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core::scoring::motif::ResPairMotif Class Reference

#include <motif_hash_stuff.hh>

Public Member Functions

 ResPairMotif ()
 
 ResPairMotif (std::string const &tag, core::pose::Pose const &pose, Real6 const &rt6, Size const &resi1, Size const &resi2, Real const &nbrs1, Real const &nbrs2, Real const &fa_atr, Real const &fa_atr_sc_bb, Real const &fa_atr_bb, Real const &hb_sc, Real const &hb_bb_sc, Real const &hb_bb, Real const &bfac1, Real const &bfac2, bool is_sspaired, RPM_Type _type)
 
bool is_reversible () const
 
ResPairMotifreverse_in_place ()
 
ResPairMotifreverse_in_place_unsafe ()
 
ResPairMotif reversed () const
 
void reset ()
 
bool valid () const
 
Xform xform () const
 
void xform (Xform const &_xform)
 
Real6 rt () const
 
void rt (Real6 const &rt)
 
Real dist2 () const
 
Real bfac1 () const
 
Real bfac2 () const
 
Real fa_atr () const
 
Real fa_atr_sc_bb () const
 
Real fa_atr_bb () const
 
Real hb_sc () const
 
Real hb_bb_sc () const
 
Real hb_bb () const
 
Real nbrs1 () const
 
Real nbrs2 () const
 
Real chi11 () const
 
Real chi12 () const
 
Real chi13 () const
 
Real chi14 () const
 
Real chi21 () const
 
Real chi22 () const
 
Real chi23 () const
 
Real chi24 () const
 
Real chi1 (Size const &ichi) const
 
Real chi2 (Size const &ichi) const
 
std::string pdb () const
 
bool check_pdb_code (std::string const &qpdb) const
 
bool check_lig_code (std::string const &qlig) const
 
void bfac1 (Real const &bfac1)
 
void bfac2 (Real const &bfac2)
 
void fa_atr (Real const &fa_atr)
 
void fa_atr_sc_bb (Real const &fa_atr_sc_bb)
 
void fa_atr_bb (Real const &fa_atr_bb)
 
void hb_sc (Real const &hb_sc)
 
void hb_bb_sc (Real const &hb_bb_sc)
 
void hb_bb (Real const &hb_bb)
 
void nbrs1 (Real const &nbrs)
 
void nbrs2 (Real const &nbrs)
 
char aa1 () const
 
char aa2 () const
 
char ss1 () const
 
char ss2 () const
 
char dssp1 () const
 
char dssp2 () const
 
Real score () const
 
RPM_Type type () const
 
RM_Type type1 () const
 
RM_Type type2 () const
 
void type (RPM_Type const &type)
 
Size resi1 () const
 
Size resi2 () const
 
Size count () const
 
void count (Size const &count)
 
void addcount ()
 
std::string tag () const
 
bool filter (RPM_FilterStats *stat=nullptr) const
 
void dump_pdb (std::ostream &out, numeric::xyzTransform< Real > const &xform=Xform::identity(), std::string tag="1") const
 
void dump_pdb (std::string const &fname="", std::string const &tag="1") const
 
Real dump_aligned_motif (std::ostream &out, core::pose::Pose const &pose1, Size const &ir, core::pose::Pose const &pose2, Size const &jr, Size &aotmno, int const &num=1, numeric::Xforms const &xforms=XsI) const
 
Real dump_aligned_motif (std::ostream &out, core::pose::Pose const &pose, Size const &ir, Size const &jr, Size &aotmno, int const &num=1, numeric::Xforms const &xforms=XsI) const
 
Real dump_aligned_motif (std::string const &fn, core::pose::Pose const &pose1, Size const &ir, core::pose::Pose const &pose2, Size const &jr, Size &aotmno, int const &num=1, numeric::Xforms const &xforms=XsI) const
 
Real dump_aligned_motif (std::string const &fn, core::pose::Pose const &pose, Size const &ir, Size const &jr, Size &aotmno, int const &num=1, numeric::Xforms const &xforms=XsI) const
 
Real dump_aligned_motif (std::ostream &out, core::pose::Pose const &pose1, Size const &ir, core::pose::Pose const &pose2, Size const &jr, int const &num=1, numeric::Xforms const &xforms=XsI) const
 
Real dump_aligned_motif (std::ostream &out, core::pose::Pose const &pose, Size const &ir, Size const &jr, int const &num=1, numeric::Xforms const &xforms=XsI) const
 
Real dump_aligned_motif (std::string const &fn, core::pose::Pose const &pose1, Size const &ir, core::pose::Pose const &pose2, Size const &jr, int const &num=1, numeric::Xforms const &xforms=XsI) const
 
Real dump_aligned_motif (std::string const &fn, core::pose::Pose const &pose, Size const &ir, Size const &jr, int const &num=1, numeric::Xforms const &xforms=XsI) const
 
void fill_pose_with_motif (core::pose::Pose &pose, int const &ir=1, int const &jr=2) const
 
core::pose::Pose get_pose (int const &ir=1, int const &jr=2) const
 
bool operator< (ResPairMotif const &other) const
 
bool operator== (ResPairMotif const &other) const
 

Static Public Member Functions

static void print_header (std::ostream &out)
 

Private Attributes

char ss1_
 
char ss2_
 
char aa1_
 
char aa2_
 
utility::fixedsizearray1
< uint16_t, 6 > 
rt6_
 
utility::fixedsizearray1
< uint8_t, 4 > 
chi1_
 
utility::fixedsizearray1
< uint8_t, 4 > 
chi2_
 
uint8_t fa_atr_
 
uint8_t fa_atr_sc_bb_
 
uint8_t fa_atr_bb_
 
uint8_t hb_sc_
 
uint8_t hb_bb_sc_
 
uint8_t hb_bb_
 
uint8_t nbrs1_
 
uint8_t nbrs2_
 
uint8_t count_
 
uint8_t type_
 
uint8_t misc1_
 
uint16_t lg1x_
 
uint16_t lg1y_
 
uint16_t lg1z_
 
uint16_t lg2x_
 
uint16_t lg2y_
 
uint16_t lg2z_
 
uint8_t bfac1_
 
uint8_t bfac2_
 
char chain1_
 
char chain2_
 
uint16_t resi1_
 
uint16_t resi2_
 
utility::fixedsizearray1
< unsigned char, 8 > 
pdb_
 

Friends

std::ostream & operator<< (std::ostream &out, ResPairMotif const &x)
 

Constructor & Destructor Documentation

core::scoring::motif::ResPairMotif::ResPairMotif ( )
core::scoring::motif::ResPairMotif::ResPairMotif ( std::string const &  tag,
core::pose::Pose const &  pose,
Real6 const &  rt6,
Size const &  resi1,
Size const &  resi2,
Real const &  nbrs1,
Real const &  nbrs2,
Real const &  fa_atr,
Real const &  fa_atr_sc_bb,
Real const &  fa_atr_bb,
Real const &  hb_sc,
Real const &  hb_bb_sc,
Real const &  hb_bb,
Real const &  bfac1,
Real const &  bfac2,
bool  is_sspaired,
RPM_Type  _type 
)

Member Function Documentation

char core::scoring::motif::ResPairMotif::aa1 ( ) const
char core::scoring::motif::ResPairMotif::aa2 ( ) const
void core::scoring::motif::ResPairMotif::addcount ( )
inline

References count_.

Real core::scoring::motif::ResPairMotif::bfac1 ( ) const
void core::scoring::motif::ResPairMotif::bfac1 ( Real const &  bfac1)
Real core::scoring::motif::ResPairMotif::bfac2 ( ) const
void core::scoring::motif::ResPairMotif::bfac2 ( Real const &  bfac2)
bool core::scoring::motif::ResPairMotif::check_lig_code ( std::string const &  qlig) const
inline
bool core::scoring::motif::ResPairMotif::check_pdb_code ( std::string const &  qpdb) const
inline

References pdb_.

Real core::scoring::motif::ResPairMotif::chi1 ( Size const &  ichi) const
Real core::scoring::motif::ResPairMotif::chi11 ( ) const
Real core::scoring::motif::ResPairMotif::chi12 ( ) const
Real core::scoring::motif::ResPairMotif::chi13 ( ) const
Real core::scoring::motif::ResPairMotif::chi14 ( ) const
Real core::scoring::motif::ResPairMotif::chi2 ( Size const &  ichi) const
Real core::scoring::motif::ResPairMotif::chi21 ( ) const
Real core::scoring::motif::ResPairMotif::chi22 ( ) const
Real core::scoring::motif::ResPairMotif::chi23 ( ) const
Real core::scoring::motif::ResPairMotif::chi24 ( ) const
Size core::scoring::motif::ResPairMotif::count ( ) const
inline

References count_.

Referenced by core::scoring::motif::operator<<().

void core::scoring::motif::ResPairMotif::count ( Size const &  count)
inline

References count(), and count_.

Referenced by count().

Real core::scoring::motif::ResPairMotif::dist2 ( ) const
char core::scoring::motif::ResPairMotif::dssp1 ( ) const
char core::scoring::motif::ResPairMotif::dssp2 ( ) const
Real core::scoring::motif::ResPairMotif::dump_aligned_motif ( std::ostream &  out,
core::pose::Pose const &  pose1,
Size const &  ir,
core::pose::Pose const &  pose2,
Size const &  jr,
Size aotmno,
int const &  num = 1,
numeric::Xforms const &  xforms = XsI 
) const
Real core::scoring::motif::ResPairMotif::dump_aligned_motif ( std::ostream &  out,
core::pose::Pose const &  pose,
Size const &  ir,
Size const &  jr,
Size aotmno,
int const &  num = 1,
numeric::Xforms const &  xforms = XsI 
) const
Real core::scoring::motif::ResPairMotif::dump_aligned_motif ( std::string const &  fn,
core::pose::Pose const &  pose1,
Size const &  ir,
core::pose::Pose const &  pose2,
Size const &  jr,
Size aotmno,
int const &  num = 1,
numeric::Xforms const &  xforms = XsI 
) const
Real core::scoring::motif::ResPairMotif::dump_aligned_motif ( std::string const &  fn,
core::pose::Pose const &  pose,
Size const &  ir,
Size const &  jr,
Size aotmno,
int const &  num = 1,
numeric::Xforms const &  xforms = XsI 
) const
Real core::scoring::motif::ResPairMotif::dump_aligned_motif ( std::ostream &  out,
core::pose::Pose const &  pose1,
Size const &  ir,
core::pose::Pose const &  pose2,
Size const &  jr,
int const &  num = 1,
numeric::Xforms const &  xforms = XsI 
) const
Real core::scoring::motif::ResPairMotif::dump_aligned_motif ( std::ostream &  out,
core::pose::Pose const &  pose,
Size const &  ir,
Size const &  jr,
int const &  num = 1,
numeric::Xforms const &  xforms = XsI 
) const
Real core::scoring::motif::ResPairMotif::dump_aligned_motif ( std::string const &  fn,
core::pose::Pose const &  pose1,
Size const &  ir,
core::pose::Pose const &  pose2,
Size const &  jr,
int const &  num = 1,
numeric::Xforms const &  xforms = XsI 
) const
Real core::scoring::motif::ResPairMotif::dump_aligned_motif ( std::string const &  fn,
core::pose::Pose const &  pose,
Size const &  ir,
Size const &  jr,
int const &  num = 1,
numeric::Xforms const &  xforms = XsI 
) const
void core::scoring::motif::ResPairMotif::dump_pdb ( std::ostream &  out,
numeric::xyzTransform< Real > const &  xform = Xform::identity(),
std::string  tag = "1" 
) const
void core::scoring::motif::ResPairMotif::dump_pdb ( std::string const &  fname = "",
std::string const &  tag = "1" 
) const
Real core::scoring::motif::ResPairMotif::fa_atr ( ) const
void core::scoring::motif::ResPairMotif::fa_atr ( Real const &  fa_atr)
Real core::scoring::motif::ResPairMotif::fa_atr_bb ( ) const
void core::scoring::motif::ResPairMotif::fa_atr_bb ( Real const &  fa_atr_bb)
Real core::scoring::motif::ResPairMotif::fa_atr_sc_bb ( ) const
void core::scoring::motif::ResPairMotif::fa_atr_sc_bb ( Real const &  fa_atr_sc_bb)
void core::scoring::motif::ResPairMotif::fill_pose_with_motif ( core::pose::Pose pose,
int const &  ir = 1,
int const &  jr = 2 
) const
bool core::scoring::motif::ResPairMotif::filter ( RPM_FilterStats stat = nullptr) const

References core::scoring::motif::aa_trustworthiness(), core::scoring::motif::BB_BB, core::scoring::motif::BB_PH, core::scoring::motif::BB_PO, core::scoring::motif::RPM_FilterStats::F_aa1, core::scoring::motif::RPM_FilterStats::F_aa2, core::scoring::motif::RPM_FilterStats::F_coorderr, core::scoring::motif::RPM_FilterStats::F_dssp1, core::scoring::motif::RPM_FilterStats::F_dssp2, core::scoring::motif::RPM_FilterStats::F_faatr, core::scoring::motif::RPM_FilterStats::F_faatr_or_hb, core::scoring::motif::RPM_FilterStats::F_faatr_or_hbbb, core::scoring::motif::RPM_FilterStats::F_hb_bb, core::scoring::motif::RPM_FilterStats::F_hb_bb_sc, core::scoring::motif::RPM_FilterStats::F_hb_sc, core::scoring::motif::RPM_FilterStats::F_lig, core::scoring::motif::RPM_FilterStats::F_max_seqsep, core::scoring::motif::RPM_FilterStats::F_maxdist2, core::scoring::motif::RPM_FilterStats::F_mindist2, core::scoring::motif::RPM_FilterStats::F_no_hb_bb, core::scoring::motif::RPM_FilterStats::F_nodisulf, core::scoring::motif::RPM_FilterStats::F_noloops, core::scoring::motif::RPM_FilterStats::F_not_restype, core::scoring::motif::RPM_FilterStats::F_not_restype_one, core::scoring::motif::RPM_FilterStats::F_oneloop, core::scoring::motif::RPM_FilterStats::F_pdb, core::scoring::motif::RPM_FilterStats::F_restype, core::scoring::motif::RPM_FilterStats::F_restype1, core::scoring::motif::RPM_FilterStats::F_restype2, core::scoring::motif::RPM_FilterStats::F_restype_one, core::scoring::motif::RPM_FilterStats::F_score, core::scoring::motif::RPM_FilterStats::F_seqsep, core::scoring::motif::RPM_FilterStats::F_ss1, core::scoring::motif::RPM_FilterStats::F_ss2, core::scoring::motif::RPM_FilterStats::F_type_BB_BB, core::scoring::motif::RPM_FilterStats::F_type_BB_PH, core::scoring::motif::RPM_FilterStats::F_type_BB_PO, core::scoring::motif::RPM_FilterStats::F_type_PH_PO, core::scoring::motif::RPM_FilterStats::F_type_SC_BB, core::scoring::motif::RPM_FilterStats::F_type_SC_PH, core::scoring::motif::RPM_FilterStats::F_type_SC_PO, core::scoring::motif::RPM_FilterStats::F_type_SC_SC, core::scoring::motif::RPM_FilterStats::F_uniformfrag, core::scoring::fa_atr, core::scoring::motif::MOTIF_HASH_CART_SIZE, core::chemical::element::N, core::scoring::motif::RPM_FilterStats::P_aa1, core::scoring::motif::RPM_FilterStats::P_aa2, core::scoring::motif::RPM_FilterStats::P_coorderr, core::scoring::motif::RPM_FilterStats::P_dssp1, core::scoring::motif::RPM_FilterStats::P_dssp2, core::scoring::motif::RPM_FilterStats::P_faatr, core::scoring::motif::RPM_FilterStats::P_faatr_or_hb, core::scoring::motif::RPM_FilterStats::P_faatr_or_hbbb, core::scoring::motif::RPM_FilterStats::P_hb_bb, core::scoring::motif::RPM_FilterStats::P_hb_bb_sc, core::scoring::motif::RPM_FilterStats::P_hb_sc, core::scoring::motif::RPM_FilterStats::P_lig, core::scoring::motif::RPM_FilterStats::P_max_seqsep, core::scoring::motif::RPM_FilterStats::P_maxdist2, core::scoring::motif::RPM_FilterStats::P_mindist2, core::scoring::motif::RPM_FilterStats::P_no_hb_bb, core::scoring::motif::RPM_FilterStats::P_nodisulf, core::scoring::motif::RPM_FilterStats::P_noloops, core::scoring::motif::RPM_FilterStats::P_not_restype, core::scoring::motif::RPM_FilterStats::P_not_restype_one, core::scoring::motif::RPM_FilterStats::P_oneloop, core::scoring::motif::RPM_FilterStats::P_pdb, core::scoring::motif::RPM_FilterStats::P_restype, core::scoring::motif::RPM_FilterStats::P_restype1, core::scoring::motif::RPM_FilterStats::P_restype2, core::scoring::motif::RPM_FilterStats::P_restype_one, core::scoring::motif::RPM_FilterStats::P_score, core::scoring::motif::RPM_FilterStats::P_seqsep, core::scoring::motif::RPM_FilterStats::P_ss1, core::scoring::motif::RPM_FilterStats::P_ss2, core::scoring::motif::RPM_FilterStats::P_type_BB_BB, core::scoring::motif::RPM_FilterStats::P_type_BB_PH, core::scoring::motif::RPM_FilterStats::P_type_BB_PO, core::scoring::motif::RPM_FilterStats::P_type_PH_PO, core::scoring::motif::RPM_FilterStats::P_type_SC_BB, core::scoring::motif::RPM_FilterStats::P_type_SC_PH, core::scoring::motif::RPM_FilterStats::P_type_SC_PO, core::scoring::motif::RPM_FilterStats::P_type_SC_SC, core::scoring::motif::RPM_FilterStats::P_uniformfrag, core::scoring::motif::PH_PO, core::scoring::motif::SC_BB, core::scoring::motif::SC_PH, core::scoring::motif::SC_PO, core::scoring::motif::SC_SC, protocols::hybridization::score, and core::scoring::motif::uint16_to_real().

core::pose::Pose core::scoring::motif::ResPairMotif::get_pose ( int const &  ir = 1,
int const &  jr = 2 
) const
Real core::scoring::motif::ResPairMotif::hb_bb ( ) const
void core::scoring::motif::ResPairMotif::hb_bb ( Real const &  hb_bb)
Real core::scoring::motif::ResPairMotif::hb_bb_sc ( ) const
void core::scoring::motif::ResPairMotif::hb_bb_sc ( Real const &  hb_bb_sc)
Real core::scoring::motif::ResPairMotif::hb_sc ( ) const
void core::scoring::motif::ResPairMotif::hb_sc ( Real const &  hb_sc)
bool core::scoring::motif::ResPairMotif::is_reversible ( ) const
inline
Real core::scoring::motif::ResPairMotif::nbrs1 ( ) const
void core::scoring::motif::ResPairMotif::nbrs1 ( Real const &  nbrs)
Real core::scoring::motif::ResPairMotif::nbrs2 ( ) const
void core::scoring::motif::ResPairMotif::nbrs2 ( Real const &  nbrs)
bool core::scoring::motif::ResPairMotif::operator< ( ResPairMotif const &  other) const
bool core::scoring::motif::ResPairMotif::operator== ( ResPairMotif const &  other) const
std::string core::scoring::motif::ResPairMotif::pdb ( ) const
inline

References pdb_.

Referenced by core::scoring::motif::operator<<().

void core::scoring::motif::ResPairMotif::print_header ( std::ostream &  out)
static
void core::scoring::motif::ResPairMotif::reset ( )
Size core::scoring::motif::ResPairMotif::resi1 ( ) const
inline
Size core::scoring::motif::ResPairMotif::resi2 ( ) const
inline
ResPairMotif & core::scoring::motif::ResPairMotif::reverse_in_place ( )
ResPairMotif & core::scoring::motif::ResPairMotif::reverse_in_place_unsafe ( )

References core::id::swap().

ResPairMotif core::scoring::motif::ResPairMotif::reversed ( ) const
Real6 core::scoring::motif::ResPairMotif::rt ( ) const
void core::scoring::motif::ResPairMotif::rt ( Real6 const &  rt)
Real core::scoring::motif::ResPairMotif::score ( ) const
char core::scoring::motif::ResPairMotif::ss1 ( ) const
char core::scoring::motif::ResPairMotif::ss2 ( ) const
std::string core::scoring::motif::ResPairMotif::tag ( ) const
RPM_Type core::scoring::motif::ResPairMotif::type ( ) const
void core::scoring::motif::ResPairMotif::type ( RPM_Type const &  type)
inline

References type_.

RM_Type core::scoring::motif::ResPairMotif::type1 ( ) const
RM_Type core::scoring::motif::ResPairMotif::type2 ( ) const
bool core::scoring::motif::ResPairMotif::valid ( ) const
Xform core::scoring::motif::ResPairMotif::xform ( ) const
void core::scoring::motif::ResPairMotif::xform ( Xform const &  _xform)

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
ResPairMotif const &  x 
)
friend

Member Data Documentation

char core::scoring::motif::ResPairMotif::aa1_
private
char core::scoring::motif::ResPairMotif::aa2_
private
uint8_t core::scoring::motif::ResPairMotif::bfac1_
private
uint8_t core::scoring::motif::ResPairMotif::bfac2_
private
char core::scoring::motif::ResPairMotif::chain1_
private
char core::scoring::motif::ResPairMotif::chain2_
private
utility::fixedsizearray1<uint8_t,4> core::scoring::motif::ResPairMotif::chi1_
private
utility::fixedsizearray1<uint8_t,4> core::scoring::motif::ResPairMotif::chi2_
private
uint8_t core::scoring::motif::ResPairMotif::count_
private

Referenced by addcount(), and count().

uint8_t core::scoring::motif::ResPairMotif::fa_atr_
private
uint8_t core::scoring::motif::ResPairMotif::fa_atr_bb_
private
uint8_t core::scoring::motif::ResPairMotif::fa_atr_sc_bb_
private
uint8_t core::scoring::motif::ResPairMotif::hb_bb_
private
uint8_t core::scoring::motif::ResPairMotif::hb_bb_sc_
private
uint8_t core::scoring::motif::ResPairMotif::hb_sc_
private
uint16_t core::scoring::motif::ResPairMotif::lg1x_
private
uint16_t core::scoring::motif::ResPairMotif::lg1y_
private
uint16_t core::scoring::motif::ResPairMotif::lg1z_
private
uint16_t core::scoring::motif::ResPairMotif::lg2x_
private
uint16_t core::scoring::motif::ResPairMotif::lg2y_
private
uint16_t core::scoring::motif::ResPairMotif::lg2z_
private
uint8_t core::scoring::motif::ResPairMotif::misc1_
private
uint8_t core::scoring::motif::ResPairMotif::nbrs1_
private
uint8_t core::scoring::motif::ResPairMotif::nbrs2_
private
utility::fixedsizearray1<unsigned char,8> core::scoring::motif::ResPairMotif::pdb_
private

Referenced by check_lig_code(), check_pdb_code(), and pdb().

uint16_t core::scoring::motif::ResPairMotif::resi1_
private
uint16_t core::scoring::motif::ResPairMotif::resi2_
private
utility::fixedsizearray1<uint16_t,6> core::scoring::motif::ResPairMotif::rt6_
private
char core::scoring::motif::ResPairMotif::ss1_
private
char core::scoring::motif::ResPairMotif::ss2_
private
uint8_t core::scoring::motif::ResPairMotif::type_
private

Referenced by type().


The documentation for this class was generated from the following files: