MTK++ Latest version: 0.2.0

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

Reads and writes MOL format files. More...

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

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

Public Member Functions

 molParser ()
 molParser Constructor
 ~molParser ()
 molParser Destructor
void Read (const std::string &i, molecule *m, const bool &bohr=false)
 Read MOL formatted file.
void Read (const std::string &i, collection *c, const bool &bohr=false)
 Read MOL formatted file.
void Write (const std::string &o, molecule *m)
 Write MOL formatted file.
void Write (const std::string &o, molecule *m, std::vector< vector3d > &coordinates)
 Write MOL formatted file.
void Write (const std::string &o, collection *c, const int &molID)
 Write MOL formatted 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 Member Functions

bool ReadAtomLine (std::string &fileline, AtomLine *pthisAtom)
 Read a single line of the input file.
int getAtom (int i)
 Get atom.

Protected Attributes

moleculepMolecule
 molecule pointer
submoleculepSubMolecule
 submolecule pointer
atompAtom
 atom pointer
BondpBond
 Bond pointer.
atompBondAtom1
 atom pointer used in bonding section
atompBondAtom2
 atom pointer used in bonding section
std::map< int, int > itsAtomMap
 internal atom mapping local to molParser
connectionspConnections
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 MOL format files.

Author:
Martin Peters
Version:
0.1
Date:
2005

Constructor & Destructor Documentation

MTKpp::molParser::molParser ( )
MTKpp::molParser::~molParser ( )

molParser Destructor

References pConnections.


Member Function Documentation

void MTKpp::molParser::Read ( const std::string &  i,
molecule m,
const bool &  bohr = false 
)
void MTKpp::molParser::Read ( const std::string &  i,
collection c,
const bool &  bohr = false 
)

Read MOL formatted file.

Parameters:
iInput file
ccollection pointer
bohrConvert coordinates to Bohr or not

References MTKpp::collection::addMolecule(), pConnections, pMolecule, and MTKpp::baseParser::Read().

void MTKpp::molParser::Write ( const std::string &  o,
molecule m 
)

Write MOL formatted file.

Parameters:
oOutput file
mmolecule pointer

References MTKpp::molecule::getCoordinates(), and MTKpp::baseParser::Write().

Referenced by main().

void MTKpp::molParser::Write ( const std::string &  o,
molecule m,
std::vector< vector3d > &  coordinates 
)
void MTKpp::molParser::Write ( const std::string &  o,
collection c,
const int &  molID 
)

Write MOL formatted file.

Parameters:
oOutput file
ccollection pointer
molIDThe ID of the molecule in the collection

References MTKpp::molecule::getCoordinates(), MTKpp::collection::getMolecule(), pMolecule, and MTKpp::baseParser::Write().

bool MTKpp::molParser::ReadAtomLine ( std::string &  fileline,
AtomLine pthisAtom 
) [protected]

Read a single line of the input file.

Parameters:
filelineActual line
pthisAtomAtomLine struct to temporary store atom info

References MTKpp::AtomLine::element, MTKpp::FieldExists(), MTKpp::removeCharacter(), MTKpp::AtomLine::x, MTKpp::AtomLine::y, and MTKpp::AtomLine::z.

Referenced by Read().

int MTKpp::molParser::getAtom ( int  i) [protected]

Get atom.

Parameters:
iatom index in itsAtomMap

References itsAtomMap.

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

Read function.

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

molecule pointer

Referenced by molParser(), Read(), and Write().

submolecule pointer

Referenced by molParser(), and Read().

atom pointer

Referenced by Read(), and Write().

Bond pointer.

Referenced by molParser(), Read(), and Write().

atom pointer used in bonding section

Referenced by molParser(), and Read().

atom pointer used in bonding section

Referenced by molParser(), and Read().

std::map<int, int> MTKpp::molParser::itsAtomMap [protected]

internal atom mapping local to molParser

Referenced by getAtom(), and Write().

Referenced by molParser(), Read(), and ~molParser().

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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