protocols::abinitio::abscript::AbscriptMover::parse_stage_id(), protocols::loophash::LoopHashMap::radial_lookup(), protocols::loophash::BackboneDB::read_db(), protocols::loophash::LoopHashMap::read_db(), protocols::noesy_assign::PeakAssignmentParameters::register_options(), protocols::canonical_sampling::TemperingBase::register_options(), protocols::relax::RangeRelaxMover::repack_sequence_window(), protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::set_angle_range_from_init_torsions(), core::select::residue_selector::ResidueIndexSelector::set_index_range(), protocols::noesy_assign::PeakAssignmentParameters::set_options_from_cmdline(), core::scoring::netcharge_energy::NetChargeConstraint::show_def(), core::scoring::aa_composition_energy::AACompositionConstraint::show_def(), core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::show_def(), protocols::membrane::SpinAroundPartnerMover::SpinAroundPartnerMover(), protocols::fold_from_loops::utils::split_mid_ranges(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::split_pose(), and core::scoring::PolymerBondedEnergyContainer::upper_neighbor_iterator_begin().

bool protocols::sic_dock::read_biounit ( std::string const &  fname,
core::pose::Pose pose,
utility::vector1< core::Real > &  bfactors,
utility::vector1< core::Real > &  occupancy,
int  max_res = 9999999,
bool  debug = false 
)

References read_biounit().

bool protocols::sic_dock::read_biounit ( std::string const &  fname,
core::pose::Pose pose,
utility::vector1< core::Real > &  bfactors,
utility::vector1< core::Real > &  occupancy,
utility::vector1< int > &  pdbres,
std::map< int, char > &  pdbchain,
int &  nresmodel1,
int  max_res = 9999999,
bool  debug = false 
)
bool protocols::sic_dock::read_biounit ( string const &  fname,
Pose pose,
int  max_res,
bool  debug 
)

Referenced by read_biounit().

bool protocols::sic_dock::read_biounit ( string const &  fname,
Pose pose,
utility::vector1< Real > &  bfactors,
utility::vector1< Real > &  occupancy,
int  max_res,
bool  debug 
)

References read_biounit().

bool protocols::sic_dock::read_biounit ( string const &  fname,
Pose pose,
vector1< Real > &  bfactors,
vector1< Real > &  occupancy,
vector1< int > &  pdbres,
std::map< int, char > &  pdbchain,
int &  nresmodel1,
int  max_res,
bool  debug 
)
core::Real protocols::sic_dock::refine_mindis_with_xyzHash ( xyzStripeHashPose *  xh,
Xform const &  xform_to_struct2_start,
vector1< Vec > const &  pa,
vector1< Real > const &  radii,
Vec const &  ori,
core::Real const &  clash_dis_sq,
core::Real const &  mindis_approx 
)
inline
bool protocols::sic_dock::residue_is_floppy ( core::pose::Pose const &  pose,
core::Size const  ir,
Real const  ttrim_cut,
core::Size const  nfold 
)
void protocols::sic_dock::rot_pose ( core::pose::Pose pose,
numeric::xyzMatrix< core::Real > const &  rot,
core::Size  start = 1,
core::Size  end = 0 
)
void protocols::sic_dock::rot_pose ( core::pose::Pose pose,
numeric::xyzMatrix< core::Real > const &  rot,
numeric::xyzVector< core::Real > const &  cen,
core::Size  start = 1,
core::Size  end = 0 
)
void protocols::sic_dock::rot_pose ( core::pose::Pose pose,
numeric::xyzVector< core::Real > const &  axis,
core::Real const &  ang,
core::Size  start = 1,
core::Size  end = 0 
)
void protocols::sic_dock::rot_pose ( core::pose::Pose pose,
numeric::xyzVector< core::Real > const &  axis,
core::Real const &  ang,
numeric::xyzVector< core::Real > const &  cen,
core::Size  start = 1,
core::Size  end = 0 
)
void protocols::sic_dock::rot_pose ( Pose pose,
Mat const &  rot,
core::Size  start,
core::Size  end 
)
void protocols::sic_dock::rot_pose ( Pose pose,
Mat const &  rot,
Vec const &  cen,
core::Size  start,
core::Size  end 
)

References rot_pose(), and trans_pose().

void protocols::sic_dock::rot_pose ( Pose pose,
Vec const &  axis,
Real const &  ang,
core::Size  start,
core::Size  end 
)

References rot_pose().

void protocols::sic_dock::rot_pose ( Pose pose,
Vec const &  axis,
Real const &  ang,
Vec const &  cen,
core::Size  start,
core::Size  end 
)

References rot_pose().

core::Real protocols::sic_dock::slide_into_contact_and_score ( protocols::sic_dock::SICFast const &  sic,
protocols::sic_dock::RigidScore const &  sfxn,
Xform xa,
Xform const &  xb,
numeric::xyzVector< core::Real > const &  ori,
core::Real score 
)
core::Real protocols::sic_dock::slide_into_contact_and_score_DEPRICATED ( protocols::sic_dock::SICFast const &  sic,
protocols::sic_dock::RigidScore const &  sfxn,
core::kinematics::Stub xa,
core::kinematics::Stub const &  xb,
numeric::xyzVector< core::Real > const &  ori,
core::Real score 
)
template<typename T >
T protocols::sic_dock::sqr ( x)
inline
static basic::Tracer protocols::sic_dock::TR ( "protocols.sic_dock.util"  )
static
static basic::Tracer protocols::sic_dock::TR ( "protocols.sic_dock.RigidScore"  )
static
void protocols::sic_dock::trans_pose ( core::pose::Pose pose,
numeric::xyzVector< core::Real > const &  trans,
core::Size  start = 1,
core::Size  end = 0 
)
void protocols::sic_dock::trans_pose ( Pose pose,
Vec const &  trans,
core::Size  start,
core::Size  end 
)
Xform protocols::sic_dock::vec3_to_stub ( Vec3 const &  v3)
Xform protocols::sic_dock::vec3_to_stub ( Xform const &  xform,
Vec3 const &  v3 
)
void protocols::sic_dock::xform_pose ( core::pose::Pose pose,
core::kinematics::Stub const &  s,
core::Size  sres,
core::Size  eres 
)
void protocols::sic_dock::xform_pose ( core::pose::Pose pose,
numeric::xyzTransform< core::Real > const &  s,
core::Size  sres,
core::Size  eres 
)
void protocols::sic_dock::xform_pose_rev ( core::pose::Pose pose,
core::kinematics::Stub const &  s 
)
void protocols::sic_dock::xform_pose_rev ( core::pose::Pose pose,
numeric::xyzTransform< core::Real > const &  s 
)