Module _protocols_sic_dock_

KMGT( (float)x, (int)w, (int)d) -> str :
    protocols/sic_dock/util.hh:131

    C++ signature :
        std::string KMGT(double,int,int)

alignaxis( (Pose)pose, (xyzVector_Real)newaxis, (xyzVector_Real)oldaxis, (xyzVector_Real)cen) -> None :
    protocols/sic_dock/util.hh:118

    C++ signature :
        void alignaxis(core::pose::Pose {lvalue},numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>)

alignaxis_xform( (xyzVector_Real)newaxis, (xyzVector_Real)oldaxis, (xyzVector_Real)cen) -> xyzTransform_T_double_T :
    protocols/sic_dock/util.hh:119

    C++ signature :
        numeric::xyzTransform<double> alignaxis_xform(numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>)

auto_trim_floppy_termini( (Pose)pose [, (float)ttrim_cut=1.0 [, (int)nfold=1]]) -> None :
    protocols/sic_dock/util.hh:108

    C++ signature :
        void auto_trim_floppy_termini(core::pose::Pose {lvalue} [,double=1.0 [,unsigned long=1]])

cb_weight( (Pose)pose, (int)ires [, (float)distance_threshold=10.0]) -> float :
    protocols/sic_dock/util.hh:50

    C++ signature :
        double cb_weight(core::pose::Pose,unsigned long [,double=10.0])

cb_weight_map_from_pose( (Pose)pose) -> AtomID_Map_T_double_T :
    protocols/sic_dock/util.hh:79

    C++ signature :
        core::id::AtomID_Map<double> cb_weight_map_from_pose(core::pose::Pose)

cb_weights_from_map( (Pose)pose, (AtomID_Map_T_double_T)map) -> vector1_Real :
    protocols/sic_dock/util.hh:85

    C++ signature :
        utility::vector1<double, std::allocator<double> > cb_weights_from_map(core::pose::Pose,core::id::AtomID_Map<double>)

cb_weights_from_pose( (Pose)pose) -> vector1_Real :
    protocols/sic_dock/util.hh:84

    C++ signature :
        utility::vector1<double, std::allocator<double> > cb_weights_from_pose(core::pose::Pose)

center_of_geom( (Pose)pose [, (int)str=1 [, (int)end=0]]) -> xyzVector_Real :
    protocols/sic_dock/util.hh:110

    C++ signature :
        numeric::xyzVector<double> center_of_geom(core::pose::Pose [,unsigned long=1 [,unsigned long=0]])

count_CBs( (Pose)pose) -> int :
    protocols/sic_dock/util.hh:77

    C++ signature :
        unsigned long count_CBs(core::pose::Pose)

count_linkers( (xyzTransform_T_double_T)lower, (xyzTransform_T_double_T)upper, (object)loop_hash_library, (vector1_Size)loopsizes [, (int)radius=0]) -> int :
    protocols/sic_dock/loophash_util.hh:60

    C++ signature :
        unsigned long count_linkers(numeric::xyzTransform<double>,numeric::xyzTransform<double>,boost::shared_ptr<protocols::loophash::LoopHashLibrary>,utility::vector1<unsigned long, std::allocator<unsigned long> > [,unsigned long=0])

dump_loophash_linkers( (xyzTransform_T_double_T)lower, (xyzTransform_T_double_T)upper, (object)loop_hash_library, (vector1_Size)loopsizes [, (int)radius=0 [, (str)outtag='']]) -> int :
    protocols/sic_dock/loophash_util.hh:72

    C++ signature :
        unsigned long dump_loophash_linkers(numeric::xyzTransform<double>,numeric::xyzTransform<double>,boost::shared_ptr<protocols::loophash::LoopHashLibrary>,utility::vector1<unsigned long, std::allocator<unsigned long> > [,unsigned long=0 [,std::string='']])

dump_points_pdb( (vector1_xyzVector_Real)p, (xyzVector_Real)t, (str)fn) -> None :
    protocols/sic_dock/util.hh:112

    C++ signature :
        void dump_points_pdb(utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > >,numeric::xyzVector<double>,std::string)

dump_points_pdb( (vector1_xyzVector_Real)p, (str)fn) -> None :
    protocols/sic_dock/util.hh:111

    C++ signature :
        void dump_points_pdb(utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > >,std::string)

flood_fill3D( (int)i, (int)j, (int)k, (object)grid, (float)t) -> int :
    protocols/sic_dock/util.hh:94

    C++ signature :
        int flood_fill3D(int,int,int,ObjexxFCL::FArray3D<double> {lvalue},double)

get_CB_Vecs_from_map( (Pose)pose, (AtomID_Map_T_double_T)map) -> vector1_xyzVector_Real :
    protocols/sic_dock/util.hh:82

    C++ signature :
        utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > > get_CB_Vecs_from_map(core::pose::Pose,core::id::AtomID_Map<double>)

get_CB_Vecs_from_pose( (Pose)pose) -> vector1_xyzVector_Real :
    protocols/sic_dock/util.hh:81

    C++ signature :
        utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > > get_CB_Vecs_from_pose(core::pose::Pose)

get_leap_6dof( (xyzTransform_T_double_T)lower, (xyzTransform_T_double_T)upper) -> object :
    protocols/sic_dock/loophash_util.hh:52

    C++ signature :
        utility::fixedsizearray1<double, 6ul> get_leap_6dof(numeric::xyzTransform<double>,numeric::xyzTransform<double>)

get_leap_lower_stub( (Pose)pose, (int)ir) -> Vec3 :
    protocols/sic_dock/util.hh:92

    C++ signature :
        protocols::sic_dock::Vec3 get_leap_lower_stub(core::pose::Pose,unsigned long)

get_leap_upper_stub( (Pose)pose, (int)ir) -> Vec3 :
    protocols/sic_dock/loophash_util.hh:31

    C++ signature :
        protocols::sic_dock::Vec3 get_leap_upper_stub(core::pose::Pose,unsigned long)

get_rg( (Pose)p) -> float :
    protocols/sic_dock/util.hh:36

    C++ signature :
        double get_rg(core::pose::Pose)

get_termini_from_pose( (Pose)pose, (object)lowers, (object)uppers) -> None :
    protocols/sic_dock/loophash_util.hh:47

    C++ signature :
        void get_termini_from_pose(core::pose::Pose,utility::vector1<std::pair<unsigned long, protocols::sic_dock::Vec3>, std::allocator<std::pair<unsigned long, protocols::sic_dock::Vec3> > > {lvalue},utility::vector1<std::pair<unsigned long, protocols::sic_dock::Vec3>, std::allocator<std::pair<unsigned long, protocols::sic_dock::Vec3> > > {lvalue})

get_termini_from_pose( (Pose)pose, (int)ir, (object)lowers, (object)uppers) -> None :
    protocols/sic_dock/loophash_util.hh:41

    C++ signature :
        void get_termini_from_pose(core::pose::Pose,unsigned long,utility::vector1<std::pair<unsigned long, protocols::sic_dock::Vec3>, std::allocator<std::pair<unsigned long, protocols::sic_dock::Vec3> > > {lvalue},utility::vector1<std::pair<unsigned long, protocols::sic_dock::Vec3>, std::allocator<std::pair<unsigned long, protocols::sic_dock::Vec3> > > {lvalue})

get_xform_stats( (xyzTransform_T_double_T)sir, (xyzTransform_T_double_T)sjr, (float)dx, (float)dy, (float)dz, (float)ex, (float)ey, (float)ez) -> None :
    protocols/sic_dock/designability_score.hh:26

    C++ signature :
        void get_xform_stats(numeric::xyzTransform<double>,numeric::xyzTransform<double>,double {lvalue},double {lvalue},double {lvalue},double {lvalue},double {lvalue},double {lvalue})

getxform( (Residue)move_resi, (Residue)fixd_resi) -> Stub :
    protocols/sic_dock/util.hh:127

    C++ signature :
        core::kinematics::Stub getxform(core::conformation::Residue,core::conformation::Residue)

invstub( (xyzTransform_T_double_T)a) -> xyzTransform_T_double_T :
    protocols/sic_dock/util.hh:101

    C++ signature :
        numeric::xyzTransform<double> invstub(numeric::xyzTransform<double>)

linker_count2score( (int)count) -> float :
    protocols/sic_dock/loophash_util.hh:77

    C++ signature :
        double linker_count2score(unsigned long)

make_Cx( (Pose)pose, (int)N, (xyzVector_Real)axis) -> None :
    protocols/sic_dock/util.hh:52

    C++ signature :
        void make_Cx(core::pose::Pose {lvalue},int,numeric::xyzVector<double>)

multstubs( (xyzTransform_T_double_T)a, (xyzTransform_T_double_T)b) -> xyzTransform_T_double_T :
    protocols/sic_dock/util.hh:98

    C++ signature :
        numeric::xyzTransform<double> multstubs(numeric::xyzTransform<double>,numeric::xyzTransform<double>)

neighbor_count( (Pose)pose, (int)ires [, (float)distance_threshold=10.0]) -> int :
    protocols/sic_dock/util.hh:43

    C++ signature :
        int neighbor_count(core::pose::Pose,int [,double=10.0])

pose1_has_most_CBs( (Pose)pose1, (Pose)pose2) -> bool :
    protocols/sic_dock/util.hh:75

    C++ signature :
        bool pose1_has_most_CBs(core::pose::Pose,core::pose::Pose)

pose_with_most_CBs( (Pose)pose1, (Pose)pose2) -> Pose :
    protocols/sic_dock/util.hh:74

    C++ signature :
        core::pose::Pose pose_with_most_CBs(core::pose::Pose,core::pose::Pose)

projperp( (xyzVector_Real)u, (xyzVector_Real)v) -> xyzVector_Real :
    protocols/sic_dock/util.hh:122

    C++ signature :
        numeric::xyzVector<double> projperp(numeric::xyzVector<double>,numeric::xyzVector<double>)

range( (int)beg, (int)end) -> vector1_Size :
    protocols/sic_dock/util.hh:87

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > range(unsigned long,unsigned long)

read_biounit( (str)fname, (Pose)pose, (vector1_Real)bfactors, (vector1_Real)occupancy, (vector1_int)pdbres, (object)pdbchain, (int)nresmodel1 [, (int)max_res=9999999 [, (bool)DEBUG=False]]) -> bool :
    protocols/sic_dock/read_biounit.hh:50

    C++ signature :
        bool read_biounit(std::string,core::pose::Pose {lvalue},utility::vector1<double, std::allocator<double> > {lvalue},utility::vector1<double, std::allocator<double> > {lvalue},utility::vector1<int, std::allocator<int> > {lvalue},std::map<int, char, std::less<int>, std::allocator<std::pair<int const, char> > > {lvalue},int {lvalue} [,int=9999999 [,bool=False]])

read_biounit( (str)fname, (Pose)pose, (vector1_Real)bfactors, (vector1_Real)occupancy [, (int)max_res=9999999 [, (bool)DEBUG=False]]) -> bool :
    protocols/sic_dock/read_biounit.hh:37

    C++ signature :
        bool read_biounit(std::string,core::pose::Pose {lvalue},utility::vector1<double, std::allocator<double> > {lvalue},utility::vector1<double, std::allocator<double> > {lvalue} [,int=9999999 [,bool=False]])

read_biounit( (str)fname, (Pose)pose [, (int)max_res=9999999 [, (bool)DEBUG=False]]) -> bool :
    protocols/sic_dock/read_biounit.hh:27

    C++ signature :
        bool read_biounit(std::string,core::pose::Pose {lvalue} [,int=9999999 [,bool=False]])

residue_is_floppy( (Pose)pose, (int)ir [, (float)ttrim_cut=1.0 [, (int)nfold=1]]) -> bool :
    protocols/sic_dock/util.hh:106

    C++ signature :
        bool residue_is_floppy(core::pose::Pose,unsigned long [,double=1.0 [,unsigned long=1]])

rot_pose( (Pose)pose, (xyzVector_Real)axis, (float)ang, (xyzVector_Real)cen [, (int)start=1 [, (int)end=0]]) -> None :
    protocols/sic_dock/util.hh:117

    C++ signature :
        void rot_pose(core::pose::Pose {lvalue},numeric::xyzVector<double>,double,numeric::xyzVector<double> [,unsigned long=1 [,unsigned long=0]])

rot_pose( (Pose)pose, (xyzVector_Real)axis, (float)ang [, (int)start=1 [, (int)end=0]]) -> None :
    protocols/sic_dock/util.hh:116

    C++ signature :
        void rot_pose(core::pose::Pose {lvalue},numeric::xyzVector<double>,double [,unsigned long=1 [,unsigned long=0]])

rot_pose( (Pose)pose, (xyzMatrix_Real)rot, (xyzVector_Real)cen [, (int)start=1 [, (int)end=0]]) -> None :
    protocols/sic_dock/util.hh:115

    C++ signature :
        void rot_pose(core::pose::Pose {lvalue},numeric::xyzMatrix<double>,numeric::xyzVector<double> [,unsigned long=1 [,unsigned long=0]])

rot_pose( (Pose)pose, (xyzMatrix_Real)rot [, (int)start=1 [, (int)end=0]]) -> None :
    protocols/sic_dock/util.hh:114

    C++ signature :
        void rot_pose(core::pose::Pose {lvalue},numeric::xyzMatrix<double> [,unsigned long=1 [,unsigned long=0]])

slide_into_contact_and_score( (SICFast)sic, (RigidScore)sfxn, (xyzTransform_T_double_T)xa, (xyzTransform_T_double_T)xb, (xyzVector_Real)ori, (float)score) -> float :
    protocols/sic_dock/util.hh:62

    C++ signature :
        double slide_into_contact_and_score(protocols::sic_dock::SICFast,protocols::sic_dock::RigidScore,numeric::xyzTransform<double> {lvalue},numeric::xyzTransform<double>,numeric::xyzVector<double>,double {lvalue})

slide_into_contact_and_score_DEPRICATED( (SICFast)sic, (RigidScore)sfxn, (Stub)xa, (Stub)xb, (xyzVector_Real)ori, (float)score) -> float :
    protocols/sic_dock/util.hh:72

    C++ signature :
        double slide_into_contact_and_score_DEPRICATED(protocols::sic_dock::SICFast,protocols::sic_dock::RigidScore,core::kinematics::Stub {lvalue},core::kinematics::Stub,numeric::xyzVector<double>,double {lvalue})

trans_pose( (Pose)pose, (xyzVector_Real)trans [, (int)start=1 [, (int)end=0]]) -> None :
    protocols/sic_dock/util.hh:113

    C++ signature :
        void trans_pose(core::pose::Pose {lvalue},numeric::xyzVector<double> [,unsigned long=1 [,unsigned long=0]])

vec3_to_stub( (xyzTransform_T_double_T)xform, (Vec3)v3) -> xyzTransform_T_double_T :
    protocols/sic_dock/loophash_util.hh:33

    C++ signature :
        numeric::xyzTransform<double> vec3_to_stub(numeric::xyzTransform<double>,protocols::sic_dock::Vec3)

vec3_to_stub( (Vec3)v3) -> xyzTransform_T_double_T :
    protocols/sic_dock/loophash_util.hh:32

    C++ signature :
        numeric::xyzTransform<double> vec3_to_stub(protocols::sic_dock::Vec3)

xform_pose( (Pose)pose, (xyzTransform_T_double_T)s [, (int)sres=1 [, (int)eres=0]]) -> None :
    protocols/sic_dock/util.hh:125

    C++ signature :
        void xform_pose(core::pose::Pose {lvalue},numeric::xyzTransform<double> [,unsigned long=1 [,unsigned long=0]])

xform_pose( (Pose)pose, (Stub)s [, (int)sres=1 [, (int)eres=0]]) -> None :
    protocols/sic_dock/util.hh:124

    C++ signature :
        void xform_pose(core::pose::Pose {lvalue},core::kinematics::Stub [,unsigned long=1 [,unsigned long=0]])