MTKpp::sdfParser Class Reference

Reads and writes SDF format files. More...

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

Inheritance diagram for MTKpp::sdfParser:

Collaboration diagram for MTKpp::sdfParser:

List of all members.

Public Member Functions
	sdfParser ()
	sdfParser Constructor
	~sdfParser ()
	sdfParser Destructor
void	Read (const std::string &i, collection *c, const bool &bohr=false)
	Read SDF formatted files.
int	ReadMolecule (std::ifstream &os, molecule *m, const bool &bohr=false)
	Read a molecule from a sd files.
int	numMolecules (const std::string &i)
	Determine the number of molecules in an sd file.
void	Write (const std::string &o, collection *c)
	Write SDF formatted file.
void	Write (std::ostream &os, molecule *m)
	Write SDF 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 Types
typedef std::vector< molecule * > ::iterator	moleculeIterator
	molecule iterator
typedef std::vector < submolecule * >::iterator	subMoleculeIterator
	submolecule iterator
typedef std::vector< atom * > ::iterator	atomIterator
	atom iterator
typedef std::map< int, Bond * > ::iterator	BondMapIterator
	Bond Map Iterator.
Protected Member Functions
bool	ReadAtomLine (std::string &fileline, AtomLine *pthisAtom)
int	getAtom (int i)
	Get atom.
Protected Attributes
collection *	pCollection
	collection pointer
molecule *	pMolecule
	molecule pointer
submolecule *	pSubMolecule
	submolecule pointer
atom *	pAtom
	atom pointer
Bond *	pBond
	Bond pointer.
atom *	pBondAtom1
	atom pointer used in bonding section
atom *	pBondAtom2
	atom pointer used in bonding section
std::map< int, int >	itsAtomMap
	internal atom mapping local to molParser
connections *	pConnections
std::map< int, Bond * >	moleculeBondMap
	Bond Map.
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 SDF format files.

Author:

Martin Peters

Version:

0.1

Date:

2005

Sdf File Example

• File Contents

  1,2,2,5,5-Pentamethyl-3-imidazoline 3-oxide
    CDK    1/18/06,2:25
  NMRShiftDB 2189 http://www.nmrshiftdb.org:8080/portal/_kbohn_Fri Nov 08 10:04:07
   11 11  0  0  0  0  0  0  0  0999 V2000
     -0.0897    1.5477   -0.1004 N   0  0  0  0  0  0  0  0  0  0  0  0
      0.0827    0.2946    0.0756 C   0  0  0  0  0  0  0  0  0  0  0  0
     -1.2603   -0.3941    0.1731 C   0  0  0  0  0  0  0  0  0  0  0  0
     -2.2226    0.5932   -0.3763 N   0  0  0  0  0  0  0  0  0  0  0  0
     -1.5189    1.8781   -0.1370 C   0  0  0  0  0  0  0  0  0  0  0  0
     -1.9639    2.4834    1.1958 C   0  0  0  0  0  0  0  0  0  0  0  0
     -1.8006    2.8552   -1.2801 C   0  0  0  0  0  0  0  0  0  0  0  0
      0.9570    2.4917   -0.2359 O   0  0  0  0  0  0  0  0  0  0  0  0
     -1.2676   -1.6724   -0.6676 C   0  0  0  0  0  0  0  0  0  0  0  0
     -1.5939   -0.7107    1.6323 C   0  0  0  0  0  0  0  0  0  0  0  0
     -3.3909    0.5845    0.5141 C   0  0  0  0  0  0  0  0  0  0  0  0
    1  2  2  0  0  0  0
    5  6  1  0  0  0  0
    5  7  1  0  0  0  0
    2  3  1  0  0  0  0
    1  8  1  0  0  0  0
    3  4  1  0  0  0  0
    3  9  1  0  0  0  0
    4  5  1  0  0  0  0
    3 10  1  0  0  0  0
    5  1  1  0  0  0  0
    4 11  1  0  0  0  0
  M  CHG  1   1   1
  M  CHG  1   8  -1
  M  END
  > <Spectrum 13C 0>
  132.1;0.0D;1|23.3;0.0Q;8|23.3;0.0Q;9|23.5;0.0Q;5|23.5;0.0Q;6|26.1;0.0Q;10|60.5;0.0S;2|90.0;0.0S;4|
  
  > <Field Strength [MHz]>
  0:50.328
  
  > <Solvent>
  0:Acetone-D6 ((CD3)2CO)
  
  > <Temperature [K]>
  0:298
  
  $$$$
      

• First line is the compound name

• Second Line contains initials, program, date, dimension, scale factors, energy, reg name

• Third line contains comments

• Fourth line provides Number of atoms(N), Number of bonds(B), atlist, obs, chiral, nentries, obs, obs, obs, obs, nprop

• Fifth line onwards provides the x, y, z, atom symbol, massdiff, charge, stereo, hcount, stcare, valence, for each atom

• (N+5)th line starts the bonding info (at1 at2 type stereo topology)

• Charges are set after the bonding info. e.g M CHG 1 1 1

• Info after "M END" is user defined and in this case come from the nmrshiftdb

• Now take a look at it graphically
  

---

Member Typedef Documentation

typedef std::vector<molecule*>::iterator MTKpp::sdfParser::moleculeIterator [protected]

molecule iterator

typedef std::vector<submolecule*>::iterator MTKpp::sdfParser::subMoleculeIterator [protected]

submolecule iterator

typedef std::vector<atom*>::iterator MTKpp::sdfParser::atomIterator [protected]

atom iterator

typedef std::map<int, Bond*>::iterator MTKpp::sdfParser::BondMapIterator [protected]

Bond Map Iterator.

---

Constructor & Destructor Documentation

MTKpp::sdfParser::sdfParser

(

)

sdfParser Constructor

References pBond, pBondAtom1, pBondAtom2, pConnections, pMolecule, and pSubMolecule.

MTKpp::sdfParser::~sdfParser

(

)

sdfParser Destructor

References pConnections.

---

Member Function Documentation

void MTKpp::sdfParser::Read	(	const std::string &	i,
		collection *	c,
		const bool &	bohr = false
	)

Read SDF formatted files.

Parameters:

i	Input file
c	collection pointer
bohr	Convert coordinates to Bohr or not

References MTKpp::submolecule::addAtom(), MTKpp::molecule::addBond(), MTKpp::atom::addBondedAtom(), MTKpp::collection::addMolecule(), MTKpp::molecule::addProperty(), MTKpp::molecule::addSubMolecule(), MTKpp::ANG2BOHR, MTKpp::connections::assignAngles(), MTKpp::connections::assignImpropers(), MTKpp::connections::assignTorsions(), MTKpp::AtomLine::element, MTKpp::molecule::getAtom(), MTKpp::elements::getElement(), MTKpp::collection::getNumberMolecules(), MTKpp::molecule::getNumSubMolecules(), MTKpp::molecule::inFileType, pAtom, pBond, pBondAtom1, pBondAtom2, pConnections, MTKpp::collection::pElements, pMolecule, pSubMolecule, ReadAtomLine(), MTKpp::atom::setCoords(), MTKpp::atom::setElement(), MTKpp::atom::setFileID(), MTKpp::atom::setFormalCharge(), MTKpp::molecule::setMolId(), MTKpp::molecule::setName(), MTKpp::submolecule::setName(), MTKpp::submolecule::setSubMolId(), MTKpp::molecule::setTotalCharge(), MTKpp::splitString(), MTKpp::string2UInt(), MTKpp::AtomLine::x, MTKpp::AtomLine::y, and MTKpp::AtomLine::z.

Referenced by main().

int MTKpp::sdfParser::ReadMolecule	(	std::ifstream &	os,
		molecule *	m,
		const bool &	bohr = false
	)

Read a molecule from a sd files.

Parameters:

os	input stream
m	molecule pointer
bohr	Convert coordinates to Bohr or not

References MTKpp::submolecule::addAtom(), MTKpp::molecule::addBond(), MTKpp::atom::addBondedAtom(), MTKpp::molecule::addProperty(), MTKpp::molecule::addSubMolecule(), MTKpp::ANG2BOHR, MTKpp::connections::assignAngles(), MTKpp::connections::assignImpropers(), MTKpp::connections::assignTorsions(), MTKpp::AtomLine::element, MTKpp::molecule::getAtom(), MTKpp::elements::getElement(), MTKpp::collection::getNumberMolecules(), MTKpp::molecule::getNumSubMolecules(), MTKpp::molecule::getParent(), MTKpp::molecule::inFileType, pAtom, pBond, pBondAtom1, pBondAtom2, pCollection, pConnections, MTKpp::collection::pElements, pSubMolecule, ReadAtomLine(), MTKpp::atom::setCoords(), MTKpp::atom::setElement(), MTKpp::atom::setFileID(), MTKpp::molecule::setMolId(), MTKpp::molecule::setName(), MTKpp::submolecule::setName(), MTKpp::submolecule::setSubMolId(), MTKpp::AtomLine::x, MTKpp::AtomLine::y, and MTKpp::AtomLine::z.

Referenced by main().

int MTKpp::sdfParser::numMolecules

(

const std::string &

i

)

Determine the number of molecules in an sd file.

Parameters:

i	Input file

void MTKpp::sdfParser::Write	(	const std::string &	o,
		collection *	c
	)

Write SDF formatted file.

Parameters:

o	Output file
c	collection pointer

References MTKpp::Bond::atom1, MTKpp::Bond::atom2, MTKpp::molecule::getAtomList(), MTKpp::molecule::getBondMap(), MTKpp::atom::getColIndex(), MTKpp::atom::getElement(), MTKpp::atom::getFormalCharge(), MTKpp::collection::getMoleculeList(), MTKpp::molecule::getName(), MTKpp::molecule::getNumAtoms(), MTKpp::molecule::getNumBonds(), MTKpp::molecule::getProperties(), MTKpp::atom::getX(), MTKpp::atom::getY(), MTKpp::atom::getZ(), itsAtomMap, moleculeBondMap, pAtom, pBond, pMolecule, MTKpp::Bond::stereo, MTKpp::element::symbol, MTKpp::Bond::topology, and MTKpp::Bond::type.

Referenced by main().

void MTKpp::sdfParser::Write	(	std::ostream &	os,
		molecule *	m
	)

Write SDF formatted file.

Parameters:

os	Output stream
m	molecule pointer

References MTKpp::Bond::atom1, MTKpp::Bond::atom2, MTKpp::molecule::getAtomList(), MTKpp::molecule::getBondMap(), MTKpp::atom::getColIndex(), MTKpp::atom::getElement(), MTKpp::atom::getFormalCharge(), MTKpp::molecule::getName(), MTKpp::molecule::getNumAtoms(), MTKpp::molecule::getNumBonds(), MTKpp::molecule::getProperties(), MTKpp::atom::getX(), MTKpp::atom::getY(), MTKpp::atom::getZ(), itsAtomMap, moleculeBondMap, pAtom, pBond, MTKpp::Bond::stereo, MTKpp::element::symbol, MTKpp::Bond::topology, and MTKpp::Bond::type.

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

\ Read a single line of the input file

Parameters:

fileline	Actual line
pthisAtom	AtomLine 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(), and ReadMolecule().

int MTKpp::sdfParser::getAtom

(

int

i

)

[protected]

Get atom.

Parameters:

i	atom index in itsAtomMap

References itsAtomMap.

void MTKpp::baseParser::Read

(

)

[virtual, inherited]

Read function.

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

void MTKpp::baseParser::Write

(

)

[virtual, inherited]

Write function.

Referenced by MTKpp::gaussianParser::Write(), MTKpp::molParser::Write(), MTKpp::zmatParser::Write(), and MTKpp::dcParser::Write().

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]

Error handling within Parsers.

Parameters:

i

error

References MTKpp::baseParser::bError.

Referenced by MTKpp::dcParser::dcParser(), MTKpp::prepParser::openFile(), MTKpp::paramParser::paramParser(), MTKpp::pamParser::Read(), MTKpp::pdbParser::Read(), MTKpp::prepParser::Read(), MTKpp::dcParser::Read(), MTKpp::dcParser::ReadElecEnergy(), MTKpp::dcParser::ReadHOF(), MTKpp::stdLibParser::stdLibParser(), and MTKpp::prepParser::Write().

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]

Error handling within Parsers.

Parameters:

s	error message

References MTKpp::baseParser::errorMessage.

Referenced by MTKpp::prepParser::openFile(), MTKpp::paramParser::paramParser(), MTKpp::pamParser::Read(), MTKpp::pdbParser::Read(), MTKpp::prepParser::Read(), MTKpp::dcParser::ReadElecEnergy(), MTKpp::dcParser::ReadHOF(), MTKpp::stdLibParser::stdLibParser(), and MTKpp::prepParser::Write().

std::string MTKpp::baseParser::getErrorMessage

(

)

[inline, inherited]

Error handling within Parsers.

Returns:

error message

References MTKpp::baseParser::errorMessage.

Referenced by main().

---

Member Data Documentation

collection* MTKpp::sdfParser::pCollection [protected]

collection pointer

Referenced by ReadMolecule().

molecule* MTKpp::sdfParser::pMolecule [protected]

molecule pointer

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

submolecule* MTKpp::sdfParser::pSubMolecule [protected]

submolecule pointer

Referenced by Read(), ReadMolecule(), and sdfParser().

atom* MTKpp::sdfParser::pAtom [protected]

atom pointer

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

Bond* MTKpp::sdfParser::pBond [protected]

Bond pointer.

Referenced by Read(), ReadMolecule(), sdfParser(), and Write().

atom* MTKpp::sdfParser::pBondAtom1 [protected]

atom pointer used in bonding section

Referenced by Read(), ReadMolecule(), and sdfParser().

atom* MTKpp::sdfParser::pBondAtom2 [protected]

atom pointer used in bonding section

Referenced by Read(), ReadMolecule(), and sdfParser().

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

internal atom mapping local to molParser

Referenced by getAtom(), and Write().

connections* MTKpp::sdfParser::pConnections [protected]

Referenced by Read(), ReadMolecule(), sdfParser(), and ~sdfParser().

std::map<int, Bond*> MTKpp::sdfParser::moleculeBondMap [protected]

Bond Map.

Referenced by Write().

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

Output File Stream.

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

bool MTKpp::baseParser::bError [protected, inherited]

Error occured.

Referenced by MTKpp::baseParser::baseParser(), MTKpp::baseParser::getError(), and MTKpp::baseParser::setError().

std::string MTKpp::baseParser::errorMessage [protected, inherited]

Error message.

Referenced by MTKpp::baseParser::baseParser(), MTKpp::baseParser::getErrorMessage(), MTKpp::prepParser::openFile(), MTKpp::paramParser::paramParser(), MTKpp::pamParser::Read(), MTKpp::pdbParser::Read(), MTKpp::prepParser::Read(), MTKpp::prepParser::readFragment(), MTKpp::baseParser::setErrorMessage(), MTKpp::stdLibParser::stdLibParser(), and MTKpp::prepParser::Write().

unsigned int MTKpp::baseParser::NUM_INDENTS_PER_SPACE [protected, inherited]

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

---

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

• sdfParser.h
• sdfParser.cpp