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
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 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<int, InnerHBondMap > protocols::sparta::PDB::HBondMap

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

(

)

References protocols::hybridization::r1.

protocols::sparta::PDB::PDB

(

const std::string &

fileName

)

References protocols::hybridization::r1.

Member Function Documentation

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

private

void protocols::sparta::PDB::calc_ElectricField

(

)

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

void protocols::sparta::PDB::calc_HN_S2

(

)

References protocols::sparta::PDB_Entry::atomName, protocols::match::upstream::b, core::sequence::end, core::chemical::element::H, protocols::hybridization::r1, and protocols::sparta::PDB_Entry::resNum.

void protocols::sparta::PDB::calcPlane

(

RingData *

ringP

)

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

)

References protocols::sparta::PDB_Entry::atomName, protocols::sparta::PDB_Entry::atomNum, protocols::match::upstream::b, protocols::sparta::PDB_Entry::Coord, core::sequence::end, protocols::hybridization::r1, and protocols::sparta::PDB_Entry::resNum.

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
	)

References core::pose::motif::a().

void protocols::sparta::PDB::collect_HN_S2_and_EF

(

)

References protocols::sparta::PDB_Entry::atomName, protocols::match::upstream::b, core::sequence::end, core::chemical::element::H, protocols::hybridization::r1, RADS_PER_DEG, and protocols::sparta::PDB_Entry::resNum.

void protocols::sparta::PDB::findNeighors

(

float

rad_sol

)

References core::pose::motif::a(), protocols::sparta::PDB_Entry::atomName, protocols::sparta::PDB_Entry::atomNum, protocols::match::upstream::b, and core::sequence::end.

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

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

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

References protocols::sparta::PDB_Entry::Coord.

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
	)

References protocols::sparta::PDB_Entry::atomName, core::scoring::co, core::io::pose_from_sfr::sgn(), SPARTA_MAXNUM, protocols::sparta::PDB_Entry::X, protocols::sparta::PDB_Entry::Y, and protocols::sparta::PDB_Entry::Z.

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

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

References protocols::sparta::PDB_Entry::Coord.

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

)

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

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
	)

References protocols::match::upstream::b, core::conformation::membrane::center, protocols::hybridization::r1, and protocols::hybridization::r2.

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
	)

References protocols::comparative_modeling::features::A, core::pose::motif::a(), protocols::sparta::PDB_Entry::atomName, protocols::sparta::PDB_Entry::atomNum, core::id::D, core::sequence::end, and protocols::sparta::PDB_Entry::resNum.

void protocols::sparta::PDB::initOrbitalShift

(

)

References protocols::sparta::PDB_Entry::atomName, protocols::sparta::PDB_Entry::Coord, and core::sequence::end.

PDB_Entry protocols::sparta::PDB::isAcceptor

(

PDB_Entry

A

)

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

PDB_Entry protocols::sparta::PDB::isDonor

(

PDB_Entry

D

)

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

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

References protocols::sparta::PDB_Entry::Coord, and core::sequence::end.

void protocols::sparta::PDB::loadPDB

(

const std::string &

fileName

)

References protocols::sparta::tr().

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

void protocols::sparta::PDB::loadPDB

(

std::istream &

file

)

References protocols::sparta::PDB_Entry::atomName, protocols::sparta::PDB_Entry::atomNum, protocols::sparta::PDB_Entry::chainName, core::sequence::end, protocols::hybridization::r1, protocols::sparta::PDB_Entry::resName, protocols::sparta::PDB_Entry::resNum, and protocols::kinmatch::str().

void protocols::sparta::PDB::loadPDB

(

core::pose::Pose const &

pose

)

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

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

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

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

References core::pose::motif::a().

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

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

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

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

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

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

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

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:

• src/protocols/sparta/PDB.hh
• src/protocols/sparta/PDB.cc