MTK++ Latest version: 0.2.0

Public Member Functions | Protected Attributes
MTKpp::amberParser Class Reference

Reads and writes amber prmtop/crd files. More...

#include <mtkpp/src/Parsers/amberParser.h>

Inheritance diagram for MTKpp::amberParser:
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Collaboration diagram for MTKpp::amberParser:
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List of all members.

Public Member Functions

 amberParser ()
 amberParser Constructor
 ~amberParser ()
 amberParser Destructor
void Write (const std::string &inpcrd, const std::string &prmtop, collection *c)
 Write amber prmtop file.
virtual void Read ()
 Read function.
virtual void Write ()
 Write function.
std::ofstream & OpenFile (std::string fileName)
 Write function.
std::string determineElement (std::string &name)
 Preceive element symbol from the atom name.
void setError (int i)
 Error handling within Parsers.
bool getError ()
 Error handling within dcParser.
void setErrorMessage (std::string s)
 Error handling within Parsers.
std::string getErrorMessage ()
 Error handling within Parsers.

Protected Attributes

std::ofstream outputFileStream
 Output File Stream.
bool bError
 Error occured.
std::string errorMessage
 Error message.
unsigned int NUM_INDENTS_PER_SPACE

Detailed Description

Reads and writes amber prmtop/crd files.

Author:
Martin Peters
Version:
0.1
Date:
2007

Constructor & Destructor Documentation

MTKpp::amberParser::amberParser ( )

amberParser Constructor

MTKpp::amberParser::~amberParser ( )

amberParser Destructor


Member Function Documentation

void MTKpp::amberParser::Write ( const std::string &  inpcrd,
const std::string &  prmtop,
collection c 
)

Write amber prmtop file.

Parameters:
inpcrdoutput inpcrd file
prmtopoutput prmtop file
ccollection pointer

References MTKpp::stdAtom::atmCharge, MTKpp::Angle::atom1, MTKpp::Torsion::atom1, MTKpp::Improper::atom1, MTKpp::Bond::atom1, MTKpp::Angle::atom2, MTKpp::Torsion::atom2, MTKpp::Improper::atom2, MTKpp::Bond::atom2, MTKpp::Angle::atom3, MTKpp::Torsion::atom3, MTKpp::Improper::atom3, MTKpp::Torsion::atom4, MTKpp::Improper::atom4, MTKpp::parameters::calculateSigmaEpsilon(), MTKpp::stdAtom::chain, MTKpp::E2KCAL, MTKpp::LJ612SE::epsilon, MTKpp::metalCenter::getAngleMap(), MTKpp::molecule::getAngleMap(), MTKpp::collection::getAtomList(), MTKpp::metalCenter::getBondMap(), MTKpp::molecule::getBondMap(), MTKpp::atom::getElementSymbol(), MTKpp::molecule::getImproperMap(), MTKpp::parameters::getImproperParamList(), MTKpp::parameters::getLJ612SE(), MTKpp::collection::getMetalCenters(), MTKpp::collection::getMoleculeList(), MTKpp::collection::getName(), MTKpp::submolecule::getName(), MTKpp::collection::getNumAnglesWithH(), MTKpp::collection::getNumAnglesWithOutH(), MTKpp::collection::getNumBondsWithH(), MTKpp::collection::getNumBondsWithOutH(), MTKpp::collection::getNumDihedralsWithH(), MTKpp::collection::getNumDihedralsWithOutH(), MTKpp::collection::getNumUniqueAngleTypes(), MTKpp::collection::getNumUniqueAtomTypes(), MTKpp::collection::getNumUniqueBondTypes(), MTKpp::collection::getNumUniqueDihedralTypes(), MTKpp::collection::getParameters(), MTKpp::atom::getParent(), MTKpp::atom::getStdAtom(), MTKpp::molecule::getSubMoleculeList(), MTKpp::molecule::getTorsionMap(), MTKpp::parameters::getTorsionParamList(), MTKpp::collection::getUniqueAngleTypes(), MTKpp::collection::getUniqueAtomTypes(), MTKpp::collection::getUniqueBondTypes(), MTKpp::collection::getUniqueImproperTypes(), MTKpp::collection::getUniqueTorsionTypes(), MTKpp::atom::has13BondedAtom(), MTKpp::atom::has14BondedAtom(), MTKpp::atom::hasBondedAtom(), MTKpp::collection::largestResidueSize(), MTKpp::Angle::pAngleParam, MTKpp::Bond::pBondParam, MTKpp::parameters::removeProlineTorsion(), MTKpp::LJ612SE::sigma, MTKpp::Angle::size, and MTKpp::stdAtom::type.

Referenced by main().

void MTKpp::baseParser::Read ( ) [virtual, inherited]

Read function.

Referenced by MTKpp::acParser::Read(), and MTKpp::molParser::Read().

void MTKpp::baseParser::Write ( ) [virtual, inherited]
std::ofstream & MTKpp::baseParser::OpenFile ( std::string  fileName) [inherited]

Write function.

References MTKpp::baseParser::outputFileStream.

Referenced by main().

std::string MTKpp::baseParser::determineElement ( std::string &  name) [inherited]

Preceive element symbol from the atom name.

References MTKpp::GetAlphaChar(), and MTKpp::removeCharacter().

Referenced by MTKpp::pdbParser::Read(), and MTKpp::prepParser::readFragment().

void MTKpp::baseParser::setError ( int  i) [inline, inherited]
bool MTKpp::baseParser::getError ( ) [inline, inherited]

Error handling within dcParser.

Returns:
error

References MTKpp::baseParser::bError.

Referenced by main().

void MTKpp::baseParser::setErrorMessage ( std::string  s) [inline, inherited]
std::string MTKpp::baseParser::getErrorMessage ( ) [inline, inherited]

Error handling within Parsers.

Returns:
error message

References MTKpp::baseParser::errorMessage.

Referenced by main().


Member Data Documentation

std::ofstream MTKpp::baseParser::outputFileStream [protected, inherited]

Output File Stream.

Referenced by MTKpp::baseParser::OpenFile().

bool MTKpp::baseParser::bError [protected, inherited]
std::string MTKpp::baseParser::errorMessage [protected, inherited]
unsigned int MTKpp::baseParser::NUM_INDENTS_PER_SPACE [protected, inherited]

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

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