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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_Entry
AtomEntries
 
typedef boost::unordered_map
< int, AtomEntries
EntryMap
 
typedef boost::unordered_map
< int, EntryMap
AtomsMap
 
typedef std::map< int, int > PairList
 
typedef std::map< std::string,
float > 
InnerHBondMap
 
typedef std::map< int,
InnerHBondMap
HBondMap
 

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
 
PDB_Entry EMPTY
 
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
 
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
 

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

typedef boost::unordered_map< std::string, PDB_Entry> protocols::sparta::PDB::AtomEntries
typedef boost::unordered_map<int, EntryMap > protocols::sparta::PDB::AtomsMap
typedef boost::unordered_map<int, AtomEntries > protocols::sparta::PDB::EntryMap
typedef std::map< std::string, float > protocols::sparta::PDB::InnerHBondMap
typedef std::map< int, int > protocols::sparta::PDB::PairList

Constructor & Destructor Documentation

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

Member Function Documentation

float protocols::sparta::PDB::arccos_ ( float  x)
private
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 ( 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 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 ( const std::string &  fileName)
void protocols::sparta::PDB::loadPDB ( std::istream &  file)
void protocols::sparta::PDB::loadPDB ( core::pose::Pose const &  pose)
void protocols::sparta::PDB::loadPDB_Entry ( const std::string &  str,
PDB_Entry entry 
)
void protocols::sparta::PDB::Mat3VecMult ( Vec3  v,
Mat3  m 
)
private
long protocols::sparta::PDB::sgn ( float  x)
private
float protocols::sparta::PDB::Vec3Abs ( Vec3 const  v)
private
void protocols::sparta::PDB::Vec3Add ( Vec3  v1,
Vec3 const  v2 
)
private
void protocols::sparta::PDB::Vec3Copy ( Vec3  v1,
Vec3 const  v2 
)
private
void protocols::sparta::PDB::Vec3Cross ( Vec3  v1,
Vec3 const  v2 
)
private
float protocols::sparta::PDB::Vec3DiffAbs ( Vec3 const  v1,
Vec3 const  v2 
)
private
void protocols::sparta::PDB::Vec3Norm ( Vec3  v)
private
float protocols::sparta::PDB::Vec3Scalar ( Vec3 const  v1,
Vec3 const  v2 
)
private
void protocols::sparta::PDB::Vec3Scale ( Vec3  v,
float  s 
)
private
void protocols::sparta::PDB::Vec3ScaleAdd ( Vec3  v1,
float  s,
Vec3 const  v2 
)
private
void protocols::sparta::PDB::Vec3Sub ( Vec3  v1,
Vec3 const  v2 
)
private
void protocols::sparta::PDB::Vec3Zero ( Vec3  v)
private

Member Data Documentation

PairList protocols::sparta::PDB::acceptorList
AtomsMap 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
Mols protocols::sparta::PDB::Conformers
PairList protocols::sparta::PDB::donorList
boost::unordered_map<int, boost::unordered_map< std::string, float> > protocols::sparta::PDB::ElectricField
PDB_Entry protocols::sparta::PDB::EMPTY
HBondMap protocols::sparta::PDB::HB_DHO_AngleList
HBondMap protocols::sparta::PDB::HB_HOA_AngleList
HBondMap protocols::sparta::PDB::HBDistList
HBondMap protocols::sparta::PDB::HBEnergyList
boost::unordered_map<int, float> protocols::sparta::PDB::HN_S2
boost::unordered_map< int, utility::vector0<int> > protocols::sparta::PDB::NeighborList
std::string protocols::sparta::PDB::PDBfileName
int protocols::sparta::PDB::r1
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
int protocols::sparta::PDB::RingNo
RingData protocols::sparta::PDB::Rings[2000]
int protocols::sparta::PDB::rN
int protocols::sparta::PDB::SpherePointNo
Vec3* protocols::sparta::PDB::SpherePoints
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: