PdbChain Class Reference

One molecule in a PDB structure. More...

#include <Pdb.h>

List of all members.

Public Member Functions
	PdbChain (char id= ' ')
	PdbChain (const Compound &compound, const Transform &transform=Transform())
	PdbChain (const State &state, const Compound &compound, const Transform &transform=Transform())
std::ostream &	write (std::ostream &os, int &nextAtomSerialNumber, const Transform &transform=Transform()) const
bool	hasResidue (PdbResidueId pdbResidueId) const
bool	hasAtom (String atomName, PdbResidueId residueId) const
const PdbAtom &	getAtom (String atomName, PdbResidueId residueId) const
PdbAtom &	updAtom (String atomName, PdbResidueId residueId)
PdbResidue &	appendResidue (const PdbResidue &residue)
size_t	getNumResidues () const
const PdbResidue &	getResidue (Pdb::ResidueIndex resIx) const
size_t	getNumAtoms () const
char	getChainId () const
size_t	getNResidues () const
size_t	getNAtoms () const
Protected Member Functions
void	parsePdbLine (const String &line)
Friends
class	PdbModel

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Detailed Description

One molecule in a PDB structure.

One exception is that all of the water molecules in a structure may share a single chainId

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Constructor & Destructor Documentation

PdbChain

(

char

id = ' '

)

[inline, explicit]

PdbChain	(	const Compound &	compound,
		const Transform &	transform = Transform()
	)			[explicit]

PdbChain	(	const State &	state,
		const Compound &	compound,
		const Transform &	transform = Transform()
	)			[explicit]

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Member Function Documentation

PdbResidue& appendResidue

(

const PdbResidue &

residue

)

[inline]

References PdbResidue::getResidueId(), and SimTK_THROW1.

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

char getChainId

(

)

const [inline]

size_t getNAtoms

(

)

const [inline]

size_t getNResidues

(

)

const [inline]

size_t getNumAtoms

(

)

const [inline]

size_t getNumResidues

(

)

const [inline]

const PdbResidue& getResidue

(

Pdb::ResidueIndex

resIx

)

const [inline]

bool hasAtom	(	String	atomName,
		PdbResidueId	residueId
	)			const

bool hasResidue

(

PdbResidueId

pdbResidueId

)

const

void parsePdbLine

(

const String &

line

)

[protected]

PdbAtom& updAtom	(	String	atomName,
		PdbResidueId	residueId
	)

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

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Friends And Related Function Documentation

friend class PdbModel [friend]

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

• Pdb.h