PdbAtom Class Reference

One atom, which may have more than one location, in the case of static or dynamic disorder in an X-ray structure. More...

#include <Pdb.h>

List of all members.

Public Member Functions
	PdbAtom (const SimTK::String &name, const Element &e)
	PdbAtom (const class Compound &compound, const String &atomName, const Transform &transform=Transform())
	PdbAtom (const State &state, const class Compound &compound, const String &atomName, const Transform &transform=Transform())
std::ostream &	write (std::ostream &os, int &nextAtomSerialNumber, const char residueName[4], PdbResidueId residueId, char chainId, const Transform &transform) const
bool	hasLocation (char altLoc) const
bool	hasLocation () const
Vec3	getLocation (char altLoc) const
Vec3	getLocation () const
PdbAtom &	setLocation (const PdbAtomLocation &loc)
const String &	getName () const
const PdbAtomLocation &	getPdbAtomLocation () const
const Vec3 &	getCoordinates () const
char	getAlternateLocationIndicator () const
SimTK::Real	getTemperatureFactor () const
SimTK::Real	getOccupancy () const
Protected Member Functions
void	parsePdbLine (const String &line)
Static Protected Member Functions
static String	canonicalizeAtomName (const String &casualName)
	create upper-case four-character PDB-style atom name, given a more free-form atom name
static std::vector< SimTK::String >	generatePossibleAtomNames (SimTK::String name)
	Try to be smart about guessing correct atom name for names that are not 4 characters long.
Friends
class	PdbResidue

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Detailed Description

One atom, which may have more than one location, in the case of static or dynamic disorder in an X-ray structure.

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Constructor & Destructor Documentation

PdbAtom	(	const SimTK::String &	name,
		const Element &	e
	)			[explicit]

PdbAtom	(	const class Compound &	compound,
		const String &	atomName,
		const Transform &	transform = Transform()
	)			[explicit]

PdbAtom	(	const State &	state,
		const class Compound &	compound,
		const String &	atomName,
		const Transform &	transform = Transform()
	)			[explicit]

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Member Function Documentation

static String canonicalizeAtomName

(

const String &

casualName

)

[static, protected]

create upper-case four-character PDB-style atom name, given a more free-form atom name

static std::vector<SimTK::String> generatePossibleAtomNames

(

SimTK::String

name

)

[static, protected]

Try to be smart about guessing correct atom name for names that are not 4 characters long.

char getAlternateLocationIndicator

(

)

const [inline]

const Vec3& getCoordinates

(

)

const [inline]

Vec3 getLocation

(

)

const

Vec3 getLocation

(

char

altLoc

)

const

const String& getName

(

)

const [inline]

SimTK::Real getOccupancy

(

)

const [inline]

const PdbAtomLocation& getPdbAtomLocation

(

)

const [inline]

SimTK::Real getTemperatureFactor

(

)

const [inline]

bool hasLocation

(

)

const

bool hasLocation

(

char

altLoc

)

const

void parsePdbLine

(

const String &

line

)

[protected]

PdbAtom& setLocation

(

const PdbAtomLocation &

loc

)

[inline]

References PdbAtomLocation::getAlternateLocationIndicator().

std::ostream& write	(	std::ostream &	os,
		int &	nextAtomSerialNumber,
		const char	residueName[4],
		PdbResidueId	residueId,
		char	chainId,
		const Transform &	transform
	)			const

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Friends And Related Function Documentation

friend class PdbResidue [friend]

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

• Pdb.h