protocols::sic_dock Namespace Reference

Namespaces
	scores

Classes
struct	XfoxmScore
struct	CBScoreVisitor
class	NoPoseXYX_Func
class	RigidScore
class	CBScore
class	LinkerScore
struct	AtomIDHashFunction
class	ConstraintSetScore
class	EdgeStandScore
class	HelixScore
class	BuriedPolarScore
class	JointScore
class	Rose
struct	CorrectionVisitor
class	SICFast
struct	Vec3
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< Mat >	Mats
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 >
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::Real >	cb_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::Real >	cb_weights_from_pose (core::pose::Pose const &pose)
vector1< core::Real >	cb_weights_from_map (core::pose::Pose const &pose, core::id::AtomID_Map< core::Real > const &map)
vector1< core::Size >	range (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::Real >	alignaxis_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::Real >	projperp (numeric::xyzVector< core::Real > const &u, numeric::xyzVector< core::Real > const &v)
template<typename T >
T	sqr (T x)

Typedef Documentation

CBScoreCOP

typedef utility::pointer::shared_ptr< CBScore const > protocols::sic_dock::CBScoreCOP

CBScoreOP

typedef utility::pointer::shared_ptr< CBScore > protocols::sic_dock::CBScoreOP

ConstraintSetScoreCOP

typedef utility::pointer::shared_ptr< ConstraintSetScore const > protocols::sic_dock::ConstraintSetScoreCOP

ConstraintSetScoreOP

typedef utility::pointer::shared_ptr< ConstraintSetScore > protocols::sic_dock::ConstraintSetScoreOP

JointScoreCOP

typedef utility::pointer::shared_ptr< JointScore const > protocols::sic_dock::JointScoreCOP

JointScoreOP

typedef utility::pointer::shared_ptr< JointScore > protocols::sic_dock::JointScoreOP

LinkerScoreCOP

typedef utility::pointer::shared_ptr< LinkerScore const > protocols::sic_dock::LinkerScoreCOP

LinkerScoreOP

typedef utility::pointer::shared_ptr< LinkerScore > protocols::sic_dock::LinkerScoreOP

Mat

typedef numeric::xyzMatrix< Real > protocols::sic_dock::Mat

Mats

typedef utility::vector1<Mat> protocols::sic_dock::Mats

Pose

typedef core::pose::Pose protocols::sic_dock::Pose

Real

typedef core::Real protocols::sic_dock::Real

Reals

typedef vector1< Real > protocols::sic_dock::Reals

RigidScoreCOP

typedef utility::pointer::shared_ptr< RigidScore const > protocols::sic_dock::RigidScoreCOP

RigidScoreOP

typedef utility::pointer::shared_ptr< RigidScore > protocols::sic_dock::RigidScoreOP

Scores

typedef vector1< RigidScoreCOP > protocols::sic_dock::Scores

SICFastCOP

typedef utility::pointer::shared_ptr< SICFast const > protocols::sic_dock::SICFastCOP

SICFastOP

typedef utility::pointer::shared_ptr< SICFast > protocols::sic_dock::SICFastOP

Sizes

typedef vector1< core::Size > protocols::sic_dock::Sizes

TermInfo

typedef utility::vector1<std::pair<platform::Size,Vec3> > protocols::sic_dock::TermInfo

Vec

typedef numeric::xyzVector< Real > protocols::sic_dock::Vec

Vecs

typedef vector1< Vec > protocols::sic_dock::Vecs

Xform

typedef Xform protocols::sic_dock::Xform

Xforms

typedef numeric::Xforms protocols::sic_dock::Xforms

xyzStripeHashPoseWithMetaCOP

typedef utility::pointer::shared_ptr< xyzStripeHashPoseWithMeta const > protocols::sic_dock::xyzStripeHashPoseWithMetaCOP

xyzStripeHashPoseWithMetaOP

typedef utility::pointer::shared_ptr< xyzStripeHashPoseWithMeta > protocols::sic_dock::xyzStripeHashPoseWithMetaOP

Function Documentation

alignaxis() [1/2]

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)
	)

alignaxis() [2/2]

void protocols::sic_dock::alignaxis	(	Pose &	pose,
		Vec	newaxis,
		Vec	oldaxis,
		Vec	cen
	)

References protocols::mean_field::max(), protocols::mean_field::min(), and rot_pose().

alignaxis_xform()

numeric::xyzTransform<core::Real> protocols::sic_dock::alignaxis_xform	(	numeric::xyzVector< core::Real >	newaxis,
		numeric::xyzVector< core::Real >	oldaxis,
		numeric::xyzVector< core::Real >	cen
	)

References protocols::mean_field::max(), and protocols::mean_field::min().

auto_trim_floppy_termini()

void protocols::sic_dock::auto_trim_floppy_termini	(	core::pose::Pose &	pose,
		Real const	ttrim_cut,
		core::Size const	nfold
	)

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), residue_is_floppy(), core::pose::Pose::size(), and TR().

brute_mindis()

Real protocols::sic_dock::brute_mindis	(	vector1< Vec > const &	pa,
		vector1< Vec > const &	pb,
		Vec const &	ofst = Vec(0,0,0)
	)

References protocols::mean_field::min().

cb_weight()

core::Real protocols::sic_dock::cb_weight	(	core::pose::Pose const &	pose,
		core::Size	ires,
		Real	distance_threshold
	)

References protocols::mean_field::min(), neighbor_count(), and core::pose::Pose::secstruct().

Referenced by cb_weight_map_from_pose(), and cb_weights_from_pose().

cb_weight_map_from_pose()

core::id::AtomID_Map< core::Real > protocols::sic_dock::cb_weight_map_from_pose

(

core::pose::Pose const &

pose

)

References core::conformation::Residue::atom_index(), cb_weight(), core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), and core::pose::Pose::size().

cb_weights_from_map()

utility::vector1< core::Real > protocols::sic_dock::cb_weights_from_map	(	core::pose::Pose const &	pose,
		core::id::AtomID_Map< core::Real > const &	map
	)

References core::pose::Pose::residue(), and core::pose::Pose::size().

cb_weights_from_pose()

utility::vector1< core::Real > protocols::sic_dock::cb_weights_from_pose

(

core::pose::Pose const &

pose

)

References cb_weight(), core::conformation::Residue::has(), core::pose::Pose::residue(), and core::pose::Pose::size().

CBScore_dist_score()

template<typename T >

T protocols::sic_dock::CBScore_dist_score ( T const &  sqdist, T const &  start, T const &  stop  )

inline

References protocols::loops::start, and protocols::loops::stop.

Referenced by protocols::sic_dock::scores::TrisBpyScore::score_extra(), and protocols::sic_dock::CBScoreVisitor::visit().

center_of_geom()

numeric::xyzVector< core::Real > protocols::sic_dock::center_of_geom	(	core::pose::Pose const &	pose,
		core::Size	str,
		core::Size	end
	)

References core::sequence::end, core::pose::Pose::size(), protocols::kinmatch::str(), and core::pose::Pose::xyz().

Referenced by get_rg().

count_CBs()

core::Size protocols::sic_dock::count_CBs

(

core::pose::Pose const &

pose

)

References core::conformation::Residue::has(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by pose1_has_most_CBs(), and pose_with_most_CBs().

count_linkers() [1/2]

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
	)

References get_leap_6dof(), and core::kinematics::RT::get_translation().

Referenced by protocols::sic_dock::LinkerScore::score().

count_linkers() [2/2]

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
	)

dist_score()

core::Real protocols::sic_dock::dist_score ( core::Real const &  sqdist, core::Real const &  start, core::Real const &  stop  )

inline

References protocols::loops::start, and protocols::loops::stop.

Referenced by core::energy_methods::HackAroEnergy::eval_atom_derivative_aro_aro(), core::energy_methods::MgEnergy::eval_mg_interaction(), and core::energy_methods::HackAroEnergy::residue_pair_energy_aro_aro().

dump_loophash_linkers() [1/2]

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
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::dump_pdb(), protocols::loophash::BackboneDB::get_backbone_segment(), get_leap_6dof(), get_leap_lower_stub(), protocols::loophash::LoopHashMap::get_peptide(), core::scoring::omega, protocols::loophash::LoopHashMap::radial_lookup(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::size(), vec3_to_stub(), and xform_pose().

Referenced by protocols::sic_dock::LinkerScore::dump_linkers().

dump_loophash_linkers() [2/2]

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 = ""
	)

dump_points_pdb() [1/4]

void protocols::sic_dock::dump_points_pdb	(	utility::vector1< numeric::xyzVector< core::Real > > const &	p,
		numeric::xyzVector< core::Real >	t,
		std::string	fn
	)

dump_points_pdb() [2/4]

void protocols::sic_dock::dump_points_pdb	(	utility::vector1< numeric::xyzVector< core::Real > > const &	p,
		std::string	fn
	)

dump_points_pdb() [3/4]

void protocols::sic_dock::dump_points_pdb	(	vector1< Vec > const &	p,
		std::string	fn
	)

References core::chemical::element::F, and core::chemical::element::I.

dump_points_pdb() [4/4]

void protocols::sic_dock::dump_points_pdb	(	vector1< Vec > const &	p,
		Vec	t,
		std::string	fn
	)

References core::chemical::element::F, core::chemical::element::I, and protocols::hybridization::t.

fill_plane_hash()

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

Referenced by protocols::sic_dock::SICFast::slide_into_contact().

flood_fill3D()

int protocols::sic_dock::flood_fill3D	(	int	i,
		int	j,
		int	k,
		ObjexxFCL::FArray3D< core::Real > &	grid,
		core::Real	t
	)

References protocols::hybridization::t.

get_bounds_intersection()

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

References protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by protocols::sic_dock::SICFast::slide_into_contact().

get_CB_Vecs_from_map()

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
	)

References core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

get_CB_Vecs_from_pose()

utility::vector1< numeric::xyzVector< core::Real > > protocols::sic_dock::get_CB_Vecs_from_pose

(

core::pose::Pose const &

pose

)

References core::conformation::Residue::has(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

get_leap_6dof()

numeric::geometry::hashing::Real6 protocols::sic_dock::get_leap_6dof	(	Xform const &	lower,
		Xform const &	upper
	)

References core::kinematics::RT::get_rotation(), and core::kinematics::RT::get_translation().

Referenced by count_linkers(), and dump_loophash_linkers().

get_leap_lower_stub()

Vec3 protocols::sic_dock::get_leap_lower_stub	(	core::pose::Pose const &	pose,
		core::Size	ir
	)

References protocols::sic_dock::Vec3::a, protocols::sic_dock::Vec3::b, protocols::sic_dock::Vec3::c, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by dump_loophash_linkers(), and get_termini_from_pose().

get_leap_upper_stub()

Vec3 protocols::sic_dock::get_leap_upper_stub	(	core::pose::Pose const &	pose,
		core::Size	ir
	)

References protocols::sic_dock::Vec3::a, protocols::sic_dock::Vec3::b, protocols::sic_dock::Vec3::c, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by get_termini_from_pose().

get_mindis_with_plane_hashes()

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

Referenced by protocols::sic_dock::SICFast::slide_into_contact().

get_rg()

core::Real protocols::sic_dock::get_rg

(

core::pose::Pose const &

pose

)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, center_of_geom(), core::pose::center_of_mass(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::pose::Pose::size().

get_termini_from_pose() [1/2]

void protocols::sic_dock::get_termini_from_pose	(	core::pose::Pose const &	pose,
		core::Size	ir,
		TermInfo &	lowers,
		TermInfo &	uppers
	)

References get_leap_lower_stub(), get_leap_upper_stub(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().

Referenced by get_termini_from_pose(), and protocols::sic_dock::LinkerScore::LinkerScore().

get_termini_from_pose() [2/2]

void protocols::sic_dock::get_termini_from_pose	(	core::pose::Pose const &	pose,
		TermInfo &	lowers,
		TermInfo &	uppers
	)

References get_termini_from_pose(), and core::pose::Pose::size().

get_xform_stats()

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
	)

Referenced by protocols::sic_dock::XfoxmScore::score().

getxform()

core::kinematics::Stub protocols::sic_dock::getxform	(	core::conformation::Residue const &	move_resi,
		core::conformation::Residue const &	fixd_resi
	)

References core::kinematics::Stub::M, core::kinematics::Stub::v, and core::conformation::Residue::xyz().

invstub()

Xform protocols::sic_dock::invstub ( Xform const &  a )

inline

References core::pose::motif::a().

Referenced by protocols::sic_dock::CBScore::score().

KMGT()

std::string protocols::sic_dock::KMGT	(	core::Real const &	x,
		int const &	w,
		int const &	d
	)

References core::chemical::element::F.

linker_count2score()

platform::Real protocols::sic_dock::linker_count2score

(

core::Size

count

)

Referenced by protocols::sic_dock::LinkerScore::score().

make_Cx()

void protocols::sic_dock::make_Cx	(	core::pose::Pose &	pose,
		int	N,
		numeric::xyzVector< core::Real >	axis
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_lower_terminus(), core::chemical::element::N, core::pose::Pose::residue(), rot_pose(), and core::pose::Pose::size().

multstubs()

Xform protocols::sic_dock::multstubs ( Xform const &  a, Xform const &  b  )

inline

References core::pose::motif::a(), and protocols::match::upstream::b.

Referenced by protocols::sic_dock::CBScore::score().

neighbor_count()

int protocols::sic_dock::neighbor_count	(	core::pose::Pose const &	pose,
		int	ires,
		core::Real	distance_threshold
	)

References protocols::mpi_refinement::distance(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by core::energy_methods::MembraneEnvSmoothEnergy::calc_energy(), core::energy_methods::FaMPEnvSmoothEnergy::calc_energy(), core::energy_methods::EnvSmoothEnergy::calc_energy(), cb_weight(), protocols::splice::neighbors_in_vector(), protocols::task_operations::ProteinCore::operator()(), protocols::optimize_weights::PNatAAOptEPositionData::print_score(), protocols::optimize_weights::PSSMOptEPositionData::print_score(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::process_score(), protocols::forge::remodel::RemodelDesignMover::reduce_task(), protocols::qsar::scoring_grid::ChargeGrid::refresh(), core::energy_methods::CovalentLabelingEnergy::residue_energy(), core::energy_methods::CovalentLabelingFAEnergy::residue_energy(), core::energy_methods::HRF_MSLabelingEnergy::residue_energy(), core::energy_methods::HRFDynamicsEnergy::residue_energy(), core::scoring::nv::NVscore::residue_energy(), core::energy_methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_file(), and protocols::optimize_weights::PNatAAOptEPositionData::write_to_file().

operator<<()

std::ostream& protocols::sic_dock::operator<<	(	std::ostream &	out,
		Vec3	v
	)

References protocols::sic_dock::Vec3::a, protocols::sic_dock::Vec3::b, protocols::sic_dock::Vec3::c, and core::conformation::membrane::out.

pose1_has_most_CBs()

bool protocols::sic_dock::pose1_has_most_CBs	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

References count_CBs().

pose_with_most_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().

projperp()

numeric::xyzVector<core::Real> protocols::sic_dock::projperp ( numeric::xyzVector< core::Real > const &  u, numeric::xyzVector< core::Real > const &  v  )

inline

References protocols::hybridization::u.

range()

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(), core::select::residue_selector::GlycanPositionSelector::add_range(), protocols::helical_bundle::BackboneGridSampler::add_torsion_to_sample(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), core::select::residue_selector::BFactorSelector::apply(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::apply(), protocols::loophash::LoopHashMap::bbdb_range(), core::scoring::PolymerBondedEnergyContainer::const_neighbor_iterator_begin(), core::scoring::PolymerBondedEnergyContainer::const_upper_neighbor_iterator_begin(), core::energy_methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::environment::claims::CutBiasClaim::CutBiasClaim(), core::energy_methods::LK_SigmoidalFunc::dfunc(), protocols::environment::claims::EnvLabelSelector::EnvLabelSelector(), 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::energy_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::LoopHashMap::read_db(), protocols::loophash::BackboneDB::read_db(), protocols::canonical_sampling::TemperingBase::register_options(), protocols::noesy_assign::PeakAssignmentParameters::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::aa_composition_energy::AACompositionConstraint::show_def(), core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::show_def(), core::scoring::netcharge_energy::NetChargeConstraint::show_def(), protocols::membrane::SpinAroundPartnerMover::SpinAroundPartnerMover(), protocols::fold_from_loops::utils::split_mid_ranges(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::split_pose(), protocols::indexed_structure_store::to_str(), protocols::environment::claims::TorsionClaim::TorsionClaim(), and core::scoring::PolymerBondedEnergyContainer::upper_neighbor_iterator_begin().

read_biounit() [1/5]

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 core::pack::interaction_graph::debug, and read_biounit().

read_biounit() [2/5]

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
	)

read_biounit() [3/5]

bool protocols::sic_dock::read_biounit	(	string const &	fname,
		Pose &	pose,
		int	max_res,
		bool	debug
	)

References core::pack::interaction_graph::debug.

Referenced by read_biounit().

read_biounit() [4/5]

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 core::pack::interaction_graph::debug, and read_biounit().

read_biounit() [5/5]

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
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::chain(), core::pose::Pose::conformation(), core::pack::interaction_graph::debug, core::conformation::Conformation::detect_disulfides(), core::pose::Pose::dump_pdb(), core::chemical::FA_STANDARD, protocols::mean_field::min(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and core::pose::Pose::size().

refine_mindis_with_xyzHash()

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

References protocols::sic_dock::CorrectionVisitor::contacts, and protocols::sic_dock::CorrectionVisitor::correction.

Referenced by protocols::sic_dock::SICFast::slide_into_contact().

residue_is_floppy()

bool protocols::sic_dock::residue_is_floppy	(	core::pose::Pose const &	pose,
		core::Size const	ir,
		Real const	ttrim_cut,
		core::Size const	nfold
	)

References core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by auto_trim_floppy_termini().

rot_pose() [1/8]

void protocols::sic_dock::rot_pose	(	core::pose::Pose &	pose,
		numeric::xyzMatrix< core::Real > const &	rot,
		core::Size	start = 1,
		core::Size	end = 0
	)

rot_pose() [2/8]

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
	)

rot_pose() [3/8]

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
	)

rot_pose() [4/8]

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
	)

rot_pose() [5/8]

void protocols::sic_dock::rot_pose	(	Pose &	pose,
		Mat const &	rot,
		core::Size	start,
		core::Size	end
	)

References core::sequence::end, core::pose::Pose::residue_type(), rot(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), protocols::loops::start, and core::pose::Pose::xyz().

Referenced by alignaxis(), make_Cx(), and rot_pose().

rot_pose() [6/8]

void protocols::sic_dock::rot_pose	(	Pose &	pose,
		Mat const &	rot,
		Vec const &	cen,
		core::Size	start,
		core::Size	end
	)

References core::sequence::end, rot(), rot_pose(), protocols::loops::start, and trans_pose().

rot_pose() [7/8]

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

References core::sequence::end, rot_pose(), and protocols::loops::start.

rot_pose() [8/8]

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

References core::sequence::end, rot_pose(), and protocols::loops::start.

slide_into_contact_and_score()

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
	)

References protocols::hybridization::score, protocols::sic_dock::RigidScore::score(), protocols::sic_dock::SICFast::slide_into_contact(), and protocols::hybridization::xa.

slide_into_contact_and_score_DEPRICATED()

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
	)

References core::kinematics::Stub::M, protocols::hybridization::score, protocols::sic_dock::RigidScore::score(), protocols::sic_dock::SICFast::slide_into_contact_DEPRICATED(), core::kinematics::Stub::v, and protocols::hybridization::xa.

sqr()

template<typename T >

T protocols::sic_dock::sqr ( T  x )

inline

TR() [1/2]

static basic::Tracer protocols::sic_dock::TR ( "protocols.sic_dock.RigidScore"  )

static

Referenced by auto_trim_floppy_termini(), get_termini_from_pose(), and protocols::sic_dock::LinkerScore::LinkerScore().

TR() [2/2]

static basic::Tracer protocols::sic_dock::TR ( "protocols.sic_dock.util"  )

static

trans_pose() [1/2]

void protocols::sic_dock::trans_pose	(	core::pose::Pose &	pose,
		numeric::xyzVector< core::Real > const &	trans,
		core::Size	start = 1,
		core::Size	end = 0
	)

trans_pose() [2/2]

void protocols::sic_dock::trans_pose	(	Pose &	pose,
		Vec const &	trans,
		core::Size	start,
		core::Size	end
	)

References core::sequence::end, core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), protocols::loops::start, trans(), and core::pose::Pose::xyz().

Referenced by rot_pose().

vec3_to_stub() [1/2]

Xform protocols::sic_dock::vec3_to_stub

(

Vec3 const &

v3

)

References protocols::sic_dock::Vec3::a, protocols::sic_dock::Vec3::b, and protocols::sic_dock::Vec3::c.

Referenced by protocols::sic_dock::LinkerScore::dump_linkers(), dump_loophash_linkers(), and protocols::sic_dock::LinkerScore::score().

vec3_to_stub() [2/2]

Xform protocols::sic_dock::vec3_to_stub	(	Xform const &	xform,
		Vec3 const &	v3
	)

References protocols::sic_dock::Vec3::a, protocols::sic_dock::Vec3::b, and protocols::sic_dock::Vec3::c.

xform_pose() [1/2]

void protocols::sic_dock::xform_pose	(	core::pose::Pose &	pose,
		core::kinematics::Stub const &	s,
		core::Size	sres,
		core::Size	eres
	)

References core::kinematics::Stub::local2global(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::pose::Pose::xyz().

Referenced by dump_loophash_linkers().

xform_pose() [2/2]

void protocols::sic_dock::xform_pose	(	core::pose::Pose &	pose,
		numeric::xyzTransform< core::Real > const &	s,
		core::Size	sres,
		core::Size	eres
	)

References core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::pose::Pose::xyz().

xform_pose_rev() [1/2]

void protocols::sic_dock::xform_pose_rev	(	core::pose::Pose &	pose,
		core::kinematics::Stub const &	s
	)

References core::kinematics::Stub::global2local(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::pose::Pose::xyz().

xform_pose_rev() [2/2]

void protocols::sic_dock::xform_pose_rev	(	core::pose::Pose &	pose,
		numeric::xyzTransform< core::Real > const &	s
	)

References core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::pose::Pose::xyz().