RelaxBase Class Reference

#include <relaxbase.h>

List of all members.

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Detailed Description

This class allows generation of an input file for the program Relax.

It provides the functionality to RelaxWidget.

Definition at line 43 of file relaxbase.h.

Public Types
enum	Input { AFF, MAFF }
Public Slots
void	reset ()
	Resets all widgets to their default values.
Public Member Functions
	RelaxBase (AtomSet *atomset, QWidget *parent=0, const char *name=0, bool modal=FALSE, WFlags fl=0)
	~RelaxBase ()
	The default destructor.
void	setName (const QString name)
	Sets the filename prefix of the calculation.
void	setDescription (const QString description)
	Sets the description of the calculation.
void	setDir (const QString dir)
	Sets the directory of the calculation.
void	setExtendedFormat (const bool state)
	Sets the format of the coordinates (normal/extended).
unsigned int	inputGenerationFrequency ()
	Returns the frequency with which the internal coordinates should be regenerated.
unsigned int	maxSteps ()
	Returns the maximum number of optimization steps to be done.
void	scaleFactors (vector< unsigned int > &steps, vector< double > &factors)
	Returns the scalefactors.
QStringList	generateInput (const Input type)
	Generates input for a specific program.
void	loadCML (const QDomElement *root)
	Reads the widgetdata from a QDomElement.
void	saveCML (QDomElement *root)
	Saves the widgetdata to a QDomElement.
Protected Slots
void	accept ()
	Overridden from RelaxWidget::accept().
void	reject ()
	Overridden from RelaxWidget::reject().
Protected Member Functions
void	showEvent (QShowEvent *e)
	Overridden from RelaxWidget::showEvent().
Private Types
enum	Categories {   BASIC = 0, INTERNAL = 1, CARTESIAN = 2, ADVANCED = 3,   DEBUG1 = 4, EXTRA = 5, CARTESIAN_SYMMETRY = 6, CARTESIAN_OTHER = 7,   ADVANCED_THRESHOLDS = 8, ADVANCED_OTHER = 9 }
enum	Type { PreviewAFF, ICListAFF }
Private Slots
void	showPreview ()
	Shows a preview from the widgets.
void	showPreview2 ()
	Shows a preview from the widgets.
void	readInputFile ()
	Reads a Relax AFF file into the widgets.
void	setChanged (bool state=true)
	Sets the 'changed' property of the widget.
void	selectWidget (QListViewItem *)
	Shows a widget from WidgetStackCategory depending on newItem.
void	enableAutogenWidgets ()
	Enabled/disables the widgets for configuring the (re)generation of the internal coordinates.
void	enableSFACWidgets (bool state=true)
	Enabled/disables the widgets for configuring the scale factor depending on RadioButtonSFAC{1|2}.
void	newScaleFactor ()
	Adds a new scale factor to the list.
void	deleteScaleFactor ()
	Deletes the currently selected scale factor from the list.
void	updateICEdit ()
	Updates the widgets for changing an IC with the contents of the currently selected IC in ListViewIC.
void	updateICList ()
	Updates ListViewIC with the contents of the widgets for changing an IC.
void	updateICSpecifics ()
	Updates the widgets for the specific data.
void	updateICType ()
	Does the necessary updating of all parts of an internal.
void	newIC ()
	Creates a new internal coordinate at the bottom of ListViewIC.
void	newICPart ()
	Creates a new part of an internal coordinate.
void	deleteIC ()
	Deletes the currently selected internal coordinate.
void	clearIC ()
	Deletes all internal coordinates.
void	genIC ()
	Fills the internal coordinates list with (non)redundant internal coordinates.
void	genIC2 ()
	Fills the internal coordinates list with (non)redundant internal coordinates.
void	moveICUp ()
	Moves the selected internal coordinate one place up in the list.
void	moveICDown ()
	Moves the selected internal coordinate one place down in the list.
void	newFixedAtom ()
	Adds a new atom to the list of fixed atoms.
void	deleteFixedAtom ()
	Deletes the selected atom from the list of fixed atoms.
void	checkFIXABoxes ()
	Makes sure at least 1 box stays checked for the fixed atoms.
void	enableTROTWidgets (bool state=true)
	Enables/disables the widgets for configuring the optimization of the external coordinates depending on CheckBoxTROT.
void	newExtraBond ()
	Adds a new bond to the XBON list.
void	deleteExtraBond ()
	Deletes the selected bond from the XBON list.
void	enableUPDTWidgets (bool state=true)
	Enables/disables the widgets for configuring the update of the force constants depending on CheckBoxUPDT.
void	enableSHRTWidgets (bool state=true)
	Enables/disables the widgets for configuring the short output depending on CheckBoxSHRT.
void	checkOverflow (int row, int col)
	Spans cell(row, col) over multiple columns if it contains more than 10 characters.
void	addExtraRow ()
	If a row is selected, inserts a row before the selection.
void	removeExtraRow ()
	Removes the selected rows.
void	clearSelection ()
	Clears the selected cells.
Private Member Functions
void	makeConnections ()
	Sets up the permanent connections. Called once from the constructor.
void	init ()
	Initializes the dialog.
void	saveWidgets ()
	Saves the status of the widgets to a data struct.
void	restoreWidgets ()
	Restores the status of the widgets from a data struct.
QString	icRepresentation (const unsigned int atom1, const unsigned int atom2, const unsigned int atom3=0, const int atom4=0)
	Returns a QString containing a representation of an internal coordinate from the 4 atom indices.
void	getAtomsFromIC (const QString textIC, unsigned int &atom1, unsigned int &atom2, unsigned int &atom3, int &atom4)
	Returns the atom numbers from a textual representation of an internal coordinate.
void	renumberICs ()
	Renumbers the internal coordinates.
QStringList	generateAFFHeader ()
	Generates input for the first part of an .aff file.
QStringList	generateBmatInput ()
	Generates input for Maff to generate non-redundant internal coordinates.
bool	makeDirCurrent (const QString dir, const QString title)
	Makes dir the current directory.
void	fillICListFromAFF (const QStringList aff)
	Adds the internal coordinates found in the latest generated aff to the IC list widget.
bool	startMAFF (const unsigned int slot)
	Initiates the generation of an AFF file using MAFF.
QStringList	readMAFFGeneratedICs ()
	Returns the internal coordinates generated by the latest MAFF run.
Private Attributes
WidgetData	data
	Contains the status of all widgets.
AtomSet *	atoms
	Pointer to the AtomSet passed in through the constructor.
vector< QString >	category
	Contains translatable names for the items in ListViewCategory.
bool	widgetChanged
	= TRUE if the dialog has been changed and needs saving.
QString	calcName
	Contains the filename prefix (maybe change to pointer to XbraboView QString.
QString	calcDescription
	Contains the description.
QString	calcDir
	Contains the directory.
bool	calcXF
	= TRUE if the calculation is to be done in extended format.
QProcess *	maffProcess
	The process for running MAFF.
Static Private Attributes
static const XMLData	xml
	Contains the XML dictRef values for all WidgetData.
Classes
struct	ICData
	A utility struct containing all data to reconstruct an internal coordinate. More...
struct	WidgetData
	A struct representing the data from all widgets. More...
struct	XMLData
	A struct representing the XML dictRef values for all the data from WidgetData. More...

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Member Enumeration Documentation

enum RelaxBase::Input

Enumerator: AFF  MAFF  Definition at line 53 of file relaxbase.h.

enum RelaxBase::Categories [private]

Enumerator: BASIC  INTERNAL  CARTESIAN  ADVANCED  DEBUG1  EXTRA  CARTESIAN_SYMMETRY  CARTESIAN_OTHER  ADVANCED_THRESHOLDS  ADVANCED_OTHER  Definition at line 126 of file relaxbase.h.

enum RelaxBase::Type [private]

Enumerator: PreviewAFF  ICListAFF  Definition at line 129 of file relaxbase.h.

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Constructor & Destructor Documentation

RelaxBase::RelaxBase (  AtomSet *  atomset, QWidget *  parent = 0, const char *  name = 0, bool  modal = FALSE, WFlags  fl = 0 )

Definition at line 77 of file relaxbase.cpp.

RelaxBase::~RelaxBase (   )

The default destructor. Definition at line 88 of file relaxbase.cpp.

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Member Function Documentation

void RelaxBase::setName (  const QString  name  )

Sets the filename prefix of the calculation. This is the basename from which all input and output files will be named. Definition at line 95 of file relaxbase.cpp.

void RelaxBase::setDescription (  const QString  description  )

Sets the description of the calculation. Definition at line 103 of file relaxbase.cpp.

void RelaxBase::setDir (  const QString  dir  )

Sets the directory of the calculation. Definition at line 110 of file relaxbase.cpp.

void RelaxBase::setExtendedFormat (  const bool  state  )

Sets the format of the coordinates (normal/extended). Definition at line 117 of file relaxbase.cpp.

unsigned int RelaxBase::inputGenerationFrequency (   )

Returns the frequency with which the internal coordinates should be regenerated. 0 means just once at the beginning. Definition at line 124 of file relaxbase.cpp.

unsigned int RelaxBase::maxSteps (   )

Returns the maximum number of optimization steps to be done. 0 means no limit. Definition at line 137 of file relaxbase.cpp.

void RelaxBase::scaleFactors (  vector< unsigned int > &  steps, vector< double > &  factors )

Returns the scalefactors. Get it from the data struct (easier). Definition at line 145 of file relaxbase.cpp.

QStringList RelaxBase::generateInput (  const Input  type  )

Generates input for a specific program. AFF: complete .aff in case of manual input or just the header if using MAFF MAFF: input for a call to the program MAFF Definition at line 171 of file relaxbase.cpp.

void RelaxBase::loadCML (  const QDomElement *  root  )

Reads the widgetdata from a QDomElement. Definition at line 214 of file relaxbase.cpp.

void RelaxBase::saveCML (  QDomElement *  root  )

Saves the widgetdata to a QDomElement. Definition at line 485 of file relaxbase.cpp.

void RelaxBase::reset (   )  [slot]

Resets all widgets to their default values. Definition at line 629 of file relaxbase.cpp.

void RelaxBase::showEvent (  QShowEvent *  e  )  [protected]

Overridden from RelaxWidget::showEvent(). Definition at line 746 of file relaxbase.cpp.

void RelaxBase::accept (   )  [protected, slot]

Overridden from RelaxWidget::accept(). Definition at line 834 of file relaxbase.cpp.

void RelaxBase::reject (   )  [protected, slot]

Overridden from RelaxWidget::reject(). Definition at line 848 of file relaxbase.cpp.

void RelaxBase::showPreview (   )  [private, slot]

Shows a preview from the widgets. This function only starts MAFF if needed. The actual showing is done by showPreview2. Definition at line 865 of file relaxbase.cpp.

void RelaxBase::showPreview2 (   )  [private, slot]

Shows a preview from the widgets. This function is either called directly by showPreview if IC's are not generated or as a slot when the MAFF process is finished. Definition at line 884 of file relaxbase.cpp.

void RelaxBase::readInputFile (   )  [private, slot]

Reads a Relax AFF file into the widgets. Definition at line 921 of file relaxbase.cpp.

void RelaxBase::setChanged (  bool  state = true  )  [private, slot]

Sets the 'changed' property of the widget. Definition at line 1163 of file relaxbase.cpp.

void RelaxBase::selectWidget (  QListViewItem *   )  [private, slot]

Shows a widget from WidgetStackCategory depending on newItem. Definition at line 1170 of file relaxbase.cpp.

void RelaxBase::enableAutogenWidgets (   )  [private, slot]

Enabled/disables the widgets for configuring the (re)generation of the internal coordinates. Definition at line 1215 of file relaxbase.cpp.

void RelaxBase::enableSFACWidgets (  bool  state = true  )  [private, slot]

Enabled/disables the widgets for configuring the scale factor depending on RadioButtonSFAC{1|2}. Definition at line 1225 of file relaxbase.cpp.

void RelaxBase::newScaleFactor (   )  [private, slot]

Adds a new scale factor to the list. Definition at line 1240 of file relaxbase.cpp.

void RelaxBase::deleteScaleFactor (   )  [private, slot]

Deletes the currently selected scale factor from the list. Definition at line 1253 of file relaxbase.cpp.

void RelaxBase::updateICEdit (   )  [private, slot]

Updates the widgets for changing an IC with the contents of the currently selected IC in ListViewIC. Definition at line 1263 of file relaxbase.cpp.

void RelaxBase::updateICList (   )  [private, slot]

Updates ListViewIC with the contents of the widgets for changing an IC. It blocks calls to updateICEdit to prevent infinite recursion. Definition at line 1351 of file relaxbase.cpp.

void RelaxBase::updateICSpecifics (   )  [private, slot]

Updates the widgets for the specific data. Definition at line 1408 of file relaxbase.cpp.

void RelaxBase::updateICType (   )  [private, slot]

Does the necessary updating of all parts of an internal. Definition at line 1479 of file relaxbase.cpp.

void RelaxBase::newIC (   )  [private, slot]

Creates a new internal coordinate at the bottom of ListViewIC. Definition at line 1610 of file relaxbase.cpp.

void RelaxBase::newICPart (   )  [private, slot]

Creates a new part of an internal coordinate. Definition at line 1645 of file relaxbase.cpp.

void RelaxBase::deleteIC (   )  [private, slot]

Deletes the currently selected internal coordinate. Definition at line 1685 of file relaxbase.cpp.

void RelaxBase::clearIC (   )  [private, slot]

Deletes all internal coordinates. Definition at line 1728 of file relaxbase.cpp.

void RelaxBase::genIC (   )  [private, slot]

Fills the internal coordinates list with (non)redundant internal coordinates. This function only starts MAFF. The reuslting file is parsed in genIC2. Definition at line 1737 of file relaxbase.cpp.

void RelaxBase::genIC2 (   )  [private, slot]

Fills the internal coordinates list with (non)redundant internal coordinates. It is only called when a MAFF run has ended. Definition at line 1749 of file relaxbase.cpp.

void RelaxBase::moveICUp (   )  [private, slot]

Moves the selected internal coordinate one place up in the list. Definition at line 1765 of file relaxbase.cpp.

void RelaxBase::moveICDown (   )  [private, slot]

Moves the selected internal coordinate one place down in the list. Definition at line 1798 of file relaxbase.cpp.

void RelaxBase::newFixedAtom (   )  [private, slot]

Adds a new atom to the list of fixed atoms. Definition at line 1819 of file relaxbase.cpp.

void RelaxBase::deleteFixedAtom (   )  [private, slot]

Deletes the selected atom from the list of fixed atoms. Definition at line 1865 of file relaxbase.cpp.

void RelaxBase::checkFIXABoxes (   )  [private, slot]

Makes sure at least 1 box stays checked for the fixed atoms. Otherwise nothing would be actually fixed. Definition at line 1877 of file relaxbase.cpp.

void RelaxBase::enableTROTWidgets (  bool  state = true  )  [private, slot]

Enables/disables the widgets for configuring the optimization of the external coordinates depending on CheckBoxTROT. Definition at line 1910 of file relaxbase.cpp.

void RelaxBase::newExtraBond (   )  [private, slot]

Adds a new bond to the XBON list. Definition at line 1924 of file relaxbase.cpp.

void RelaxBase::deleteExtraBond (   )  [private, slot]

Deletes the selected bond from the XBON list. Definition at line 1947 of file relaxbase.cpp.

void RelaxBase::enableUPDTWidgets (  bool  state = true  )  [private, slot]

Enables/disables the widgets for configuring the update of the force constants depending on CheckBoxUPDT. Definition at line 1958 of file relaxbase.cpp.

void RelaxBase::enableSHRTWidgets (  bool  state = true  )  [private, slot]

Enables/disables the widgets for configuring the short output depending on CheckBoxSHRT. Definition at line 1967 of file relaxbase.cpp.

void RelaxBase::checkOverflow (  int  row, int  col )  [private, slot]

Spans cell(row, col) over multiple columns if it contains more than 10 characters. Definition at line 1983 of file relaxbase.cpp.

void RelaxBase::addExtraRow (   )  [private, slot]

If a row is selected, inserts a row before the selection. If no row is selected, adds a row at the end. Definition at line 1991 of file relaxbase.cpp.

void RelaxBase::removeExtraRow (   )  [private, slot]

Removes the selected rows. Definition at line 1999 of file relaxbase.cpp.

void RelaxBase::clearSelection (   )  [private, slot]

Clears the selected cells. Definition at line 2007 of file relaxbase.cpp.

void RelaxBase::makeConnections (   )  [private]

Sets up the permanent connections. Called once from the constructor. Definition at line 2020 of file relaxbase.cpp.

void RelaxBase::init (   )  [private]

Initializes the dialog. Called once from the constructor. Connections should be up. Definition at line 2188 of file relaxbase.cpp.

void RelaxBase::saveWidgets (   )  [private]

Saves the status of the widgets to a data struct. Definition at line 2322 of file relaxbase.cpp.

void RelaxBase::restoreWidgets (   )  [private]

Restores the status of the widgets from a data struct. Definition at line 2465 of file relaxbase.cpp.

QString RelaxBase::icRepresentation (  const unsigned int  atom1, const unsigned int  atom2, const unsigned int  atom3 = 0, const int  atom4 = 0 )  [private]

Returns a QString containing a representation of an internal coordinate from the 4 atom indices. A zero value will not be added. Definition at line 2590 of file relaxbase.cpp.

void RelaxBase::getAtomsFromIC (  const QString  textIC, unsigned int &  atom1, unsigned int &  atom2, unsigned int &  atom3, int &  atom4 )  [private]

Returns the atom numbers from a textual representation of an internal coordinate. Definition at line 2614 of file relaxbase.cpp.

void RelaxBase::renumberICs (   )  [private]

Renumbers the internal coordinates. Definition at line 2638 of file relaxbase.cpp.

QStringList RelaxBase::generateAFFHeader (   )  [private]

Generates input for the first part of an .aff file. Definition at line 2654 of file relaxbase.cpp.

QStringList RelaxBase::generateBmatInput (   )  [private]

Generates input for Maff to generate non-redundant internal coordinates. Only generates the actual input for the IC definitions. The input for the initial questions is generated in generateICs. Definition at line 2957 of file relaxbase.cpp.

bool RelaxBase::makeDirCurrent (  const QString  dir, const QString  title )  [private]

Makes dir the current directory. Shows a messagebox with the error and title when something goes wrong. Definition at line 3224 of file relaxbase.cpp.

void RelaxBase::fillICListFromAFF (  const QStringList  aff  )  [private]

Adds the internal coordinates found in the latest generated aff to the IC list widget. Definition at line 3246 of file relaxbase.cpp.

bool RelaxBase::startMAFF (  const unsigned int  slot  )  [private]

Initiates the generation of an AFF file using MAFF. Upon completion a specific slot will be called. Definition at line 3420 of file relaxbase.cpp.

QStringList RelaxBase::readMAFFGeneratedICs (   )  [private]

Returns the internal coordinates generated by the latest MAFF run. Definition at line 3495 of file relaxbase.cpp.

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Member Data Documentation

WidgetData RelaxBase::data [private]

Contains the status of all widgets. Definition at line 357 of file relaxbase.h.

const RelaxBase::XMLData RelaxBase::xml [static, private]

Contains the XML dictRef values for all WidgetData. Definition at line 358 of file relaxbase.h.

AtomSet* RelaxBase::atoms [private]

Pointer to the AtomSet passed in through the constructor. Definition at line 359 of file relaxbase.h.

vector<QString> RelaxBase::category [private]

Contains translatable names for the items in ListViewCategory. Definition at line 360 of file relaxbase.h.

bool RelaxBase::widgetChanged [private]

= TRUE if the dialog has been changed and needs saving. Definition at line 361 of file relaxbase.h.

QString RelaxBase::calcName [private]

Contains the filename prefix (maybe change to pointer to XbraboView QString. Definition at line 362 of file relaxbase.h.

QString RelaxBase::calcDescription [private]

Contains the description. Definition at line 363 of file relaxbase.h.

QString RelaxBase::calcDir [private]

Contains the directory. Definition at line 364 of file relaxbase.h.

bool RelaxBase::calcXF [private]

= TRUE if the calculation is to be done in extended format. Definition at line 365 of file relaxbase.h.

QProcess* RelaxBase::maffProcess [private]

The process for running MAFF. Definition at line 366 of file relaxbase.h.

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