Inherited by CSite.

Public Member Functions
	CIO ()

	CIO (delphi_real fDielecIn, delphi_real fEPKTIn)

	~CIO ()

void	readForceFile (const string &strFile)

void	readPdbFile (const string &strPdbFile, const int &iPdbFormat, const bool &bPdbUnformat)

void	writeUnformatPdb (const string &strPdbFile)

void	writeModifiedPdb (const string &strPdbFile, const int &iModPdbFormatOut)

void	setDelphiAtom (const bool &bSolvePB, const bool &bSurfCrgInSite, const string &strSizeFile, const string &strCrgFile, const string &strPdbFile, const int &iPdbFormat, const bool &bPdbUnformat)

SGrid< delphi_real >	readFrcFile (const string &strFrcFile, const SGrid< delphi_real > &fgOffCenter, const delphi_real &fScale)

void	writeEpsMap (const delphi_integer &iAtomNumIn, const delphi_integer &iObjectNumIn, const delphi_integer &iGrid, const delphi_real &fScale, const SGrid< delphi_real > &fgBoxCenter, const vector< SGrid< delphi_integer > > &vctigEpsMap, const vector< bool > &vctbDielecMap, const string &strEpsFile)

Public Attributes
delphi_integer	iMediaNum

delphi_integer	iObjectNum

delphi_integer	iAtomNum

delphi_integer	iResidueNum

bool	bOnlyMolecule

vector< CAtomPdb >	vctapAtomPdb

vector< delphi_real >	vctfMediaEps

vector< string >	vctstrObject

vector< delphi_integer >	vctiAtomMediaNum

Protected Member Functions
string	toUpperCase (const string &strLine)

string	removeSpace (const string &strLine)

bool	checkFileFormat (const string &strFile)

void	readFileInNotPKFormat (ifstream &ifFileStream, const int &iFileType)

void	readFileInPKFormat (ifstream &ifFileStream, const int &iFileType)

delphi_integer	FindRecordIndex (const string &strAtom, const string &strResidue, const string &strResidueNum, const string &strChain, const delphi_integer &iRecordNum, vector< CForce > *prgaf)

delphi_integer	FindRecord (const string &strAtom, const string &strResidue, const string &strResidueNum, const string &strChain, const int &iFileType, delphi_real &fValue)

void	readStdPdbFile (ifstream &ifPdbFileStream)

void	readModFile1 (ifstream &ifPdbFileStream)

void	readModFile4 (ifstream &ifPdbFileStream)

void	readPqrFile (ifstream &ifPdbFileStream)

void	readMod4File (ifstream &ifPdbFileStream)

void	readPqr4File (ifstream &ifPdbFileStream)

void	readUnformattedPdb (const string &strPdbFile, ifstream &ifPdbFileStream, bool &bPostProcess)

Protected Attributes
const delphi_real	fDielec

const delphi_real	fEPKT

delphi_integer	iObjectMediaNum

bool	bExistRadiiInfo

vector< delphi_integer >	prgiObjectMediaNum

Static Protected Attributes
static delphi_integer	iRadiusNum = 0

static vector< CForce >	prgas

static delphi_integer	iCrgNum = 0

static vector< CForce >	prgac

Constructor & Destructor Documentation

CIO::CIO ( )

inline

constructor I using default Dielectric constant and epkt values

CIO::CIO	(	delphi_real	fDielecIn,
		delphi_real	fEPKTIn
	)

inline

constructor II using user-specified Dielectric constant and epkt values

CIO::~CIO ( )

inline

destructor

Member Function Documentation

bool CIO::checkFileFormat ( const string & strFile )

protected

function to check if the input file is formatted or not

Parameters

strFile name of the input file

Returns: true if the file formatted, false otherwise.

delphi_integer CIO::FindRecord	(	const string &	strAtom,
		const string &	strResidue,
		const string &	strResidueNum,
		const string &	strChain,
		const int &	iFileType,
		delphi_real &	fValue
	)

protected

function to find a particular record matching the specified atom

Parameters

strAtom	atom name
strResidue	residue name
strResidueNum	residue number
strChain	chain name
iFileType	file type
fValue	value (charge or radius) associated with this atom

Returns: -1 if unfounded, index otherwise

delphi_integer CIO::FindRecordIndex	(	const string &	strAtom,
		const string &	strResidue,
		const string &	strResidueNum,
		const string &	strChain,
		const delphi_integer &	iRecordNum,
		vector< CForce > *	prgaf
	)

protected

function to get index of a specified atom in the record

Parameters

strAtom	atom name
strResidue	residue name
strResidueNum	residue number
strChain	chain name
iRecordNum	total number of records
prgaf	pointer to the vector of records

Returns: -1 if no record is found, index otherwise.

void CIO::readFileInNotPKFormat	(	ifstream &	ifFileStream,
		const int &	iFileType
	)

protected

read a .siz or .crg file in non-PK format

Parameters

ifFileStream	input file stream
iFileType	input file type

void CIO::readFileInPKFormat	(	ifstream &	ifFileStream,
		const int &	iFileType
	)

protected

read a .siz or .crg file in PK format

Parameters

ifFileStream	input file stream
iFileType	input file type

void CIO::readForceFile ( const string & strFile )

function for reading atom force (radii/size and charge) file

Parameters

strFile file name

SGrid< delphi_real > CIO::readFrcFile	(	const string &	strFrcFile,
		const SGrid< delphi_real > &	fgOffCenter,
		const delphi_real &	fScale
	)

function for reading FRC file

Parameters

strFrcFile	name of frc file
fgOffCenter	offset from box center
fScale	scale used for calculations

Returns: position of box center

void CIO::readMod4File ( ifstream & ifPdbFileStream )

protected

function to read mod4 pdb file

Parameters

ifPdbFileStream input .pdb file stream

void CIO::readModFile1 ( ifstream & ifPdbFileStream )

protected

function to read modified .pdb file (type = 1)

Parameters

ifPdbFileStream input .pdb file stream

void CIO::readModFile4 ( ifstream & ifPdbFileStream )

protected

function to read modified .pdb file (type = 4)

Parameters

ifPdbFileStream input .pdb file stream

void CIO::readPdbFile	(	const string &	strPdbFile,
		const int &	iPdbFormat,
		const bool &	bPdbUnformat
	)

function for reading PDB file in various formats

Parameters

strPdbFile	pdb file name
iPdbFormat	pdb file format
bPdbUnformat	true if unformatted pdb file

void CIO::readPqr4File ( ifstream & ifPdbFileStream )

protected

function to read pqr4 file

Parameters

ifPdbFileStream input .pdb file stream

void CIO::readPqrFile ( ifstream & ifPdbFileStream )

protected

function to read .pqr file

Parameters

ifPdbFileStream input .pqr file stream

void CIO::readStdPdbFile ( ifstream & ifPdbFileStream )

protected

function to read standard .pdb file

Parameters

ifPdbFileStream input .pdb file stream

void CIO::readUnformattedPdb	(	const string &	strPdbFile,
		ifstream &	ifPdbFileStream,
		bool &	bPostProcess
	)

protected

function to read unformatted pdb file

Parameters

strPdbFile	input .pdb file name
ifPdbFileStream	input .pdb file stream
bPostProcess	flag for post processing

string CIO::removeSpace ( const string & strLine )

protected

function to remove spaces from a string

Parameters

strLine input string

Returns: converted string without spaces

void CIO::setDelphiAtom	(	const bool &	bSolvePB,
		const bool &	bSurfCrgInSite,
		const string &	strSizeFile,
		const string &	strCrgFile,
		const string &	strPdbFile,
		const int &	iPdbFormat,
		const bool &	bPdbUnformat
	)

function to set DelPhi-style atom list vctapAtomPdb(iAtomNum), i.e, (delphipdb(natom))

Parameters

bSolvePB	true if solving PB equation
bSurfCrgInSite	true if writing surface chagre info into site file
strSizeFile	name of .siz file
strCrgFile	name of .crg file
strPdbFile	name of .pdb file
iPdbFormat	.pdb file format
bPdbUnformat	true if unformatted pdb file

string CIO::toUpperCase ( const string & strLine )

protected

function to convert a string to upper case

Parameters

strLine input string

Returns: converted string in upper case

void CIO::writeEpsMap	(	const delphi_integer &	iAtomNumIn,
		const delphi_integer &	iObjectNumIn,
		const delphi_integer &	iGrid,
		const delphi_real &	fScale,
		const SGrid< delphi_real > &	fgBoxCenter,
		const vector< SGrid< delphi_integer > > &	vctigEpsMap,
		const vector< bool > &	vctbDielecMap,
		const string &	strEpsFile
	)

function for writing EPS file

Parameters

iAtomNumIn	number of atoms
iObjectNumIn	number of objects
iGrid	number of grid points on each direction
fScale	scale used for calculations
fgBoxCenter	position of box center
vctigEpsMap	vector of epsilon map
vctbDielecMap	vector of dielectric constants map
strEpsFile	output eps file name

void CIO::writeModifiedPdb	(	const string &	strPdbFile,
		const int &	iModPdbFormatOut
	)

function for writing modified pdb file

Parameters

strPdbFile	pdb file name
iModPdbFormatOut	file format

void CIO::writeUnformatPdb ( const string & strPdbFile )

function for writing unformatted pdb file

Parameters

strPdbFile pdb file name

Member Data Documentation

bool CIO::bExistRadiiInfo

protected

F95 var.: iatrad whether there is radius info

bool CIO::bOnlyMolecule

F95 var.: ionlymol true if there are only molecules in the system (no objects)

const delphi_real CIO::fDielec

protected

F95 var.: repsin

const delphi_real CIO::fEPKT

protected

F95 var.: epkt

delphi_integer CIO::iAtomNum

F95 var.: natom

of atoms

delphi_integer CIO::iCrgNum = 0

staticprotected

F95 var.: nchrec

of entries in charge file

delphi_integer CIO::iMediaNum

F95 var.: nmedia

of media

delphi_integer CIO::iObjectMediaNum

protected

F95 var.: imedianumb number of objects read from .pdb file

delphi_integer CIO::iObjectNum

F95 var.: nobject

of objects

delphi_integer CIO::iRadiusNum = 0

staticprotected

F95 var.: nrmax

of entries in radius file

delphi_integer CIO::iResidueNum

F95 var.: resnummax maximum residue number

vector< CForce > CIO::prgac

staticprotected

F95 var.: charge(:) a vector containing all charges read from .crg file

vector< CForce > CIO::prgas

staticprotected

F95 var.: radii(:) a vector containing all radius read from .siz file

vector<delphi_integer> CIO::prgiObjectMediaNum

protected

F95 var.: tmpiatmmed(nobjectmax) vector containing internal media-number per object

vector<CAtomPdb> CIO::vctapAtomPdb

F95 var.: delphipdb(Natom) array of structure to store info read from pdb file

vector<delphi_real> CIO::vctfMediaEps

F95 var.: medeps(0:nmediamax) vector containing correspondence media<->epsilon/epkt

vector<delphi_integer> CIO::vctiAtomMediaNum

F95 var.: iatmmed(Natom+Nobjectmax) vector containing internal media-number per atom and object

vector<string> CIO::vctstrObject

F95 var.: dataobject(nobjectmax,2) vector containing string with object data, and pre-elab data changed it to vctstrObject(2*nobjectmax)

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

io.h
io_epsmap.cpp
io_force.cpp
io_frc.cpp
io_misc.cpp
io_pdb.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Static Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

of atoms

of entries in charge file

of media

of objects

of entries in radius file