Molmodel
Public Member Functions | Protected Member Functions | Friends

SimTK::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 PdbAtomgetAtom (String atomName, PdbResidueId residueId) const
PdbAtomupdAtom (String atomName, PdbResidueId residueId)
PdbResidueappendResidue (const PdbResidue &residue)
size_t getNumResidues () const
const PdbResiduegetResidue (Pdb::ResidueIndex resIx) const
size_t getNumAtoms () const
char getChainId () const

Protected Member Functions

void parsePdbLine (const String &line)

Friends

class PdbModel

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


Constructor & Destructor Documentation

SimTK::PdbChain::PdbChain ( char  id = ' ') [inline, explicit]
SimTK::PdbChain::PdbChain ( const Compound compound,
const Transform transform = Transform() 
) [explicit]
SimTK::PdbChain::PdbChain ( const State state,
const Compound compound,
const Transform transform = Transform() 
) [explicit]

Member Function Documentation

std::ostream& SimTK::PdbChain::write ( std::ostream &  os,
int &  nextAtomSerialNumber,
const Transform transform = Transform() 
) const
bool SimTK::PdbChain::hasResidue ( PdbResidueId  pdbResidueId) const
bool SimTK::PdbChain::hasAtom ( String  atomName,
PdbResidueId  residueId 
) const
const PdbAtom& SimTK::PdbChain::getAtom ( String  atomName,
PdbResidueId  residueId 
) const
PdbAtom& SimTK::PdbChain::updAtom ( String  atomName,
PdbResidueId  residueId 
)
PdbResidue& SimTK::PdbChain::appendResidue ( const PdbResidue residue) [inline]
size_t SimTK::PdbChain::getNumResidues ( ) const [inline]
const PdbResidue& SimTK::PdbChain::getResidue ( Pdb::ResidueIndex  resIx) const [inline]
size_t SimTK::PdbChain::getNumAtoms ( ) const [inline]
char SimTK::PdbChain::getChainId ( ) const [inline]
void SimTK::PdbChain::parsePdbLine ( const String line) [protected]

Friends And Related Function Documentation

friend class PdbModel [friend]

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