PdbModel Class Reference

PDB structure containing one or more molecules (chains), corresponding to one member of an NMR ensemble of alternate structures, or to one frame of a molecular dynamics simulation. More...

#include <Pdb.h>

List of all members.

Public Member Functions
	PdbModel (const Compound &compound, int number=1, const Transform &transform=Transform())
	PdbModel (const State &state, const Compound &compound, int number=1, const Transform &transform=Transform())
	PdbModel (int number)
std::ostream &	write (std::ostream &os, const Transform &transform) const
bool	hasChain (char id) const
bool	hasAtom (String atomName, PdbResidueId residueId, char chainId) const
const PdbAtom &	getAtom (String atomName, PdbResidueId residueId, char chainId) const
PdbAtom &	updAtom (String atomName, PdbResidueId residueId, char chainId)
size_t	getNumChains () const
const PdbChain &	getChain (Pdb::ChainIndex chainIx) const
const PdbChain &	getChain (char chainId) const
size_t	getNChains () const
Protected Member Functions
void	parsePdbLine (const String &line)
PdbChain &	updOrCreateChain (char chainId)
Friends
class	PdbStructure

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Detailed Description

PDB structure containing one or more molecules (chains), corresponding to one member of an NMR ensemble of alternate structures, or to one frame of a molecular dynamics simulation.

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Constructor & Destructor Documentation

PdbModel	(	const Compound &	compound,
		int	number = 1,
		const Transform &	transform = Transform()
	)			[explicit]

PdbModel	(	const State &	state,
		const Compound &	compound,
		int	number = 1,
		const Transform &	transform = Transform()
	)			[explicit]

PdbModel

(

int

number

)

[inline, explicit]

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Member Function Documentation

const PdbAtom& getAtom	(	String	atomName,
		PdbResidueId	residueId,
		char	chainId
	)			const

const PdbChain& getChain

(

char

chainId

)

const

const PdbChain& getChain

(

Pdb::ChainIndex

chainIx

)

const [inline]

Referenced by Protein::loadFromPdbStructure(), and RNA::RNA().

size_t getNChains

(

)

const [inline]

size_t getNumChains

(

)

const [inline]

bool hasAtom	(	String	atomName,
		PdbResidueId	residueId,
		char	chainId
	)			const

bool hasChain

(

char

id

)

const

void parsePdbLine

(

const String &

line

)

[protected]

PdbAtom& updAtom	(	String	atomName,
		PdbResidueId	residueId,
		char	chainId
	)

PdbChain& updOrCreateChain

(

char

chainId

)

[protected]

std::ostream& write	(	std::ostream &	os,
		const Transform &	transform
	)			const

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Friends And Related Function Documentation

friend class PdbStructure [friend]

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

• Pdb.h