Public Types | Public Member Functions | Public Attributes | Private Member Functions | List of all members
protocols::sparta::PDB Class Reference

#include <PDB.hh>

Public Types

typedef boost::unordered_map< std::string, PDB_EntryAtomEntries
typedef boost::unordered_map< int, AtomEntriesEntryMap
typedef boost::unordered_map< int, EntryMapAtomsMap
typedef std::map< int, int > PairList
typedef std::map< std::string, float > InnerHBondMap
typedef std::map< int, InnerHBondMapHBondMap

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 (core::Real x0, core::Real y0, core::Real z0, core::Real x1, core::Real y1, core::Real z1, core::Real x2, core::Real y2, core::Real 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
Mols Conformers
AtomsMap ATOMS
std::map< int, std::string > residList
std::map< int, std::string > residListOne
int r1
int rN
PairList acceptorList
PairList donorList
HBondMap HBDistList
HBondMap HBEnergyList
HBondMap HB_DHO_AngleList
HBondMap HB_HOA_AngleList
int SpherePointNo
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 const v2)
float Vec3Abs (Vec3 const v)
float Vec3DiffAbs (Vec3 const v1, Vec3 const v2)
void Vec3Norm (Vec3 v)
void Vec3Scale (Vec3 v, float s)
void Vec3Add (Vec3 v1, Vec3 const v2)
void Vec3Sub (Vec3 v1, Vec3 const v2)
float Vec3Scalar (Vec3 const v1, Vec3 const v2)
void Vec3Cross (Vec3 v1, Vec3 const v2)
void Mat3VecMult (Vec3 v, Mat3 m)
void Vec3ScaleAdd (Vec3 v1, float s, Vec3 const v2)

Member Typedef Documentation

◆ AtomEntries

typedef boost::unordered_map< std::string, PDB_Entry> protocols::sparta::PDB::AtomEntries

◆ AtomsMap

typedef boost::unordered_map<int, EntryMap > protocols::sparta::PDB::AtomsMap

◆ EntryMap

typedef boost::unordered_map<int, AtomEntries > protocols::sparta::PDB::EntryMap

◆ HBondMap

◆ InnerHBondMap

typedef std::map< std::string, float > protocols::sparta::PDB::InnerHBondMap

◆ PairList

typedef std::map< int, int > protocols::sparta::PDB::PairList

Constructor & Destructor Documentation

◆ PDB() [1/2]

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

◆ PDB() [2/2]

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

Member Function Documentation

◆ arccos_()

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

◆ calc_ElectricField()

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

◆ calc_HN_S2()

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

◆ calcPlane()

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

◆ calcSurface()

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

◆ calcTriangles()

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

◆ collect_HN_S2_and_EF()

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

◆ findNeighors()

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

◆ getBondAngle() [1/2]

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

◆ getBondAngle() [2/2]

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

◆ getChi1()

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


◆ getChi2()

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


◆ getDihedralAngle()

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

◆ getDist() [1/2]

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

◆ getDist() [2/2]

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

◆ getEntry() [1/2]

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

◆ getEntry() [2/2]

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

◆ getField()

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

◆ getHBondDist() [1/2]

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

◆ getHBondDist() [2/2]

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

References core::id::D.

◆ getOmega()

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

◆ getOneAAName()

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

◆ getOrbitalShift()

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

◆ getPhi()

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

◆ getPsi()

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

◆ getThreeAAName()

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

◆ initHBond()

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

◆ initOrbitalShift()

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

◆ isAcceptor()

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

◆ isDonor()

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

References core::id::D.

◆ isSSBonded()

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

◆ loadPDB() [1/3]

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

◆ loadPDB() [2/3]

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

◆ loadPDB() [3/3]

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

◆ loadPDB_Entry()

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

◆ Mat3VecMult()

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

◆ sgn()

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

◆ Vec3Abs()

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

◆ Vec3Add()

void protocols::sparta::PDB::Vec3Add ( Vec3  v1,
Vec3 const  v2 

◆ Vec3Copy()

void protocols::sparta::PDB::Vec3Copy ( Vec3  v1,
Vec3 const  v2 

◆ Vec3Cross()

void protocols::sparta::PDB::Vec3Cross ( Vec3  v1,
Vec3 const  v2 

◆ Vec3DiffAbs()

float protocols::sparta::PDB::Vec3DiffAbs ( Vec3 const  v1,
Vec3 const  v2 

◆ Vec3Norm()

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

◆ Vec3Scalar()

float protocols::sparta::PDB::Vec3Scalar ( Vec3 const  v1,
Vec3 const  v2 

◆ Vec3Scale()

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

◆ Vec3ScaleAdd()

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

◆ Vec3Sub()

void protocols::sparta::PDB::Vec3Sub ( Vec3  v1,
Vec3 const  v2 

◆ Vec3Zero()

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

Member Data Documentation

◆ acceptorList

PairList protocols::sparta::PDB::acceptorList


AtomsMap protocols::sparta::PDB::ATOMS

◆ AtomSurfaceFullList

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

◆ AtomSurfacePartList

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

◆ Conformers

Mols protocols::sparta::PDB::Conformers

◆ donorList

PairList protocols::sparta::PDB::donorList

◆ ElectricField

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


PDB_Entry protocols::sparta::PDB::EMPTY

◆ HB_DHO_AngleList

HBondMap protocols::sparta::PDB::HB_DHO_AngleList

◆ HB_HOA_AngleList

HBondMap protocols::sparta::PDB::HB_HOA_AngleList

◆ HBDistList

HBondMap protocols::sparta::PDB::HBDistList

◆ HBEnergyList

HBondMap protocols::sparta::PDB::HBEnergyList

◆ HN_S2

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

◆ NeighborList

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

◆ PDBfileName

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

◆ r1

int protocols::sparta::PDB::r1

◆ residList

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

◆ residListOne

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

◆ ResSurfaceFullList

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

◆ ResSurfacePartList

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

◆ RingNo

int protocols::sparta::PDB::RingNo

◆ Rings

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

◆ rN

int protocols::sparta::PDB::rN

◆ SpherePointNo

int protocols::sparta::PDB::SpherePointNo

◆ SpherePoints

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

◆ SurfPrec

int protocols::sparta::PDB::SurfPrec


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

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