ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.
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ProtoMol::OutputDihedrals Class Reference

#include <OutputDihedrals.h>

Inheritance diagram for ProtoMol::OutputDihedrals:

ProtoMol::OutputFile ProtoMol::Output ProtoMol::Makeable List of all members.

Public Member Functions

 OutputDihedrals ()
 OutputDihedrals (const std::string &filename, int freq, int cacheFreq, int cacheSize, Real closeTime, int index, bool dihset, std::string dsetfile)
 ~OutputDihedrals ()
void getbackbonedihedrals ()
void getdihedralsfromatomset ()
virtual std::string getIdNoAlias () const
virtual unsigned int getParameterSize () const
virtual bool adjustWithDefaultParameters (std::vector< Value > &values, const Configuration *config) const
virtual void getParameters (std::vector< Parameter > &parameter) const

Static Public Attributes

const std::string keyword

Private Member Functions

virtual void doRunCached (int step)
virtual Output * doMake (std::string &errMsg, const std::vector< Value > &values) const
virtual void doInitialize ()
virtual void doFinalize (int step)

Private Attributes

int myDihedralIndex
bool myDihedralsSet
std::string myDihedralsSetfile
std::vector< int > myDihedrals
std::vector< std::vector<
Real > > 		myMaximas
std::vector< std::vector<
Real > > 		myMinimas
std::set< std::string > myConfstrings
DCDTrajectoryWriter * myDCD
std::vector< std::string > confstrings
std::vector< int > confstringsCounter

Detailed Description

Writes the dihedral values to a file at given freqeuncy.

Constructor & Destructor Documentation

ProtoMol::OutputDihedrals::OutputDihedrals (   ) 
 

ProtoMol::OutputDihedrals::OutputDihedrals (  const std::string &  filename,
int  freq,
int  cacheFreq,
int  cacheSize,
Real  closeTime,
int  index,
bool  dihset,
std::string  dsetfile
) 
 

ProtoMol::OutputDihedrals::~OutputDihedrals (   ) 
 

Member Function Documentation

bool ProtoMol::OutputDihedrals::adjustWithDefaultParameters (  std::vector< Value > &  values,
const Configuration *  config
)  const [virtual]
 

Reimplemented from ProtoMol::OutputFile.

void ProtoMol::OutputDihedrals::doFinalize (  int  step  )  [private, virtual]
 

Hook method of finalize, implemented in the concrete class.

Reimplemented from ProtoMol::OutputFile.

void ProtoMol::OutputDihedrals::doInitialize (   )  [private, virtual]
 

Hook method of initialize, implemented in the concrete class.

Implements ProtoMol::Output.

Output * ProtoMol::OutputDihedrals::doMake (  std::string &  errMsg,
const std::vector< Value > &  values
)  const [private, virtual]
 

Implements ProtoMol::Output.

void ProtoMol::OutputDihedrals::doRunCached (  int  step  )  [private, virtual]
 

new implementation of run method

Implements ProtoMol::OutputFile.

void ProtoMol::OutputDihedrals::getbackbonedihedrals (   ) 
 

This function can be used to get an approximate set of backbone dihedrals based on the weights of the atoms in each dihedral. The function can be called during initialization by uncommenting the call and recompiling

void ProtoMol::OutputDihedrals::getdihedralsfromatomset (   ) 
 

PRB Feb05 This function takes in a set of atom indices for select protein structures (backbone, alpha helix, etc...) and returns the Protomol indices for the matching dihedrals !the method may return extra dihedrals!

virtual std::string ProtoMol::OutputDihedrals::getIdNoAlias (   )  const [inline, virtual]
 

Implements ProtoMol::Makeable.

void ProtoMol::OutputDihedrals::getParameters (  std::vector< Parameter > &  parameter  )  const [virtual]
 

retrieve all parameters

Reimplemented from ProtoMol::OutputFile.

virtual unsigned int ProtoMol::OutputDihedrals::getParameterSize (   )  const [inline, virtual]
 

number of parameters

Implements ProtoMol::Makeable.

Member Data Documentation

std::vector< std::string > ProtoMol::OutputDihedrals::confstrings [private]
 

std::vector< int > ProtoMol::OutputDihedrals::confstringsCounter [private]
 

const string ProtoMol::OutputDihedrals::keyword [static]
 

std::set< std::string > ProtoMol::OutputDihedrals::myConfstrings [private]
 

DCDTrajectoryWriter* ProtoMol::OutputDihedrals::myDCD [private]
 

int ProtoMol::OutputDihedrals::myDihedralIndex [private]
 

std::vector< int > ProtoMol::OutputDihedrals::myDihedrals [private]
 

bool ProtoMol::OutputDihedrals::myDihedralsSet [private]
 

std::string ProtoMol::OutputDihedrals::myDihedralsSetfile [private]
 

std::vector< std::vector< Real > > ProtoMol::OutputDihedrals::myMaximas [private]
 

std::vector< std::vector< Real > > ProtoMol::OutputDihedrals::myMinimas [private]
 

The documentation for this class was generated from the following files: Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of Bergen, Norway.