Rosetta 3.4
Public Member Functions | Public Attributes
protocols::sparta::PDB Class Reference

#include <PDB.hh>

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List of all members.

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, intacceptorList
boost::unordered_map< int, intdonorList
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
Vec3SpherePoints
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

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::sparta::PDB::calc_ElectricField ( )
void protocols::sparta::PDB::calc_HN_S2 ( )
void protocols::sparta::PDB::calcPlane ( RingData ringP)
void protocols::sparta::PDB::calcSurface ( float  rad_sol)
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 
)
void protocols::sparta::PDB::collect_HN_S2_and_EF ( )
void protocols::sparta::PDB::findNeighors ( float  rad_sol)
float protocols::sparta::PDB::getBondAngle ( Vec3  A,
Vec3  B,
Vec3  C 
)
float protocols::sparta::PDB::getBondAngle ( PDB_Entry  a,
PDB_Entry  b,
PDB_Entry  c 
)
float protocols::sparta::PDB::getChi1 ( int  conformerID,
int  resNum 
)

References SPARTA_MAXNUM.

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

References SPARTA_MAXNUM.

float protocols::sparta::PDB::getDihedralAngle ( PDB_Entry  a,
PDB_Entry  b,
PDB_Entry  c,
PDB_Entry  d 
)
float protocols::sparta::PDB::getDist ( Vec3  A,
Vec3  B 
)
float protocols::sparta::PDB::getDist ( PDB_Entry  A,
PDB_Entry  B 
)
PDB_Entry protocols::sparta::PDB::getEntry ( int  conformerID,
int  rNum,
const std::string &  aName 
)
PDB_Entry protocols::sparta::PDB::getEntry ( int  conformerID,
int  aNum 
)
string protocols::sparta::PDB::getField ( const std::string &  str,
int  index 
)
float protocols::sparta::PDB::getHBondDist ( PDB_Entry  D)
float protocols::sparta::PDB::getHBondDist ( int  resNum,
std::string  atomName 
)
float protocols::sparta::PDB::getOmega ( int  conformerID,
int  resNum 
)
string protocols::sparta::PDB::getOneAAName ( const std::string &  a)
float protocols::sparta::PDB::getOrbitalShift ( int  conformerID,
int  resNum,
const std::string &  aName 
)
float protocols::sparta::PDB::getPhi ( int  conformerID,
int  resNum 
)
float protocols::sparta::PDB::getPsi ( int  conformerID,
int  resNum 
)
string protocols::sparta::PDB::getThreeAAName ( char  a)
void protocols::sparta::PDB::initHBond ( float  DIST = 3.5,
float  ANGLE = 35 
)
void protocols::sparta::PDB::initOrbitalShift ( )
PDB_Entry protocols::sparta::PDB::isAcceptor ( PDB_Entry  A)
PDB_Entry protocols::sparta::PDB::isDonor ( PDB_Entry  D)
bool protocols::sparta::PDB::isSSBonded ( int  conformerID,
int  resNum 
)
void protocols::sparta::PDB::loadPDB ( std::istream &  file)
void protocols::sparta::PDB::loadPDB ( const std::string &  fileName)
void protocols::sparta::PDB::loadPDB ( core::pose::Pose const &  pose)
void protocols::sparta::PDB::loadPDB_Entry ( const std::string &  str,
PDB_Entry entry 
)

Member Data Documentation

boost::unordered_map<int, boost::unordered_map<int, boost::unordered_map< std::string, PDB_Entry> > > protocols::sparta::PDB::ATOMS
boost::unordered_map<int, boost::unordered_map< std::string,float> > protocols::sparta::PDB::AtomSurfaceFullList
boost::unordered_map<int, boost::unordered_map< std::string,float> > protocols::sparta::PDB::AtomSurfacePartList
boost::unordered_map<int, int> protocols::sparta::PDB::donorList
boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::ElectricField
boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::HB_DHO_AngleList
boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::HB_HOA_AngleList
boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::HBDistList
boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::HBEnergyList
boost::unordered_map<int, float> protocols::sparta::PDB::HN_S2
std::map<int, std::string> protocols::sparta::PDB::residList
std::map<int, std::string> protocols::sparta::PDB::residListOne
boost::unordered_map< int,float> protocols::sparta::PDB::ResSurfaceFullList
boost::unordered_map< int,float> protocols::sparta::PDB::ResSurfacePartList
boost::unordered_map< std::string, float > protocols::sparta::PDB::VDW_RAD

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