BALL::VIEW::MolecularStructure Class Reference
[Modular
Widgets]
MolecularStructure
provides means to modify molecular structures and do several
calculations. More...
#include <molecularStructure.h>
Public Types |
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| enum | { AMBER_FF = 0, CHARMM_FF, MMFF94_FF } |
Public Member Functions |
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Constructors
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| MolecularStructure (QWidget *parent=0, const char *name=0) | |
| Default Constructor. |
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| MolecularStructure (const MolecularStructure &m) | |
| only needed for Python Interface,
dont call it! |
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Destructors
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| virtual | ~MolecularStructure () |
| Destructor. |
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Accessors: inspectors and mutators |
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| virtual void | onNotify (Message *message) |
| Handles messages sent by other
registered
ConnectionObject objects. |
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| virtual void | checkMenu (MainControl &main_control) |
| Check the menu entries. |
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| virtual void | initializeWidget (MainControl &main_control) |
| Initialize the popup menus for this
Widget. |
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| ForceField & | getForceField () |
| Get the currently selected force
field instance. |
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| AmberFF & | getAmberFF () |
| Get the instance of the AMBER
forcefield. |
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| CharmmFF & | getCharmmFF () |
| Get the instance of the CHARMM
forcefield. |
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| MMFF94 & | getMMFF94 () |
| AmberConfigurationDialog & | getAmberConfigurationDialog () |
| Get an instance of an dialog to
setup the AMBER forcefield. |
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| CharmmConfigurationDialog & | getCharmmConfigurationDialog () |
| Get an instance of an dialog to
setup the CHARMM forcefield. |
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| MMFF94ConfigurationDialog & | getMMFF94ConfigurationDialog () |
| virtual void | fetchPreferences (INIFile &inifile) |
| Fetch the widgets preferences from
the INIfile. |
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| virtual void | writePreferences (INIFile &inifile) |
| Writes the widgets preferences to
the INIFile. |
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| MolecularDynamicsDialog & | getMDSimulationDialog () |
| MinimizationDialog & | getMinimizationDialog () |
| FDPBDialog * | getFDPBDialog () |
| AssignBondOrderConfigurationDialog & | getBondOrderDialog () |
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const AssignBondOrderConfigurationDialog & |
getBondOrderDialog () const |
| AssignBondOrderResultsDialog & | getBondOrderResultsDialog () |
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const AssignBondOrderResultsDialog & |
getBondOrderResultsDialog () const |
| void | centerCamera (Composite *composite=0) |
| Centers the camera of
Scene to the geometric center of the molecular objects
in the selection list. |
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| void | buildBonds () |
| Creates bonds. |
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| void | runBondOrderAssignment (bool show_dialog=true) |
| Assigns bond orders. |
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| void | showBondOrderAssignmentResults (AssignBondOrderProcessor &bop) |
| Shows the results of the given
BondOrderAssigner. |
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| void | addHydrogens () |
| Adds hydrogens. |
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| virtual bool | checkResidue () |
| Check the residues. |
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| virtual void | createGridFromDistance () |
| Create a RegularData3D instance with
the distance from the geometric center. |
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| virtual void | createGridFromCameraDistance () |
| virtual void | calculateSecondaryStructure () |
| Calculate the secondary structure
for a protein. |
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| virtual void | mapProteins () |
| Map two Proteins and apply the
resulting transformation matrix. |
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| virtual void | calculateRMSD () |
| Calculate the RMSD between two
Molecules. |
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| void | buildPeptide () |
| Build a Peptide from a amino acid
sequence. |
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| void | calculateHBonds () |
| Calculate the H-Bonds for a
Protein. |
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| void | calculateRamachandranPlot () |
| Calculate a Ramachandran
Plot. |
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| void | calculateForceFieldEnergy () |
| Calculate the energy for the
currently selected force field. |
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| void | runMinimization (bool show_dialog_=true) |
| Run a energy minization with the
currently selected force field. |
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| void | MDSimulation (bool show_dialog_=true) |
| Perfomr a molecular dynamics
simulation with the currently selected force
field. |
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| void | showAmberForceFieldOptions () |
| Show the dialog to setup the AMBER
force field. |
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| void | showCharmmForceFieldOptions () |
| Show the dialog to setup the CHARMM
force field. |
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| void | showMMFF94ForceFieldOptions () |
| void | chooseAmberFF () |
| Slot for a menu entry to select the
AMBER force field. |
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| void | chooseCharmmFF () |
| Slot for a menu entry to select the
CHARMM force field. |
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| void | chooseMMFF94 () |
| Slot for a menu entry to select the
MMFF94 force
field. |
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| void | chooseForceField (Position nr) |
| void | setupForceField () |
| Show a dialog to setup the currently
selected force field. |
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| bool | calculateFDPB (bool show=true) |
Detailed Description
MolecularStructure provides means to modify molecular structures and do several calculations.To do so, it contains the MMFF94, AMBER and CHARMM forcefields and dialogs to do the setup. The widget itself is invisible, but it has several menu entries, e.g.:
- checkResidue
- centerCamera
- buildBonds
- assignBondOrders
- addHydrogens
- createGridFromDistance
- calculateSecondaryStructure This class is also necessary
to add certain properties to new Composite objects, which were opened
with the MolecularFileDialog.
So it reacts to Messages itself and converts some to other
Message objects. Further
it converts the geometric selection sent by
Scene to a molecular selection whose objects can be
given a new graphical representation by the
DisplayProperties dialog. See onNotify for information
concerning the conversion mechanism.
Constructor & Destructor Documentation
| BALL::VIEW::MolecularStructure::MolecularStructure | ( | QWidget * | parent =
0, |
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| const char * | name =
0 |
|||
| ) |
Member Function Documentation
| void BALL::VIEW::MolecularStructure::addHydrogens | ( | ) | [slot] |
Adds hydrogens.
If selected molecular objects are available hydrogens will be created for each object in the selection list using the add_hydrogens processor of the FragmentDB. A CompositeMessage will be sent for each object in the selection list. The number of hydrogens created will be written into the Log object.
| void BALL::VIEW::MolecularStructure::buildBonds | ( | ) | [slot] |
Creates bonds.
If selected molecular objects are available Bond objects will be created for each object in the selection list using the build_bonds processor of the FragmentDB. A CompositeMessage will be sent for each object in the selection list. The number of bonds created will be written into the Log object.
| void BALL::VIEW::MolecularStructure::centerCamera | ( | Composite * | composite =
0 |
) | [slot] |
Centers the camera of Scene to the geometric center of the molecular objects in the selection list.
A SceneMessage will be sent to inform the Scene.
| virtual void BALL::VIEW::MolecularStructure::checkMenu | ( | MainControl & | main_control | ) | [virtual] |
Check the menu entries.
The menus Select, Deselect, Add Hydrogens and Build Bonds will be enabled if the selection of molecular objects is not empty. The menu Focus camera will be enabled only if only one molecular object is in the selection list.
Reimplemented from BALL::VIEW::ModularWidget.
| virtual void BALL::VIEW::MolecularStructure::fetchPreferences | ( | INIFile & | inifile | ) | [virtual] |
Fetch the widgets preferences from the INIfile.
- Parameters:
-
inifile the INIFile that contains the required values
Reimplemented from BALL::VIEW::ModularWidget.
| AmberFF& BALL::VIEW::MolecularStructure::getAmberFF | ( | ) |
Get the instance of the AMBER forcefield.
The forcefield will be created, when this function is called the first time.
| CharmmFF& BALL::VIEW::MolecularStructure::getCharmmFF | ( | ) |
Get the instance of the CHARMM forcefield.
The forcefield will be created, when this function is called the first time.
| ForceField& BALL::VIEW::MolecularStructure::getForceField | ( | ) |
Get the currently selected force field instance.
This returns either a reference to the amber_ff_ member or to the charmm_ff_ member, depending on the value of use_amber_.
| virtual void BALL::VIEW::MolecularStructure::initializeWidget | ( | MainControl & | main_control | ) | [virtual] |
Initialize the popup menus for this Widget.
This method is called automatically immediately before the main application is started by MainControl::show().
- Parameters:
-
main_control the MainControl object to be initialized
- See also:
- finalizeWidget
Reimplemented from BALL::VIEW::ModularWidget.
| virtual void BALL::VIEW::MolecularStructure::onNotify | ( | Message * | message | ) | [virtual] |
Handles messages sent by other registered ConnectionObject objects.
Converts CompositeMessage if the retrieved Composite object is kind of AtomContainer and applies molecular properties to it (like normalize_names and build_bonds).
- Parameters:
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message the pointer to the message that should be processed
Reimplemented from BALL::VIEW::ConnectionObject.
| void BALL::VIEW::MolecularStructure::runBondOrderAssignment | ( | bool | show_dialog =
true |
) | [slot] |
Assigns bond orders.
If a single selected molecular object is available Bond Orders will be set for each bond object of the selected AtomContainer using the assign_bond_order processor. A CompositeMessage will be sent for the object in the selection list. The number of bond orders changed will be written into the Log object.
| void BALL::VIEW::MolecularStructure::showBondOrderAssignmentResults | ( | AssignBondOrderProcessor & | bop | ) | [slot] |
Shows the results of the given BondOrderAssigner.
All bond order assignment sets found by the given BondOrderAssigner will be presented as structural sketch, additional scoring information is provided by click on the entry. A single assignment can either be applied to the selected AtomContainer, or a copy of the original system with the bond order assignment of the current result is added to the Structure list.
| virtual void BALL::VIEW::MolecularStructure::writePreferences | ( | INIFile & | inifile | ) | [virtual] |
Writes the widgets preferences to the INIFile.
- Parameters:
-
inifile the INIFile that contains the needed values
Reimplemented from BALL::VIEW::ModularWidget.
