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CData Class Reference

#include <ReadData.h>

List of all members.

Public Member Functions

 CData ()
 ~CData ()
void Read (char *name)
void Delete ()
void PrintSelf ()
void Prepare ()
void Postpare ()
void CheckAllRestraints ()
int GetNumber (int id, int *idFrg, int *idLoc)
void EnergyFunction (int ndim, const ColumnVector &X, REAL &E, int &result)
void InitComputation (int ndim, ColumnVector &x)
void SetFilenamePDBall (CSmallString &str)
void SetFilenamePDBfinal (CSmallString &str)
CSmallString & GetFilenamePDBall ()
CSmallString & GetFilenamePDBfinal ()
void SetFilenameEnergyGraph (CSmallString &str)
CSmallString & GetFilenameEnergyGraph ()
void ApplyTransformsToAllAtoms (const ColumnVector &X)
void ExportDataPDB (const ColumnVector &X, FILE *fout)
void ExportDataPDB (const ColumnVector &X, char *name)
void ExportDataXML (const ColumnVector &X, char *name)
void SetNumIterations (int a)
void IncrementNumIterations (int a=1)

Public Attributes

int numFragments
int * nF
CSmallString * idF
int masterFragment
Atom ** Atoms
int ** changingAtoms
int * cntChangeAtom
Point ** points
Point * centerF
REAL * chargeF
bool * distribF
int numRestrains
CRestrain ** restrains
CContrELECT * contrEl
CSmallString strFilePDBall
CSmallString strFilePDBfinal
CSmallString strFileEnergyGraph
int numIterations

Detailed Description

Basic class for manipulating with data

Constructor & Destructor Documentation

CData::CData (   ) 
 

construcor

CData::~CData (   ) 
 

destrucor

Member Function Documentation

void CData::ApplyTransformsToAllAtoms (  const ColumnVector &  X  ) 
 

Applies transformations driven by vector X to all atoms in fragments

Parameters:
X vector from parametric space

void CData::CheckAllRestraints (   ) 
 

Function check if the restraints are well defined if yes the computation goes on otherwise the program ends

void CData::Delete (   ) 
 

Release memory

void CData::EnergyFunction (  int  ndim,
const ColumnVector &  X,
REAL &  E,
int &  result
) 
 

Energy funcion for searching global minimum

Parameters:
ndim dimension of the parametric space (usually $6(numFragments-1)$
X vector from parametric space
E value of the energetic funciton
result value if error flag
See also:
InitComputation()

void CData::ExportDataPDB (  const ColumnVector &  X,
char *  name
) 
 

Export data to PDB file

Parameters:
name name of the file

void CData::ExportDataPDB (  const ColumnVector &  X,
FILE *  fout
) 
 

Export data to PDB file

Parameters:
fout handler to file

void CData::ExportDataXML (  const ColumnVector &  X,
char *  name
) 
 

Export data to XML file

Parameters:
name name of the file

CSmallString& CData::GetFilenameEnergyGraph (   )  [inline]
 

Returns filename to save energy graph

CSmallString& CData::GetFilenamePDBall (   )  [inline]
 

Returns filename to save all frames of computation to PDB-file

CSmallString& CData::GetFilenamePDBfinal (   )  [inline]
 

Returns filename to save final (optimized) constitution

int CData::GetNumber (  int  id,
int *  idFrg,
int *  idLoc
) 
 

Get number of fragment and position of atom in this fragment

Parameters:
id uniq identificator of the atom in the file
idFrg return value - number of fragment
idLoc return value - ordinary number of atom in fragment

void CData::InitComputation (  int  ndim,
ColumnVector &  x
) 
 

Initial setting for optimalization procedure

Parameters:
ndim dimension of the parametric space (usually $6(numFragments-1)$
x vector from parametric space
See also:
EnergyFunction()

void CData::Postpare (   ) 
 

Function called after optimalization

void CData::Prepare (   ) 
 

Prepare data for optimalization (creates some temporary tables)

void CData::PrintSelf (   ) 
 

Print Information and content of this class

void CData::Read (  char *  name  ) 
 

Reads data from XML file

Parameters:
name name of the XML file
Example of XML file: 
<?xml version="1.0" encoding="ISO-8859-1"?>
<!-- testovaci soubor s daty //-->
<FIT>
<FRAGMENTS>
 <FRAGMENT id="F1" elementarcharge="1" distribute="no">
  <ATOM x="-2" y="0" z="0" type="H" id="1" />  
  <ATOM x="0" y="0" z="0" type="O" id="2"/>
  <ATOM x="2" y="0" z="0" type="H" id="3"/>
 </FRAGMENT>
 <FRAGMENT id="F2" master="yes" elementarcharge="1" distribute="no">
  <ATOM x="10" y="-2" z="-6" type="H" id="4"/>
  <ATOM x="10" y="0" z="-6" type="C" id="5"/>
  <ATOM x="10" y="2" z="-6" type="H" id="6"/>
 </FRAGMENT>
</FRAGMENTS>
<RESTRAINTS>
 <RESTRAINT type="DIST" part1="2" part2="5" value="5" k="1" />
 <RESTRAINT type="ANGLE" part1="1" part2="2" part3="2" part4="5" value="1.57" k="1" disabled="yes" />
 <RESTRAINT type="TORSION" part1="1" part2="2" part3="5" part4="6" value="1.57" k="100" disabled="no"/>
 <RESTRAINT type="ELECTROSTATIC" disabled="no" k="10" eps="0.1"/>
</RESTRAINTS>
</FIT>

void CData::SetFilenameEnergyGraph (  CSmallString &  str  )  [inline]
 

Set filename for energy graph

void CData::SetFilenamePDBall (  CSmallString &  str  )  [inline]
 

Set filename for PDB output for sequence

void CData::SetFilenamePDBfinal (  CSmallString &  str  )  [inline]
 

Set filename for PDB output for final constitution

The documentation for this class was generated from the following file:
Generated on Tue Apr 20 11:53:39 2004 for FragmentsFitting by doxygen 1.3.4