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protocols::sparta::PDB Class Reference

#include <PDB.hh>

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Public Member Functions

 PDB ()
 
 PDB (const std::string &fileName)
 
std::string getThreeAAName (char a)
 
std::string getOneAAName (const std::string &a)
 
void loadPDB (const std::string &fileName)
 
void loadPDB (std::istream &file)
 
void loadPDB (core::pose::Pose const &pose)
 
void loadPDB_Entry (const std::string &str, PDB_Entry &entry)
 
std::string getField (const std::string &str, int index)
 
PDB_Entry getEntry (int conformerID, int rNum, const std::string &aName)
 
PDB_Entry getEntry (int conformerID, int aNum)
 
float getBondAngle (Vec3 A, Vec3 B, Vec3 C)
 
float getBondAngle (PDB_Entry a, PDB_Entry b, PDB_Entry c)
 
float getDihedralAngle (PDB_Entry a, PDB_Entry b, PDB_Entry c, PDB_Entry d)
 
float getPhi (int conformerID, int resNum)
 
float getPsi (int conformerID, int resNum)
 
float getOmega (int conformerID, int resNum)
 
float getChi1 (int conformerID, int resNum)
 
float getChi2 (int conformerID, int resNum)
 
float getDist (Vec3 A, Vec3 B)
 
float getDist (PDB_Entry A, PDB_Entry B)
 
bool isSSBonded (int conformerID, int resNum)
 
void initOrbitalShift ()
 
float getOrbitalShift (int conformerID, int resNum, const std::string &aName)
 
void calcPlane (RingData *ringP)
 
void initHBond (float DIST=3.5, float ANGLE=35)
 
float getHBondDist (PDB_Entry D)
 
float getHBondDist (int resNum, std::string atomName)
 
PDB_Entry isAcceptor (PDB_Entry A)
 
PDB_Entry isDonor (PDB_Entry D)
 
void calcTriangles (double x0, double y0, double z0, double x1, double y1, double z1, double x2, double y2, double z2, int rowStartA[], int rowNo, int quad, int row0, int ind0, int ind1, int row2, int ind2, Vec3 *pointA)
 
void findNeighors (float rad_sol)
 
void calcSurface (float rad_sol)
 
void calc_HN_S2 ()
 
void calc_ElectricField ()
 
void collect_HN_S2_and_EF ()
 

Public Attributes

std::string PDBfileName
 
RingData Rings [2000]
 
int RingNo
 
PDB_Entry EMPTY
 
Mols Conformers
 
boost::unordered_map< int,
boost::unordered_map< int,
boost::unordered_map
< std::string, PDB_Entry > > > 		ATOMS
 
std::map< int, std::string > residList
 
std::map< int, std::string > residListOne
 
int r1
 
int rN
 
boost::unordered_map< int, int > acceptorList
 
boost::unordered_map< int, int > donorList
 
boost::unordered_map< int,
boost::unordered_map
< std::string, float > > 		HBDistList
 
boost::unordered_map< int,
boost::unordered_map
< std::string, float > > 		HBEnergyList
 
boost::unordered_map< int,
boost::unordered_map
< std::string, float > > 		HB_DHO_AngleList
 
boost::unordered_map< int,
boost::unordered_map
< std::string, float > > 		HB_HOA_AngleList
 
int SpherePointNo
 
Vec3 * SpherePoints
 
int SurfPrec
 
boost::unordered_map< int,
utility::vector0< int > > 		NeighborList
 
boost::unordered_map< int, float > ResSurfaceFullList
 
boost::unordered_map< int, float > ResSurfacePartList
 
boost::unordered_map< int,
boost::unordered_map
< std::string, float > > 		AtomSurfaceFullList
 
boost::unordered_map< int,
boost::unordered_map
< std::string, float > > 		AtomSurfacePartList
 
boost::unordered_map
< std::string, float > 		VDW_RAD
 
boost::unordered_map< int, float > HN_S2
 
boost::unordered_map< int,
boost::unordered_map
< std::string, float > > 		ElectricField
 

Private Member Functions

long sgn (float x)
 
float arccos_ (float x)
 
void Vec3Zero (Vec3 v)
 
void Vec3Copy (Vec3 v1, Vec3 v2)
 
float Vec3Abs (Vec3 v)
 
float Vec3DiffAbs (Vec3 v1, Vec3 v2)
 
void Vec3Norm (Vec3 v)
 
void Vec3Scale (Vec3 v, float s)
 
void Vec3Add (Vec3 v1, Vec3 v2)
 
void Vec3Sub (Vec3 v1, Vec3 v2)
 
float Vec3Scalar (Vec3 v1, Vec3 v2)
 
void Vec3Cross (Vec3 v1, Vec3 v2)
 
void Mat3VecMult (Vec3 v, Mat3 m)
 
void Vec3ScaleAdd (Vec3 v1, float s, Vec3 v2)
 

Detailed Description

Definition at line 64 of file PDB.hh.

Constructor & Destructor Documentation

protocols::sparta::PDB::PDB ( )

Definition at line 41 of file PDB.cc.

protocols::sparta::PDB::PDB ( const std::string &  fileName)

Definition at line 47 of file PDB.cc.

Member Function Documentation

float protocols::sparta::PDB::arccos_ ( float  x)
private

Definition at line 799 of file PDB.cc.

void protocols::sparta::PDB::calc_ElectricField ( )

Definition at line 1407 of file PDB.cc.

References protocols::sparta::CORdata::atomName, protocols::match::upstream::b, core::pack::dunbrack::c, and protocols::sparta::CORdata::resNum.

void protocols::sparta::PDB::calc_HN_S2 ( )

Definition at line 1350 of file PDB.cc.

References protocols::sparta::CORdata::atomName, protocols::match::upstream::b, and protocols::sparta::CORdata::resNum.

void protocols::sparta::PDB::calcPlane ( RingData *  ringP)

Definition at line 522 of file PDB.cc.

References protocols::sparta::RingData::atomNo, protocols::sparta::RingData::center, protocols::sparta::RingData::coordA, protocols::sparta::RingData::norm, protocols::sparta::RingData::rad, and protocols::sparta::RingData::transM.

void protocols::sparta::PDB::calcSurface ( float  rad_sol)

Definition at line 971 of file PDB.cc.

References protocols::sparta::CORdata::atomName, protocols::sparta::CORdata::atomNum, protocols::match::upstream::b, protocols::sparta::CORdata::Coord, and protocols::sparta::CORdata::resNum.

void protocols::sparta::PDB::calcTriangles ( double  x0,
double  y0,
double  z0,
double  x1,
double  y1,
double  z1,
double  x2,
double  y2,
double  z2,
int  rowStartA[],
int  rowNo,
int  quad,
int  row0,
int  ind0,
int  ind1,
int  row2,
int  ind2,
Vec3 *  pointA 
)

Definition at line 1131 of file PDB.cc.

void protocols::sparta::PDB::collect_HN_S2_and_EF ( )

Definition at line 1469 of file PDB.cc.

References protocols::sparta::CORdata::atomName, protocols::match::upstream::b, and protocols::sparta::CORdata::resNum.

void protocols::sparta::PDB::findNeighors ( float  rad_sol)

Definition at line 1086 of file PDB.cc.

References protocols::sparta::CORdata::atomName, protocols::sparta::CORdata::atomNum, and protocols::match::upstream::b.

float protocols::sparta::PDB::getBondAngle ( Vec3  A,
Vec3  B,
Vec3  C 
)

Definition at line 224 of file PDB.cc.

References core::pack::dunbrack::c.

float protocols::sparta::PDB::getBondAngle ( PDB_Entry  a,
PDB_Entry  b,
PDB_Entry  c 
)

Definition at line 243 of file PDB.cc.

References protocols::sparta::CORdata::Coord.

float protocols::sparta::PDB::getChi1 ( int  conformerID,
int  resNum 
)

Definition at line 303 of file PDB.cc.

References SPARTA_MAXNUM.

float protocols::sparta::PDB::getChi2 ( int  conformerID,
int  resNum 
)

Definition at line 329 of file PDB.cc.

References SPARTA_MAXNUM.

float protocols::sparta::PDB::getDihedralAngle ( PDB_Entry  a,
PDB_Entry  b,
PDB_Entry  c,
PDB_Entry  d 
)

Definition at line 249 of file PDB.cc.

References protocols::sparta::CORdata::atomName, core::scoring::co, SPARTA_MAXNUM, protocols::sparta::CORdata::X, protocols::sparta::CORdata::Y, and protocols::sparta::CORdata::Z.

float protocols::sparta::PDB::getDist ( Vec3  A,
Vec3  B 
)

Definition at line 648 of file PDB.cc.

float protocols::sparta::PDB::getDist ( PDB_Entry  A,
PDB_Entry  B 
)

Definition at line 641 of file PDB.cc.

References protocols::sparta::CORdata::Coord.

PDB_Entry protocols::sparta::PDB::getEntry ( int  conformerID,
int  rNum,
const std::string &  aName 
)

Definition at line 211 of file PDB.cc.

PDB_Entry protocols::sparta::PDB::getEntry ( int  conformerID,
int  aNum 
)

Definition at line 218 of file PDB.cc.

string protocols::sparta::PDB::getField ( const std::string &  str,
int  index 
)

Definition at line 57 of file PDB.cc.

float protocols::sparta::PDB::getHBondDist ( PDB_Entry  D)

Definition at line 731 of file PDB.cc.

References protocols::sparta::CORdata::atomName, and protocols::sparta::CORdata::resNum.

float protocols::sparta::PDB::getHBondDist ( int  resNum,
std::string  atomName 
)

Definition at line 738 of file PDB.cc.

float protocols::sparta::PDB::getOmega ( int  conformerID,
int  resNum 
)

Definition at line 294 of file PDB.cc.

string protocols::sparta::PDB::getOneAAName ( const std::string &  a)

Definition at line 403 of file PDB.cc.

float protocols::sparta::PDB::getOrbitalShift ( int  conformerID,
int  resNum,
const std::string &  aName 
)

Definition at line 578 of file PDB.cc.

References protocols::match::upstream::b.

float protocols::sparta::PDB::getPhi ( int  conformerID,
int  resNum 
)

Definition at line 276 of file PDB.cc.

float protocols::sparta::PDB::getPsi ( int  conformerID,
int  resNum 
)

Definition at line 285 of file PDB.cc.

string protocols::sparta::PDB::getThreeAAName ( char  a)

Definition at line 371 of file PDB.cc.

void protocols::sparta::PDB::initHBond ( float  DIST = 3.5,
float  ANGLE = 35 
)

Definition at line 660 of file PDB.cc.

References protocols::comparative_modeling::features::A, protocols::sparta::CORdata::atomName, protocols::sparta::CORdata::atomNum, core::id::D, and protocols::sparta::CORdata::resNum.

void protocols::sparta::PDB::initOrbitalShift ( )

Definition at line 434 of file PDB.cc.

References protocols::sparta::CORdata::atomName, and protocols::sparta::CORdata::Coord.

PDB_Entry protocols::sparta::PDB::isAcceptor ( PDB_Entry  A)

Definition at line 745 of file PDB.cc.

References protocols::sparta::CORdata::atomName, protocols::sparta::CORdata::resName, and protocols::sparta::CORdata::resNum.

PDB_Entry protocols::sparta::PDB::isDonor ( PDB_Entry  D)

Definition at line 764 of file PDB.cc.

References protocols::sparta::CORdata::atomName, protocols::sparta::CORdata::resName, and protocols::sparta::CORdata::resNum.

bool protocols::sparta::PDB::isSSBonded ( int  conformerID,
int  resNum 
)

Definition at line 192 of file PDB.cc.

References protocols::sparta::CORdata::Coord.

void protocols::sparta::PDB::loadPDB ( const std::string &  fileName)

Definition at line 101 of file PDB.cc.

References protocols::sparta::tr().

Referenced by protocols::sparta::Sparta::SpartaLib::setup_for_scoring().

void protocols::sparta::PDB::loadPDB ( std::istream &  file)

Definition at line 121 of file PDB.cc.

References protocols::sparta::CORdata::atomName, protocols::sparta::CORdata::atomNum, protocols::sparta::CORdata::chainName, protocols::sparta::CORdata::resName, protocols::sparta::CORdata::resNum, and protocols::kinmatch::str().

void protocols::sparta::PDB::loadPDB ( core::pose::Pose const &  pose)

Definition at line 114 of file PDB.cc.

References core::pose::Pose::dump_pdb().

void protocols::sparta::PDB::loadPDB_Entry ( const std::string &  str,
PDB_Entry &  entry 
)

Definition at line 78 of file PDB.cc.

References protocols::sparta::CORdata::atomName, protocols::sparta::CORdata::atomNum, protocols::sparta::CORdata::B_Factor, protocols::sparta::CORdata::chainName, protocols::sparta::CORdata::Coord, protocols::sparta::CORdata::resName, protocols::sparta::CORdata::resNum, protocols::sparta::simplifyWhiteSpace(), protocols::sparta::CORdata::X, protocols::sparta::CORdata::Y, and protocols::sparta::CORdata::Z.

void protocols::sparta::PDB::Mat3VecMult ( Vec3  v,
Mat3  m 
)
private

Definition at line 890 of file PDB.cc.

long protocols::sparta::PDB::sgn ( float  x)
private

Definition at line 793 of file PDB.cc.

float protocols::sparta::PDB::Vec3Abs ( Vec3  v)
private

Definition at line 830 of file PDB.cc.

void protocols::sparta::PDB::Vec3Add ( Vec3  v1,
Vec3  v2 
)
private

Definition at line 859 of file PDB.cc.

void protocols::sparta::PDB::Vec3Copy ( Vec3  v1,
Vec3  v2 
)
private

Definition at line 823 of file PDB.cc.

void protocols::sparta::PDB::Vec3Cross ( Vec3  v1,
Vec3  v2 
)
private

Definition at line 879 of file PDB.cc.

float protocols::sparta::PDB::Vec3DiffAbs ( Vec3  v1,
Vec3  v2 
)
private

Definition at line 836 of file PDB.cc.

void protocols::sparta::PDB::Vec3Norm ( Vec3  v)
private

Definition at line 844 of file PDB.cc.

float protocols::sparta::PDB::Vec3Scalar ( Vec3  v1,
Vec3  v2 
)
private

Definition at line 873 of file PDB.cc.

void protocols::sparta::PDB::Vec3Scale ( Vec3  v,
float  s 
)
private

Definition at line 852 of file PDB.cc.

void protocols::sparta::PDB::Vec3ScaleAdd ( Vec3  v1,
float  s,
Vec3  v2 
)
private

Definition at line 903 of file PDB.cc.

void protocols::sparta::PDB::Vec3Sub ( Vec3  v1,
Vec3  v2 
)
private

Definition at line 866 of file PDB.cc.

void protocols::sparta::PDB::Vec3Zero ( Vec3  v)
private

Definition at line 816 of file PDB.cc.

Member Data Documentation

boost::unordered_map<int, int> protocols::sparta::PDB::acceptorList

Definition at line 99 of file PDB.hh.

boost::unordered_map<int, boost::unordered_map<int, boost::unordered_map< std::string, PDB_Entry> > > protocols::sparta::PDB::ATOMS

Definition at line 93 of file PDB.hh.

boost::unordered_map<int, boost::unordered_map< std::string,float> > protocols::sparta::PDB::AtomSurfaceFullList

Definition at line 115 of file PDB.hh.

boost::unordered_map<int, boost::unordered_map< std::string,float> > protocols::sparta::PDB::AtomSurfacePartList

Definition at line 115 of file PDB.hh.

Mols protocols::sparta::PDB::Conformers

Definition at line 91 of file PDB.hh.

boost::unordered_map<int, int> protocols::sparta::PDB::donorList

Definition at line 100 of file PDB.hh.

boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::ElectricField

Definition at line 120 of file PDB.hh.

PDB_Entry protocols::sparta::PDB::EMPTY

Definition at line 88 of file PDB.hh.

boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::HB_DHO_AngleList

Definition at line 103 of file PDB.hh.

boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::HB_HOA_AngleList

Definition at line 104 of file PDB.hh.

boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::HBDistList

Definition at line 101 of file PDB.hh.

boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::HBEnergyList

Definition at line 102 of file PDB.hh.

boost::unordered_map<int, float> protocols::sparta::PDB::HN_S2

Definition at line 119 of file PDB.hh.

boost::unordered_map< int, utility::vector0<int> > protocols::sparta::PDB::NeighborList

Definition at line 110 of file PDB.hh.

std::string protocols::sparta::PDB::PDBfileName

Definition at line 83 of file PDB.hh.

int protocols::sparta::PDB::r1

Definition at line 97 of file PDB.hh.

Referenced by protocols::sparta::Sparta::SpartaLib::setup_for_scoring().

std::map<int, std::string> protocols::sparta::PDB::residList

Definition at line 96 of file PDB.hh.

std::map<int, std::string> protocols::sparta::PDB::residListOne

Definition at line 96 of file PDB.hh.

Referenced by protocols::sparta::Sparta::SpartaLib::setup_for_scoring().

boost::unordered_map< int,float> protocols::sparta::PDB::ResSurfaceFullList

Definition at line 112 of file PDB.hh.

boost::unordered_map< int,float> protocols::sparta::PDB::ResSurfacePartList

Definition at line 112 of file PDB.hh.

int protocols::sparta::PDB::RingNo

Definition at line 86 of file PDB.hh.

RingData protocols::sparta::PDB::Rings[2000]

Definition at line 85 of file PDB.hh.

int protocols::sparta::PDB::rN

Definition at line 97 of file PDB.hh.

Referenced by protocols::sparta::Sparta::SpartaLib::setup_for_scoring().

int protocols::sparta::PDB::SpherePointNo

Definition at line 107 of file PDB.hh.

Vec3* protocols::sparta::PDB::SpherePoints

Definition at line 108 of file PDB.hh.

int protocols::sparta::PDB::SurfPrec

Definition at line 109 of file PDB.hh.

boost::unordered_map< std::string, float > protocols::sparta::PDB::VDW_RAD

Definition at line 117 of file PDB.hh.

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