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General Functions

The functions defined in this section provide a wide variety of functionality that is generally applicable to the application as a whole.

About

void About()

Displays information about VIDA.

AppAddCallback

unsigned int AppAddCallback(changeName, callbackFunction)

Adds a Python callback function to be called when certain changes occur within VIDA. The changeName parameter is a string, and can have the following values:

  • “ActiveChanged”
  • “DisplayChanged”
  • “LockedChanged”
  • “MarkedChanged”
  • “ObjectsAdded”
  • “ObjectsDeleted”
  • “SelectedChanged”
  • “VisibleChanged”
  • “StateReset”

The callbackFunction parameter is the actual Python function (not a string) to be called each time the specified change happens.

The return value is an integer callback ID, which can be used to remove the callback later. See AppRemoveCallback.

AppCurrentDir

std::string AppCurrentDir()

Returns the current working directory.

AppCurrentDirSet

bool AppCurrentDirSet(const std::string &name)

Sets the current working directory and returns whether or not the change was successful.

AppDir

std::string AppDir()

Returns the path of the directory where the application is installed.

AppDocDir

std::string AppDocDir()

Returns the path to the directory containing all of the documentation.

AppExampleDir

std::string AppExampleDir()

Returns the path to the directory containing all of the examples provided with the application.

AppInstallDir

std::string AppInstallDir()

Returns the path to the directory where VIDA is installed.

AppLastDirGet

std::string AppLastDirGet()

Returns the path to the last directory that was accessed by VIDA. However, if the user has the preference “Open Current Dir” specified, this function will return an empty string.

AppLastDirSet

void AppLastDirSet(const std::string &)

Stores the path to the last directory that was accessed by VIDA.

AppLastOpenDirGet

std::string AppLastOpenDirGet()

Returns the path to the last directory from which a file was opened. However, if the user has the preference “Open Current Dir” specified, this function will return an empty string.

AppLastOpenDirSet

void AppLastOpenDirSet(const std::string &)

Sets the path to the last directory from which a file was opened.

AppLastSaveDirGet

std::string AppLastSaveDirGet()

Returns the path to the last directory to which a file was saved. However, if the user has the preference “Open Current Dir” specified, this function will return an empty string.

AppLastSaveDirSet

void AppLastSaveDirSet(const std::string &)

Sets the path to the last directory to which a file was saved.

AppLicenseFile

std::string AppLicenseFile()

Returns the path to the license file being used by VIDA.

AppLicenseUpdate

void AppLicenseUpdate(bool promptonly)

Searches for a new valid license file. If promptonly is True, VIDA will prompt the user to specify the location of the license file. If it is False, VIDA will search the expected potential locations for a new valid license file before prompting. If a valid license file is found in one of these locations, that file will be used and the user will not be prompted.

AppOpenUrl

void AppOpenUrl(const std::string &url)

Opens the specified URL using the most appropriate program for the specified URL. For instance, web pages will be opened with the default web browser and files will be opened with the program that that file type is associated.

AppRemoveCallback

void AppRemoveCallback(changeName, unsigned int callbackID)

Removes a callback created using the AppAddCallback function. The callbackID argument is the value returned from AppAddCallback, and the changeName string must be the same one that was used in the call to AppAddCallback. See AppAddCallback.

AppScriptSave

bool AppScriptSave(const std::string &fname)

Saves the current scripting history to the specified file.

AppUserDir

std::string AppUserDir()

Returns the path of the application user directory containing the application preferences, settings, startup script, journal file, and license.

AppVersion

std::string AppVersion()

Returns a string representation of the complete version number

AppVersionMajor

int AppVersionMajor()

Returns the first, or major, part of the version number as an integer

AppVersionMinor

int AppVersionMinor()

Returns the second, or minor, part of the version number as an integer

AppVersionBugFix

int AppVersionBugFix()

Returns the third, or bug fix, part of the version number as an integer

CopyData

void CopyData(const std::string &data)

Copies the specified data onto the system clipboard where it can be pasted into other applications.

CopyMolecules

void CopyMolecules(const std::vector<OEPropDB::OEKey> &keys)

Copies the specified molecules onto the system clipboard where they can be pasted into other applications in a variety of formats.

CopyMoleculesScoped

void CopyMoleculesScoped(unsigned int scope = BestScope)

Copies all of the molecules in the specified scope onto the system clipboard where they can be pasted into other applications in a variety of formats.

Error

void Error(const std::string &err)

Raises an exception when called from within a script, otherwise, it reports the specified error message to the status bar.

ErrorDetailsDialog

void ErrorDetailsDialog(const std::string &title, const std::string &message,
                        const std::string &error)

Launches an error dialog that contain detailed information about the error that occurred.

ExtensionsEdit

void ExtensionsEdit()

Launches the extensions manager.

IsLicensed

bool IsLicensed(const std::string &toolkit)

Returns whether or not a valid license exists for the specified toolkit. If a valid license is present, that toolkit can be accessed from Python in VIDA. If a valid license is not present, importing that toolkit in Python will fail and throw an exception.

JournalInit

void JournalInit(bool force)

For internal use only. This function specifies the script as a “Journal Script” which forces the application to clear its current state and run the script starting from a clean state.

ObservableBool

BoolObservable &ObservableBool(const std::string &name, bool create=False)

Returns a reference to an observable boolean value.

ObservableFloat

FloatObservable &ObservableFloat(const std::string &name, bool create=False)

Returns a reference to an observable floating point value.

ObservableInt

IntObservable &ObservableInt(const std::string &name, bool create=False)

Returns a reference to an observable integer value.

ObservableKey

KeyObservable &ObservableKey(const std::string &name, bool create=False)

Returns a reference to an observable OEKey object.

ObservableString

StringObservable &ObservableString(const std::string &name, bool create=False)

Returns a reference to an observable string value.

ObservableUInt

UIntObservable &ObservableUInt(const std::string &name, bool create=False)

Returns a reference to an observable unsigned integer value.

ObservableUpdate

UpdateObservable &ObservableUpdate(const std::string &name, bool create=False)

Returns a reference to an observable updater.

ObservableVecFloat

FloatVectorObservable &ObservableVecFloat(const std::string &name,
                                          bool create=False)

Returns a reference to an observable list of floating point values.

ObservableVecInt

IntVectorObservable &ObservableVecInt(const std::string &name,
                                      bool create=False)

Returns a reference to an observable list of integer values.

ObservableVecString

StringVectorObservable &ObservableVecString(const std::string &name,
                                            bool create=False)

Returns a reference to an observable list of string values.

ObservableVecUInt

UIntVectorObservable &ObservableVecUInt(const std::string &name,
                                        bool create=False)

Returns a reference an observable list of unsigned integer values.

Open

std::vector<unsigned int> Open(const std::string &filename,
                               const std::string &type="")
std::vector<unsigned int> Open(const std::vector<std::string> &filenames,
                               const std::string &type="")

This function opens the specified file or files. The optional type parameter is the file extension to assume for this file.

OpenState

void OpenState(const std::string &filename)

This function opens the specified state file. This action will clear the current session, including deleting all the loaded molecules.

PasteMolecules

void PasteMolecules()
void PasteMolecules(const std::vector<std::string> &,
                    const std::string &format)

Pastes all of the molecules that can be found in the system clipboard into the application. Pasted molecules will appear in a new list called “Pasted”.

PreferenceDump

void PreferenceDump()

This function prints out all the current preferences.

PreferenceGetBool

bool PreferenceGetBool(const std::string &pref, bool def=False)

This function returns the current boolean value of the given preference.

PreferenceGetColor

OESystem::OEColor PreferenceGetColor(const std::string &pref,
                                     const OESystem::OEColor &def=OESystem::OEWhite)

This function returns the current color of the given preference.

PreferenceGetDouble

double PreferenceGetDouble(const std::string &pref, double def=0.0)

This function returns the double precision number (non-integral) value of the given preference.

PreferenceGetFloat

float PreferenceGetFloat(const std::string &pref, float def=0.0f)

This function returns the floating point (non-integral) value of the given preference.

PreferenceGetInt

int PreferenceGetInt(const std::string &pref, int def=0)

This function returns the integer value of the given preference.

PreferenceGetString

std::string PreferenceGetString(const std::string &pref,
                                const std::string &def="")

This function returns the string value of the given preference.

PreferenceGetVBool

std::vector<bool> PreferenceGetVBool(const std::string &pref,
                                     const std::vector<bool> &v=std::vector<bool>())

This function returns the vector of boolean values for the given preference.

PreferenceGetVDouble

std::vector<double> PreferenceGetVDouble(const std::string &pref,
                                         const std::vector<double> &v=std::vector<double>())

This function returns the vector of double precision values for the given preference.

PreferenceGetVFloat

std::vector<float> PreferenceGetVFloat(const std::string &pref,
                                       const std::vector<float> &v=std::vector<float>())

This function returns the vector of floating point values for the given preference.

PreferenceGetVInt

std::vector<int> PreferenceGetVInt(const std::string &pref,
                                   const std::vector<int> &v=std::vector<int>())

This function returns the vector of integer values for the given preference.

PreferenceIsBool

bool PreferenceIsBool(const std::string &pref)

This function returns whether the given preference is a boolean preference.

PreferenceIsColor

bool PreferenceIsColor(const std::string &pref)

This function returns whether the given preference is a color.

PreferenceIsDouble

bool PreferenceIsDouble(const std::string &pref)

This function returns whether the given preference is a double precision number.

PreferenceIsFloat

bool PreferenceIsFloat(const std::string &pref)

This function returns whether the given preference is a floating point number.

PreferenceIsInt

bool PreferenceIsInt(const std::string &pref)

This function returns whether the given preference is an integer.

PreferenceIsSet

bool PreferenceIsSet(const std::string &pref)

This function returns whether the given preference has a value.

PreferenceIsString

bool PreferenceIsString(const std::string &pref)

This function returns whether the given preference is a string.

PreferenceIsVBool

bool PreferenceIsVBool(const std::string &pref)

This function returns whether the given preference is a list of booleans.

PreferenceIsVDouble

bool PreferenceIsVDouble(const std::string &pref)

This function returns whether the given preference is a list of double precision numbers.

PreferenceIsVFloat

bool PreferenceIsVFloat(const std::string &pref)

This function returns whether the given preference is a list of floating point numbers.

PreferenceIsVInt

bool PreferenceIsVInt(const std::string &pref)

This function returns whether the given preference is a list of floating point numbers.

PreferenceMark

void PreferenceMark()

This function marks the preferences as a point for undoing.

PreferenceRemove

bool PreferenceRemove(const std::string &pref)

This function deletes a preference.

PreferenceRestore

void PreferenceRestore()

This function restores the default preferences.

PreferenceSetBool

bool PreferenceSetBool(const std::string &pref, bool v)

This function sets the boolean value of the preference.

PreferenceSetColor

bool PreferenceSetColor(const std::string &pref, const OESystem::OEColor &v)

This function sets the color value of the preference.

PreferenceSetCommand

bool PreferenceSetCommand(const std::string &pref, const std::string &cmd)

This function sets the command to activate the changes in the preference.

PreferenceSetDouble

bool PreferenceSetDouble(const std::string &pref, double v)

This function sets double precision value of the preference.

PreferenceSetFloat

bool PreferenceSetFloat(const std::string &pref, float v)

This function sets floating point value of the preference.

PreferenceSetInt

bool PreferenceSetInt(const std::string &pref, int v)

This function sets integer value of the preference.

PreferenceSetString

bool PreferenceSetString(const std::string &pref, const std::string &v)

This function sets the string value of the preference.

PreferenceSetVBool

bool PreferenceSetVBool(const std::string &pref, const std::vector<bool> &v)

This function sets value of the preference to the passed list of booleans.

PreferenceSetVDouble

bool PreferenceSetVDouble(const std::string &pref,
                          const std::vector<double> &v)

This function sets value of the preference to the passed list of double precision numbers.

PreferenceSetVFloat

bool PreferenceSetVFloat(const std::string &pref,
                         const std::vector<float> &v)

This function sets value of the preference to the passed list of floating point numbers.

PreferenceSetVInt

bool PreferenceSetVInt(const std::string &pref, const std::vector<int> &v)

This function sets value of the preference to the passed list of integers.

PreferenceValidateCommands

std::string PreferenceValidateCommands()

This function checks all the commands for the preferences to ensure that they all exist. It returns a list of Preference commands that could not be found.

PreferencesEdit

void PreferencesEdit()

This function opens the preferences dialog.

Quit

void Quit(bool force=False)
void quit(bool force=False)

Exits the application. If force is set to False, the user will be prompted before actually exiting.

Redo

void Redo()
void Redo(unsigned int steps)

This function redoes any previously undone actions.

RedoTo

bool RedoTo(const std::string &)

Redoes all the previously undone operation up to the specified location in the undo stack.

(See UndoMark.)

RunTheGauntlet

void RunTheGauntlet()

This function is designed for testing and debugging purposes. It is disabled in release distributions.

Save

void Save(const std::string &filename, const std::vector<unsigned int> &ids)
void Save(const std::string &filename,
          const std::vector<OEPropDB::OEKey> &keys)

This function saves the passed IDs or OEKeys to a file with the given filename.

SaveMiniState

void SaveMiniState(const std::string &filename, const std::string &version="")

This function saves the current application state as a “mini state” to the specified file.

SaveState

void SaveState(const std::string &filename, const std::string &version="")

This function saves the current application state to the specified file.

SaveStateFilter

void SaveStateFilter(const std::string &filename, const std::string &filter)

This function saves the state of the application to the specified file in the state file format determined by the specified filter.

SettingsGetBool

bool SettingsGetBool(const std::string &s, bool def=False)

This function returns the specified boolean setting.

SettingsGetFloat

float SettingsGetFloat(const std::string &s, float def=0.0f)

This function returns the specified float setting.

SettingsGetInt

int SettingsGetInt(const std::string &s, int def=0)

This function returns the specified int setting.

SettingsGetString

std::string SettingsGetString(const std::string &s, const std::string &def="")

This function returns the specified string setting.

SettingsRestore

void SettingsRestore()

This function returns the specified restore setting.

SettingsSetBool

bool SettingsSetBool(const std::string &s, bool v)

This function sets the specified bool setting.

SettingsSetFloat

bool SettingsSetFloat(const std::string &s, float v)

This function sets the specified float setting.

SettingsSetInt

bool SettingsSetInt(const std::string &s, int v)

This function sets the specified integer setting.

SettingsSetString

bool SettingsSetString(const std::string &s, const std::string &v)

This function sets the specified string setting.

SettingsSync

void SettingsSync()

This function synchronizes the application settings with those stored on disk. Ordinarily this function should not need to be called.

StateMark

int StateMark()

Reserved for internal use.

StatePop

int StatePop(bool load=True)

Reserved for internal use.

Undo

void Undo()
void Undo(unsigned int steps)

This function undoes the previous actions.

UndoHint

void UndoHint(const std::string &action, bool replace=True)

This function is used to name the current undo action. Ordinarily this function should not need to be called by the user.

UndoMark

bool UndoMark(const std::string &)

Sets a name for the current position in the undo stack which can be used later by the UndoTo function.

UndoTo

bool UndoTo(const std::string &)

Undoes all the previous operations up to the specified operation.

(See UndoMark.)

UpdateRedo

void UpdateRedo()

This function updates the redo menu. Ordinarily this function should not need to be called by the user.

VFSleep

void VFSleep(unsigned int seconds)

Sleeps the application for the specified number of seconds.

ViewerExportPOVRAY

void ViewerExportPOVRAY(const std::string &fname)

This function exports the current scene in the 3D display to a POV-Ray input file. The resulting file can be used as input to the POV-Ray raytracing program to generate very high quality static 3D images.

ViewerScreenshot

void ViewerScreenshot(const std::string &fname)
void ViewerScreenshot(const std::string &fname, unsigned int width,
                      unsigned int height)

This function saves a screenshot of the 3D display window to the specified file (fname) in PNG format.

WriteHistory

void WriteHistory(const std::string &filename)

Writes the current Python interpreter history to the specified filename.

Scope Functions

The functions detailed in this section enable the user to access information about and change the state of the application through the multiple different available scopes.

Active

void Active(const OEPropDB::OEKey &k)
void Active(unsigned int id, unsigned int conf=UINT_MAX)

Makes the specified object the Active or Focused object in the application. The object is specified by passing either an OEKey object or a unique ID paired with a conformer index (if dealing with multiconformer molecules).

ActiveConformer

unsigned int ActiveConformer()

Returns the index of the currently Active or Focused conformer.

ActiveID

unsigned int ActiveID()

Returns the unique ID associated with the currently Active or Focused object.

ActiveKey

OEPropDB::OEKey ActiveKey()

Returns the unique key associated with the currently Active or Focused object.

ClearActive

void ClearActive()

Clears the active / focused property from the currently active object.

ClearLocked

void ClearLocked()

Clears the locked property from all objects.

ClearMarked

void ClearMarked()

Clears the marked property from all objects.

ClearSelection

void ClearSelection()

Clears the selected property from all objects.

ClearVisible

void ClearVisible()

Clears the visible property from all objects.

ContextClear

void ContextClear()

Clears the context scope.

ContextGet

std::vector<OEPropDB::OEKey> ContextGet()

Returns the list of keys currently contained in the context scope. The “context” scope is used to determine which operations are appropriate for display in the right-click popup menu.

ContextInsert

void ContextInsert(const OEPropDB::OEKey &)
void ContextInsert(const std::vector<OEPropDB::OEKey> &)

Inserts the specified key(s) into the context scope. The “context” scope is used to determine which operations are appropriate for display in the right-click popup menu.

ContextKeysSet

void ContextKeysSet(const OEPropDB::OEKeyGroup &k)
void ContextKeysSet(const std::vector<OEPropDB::OEKey> &keys)

Sets the specified keys to be the “context” keys which are used to determine which operations are appropriate for display in the right-click popup menu.

ContextSet

void ContextSet(const OEPropDB::OEKey &)
void ContextSet(const std::string &prop)
void ContextSet(const std::vector<OEPropDB::OEKey> &)

Sets the specified key(s) to be the “context” keys which are used to determine which operations are appropriate for display in the right-click popup menu.

DefaultScopeGet

unsigned int DefaultScopeGet()

Returns the default scope of operations.

DefaultScopeSet

void DefaultScopeSet(unsigned int scope)

Sets the default scope of operations. Valid parameters are:

  • ActiveScope - operations are performed on the active / focused

    object

  • ActiveThenVisibleScope - operations are performed only on the active /

    focused object; however, if no object has that property, the operations are performed on the visible objects

  • AllScope - operations are performed on all of the currently loaded

    objects

  • BestScope - allows the application to determine the current best scope

    for operations based on the context of the operation

  • MarkedScope - operations are performed on all of the marked objects

  • ScratchScope - operations are performed on all of the objects that were

    added to the scratch scope using the ScratchInsert and the ScratchSet functions.

  • SelectedScope - operations are performed only on selected objects

  • VisibleScope - operations are performed on all of the visible objects

GetAllContextKeys

std::vector<OEPropDB::OEKey> GetAllContextKeys()

Returns all of the relevant keys of interest corresponding to the current state of the application.

GetAtomsScoped

std::vector<OEPropDB::OEKey> GetAtomsScoped(unsigned int scope)

Returns a list of all the atom keys in the specified scope.

GetBondsScoped

std::vector<OEPropDB::OEKey> GetBondsScoped(unsigned int scope)

Returns a list of all the bond keys in the specified scope.

GetContoursScoped

std::vector<OEPropDB::OEKey> GetContoursScoped(unsigned int scope)

Returns a list of all the contour keys in the specified scope.

GetGridsScoped

std::vector<OEPropDB::OEKey> GetGridsScoped(unsigned int scope)

Returns a list of all the grid keys in the specified scope.

GetMarkedAtoms

std::vector<OEPropDB::OEKey> GetMarkedAtoms()

Returns a list of keys corresponding to all of the currently marked atoms.

GetMarkedAtomsScoped

std::vector<OEPropDB::OEKey> GetMarkedAtomsScoped(unsigned int scope)

Returns a list of keys corresponding to all of the currently marked atoms that are also in the specified scope.

GetMarkedBonds

std::vector<OEPropDB::OEKey> GetMarkedBonds()

Returns a list of keys corresponding to all of the currently marked bonds.

GetMarkedBondsScoped

std::vector<OEPropDB::OEKey> GetMarkedBondsScoped(unsigned int scope)

Returns a list of keys corresponding to all of the currently marked bonds that are also in the specified scope.

GetMarkedContours

std::vector<OEPropDB::OEKey> GetMarkedContours()

Returns a list of keys corresponding to all of the currently marked contours.

GetMarkedGrids

std::vector<OEPropDB::OEKey> GetMarkedGrids()

Returns a list of keys corresponding to all of the currently marked grids.

GetMarkedMolecules

std::vector<OEPropDB::OEKey> GetMarkedMolecules()

Returns a list of keys corresponding to all of the currently marked molecules.

GetMarkedMonitors

std::vector<OEPropDB::OEKey> GetMarkedMonitors()

Returns a list of keys corresponding to all of the currently marked monitors.

GetMarkedSurfaces

std::vector<OEPropDB::OEKey> GetMarkedSurfaces()

Returns a list of keys corresponding to all of the currently marked surfaces.

GetMoleculesScoped

std::vector<OEPropDB::OEKey> GetMoleculesScoped(unsigned int scope)

Returns a list of all the molecule keys in the specified scope.

GetScoped

std::vector<OEPropDB::OEKey> GetScoped(unsigned int scope)
std::vector<OEPropDB::OEKey> GetScoped(unsigned int scope, unsigned int type)

Returns a list of all the keys in the specified scope. If a type parameter is specified, it will return a list of all keys of that type in the specified scope. The type parameter can be retrieved by calling the GetType method on an OEKey object.

GetSelectedAtom

OEPropDB::OEKey GetSelectedAtom()

Returns a key corresponding to a single selected atom. If multiple atoms are currently selected, this is equivalent to returning the first entry in list returned by GetSelectedAtoms.

GetSelectedAtoms

std::vector<OEPropDB::OEKey> GetSelectedAtoms()

Returns a list of keys corresponding to the currently selected atoms.

GetSelectedBond

OEPropDB::OEKey GetSelectedBond()

Returns a key corresponding to a single selected bond. If multiple atoms are currently selected, this is equivalent to returning the first entry in list returned by GetSelectedBondss.

GetSelectedBonds

std::vector<OEPropDB::OEKey> GetSelectedBonds()

Returns a list of keys corresponding to the currently selected bonds.

GetSelectedContours

std::vector<OEPropDB::OEKey> GetSelectedContours()

Returns a list of keys corresponding to the currently selected contours.

GetSelectedGrids

std::vector<OEPropDB::OEKey> GetSelectedGrids()

Returns a list of keys corresponding to the currently selected grids.

GetSelectedMolecules

std::vector<OEPropDB::OEKey> GetSelectedMolecules()

Returns a list of keys corresponding to the currently selected molecules.

GetSelectedMonitors

std::vector<OEPropDB::OEKey> GetSelectedMonitors()

Returns a list of keys corresponding to the currently selected monitors.

GetSelectedSurfaces

std::vector<OEPropDB::OEKey> GetSelectedSurfaces()

Returns a list of keys corresponding to the currently selected surfaces.

GetSurfacesScoped

std::vector<OEPropDB::OEKey> GetSurfacesScoped(unsigned int scope)

Returns a list of all the surface keys in the specified scope.

GetVisibleAtoms

std::vector<OEPropDB::OEKey> GetVisibleAtoms()

Returns a list of all the visible atom keys.

GetVisibleBonds

std::vector<OEPropDB::OEKey> GetVisibleBonds()

Returns a list of all the visible bond keys.

GetVisibleContours

std::vector<OEPropDB::OEKey> GetVisibleContours()

Returns a list of all the visible contour keys.

GetVisibleGrids

std::vector<OEPropDB::OEKey> GetVisibleGrids()

Returns a list of all the visible grid keys.

GetVisibleIDs

std::vector<unsigned int> GetVisibleIDs()

Returns a list of all the IDs for the current set of visible objects.

GetVisibleMolecules

std::vector<OEPropDB::OEKey> GetVisibleMolecules()

Returns a list of all the visible molecule keys.

GetVisibleMonitors

std::vector<OEPropDB::OEKey> GetVisibleMonitors()

Returns a list of all the visible monitor keys.

GetVisibleSurfaces

std::vector<OEPropDB::OEKey> GetVisibleSurfaces()

Returns a list of all the visible surface keys.

IDGet

unsigned int IDGet(const OESystem::OEBase &)

Returns the ID associated with the specified Python object.

IDTypeGet

std::string IDTypeGet(unsigned int)

Returns the name of the object type associated with the specified ID.

IsActive

bool IsActive(const OEPropDB::OEKey &k)
bool IsActive(unsigned int id, unsigned int conf=UINT_MAX)

Returns whether or not the specified object (key or ID with optional conformer index) is active/focused.

IsLocked

bool IsLocked(const OEPropDB::OEKey &k)
bool IsLocked(unsigned int id, unsigned int conf=UINT_MAX)

Returns whether or not the specified object (key or ID with optional conformer index) is locked.

IsMarked

bool IsMarked(const OEPropDB::OEKey &k)
bool IsMarked(unsigned int id, unsigned int conf=UINT_MAX)

Returns whether or not the specified object (key or ID with optional conformer index) is marked.

IsSelected

bool IsSelected(const OEPropDB::OEKey &k)
bool IsSelected(unsigned int id, unsigned int conf=UINT_MAX)

Returns whether or not the specified object (key or ID with optional conformer index) is selected.

IsTrulyVisible

bool IsTrulyVisible(const OEPropDB::OEKey &k)
bool IsTrulyVisible(unsigned int id, unsigned int conf=UINT_MAX)

Returns whether or not the specified object (key or ID with optional conformer index) is truly visible.

IsVisible

bool IsVisible(const OEPropDB::OEKey &k)
bool IsVisible(unsigned int id, unsigned int conf=UINT_MAX)

Returns whether or not the specified object (key or ID with optional conformer index) is visible.

Lock

void Lock(const std::string &k)
void Lock(const OEPropDB::OEKey &k, bool state)
void Lock(const std::vector<OEPropDB::OEKey> &keys, bool state)
void Lock(unsigned int id, bool state, unsigned int conf=UINT_MAX)

Sets the locked property on the specified object to the specified value (state). If a string value is passed to this function as opposed to an object specifier, the locked property will be set for all the objects that satisfy the specified query. For more details on the query language, see the relevant chapter in the main VIDA manual.

LockScoped

void LockScoped(bool state, unsigned int scope)

Sets the locked property to the specified value for all objects in the specified scope.

Mark

void Mark(const std::string &prop)
void Mark(const OEPropDB::OEKey &k, bool state)
void Mark(const std::vector<OEPropDB::OEKey> &keys, bool state)
void Mark(unsigned int id, bool state, unsigned int conf=UINT_MAX)
void Mark(const std::vector<OEPropDB::OEKey> &keys, bool state,
          unsigned char action)

Sets the marked property on the specified object to the specified value (state). If a string value is passed to this function as opposed to an object specifier, the marked property will be set for all the objects that satisfy the specified query. For more details on the query language, see the relevant chapter in the main VIDA manual.

MarkScoped

void MarkScoped(bool state, unsigned int scope)

Sets the marked property to the specified value for all objects in the specified scope.

MimicParentVisibilityGet

bool MimicParentVisibilityGet(const OEPropDB::OEKey &k)

Returns whether or not the visibility of the specified object is controlled by its parent’s visibility.

MimicParentVisibilitySet

void MimicParentVisibilitySet(const OEPropDB::OEKey &k, bool mimic)
void MimicParentVisibilitySet(const std::vector<OEPropDB::OEKey> &k,
                              bool mimic)

Sets whether or not the visibility of the specified object(s) is controlled by each individual’s parent’s visibility.

MimicParentVisibilitySetScoped

void MimicParentVisibilitySetScoped(const std::string &tag, bool mimic,
                                    unsigned int scope = BestScope)

Sets whether or not the visibility of a certain set of objects with the specified scope is controlled by each individual’s parent’s visibility. The set of objects is determined by the presence or absence of the specified tag on the molecule.

ScratchClear

void ScratchClear()

This function clears the ScratchScope.

ScratchGet

std::vector<OEPropDB::OEKey> ScratchGet()

Returns all of the keys currently in the ScratchScope.

ScratchInsert

void ScratchInsert(const OEPropDB::OEKey &)
void ScratchInsert(const std::vector<OEPropDB::OEKey> &)

This function adds a key to the ScratchScope.

ScratchSet

void ScratchSet(const std::string &prop)
void ScratchSet(const OEPropDB::OEKey &)
void ScratchSet(const std::vector<OEPropDB::OEKey> &)

This function sets the contents of the ScratchScope.

Select

void Select(const std::string &prop)
void Select(const OEPropDB::OEKey &k, bool state)
void Select(const std::vector<OEPropDB::OEKey> &keys, bool state)
void Select(unsigned int id, bool state, unsigned int conf=UINT_MAX)
void Select(const std::vector<OEPropDB::OEKey> &keys, bool state,
            unsigned char action)

This function selects objects according to the selection language.

SelectAllMolecules

void SelectAllMolecules()

This function selects every molecule that is currently visible.

SelectByQuery

void SelectByQuery(const std::string &query, int action=0,
                   unsigned int scope = BestScope)

This function selects every molecule in the specified scope based on whether or not it matches the specified substructure query. Valid query inputs include SMILES, SMARTS, and IUPAC as well as common names. The IUPAC and common name to structure conversion is performed by the Ogham toolkit.

SelectInvert

void SelectInvert()

This function selects the currently visible, but not selected items, and deselects the visible and selected items.

SelectKeys

void SelectKeys(const std::vector<OEPropDB::OEKey> &atomsKeys)

This function selects the objects corresponding to each of the keys specified in the parameter list keys.

SelectOERID

void SelectOERID(unsigned int id, bool selected=true)

This function sets the selected property on the object corresponding to the specified id. The selected parameter specifies whether or not the object should either be selected or unselected.

SelectResidues

void SelectResidues(const std::vector<OEPropDB::OEKey> &keys, bool state)

Set the selected state of the residues containing the specified atoms.

SelectScoped

void SelectScoped(bool state, unsigned int scope)

Select or unselect (based on the state parameter) all the objects in the specified scope.

SelectWithin

void SelectWithin(float radius, bool selected)

This function selects all molecule objects, including atoms and bonds, within the specified radius of the currently selected objects.

SelectWithout

void SelectWithout(float radius, bool selected)

This function selects all molecule objects, including atoms and bonds, outside of the specified radii of the currently selected objects.

Subset

void Subset(const std::string &name, const std::string &sel)

Creates a named subset that can be then used in the Select routine.

Visible

void Visible(const std::string &prop)
void Visible(const OEPropDB::OEKey &k, bool state)
void Visible(const std::vector<OEPropDB::OEKey> &keys, bool state)
void Visible(unsigned int id, bool state, unsigned int conf=UINT_MAX)
void Visible(const std::vector<OEPropDB::OEKey> &keys, bool state,
             unsigned char action)
bool Visible(const std::vector<unsigned int> &ids, bool visible,
             unsigned int conf=UINT_MAX)

This function sets the keys that pass the specified criteria to be visible.

VisibleScoped

void VisibleScoped(bool state, unsigned int scope)

Sets the visibility of all the objects in the specified scope based on the state parameter.

VisualizeCommandScopeGet

unsigned int VisualizeCommandScopeGet()

Reserved for future expansion.

VisualizeCommandScopeSet

void VisualizeCommandScopeSet(unsigned int scope)

Reserved for future expansion.

User Interface Functions

The functions detailed in this section provide access to information about and enable customization of the user interface.

AppComponentNameGet

std::string AppComponentNameGet()

Returns the name of which VIDA component currently has the mouse focus.

AppComponentNameSet

void AppComponentNameSet(const std::string &name)

Stores the name of which VIDA component currently has the mouse focus. This function is called internally whenever the mouse focus changes to a new widget within the application. This is primarily intended for internal use and as such should not be called.

AppGeometryGet

std::vector<unsigned int> AppGeometryGet()

Returns a list of four unsigned integers corresponding to the width, height, x and y positions of the application.

AppGeometrySet

std::vector<unsigned int> AppGeometrySet( const std::vector<unsigned int> &geom )
std::vector<unsigned int> AppGeometrySet( unsigned int width,
                                          unsigned int height,
                                          unsigned int x,
                                          unsigned int y,
                                          unsigned int mainx ,
                                          unsigned int mainy )

Sets the width, height, x position, y position, central widget width, and central widget height of the application.

AppGlobalFontGet

std::string AppGlobalFontGet()

Returns the current global font used in the application.

AppGlobalFontSet

void AppGlobalFontSet(const std::string &font)

Sets the global font to be used in the application.

AppLayoutGet

std::string AppLayoutGet()

Returns a hexadecimal encoded string representation of the current layout.

AppLayoutSet

std::string AppLayoutSet(const std::string &geom)

Sets the current layout of the application based on the hexadecimal encoded layout specified by geom. Ordinarily this function should not need to be called by the user; however, in the event that it is called, the input to this function should always be the return value from a previous call to AppLayoutGet.

AppLayoutToIcon

std::vector<std::string> AppLayoutToIcon(unsigned int width  = 24,
                                         unsigned int height = 24 )

Returns a cartoon representation of the current layout as an image of size width and height. The image is returned in XPM format.

AppMainWindowGet

std::string AppMainWindowGet()

Returns the name of the current main window.

AppMainWindowSet

std::string AppMainWindowSet(const std::string &mainWindow)

Sets the current main window. The name of the desired main window is the input to this function.

AppMovableWindowsGet

bool AppMovableWindowsGet()

Returns whether or not the layout of the individual windows in the application can be changed by clicking and dragging the window to the desired location.

AppMovableWindowsSet

bool AppMovableWindowsSet(bool)

Sets whether or not the layout of the individual windows in the application can be changed by clicking and dragging the window to the desired location.

AppPerspectiveSet

std::string AppPerspectiveSet(const std::string &perspective)

Sets the current layout of the application based on the hexadecimal encoded layout specified by perspective while maintaining the current geometry (width, height, x and y positions). Ordinarily this function should not need to be called by the user; however, in the event that it is called, the input to this function should always be the return value of a previous call to AppLayoutGet.

AppRecordWindowEventsGet

bool AppRecordWindowEventsGet()

Returns whether or not window events are currently being recorded in the application history.

AppRecordWindowEventsSet

bool AppRecordWindowEventsSet(bool record)

Sets whether or not window events are recorded in the application history.

AppShowGet

std::string AppShowGet()

Returns the display status of the application. Potential return values are:

  • “normal”
  • “minimized”
  • “maximized”
  • “fullscreen”

AppShowMenuBarGet

bool AppShowMenuBarGet()

Returns whether or not the main menubar is currently visible.

AppShowMenuBarSet

void AppShowMenuBarSet(bool)

Sets whether or not the main menubar is currently visible.

AppShowSet

void AppShowSet(const std::string &style)

Sets the display status of the application. Valid options are:

  • “normal”
  • “minimized”
  • “maximized”
  • “fullscreen”

AppShowStatusBarGet

bool AppShowStatusBarGet()

Returns whether or not the main status bar is currently visible.

AppShowStatusBarSet

void AppShowStatusBarSet(bool)

Sets whether or not the main status bar is currently visible.

AppSloppyFocusGet

bool AppSloppyFocusGet()

Returns whether or not the window focus is changed by simply positioning the mouse over a window as opposed to requiring a click in the window to change focus (the default behavior).

AppSloppyFocusSet

bool AppSloppyFocusSet(bool sloppy)

Sets whether or not the window focus is changed by simply positioning the mouse over a window as opposed to requiring a click in the window to change focus (the default behavior).

AppStatusTextSet

void AppStatusTextSet(const std::string &text, unsigned int seconds)

Sets the displayed text in the status bar of the main application window to the specified text. If the seconds parameter is 0, this text will replace the default SMILES display in the status bar. If the seconds parameter is greater than 0, the text will only be displayed for the specified period of time, returning to the default SMILES display when the time has elapsed.

AppWindowStyleGet

std::string AppWindowStyleGet()

Returns the application window display style of the application. These styles typically correspond to specific operating system window managers.

AppWindowStyleSet

std::string AppWindowStyleSet(const std::string &windowStyle)

Sets the application window display style of the application. These styles typically correspond to specific operating system window managers.

BlockBegin

void BlockBegin()

Blocks user interaction with the GUI with the exception of the abort button. This function is used internally and should only be called by the user to restore already existing blocking behavior that may have been temporarily overridden to enable user interaction within a user specified script.

BlockEnd

void BlockEnd()

Restores user interaction with the GUI that was previously blocked by BlockBegin. This function is used internally and should only be called to enable user interaction (if needed) within a user specified script. Any script which calls this function should restore the blocking behavior by calling BlockBegin once the user interaction portion is complete. However, it is important to make sure that blocking is actually active in the first place (see BlockGet) before calling this function and then later calling BlockBegin.

BlockExemptGet

bool BlockExemptGet(const std::string &name)

Returns whether or not the GUI object specified by name is exempt from GUI blocking when Python commands are being executed.

BlockExemptSet

void BlockExemptSet(const std::string &name, bool value)

Sets whether or not the GUI object specified by name is exempt from GUI blocking when Python commands are being executed.

BlockGet

bool BlockGet()

Returns whether or not user interaction with the GUI is currently being blocked. User interaction is typically blocked while Python commands and scripts are being executed.

BuilderFocusOnProperties

void BuilderFocusOnProperties()

Displays the Properties tab in the Builder Window.

BuilderFocusOnSketcher

void BuilderFocusOnSketcher()

Displays the Sketcher tab in the Builder Window.

IconGetXPM

std::vector<std::string> IconGetXPM(const std::string &name)

Returns an XPM representation of the icon specified by name.

InterpreterClear

void InterpreterClear()

Clears the contents of the scripting window.

InterpreterPopUpdateGUI

  void InterpreterPopUpdateGUI()

Specifies to the application that the normal interface updating behavior
should occur after issued commands. This function is normally called in
conjunction with
:oe:func:`InterpreterPushUpdateGUI` to
terminate the non-updating behavior triggered by that function. It is
important to note that these functions can be nested.

InterpreterPushUpdateGUI

void InterpreterPushUpdateGUI(bool update)

Specifies to the application whether or not the application should be updating the interface after this function is called. This is normally called to allow multiple commands to be issued in a row without causing an interface update after each individual call. A call to InterpreterPopUpdateGUI will resume the normal updating behavior. It is important to note that these calls can be nested.

InterpreterShowDebugTextGet

bool InterpreterShowDebugTextGet()

Returns whether or not debugging text will be displayed in the scripting window.

InterpreterShowDebugTextSet

void InterpreterShowDebugTextSet(bool show)

Sets whether or not debugging text will be displayed in the scripting window.

InterpreterTimerGet

bool InterpreterTimerGet()

Returns whether or not the application reports the time elapsed after every user entered command.

InterpreterTimerSet

bool InterpreterTimerSet(bool enable)

Sets whether or not the application reports the time elapsed after every user entered command.

InterpreterUpdatesGUI

bool InterpreterUpdatesGUI()

Returns whether or not VIDA is updating the interface after every command is completed.

LayoutCurrentGet

std::string LayoutCurrentGet()

Returns the name of the most recently applied named layout.

LayoutExists

bool LayoutExists(const std::string &name)

Returns whether or not the specified named layout exists.

LayoutGet

std::string LayoutGet(const std::string &name)

Returns a string representation of the specified name layout. The value returned by this function can be used as input to the following functions:

LayoutIcon

std::vector<std::string> LayoutIcon(const std::string &name)

Returns the icon associated with the specified named layout in XPM format.

LayoutLoad

bool LayoutLoad(const std::string &name)

Loads the specified named layout.

LayoutOrganizePrompt

std::string LayoutOrganizePrompt()

Launches the layout organization dialog.

LayoutOverrideOrder

void LayoutOverrideOrder(const std::vector<std::string> &names)

Sets the order to be used when displaying the named layouts in the layout button.

LayoutRemove

bool LayoutRemove(const std::string &name)

Removes the specified named layout.

LayoutRename

bool LayoutRename(const std::string &oldName, const std::string &newName)

Renames the specified named layout.

LayoutSaveCurrent

bool LayoutSaveCurrent(const std::string &name)

Saves the current application’s layout using the specified name.

LayoutSet

void LayoutSet(const std::string &name, const std::string &data)

Creates a named layout using the specified name and layout data. The input for the data parameter can be obtained from AppLayoutGet command.

LayoutStickyGet

bool LayoutStickyGet()

LayoutStickySet

void LayoutStickySet(bool sticky)

Layouts

std::vector<std::string> Layouts()

Returns a list of the available named layouts.

ListWindowCollapseAll

void ListWindowCollapseAll()

Collapses all the visible nodes in the List Window to show only the top-level list entries.

ListWindowCollapseCurrent

void ListWindowCollapseCurrent()

Collapses the currently active list node in the List Window to a single top-level entry.

ListWindowExpandAll

void ListWindowExpandAll()

Expands all the top-level list nodes in the List Window to show their contents.

ListWindowExpandCurrent

void ListWindowExpandCurrent()

Expands the currently active list node in the List Window to show its contents.

ListWindowFirstList

void ListWindowFirstList()

Makes active the first item in the first list.

ListWindowFirstListItem

void ListWindowFirstListItem()

Makes active the first item in the current list.

ListWindowFocusOnOERID

void ListWindowFocusOnOERID(unsigned int id)

Changes the view of the list window to ensure that the specified ID is visible.

ListWindowGetCurrentPos

std::vector<unsigned int> ListWindowGetCurrentPos()

Returns the current active position with the list window. This function is primarily intended for internal use only.

ListWindowHideColumn

void ListWindowHideColumn(unsigned int column)

Hides the specified column from view in the list window.

ListWindowIsVisible

bool ListWindowIsVisible()

Returns whether or not the list window is currently visible.

ListWindowLastList

void ListWindowLastList()

Makes active the first item in the last list.

ListWindowLastListItem

void ListWindowLastListItem()

Makes active the last item in the current list.

ListWindowNavigateChildrenGet

bool ListWindowNavigateChildrenGet()

Returns whether or not to navigate through an object’s children when browsing through the list window.

ListWindowNavigateChildrenSet

void ListWindowNavigateChildrenSet(bool nav)

Sets whether or not to navigate through an object’s children when browsing through the list window.

ListWindowNavigateLeft

void ListWindowNavigateLeft()

Navigate to a new active object as if the user had pressed the left arrow key inside of the list window.

ListWindowNavigateRight

void ListWindowNavigateRight()

Navigate to a new active object as if the user had pressed the right arrow key inside of the list window.

ListWindowNextList

bool ListWindowNextList()

Makes active the first item in the next list.

ListWindowNextListItem

bool ListWindowNextListItem()

Makes active the next item in the current list.

ListWindowPrevList

bool ListWindowPrevList()

Makes active the first item in the previous list.

ListWindowPrevListItem

bool ListWindowPrevListItem()

Makes active the previous item in the current list.

ListWindowRowColoringGet

bool ListWindowRowColoringGet()

Returns whether or not the list window uses an alternating row coloring scheme.

ListWindowRowColoringSet

void ListWindowRowColoringSet(bool on)

Sets whether or not the list window uses an alternating row coloring scheme.

ListWindowSetCurrentPos

void ListWindowSetCurrentPos(std::vector<unsigned int> pos)

Sets the current active position within the list window. This is intended for internal use only.

ListWindowShowColumn

void ListWindowShowColumn(unsigned int column)

Shows the specified column in the list window.

MainWindowScreenshot

bool MainWindowScreenshot(const std::string &filename="")

Captures an image of the current main window and saves that image to the specified file.

MainWindowScreenshotPrompt

bool MainWindowScreenshotPrompt()

Opens a dialog which allows the user to specify multiple parameters regarding the creation of a screenshot of the main window.

Pick

void Pick(unsigned int action, const std::string &source,
          const std::vector<OEPropDB::OEKey> &keys, int replicate)
void Pick(unsigned int action, unsigned int startX, unsigned int startY,
          unsigned int endX, unsigned int endY, unsigned int width,
          unsigned int height)

Picks a small rectangular region on the 3D display specified by the start and end coordinates. This function is primarily intended for internal use.

PickAgain

void PickAgain(unsigned int action)

Repeats the previous Pick action.

PopIgnoreHint

void PopIgnoreHint()

This function, paired with PushIgnoreHint, minimizes application response to the functions called between them. Every PushIgnoreHint must be matched with a PopIgnoreHint and vice versa.

PopupAddButton

std::string PopupAddButton(const std::string &button,
                           const std::string &command, bool showOnce=false)

This function adds a clickable menu entry that runs the specified command to the popup menu. The last optional parameter specifies that this menu entry should only last one show of the popup menu.

PopupAddRadioButton

std::string PopupAddRadioButton(const std::string &button,
                                const std::string &command,
                                const std::string &updateCommand,
                                bool showOnce=false)

This function adds an exclusive clickable menu entry to the popup menu. The last optional parameter specifies that this menu entry should only last one show of the popup menu. It should only be called between PopupBeginRadioGroup and PopupEndRadioGroup.

PopupAddSeparator

std::string PopupAddSeparator(bool once=false, bool conditional=false)

This function adds a non-clickable line menu entry to the popup menu. The last optional parameter specifies that this menu entry should only last one show of the popup menu.

PopupAddSetupFunc

void PopupAddSetupFunc(const std::string &function)

This function specifies a worker function to be called before the popup menu is shown. It is called with no arguments. It is designed to allow context sensitive menu entries to be added to the popup menu.

PopupAddSubmenu

std::string PopupAddSubmenu(const std::string &child, bool showOnce=false)

This function adds a submenu to the popup menu. The last optional parameter specifies that this menu entry should only last one show of the popup menu.

PopupAddToggleButton

std::string PopupAddToggleButton(const std::string &button,
                                 const std::string &command,
                                 const std::string &updateCommand,
                                 bool showOnce=false, bool state=false)

This function adds a clickable menu entry that runs the specified command to the popup menu. The last optional parameter specifies that this menu entry should only last one show of the popup menu. The state of the toggle is passed as either 0 or 1 in the variable OEInternal.MenuVal. The return value of the update command is used to set the state of the toggle. Returning 1 or True from the update function sets the toggle on.

PopupBeginRadioGroup

void PopupBeginRadioGroup()

This function specifies that the following added radio buttons are exclusive.

PopupDisplayName

void PopupDisplayName(const std::string &item, const std::string &display_name)

This function modifies the display name of a popup menu entry.

PopupEnableItem

void PopupEnableItem(const std::string &item, bool enabled)

This function enables or disables the specified popup menu entry.

PopupEnableItemCommand

void PopupEnableItemCommand(const std::string &item,
                            const std::string &command)

This function sets the update command on the given entry in the popup menu.

PopupEndRadioGroup

void PopupEndRadioGroup()

This function ends the radio group begun by PopupBeginRadioGroup.

PopupRemoveAll

void PopupRemoveAll()

This function removes all entries from the popup menu.

PopupRemoveItem

void PopupRemoveItem(const std::string &item)

This function removes the specified entry from the popup menu.

ProgressbarUpdate

bool ProgressbarUpdate(int count, int total)

Updates the application progress bar based on the specified count and total parameters.

PromptAtomicNum

unsigned int PromptAtomicNum(const std::string &caption, unsigned int def=6)

Prompts the user to specify an element from a periodic table dialog.

PromptColor

OEColor PromptColor(const OEColor &deflt=OEColor())

Prompts the user to specify a color.

PromptError

bool PromptError(const std::string &)

This function prompts the user with an error message.

PromptFilename

std::string PromptFilename(const std::string &def="",
                           const std::string &mode="Open",
                           const std::string &type="all",
                           const std::string &msg="")

This function prompts the user for a filename. The parameters specify the default value, whether it should be an ‘Open’ or ‘Save’ dialog, and what kind of file.

PromptFilenames

std::vector<std::string>
  PromptFilenames(const std::vector<std::string> &def=std::vector<std::string>(),
                  const std::string &type="all", const std::string &msg="")

This function prompts the user for a collection of filenames. The parameters specify the default value, whether it should be an ‘Open’ or ‘Save’ dialog, and what kind of files.

PromptFloat

float PromptFloat(const std::string &prompt, float def=0.0f,
                  unsigned int prec=5)

This function prompts the user for a floating point number.

PromptFont

std::string PromptFont()

Prompts the user to specify a desired font.

PromptID

unsigned int PromptID(unsigned int filters=0xF0FF, bool preview=true)
unsigned int PromptID(std::vector<std::string> filterList, bool preview=true)

This function prompts the user for an ID from the currently loaded set.

Unsigned integer filters are an OR’ed combination of the following values.

  • PromptFilter_Molecules
  • PromptFilter_Surfaces
  • PromptFilter_Grids
  • PromptFilter_Lists
  • PromptFilter_Reflections
  • PromptFilter_Selected
  • PromptFilter_Active
  • PromptFilter_Marked
  • PromptFilter_Visible
  • PromptFilter_Unknown
  • PromptFilter_All

String filters are just placed in a list:

  • ‘M’ or ‘m’ for molecules
  • ‘S’ or ‘s’ for surfaces
  • ‘R’ or ‘r’ for reflections
  • ‘G’ or ‘g’ for grids
  • ‘L’ or ‘l’ for lists
  • ‘O’ or ‘o’ for Unknown objects

For example, to prompt for Molecules and Surfaces:

id = PromptID(PromptFilter_Molecules | PromptFilter_Surfaces)

or

id = PromptID([‘M’,’S’])

PromptIDWriteFilters

std::vector<std::string> PromptIDWriteFilters(const std::string &fname)

This function returns the valid types that can be written to the type of file specified by the filename parameter.

PromptIDs

std::vector<unsigned int> PromptIDs(unsigned int filters=0xF0FF,
                                    bool preview=true)
std::vector<unsigned int> PromptIDs(const std::vector<std::string> &filterList,
                                    bool preview=true)

This function prompts the user for several IDs from the currently loaded set.

See PromptID for the list of available filters.

PromptInteger

int PromptInteger(const std::string &msg, int def=0)

This function prompts the user for an integer.

PromptKey

OEPropDB::OEKey PromptKey(unsigned int filters=0xF0FF, bool preview=true)
OEPropDB::OEKey PromptKey(const std::vector<std::string> &filterList,
                          bool preview=true)

This function prompts the user for a key.

See PromptID for the list of available filters.

PromptKeys

std::vector<OEPropDB::OEKey>
  PromptKeys(const std::vector<std::string> &filterList, bool preview=true)
std::vector<OEPropDB::OEKey> PromptKeys(unsigned int filters=0xF0FF,
                                        bool preview=true)

This function prompts the user for a collection of key.

See PromptID for the list of available filters.

PromptMessage

bool PromptMessage(const std::string &msg)

This function alerts the user with a message and an OK button.

PromptModeGet

std::string PromptModeGet()

PromptModeSet

bool PromptModeSet(const std::string &mod)

PromptFragment

std::string PromptMolecule(const std::string &caption)

Prompts the user to input a molecule fragment using the built-in molecule input dialog. Returns a hexadecimal encoded OEB string representation of the fragment. In addition to specifying a molecular fragment, the user will be required to define an attachment point, either by including a dummy atom or a selected atom or bond.

PromptMolecule

std::string PromptMolecule(const std::string &caption,
                           const std::string &def="", unsigned int options=21)

Prompts the user to specify a molecule using the built-in molecule input dialog. Returns a hexadecimal encoded OEB string representation of the molecule.

PromptMoleculeSplit

std::string PromptMoleculeSplit(unsigned int id)

Launches a dialog to assist in the splitting of the specified molecule.

PromptMulti

bool PromptMulti(const std::string &prompt, std::vector<std::string> names,
                 std::vector<std::string> types,
                 std::vector<std::string> defs,
                 std::vector<OEInterpreter::OEMultiTypeVar> &out)

This function prompts the user for several different types of variables and returns them in a list.

PromptQuery

std::string PromptQuery(const std::string &def="")

This function prompts the user for a query string for calls to ListSubsetQuery.

PromptResponseBool

void PromptResponseBool(const std::string &msg, bool v, bool forceInter)

This function pushes a boolean response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseCanceled

void PromptResponseCanceled(const std::string &)

This function pushes a cancel response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseColor

void PromptResponseColor(const std::string &type, const OESystem::OEColor &c,
                         bool forceInteractive)

This function pushes a color response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseFloat

void PromptResponseFloat(const std::string &type, float v, bool forceInter)

This function pushes a floating point response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseInt

void PromptResponseInt(const std::string &type, int v, bool forceInter=false)

This function pushes an integer response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseKey

void PromptResponseKey(const std::string &type, const OEPropDB::OEKey &key,
                       bool forceInteractive=false)

This function pushes a key response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseKeys

void PromptResponseKeys(const std::string &type,
                        std::vector<OEPropDB::OEKey> &keys,
                        bool forceInteractive=false)

This function pushes a collection of keys response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseString

void PromptResponseString(const std::string &type, const std::string &v,
                          bool forceInteractive=false)

This function pushes a string response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseUInt

void PromptResponseUInt(const std::string &type, unsigned int v,
                        bool forceInteractive=false)

This function pushes a positive integer response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseVectInt

void PromptResponseVectInt(const std::string &type,
                           const std::vector<int> &value,
                           bool forceInteractive=false)

This function pushes a list-of-integers response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseVectMulti

void PromptResponseVectMulti(const std::string &type,
                             const std::vector<OEInterpreter::OEMultiTypeVar> &value,
                             bool forceInteractive=false)

PromptResponseVectString

void PromptResponseVectString(const std::string &type,
                              const std::vector<std::string> &value,
                              bool forInteractive=false)

This function pushes a list-of-strings response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptResponseVectUInt

void PromptResponseVectUInt(const std::string &type,
                            const std::vector<unsigned int> &value,
                            bool forceInteractive=false)

This function pushes a list-of-positive-integers response to an upcoming Prompt, allowing it to be skipped in scripts. Ordinarily this function should not need to be called by the user.

PromptSaveFilename

std::string PromptSaveFilename(const std::vector<unsigned int> &ids,
                               const std::string &msg="")
std::string PromptSaveFilename(const std::vector<OEPropDB::OEKey> &keys,
                               const std::string &msg="")
std::vector<std::string> PromptSaveFilename(const std::string &filters,
                                            const std::string &msg="")

This function prompts the user to select a file for saving. The filters parameter allows for specification of filter types to be shown in the file dialog. Individual filters should be separated by a pair of semicolons like this:

“OpenEye OEBinary (.oeb);;All Files (.*)”

The msg parameter allows for specification of the caption of the file dialog. This function returns a list where the first member is the selected filename and the second is the selected filter. If the user cancels the prompt, the returned list will be empty.

See PromptID for the list of available filters.

PromptSmiles

std::string PromptSmiles(const std::string &caption, const std::string &def="",
                         unsigned int options=21)

Prompts the user to specify a molecule using the built-in molecule input dialog. The molecule is returned as a SMILES string.

PromptString

std::string PromptString(const std::string &prompt="",
                         const std::string &def="", bool lineMode=true,
                         bool editable=true)

This function prompts the user for a string.

PromptStringListFromString

void PromptStringListFromString(const std::string &in,
                                std::vector<std::string> &options,
                                unsigned int &def)

This function prompts the user for a string.

PromptStringListToString

std::string PromptStringListToString(const std::vector<std::string> &options,
                                     unsigned int def)
std::string PromptStringListToString(const std::vector<std::string> &options,
                                     const std::string &def)

This function generates a list of strings from a formatted string. Ordinarily this function should not need to be called by the user.

PromptYesNo

bool PromptYesNo(const std::string &prompt, const std::string &key="")
bool PromptYesNo(const std::string &prompt, bool &check,
                 const std::string &key="")

This function prompts the user for a yes or no answer.

PromptYesNoSetDefault

bool PromptYesNoSetDefault(const std::string &key, bool def)

This function prompts the user for a yes or no answer.

PushIgnoreHint

void PushIgnoreHint(bool ignore)

This function delays update actions for the following commands until a PopIgnoreHint is called. PushIgnoreHint and PopIgnoreHints MUST match.

SetProgressbar

void SetProgressbar(int index, int total)

This function sets the progress bar to the specified value.

ToolbarAdd

void ToolbarAdd(const std::vector<std::string> &icon,
                const std::string &command, const std::string &tooltip="",
                const std::string &toolbar="Application",
                const std::string &name="")
void ToolbarAdd(const std::string &text, const std::string &command,
                const std::string &tooltip="",
                const std::string &toolbar="Application",
                const std::string &name="", int margin=5)

Adds a single standard push button to the specified toolbar. The button can be represented by either the passed icon (in XPM format) or the passed text string. The specified command will be executed when the button is pushed.

ToolbarAddAbort

void ToolbarAddAbort(const std::string &toolbar)

Adds an abort button to the specified toolbar.

ToolbarAddCombo

void ToolbarAddCombo(const std::vector<std::string> &choices,
                     const std::vector<std::string> &commands,
                     const std::string &update,
                     const std::string &toolbar="Application",
                     const std::string &name="")

Adds a combo box (a.k.a. dropdown box) with the specified list of options and their associated commands to the specified toolbar. The update parameter contains a command that will be executed to update the widget.

ToolbarAddMenu

void ToolbarAddMenu(const std::vector<std::string> &text,
                    const std::vector<std::string> &command,
                    const std::vector<std::string> &tooltip,
                    const std::string &update,
                    const std::string &toolbar="Application",
                    const std::string &name="", int margin=5)
void ToolbarAddMenu(const std::vector<std::vector<std::string> > &icon,
                    const std::vector<std::string> &text,
                    const std::vector<std::string> &command,
                    const std::vector<std::string> &tooltip,
                    const std::string &update,
                    const std::string &toolbar="Application",
                    const std::string &name="")

Adds a button with a dropdown menu to the toolbar. Each menu item is represented by a name, a Python command, and a tooltip. One implementation also allows specification of an icon for each item. The update parameter contains a command that will be executed to update the button and the associated menu.

ToolbarAddMenuViaNamedIcons

void ToolbarAddMenuViaNamedIcons(const std::vector<std::string> &iconName,
                                 const std::vector<std::string> &text,
                                 const std::vector<std::string> &command,
                                 const std::vector<std::string> &tooltip,
                                 const std::string &update,
                                 const std::string &toolbar="Application",
                                 const std::string &name="")

Adds a button with a dropdown menu to the toolbar. Each menu item is represented by a name, a named icon, a Python command, and a tooltip. The update parameter contains a command that will be executed to update the button and the associated menu.

ToolbarAddSeparator

void ToolbarAddSeparator(const std::string &toolbar="Application")

Adds a separator to the specified toolbar.

ToolbarAddSheet

StyleSheet *ToolbarAddSheet(const std::string &icon,
                            const std::string &toolbar)

Adds a new style sheet to the specified toolbar represented by the specified icon.

ToolbarAddSlider

void ToolbarAddSlider(const std::string &applyCommand,
                      const std::string &getCount, const std::string &getMin,
                      const std::string &getMax, const std::string &getCurrent,
                      const std::string &sliderToVal,
                      const std::string &valToSlider,
                      const std::string &toolbar="Application",
                      const std::string &name="")

Adds a slider bar to the specified toolbar. The applyCommand will be executed whenever the slider bar is changed. The getCount parameter is a command that returns how many things the slider is currently controlling. The getMin, getMax, and getCurrent parameters are commands that will be executed to determine the bounds of the slider. The sliderToVal parameter is a command that converts the slider position to a meaningful value for the applyCommand function. The valToSlider parameter is a command that converts the value returned by getCurrent to a meaningful value to be shown on the slider bar.

ToolbarAddToggle

void ToolbarAddToggle(const std::string &onText, const std::string &offText,
                      const std::string &onCommand,
                      const std::string &offCommand, const std::string &desc,
                      const std::string &update,
                      const std::string &toolbar="Application",
                      const std::string &name="", int margin=5)
void ToolbarAddToggle(const std::vector<std::string> &onIcon,
                      const std::vector<std::string> &offIcon,
                      const std::string &onCommand,
                      const std::string &offCommand, const std::string &desc,
                      const std::string &update,
                      const std::string &toolbar="Application",
                      const std::string &name="")

Adds a single standard toggle button to the specified toolbar. Both on and off icons can be specified as parameters (in XPM format). Commands for both the on and off states can be specified and will be executed when the associated button enters that state.

ToolbarAddToggleViaNamedIcons

void ToolbarAddToggleViaNamedIcons(const std::string &onIconName,
                                   const std::string &ofIconfName,
                                   const std::string &onCommand,
                                   const std::string &offCommand,
                                   const std::string &desc,
                                   const std::string &update,
                                   const std::string &toolbar="Application",
                                   const std::string &name="")

Equivalent to ToolbarAddToggle except that instead of having to pass in an icon pixmaps, icons are specified by name. For a table of available icons, please see the Icons chapter in the main VIDA manual.

ToolbarAddViaNamedIcon

void ToolbarAddViaNamedIcon(const std::string &iconName,
                            const std::string &command,
                            const std::string &tooltip="",
                            const std::string &toolbar="Application",
                            const std::string &name="")

Equivalent to ToolbarAdd except that instead of having to pass in an icon pixmap, the icon is specified by name. For a table of available icons, please see the Icons chapter in the main VIDA manual.

ToolbarBeginRadio

  void ToolbarBeginRadio(const std::string &name,
                         const std::string &toolbar="Application")

Begins a named group of mutually exclusive radio buttons in the specified
toolbar.

ToolbarButtonEnableGet

bool ToolbarButtonEnableGet(const std::string &name,
                            const std::string &toolbar="Application")

Returns whether or not the specified button in the specified toolbar is currently enabled.

ToolbarButtonEnableSet

void ToolbarButtonEnableSet(const std::string &name, bool enabled,
                            const std::string &toolbar="Application")

Sets whether or not the specified button in the specified toolbar is currently enabled.

ToolbarComboAddChoice

bool ToolbarComboAddChoice(const std::string &choice,
                           const std::string &command,
                           const std::string &after,
                           const std::string toolbar="Application",
                           const std::string &combo_name="")

Adds a new option specified by choice to the specified combo box in the specified toolbar. The command parameter contains the Python function to be called when this choice is selected. The after parameter specifies after which other choice this new option should be added.

ToolbarComboClear

bool ToolbarComboClear(const std::string toolbar="Application",
                       const std::string &combo_name="")

Clears the contents of the specified combo box in the specified toolbar.

ToolbarComboRemoveChoice

bool ToolbarComboRemoveChoice(const std::string &choice,
                              const std::string toolbar="Application",
                              const std::string &combo_name="")

Removes the specified choice from the specified combo box in the specified toolbar.

ToolbarCreate

void ToolbarCreate(const std::string &toolbar)

Creates a new toolbar with the specified name.

ToolbarEnabledGet

bool ToolbarEnabledGet(const std::string &toolbar="Application")

Returns whether or not the specified toolbar is currently enabled.

ToolbarEnabledSet

bool ToolbarEnabledSet(bool vis, const std::string &toolbar="Application")

Sets whether or not the specified toolbar is currently enabled.

ToolbarEndRadio

void ToolbarEndRadio(const std::string &name,
                     const std::string &toolbar="Application")

Ends the named group of mutually exclusive radio buttons in the specified toolbar.

ToolbarGetAll

std::vector<std::string> ToolbarGetAll()

Returns a list of all the existing toolbars in VIDA.

ToolbarItemCheckedGet

bool ToolbarItemCheckedGet(const std::string &name, const std::string &toolbar)

Returns whether or not the specified toolbar item in the specified toolbar is currently checked.

ToolbarItemCheckedSet

bool ToolbarItemCheckedSet(bool, const std::string &name,
                           const std::string &toolbar)

Sets whether or not the specified toolbar item in the specified toolbar is currently checked.

ToolbarItemUpdate

void ToolbarItemUpdate(const std::string &name, const std::string &toolbar)

Causes the specified toolbar item in the specified toolbar to update itself.

ToolbarItemVisibleGet

bool ToolbarItemVisibleGet(const std::string &name, const std::string &toolbar)

Returns whether or no the specified toolbar item in the specified toolbar is currently visible.

ToolbarItemVisibleSet

bool ToolbarItemVisibleSet(bool, const std::string &name,
                           const std::string &toolbar)

Sets whether or not the specified toolbar item in the specified toolbar is currently visible.

ToolbarRemove

void ToolbarRemove(const std::string &toolbar)
void ToolbarRemove(const std::string &toolbar, const std::string &name)

Removes the specified toolbar from VIDA. Please not that when a toolbar is removed, it is deleted from the application and not simply hidden.

ToolbarUpdate

void ToolbarUpdate(const std::string &toolbar)

Updates the specified toolbar.

ToolbarVisibleGet

bool ToolbarVisibleGet(const std::string &toolbar="Application")

Returns whether or not the specified toolbar is currently visible.

ToolbarVisibleSet

bool ToolbarVisibleSet(bool vis, const std::string &toolbar="Application")

Sets whether or not the specified toolbar is currently visible.

UpdateStyleWidget

void UpdateStyleWidget()

This function notifies the style widget that it should update itself due to changes that might affect its display.

UpdateUndo

void UpdateUndo()

This function updates the undo menu. Ordinarily this function should not need to be called by the user.

ViewerActiveAnnotation

OEGLTextBox *ViewerActiveAnnotation(int x=-1, int y=-1, int w=-1, int h=-1)

Create the active annotation.

ViewerActiveAnnotationBackgroundColorGet

OESystem::OEColor ViewerActiveAnnotationBackgroundColorGet()

Return the background color for the active annotation.

ViewerActiveAnnotationBackgroundColorSet

void ViewerActiveAnnotationBackgroundColorSet(const OESystem::OEColor &clr)

Set the background color for the active annotation.

ViewerActiveAnnotationClose

void ViewerActiveAnnotationClose()

Close the active annotation window.

ViewerActiveAnnotationFontGet

std::string ViewerActiveAnnotationFontGet()

Return the font used for the active annotation.

ViewerActiveAnnotationFontSet

void ViewerActiveAnnotationFontSet(const std::string &font)

Set the font used for the active annotation. Uses fonts as returned by the PromptFont scripting command.

ViewerActiveAnnotationForegroundColorGet

OESystem::OEColor ViewerActiveAnnotationForegroundColorGet()

Returns the foreground (text) color used in the active annotation.

ViewerActiveAnnotationForegroundColorSet

void ViewerActiveAnnotationForegroundColorSet(const OESystem::OEColor &clr)

Sets the foreground (text) color for the active annotation.

ViewerActiveAnnotationVisible

bool ViewerActiveAnnotationVisible()

Returns whether or not the active annotation is visible.

ViewerActiveDataFontSizeGet

unsigned int ViewerActiveDataFontSizeGet()

Returns the font size for the active data display.

ViewerActiveDataFontSizeSet

void ViewerActiveDataFontSizeSet(unsigned int sz)

Sets the font size for the active data display.

ViewerActiveDataHide

OEGLDataView *ViewerActiveDataHide()

Hides the active data display.

ViewerActiveDataShow

OEGLDataView *ViewerActiveDataShow()
OEGLDataView *ViewerActiveDataShow(int x, int y, int h, int w)

Returns and shows the active data display.

ViewerActiveDataVisible

bool ViewerActiveDataVisible()

Returns whether or not the active data display is currently visible in the 3D display.

ViewerBookmarkWidget

OEGLHList *ViewerBookmarkWidget()

Returns a reference to the bookmark control widget.

ViewerBookmarkWidgetFontSizeGet

unsigned int ViewerBookmarkWidgetFontSizeGet()

Returns the size of the font used in the bookmark control widget.

ViewerBookmarkWidgetFontSizeSet

void ViewerBookmarkWidgetFontSizeSet(unsigned int sz)

Sets the size of the font used in the bookmark control widget.

ViewerBookmarkWidgetHide

OEGLHList *ViewerBookmarkWidgetHide()

Hides the bookmark control widget from the 3D display.

ViewerBookmarkWidgetShow

OEGLHList *ViewerBookmarkWidgetShow()

Shows the bookmark control widget in the 3D display.

ViewerButtonImage

OEGLButton *ViewerButtonImage(const std::string &image,
                              const std::string &callback,
                              int x, int y, int w=-1, int h=-1)

Creates and returns a clickable button in the 3D display. The image parameter specifies the name of the icon to be displayed on the button. The callback parameter specifies the Python function to be executed when the button is clicked on. The position and dimensions of the button are specified by the parameters x, y, w, and h.

ViewerClick

void ViewerClick(int fxn, int x, int y, int gX, int gY, int w, int h)

This function performs an action in the display corresponding to a mouse click event in the 3D display window. Ordinarily, this function should not need to be called by the user.

ViewerCursorSet

void ViewerCursorSet(const std::string &mode)

This function sets the cursor style based on the mode parameter. Valid mode parameters are:

  • arrow - sets the cursor to the standard arrow cursor
  • back diagonal arrow - sets the cursor to a backwards diagonal double-ended arrow
  • blank - sets the cursor to a blank cursor (no cursor will appear)
  • busy - sets the cursor to be a busy indicator (an hourglass on many systems)
  • closed hand - sets the cursor to be a closed hand
  • cross - sets the cursor to two crossed lines
  • double arrow - sets the cursor to two crossed double-ended arrows
  • forbidden - sets the cursor to be a circle with a cross line through it
  • forward diagonal arrow - sets the cursor to a forwards diagonal double-ended arrow
  • horizontal arrow - sets the cursor to a horizontal double-ended arrow
  • ibeam - sets the cursor to an ibeam style cursor
  • open hand - sets the cursor to be an open hand
  • pointing - sets the cursor to be a pointing hand
  • rotation - same as cross
  • split horizontal - sets the cursor to two parallel horizontal lines with perpendicular arrows coming out of each line
  • split vertical - sets the cursor to two parallel vertical lines with perpendicular arrows coming out of each line
  • translation - same as double arrow
  • up arrow - sets the cursor to an upwards point arrow
  • vertical arrow - sets the cursor to a vertical double-ended arrow
  • wait - sets the cursor to a waiting indicator (an hourglass on many systems)
  • whats this - sets the cursor to be an arrow with an adjacent question mark

ViewerDepict

OEGLImage *ViewerDepict(const OEPropDB::OEKey &key, int x, int y, int width,
                        int height)

Creates and returns a depiction widget for the 3D display. The key parameter specifies which molecule to use for the depiction. The position and dimensions of the widget are specified by the x, y, width, and height parameters.

ViewerDepictionAntiAliasGet

bool ViewerDepictionAntiAliasGet()

Returns whether or not the lines used in drawing depictions in the 3D display should be anti-aliased.

ViewerDepictionAntiAliasSet

void ViewerDepictionAntiAliasSet(bool s)

Sets whether or not the lines used in drawing depictions in the 3D display should be anti-aliased.

ViewerDepictionHeightGet

float ViewerDepictionHeightGet()

Returns the percent of the total height of the 3D display that the active depiction display uses when drawing onto the 3D display.

ViewerDepictionLineWidthGet

float ViewerDepictionLineWidthGet()

Returns the width of the lines used in drawing depictions in the 3D display.

ViewerDepictionLineWidthSet

void ViewerDepictionLineWidthSet(float lw)

Sets the width of the lines used in drawing depictions in the 3D display.

ViewerDepictionSizeSet

float ViewerDepictionSizeSet(float percent)
float ViewerDepictionSizeSet(float perc_w, float perc_h)

Sets the percents of the total width and height of the 3D display that the active depiction display uses when drawing onto the 3D display. The perc_w parameter specifies the percent width and the perc_h specifies the percent height.

ViewerDepictionWidthGet

float ViewerDepictionWidthGet()

Returns the percent of the total width of the 3D display that the active depiction display uses when drawing onto the 3D display.

ViewerLabel

OEGLLabel *ViewerLabel(const std::string &message, int x, int y)

Creates and returns a text label which is displayed in the 3D window. The text is specified by the message parameter and the position is specified by the x and y parameters.

ViewerLabelDialog

void ViewerLabelDialog(const std::string &type)

Opens a dialog which allows the user to specify what types of labels to apply to either atoms or bonds.

ViewerMouseClick

void ViewerMouseClick(unsigned int state, unsigned int action)

This function specifies the desired action that should occur when a mouse click event is generated with the associated state. The state parameter specifies which mouse buttons were clicked as well as whether any modifier keys were depressed at the same time. State parameters can be added together to specify complicated states. Valid state parameters are:

  • MouseState_None
  • MouseState_Left
  • MouseState_Middle
  • MouseState_Right
  • MouseState_Shift
  • MouseState_Control
  • MouseState_Alt

Action parameters are distinct and cannot be added together like state parameters. Valid action parameters are:

  • MouseClick_None

  • MouseClick_Menu - creates a context specific popup menu

  • MouseClick_Select - selects the object that was clicked on and clears the

    previous selection

  • MouseClick_SelectAdd - selects the object that was clicked on, but does not

    clear the previous selection

  • MouseClick_SelectGrow - extends the selection of the object that was

    clicked on: atom -> residue -> chain -> mol and clears the previous selection

  • MouseClick_SelectAddGrow - extends the selection of the object that was

    clicked on: atom -> residue -> chain -> mol and clears the previous selection

  • MouseClick_SelectToggle - toggles the selection of the object that was

    clicked on

  • MouseClick_Label - displays a context specific label corresponding to the

    object that was clicked on

ViewerMouseDoubleClick

void ViewerMouseDoubleClick(unsigned int state, unsigned int action)

This function specifies the desired action that should occur when a mouse double-click event is generated with the associated state. The state parameter specifies which mouse buttons were clicked as well as whether any modifier keys were depressed at the same time. State parameters can be added together to specify complicated states. Valid state parameters are:

  • MouseState_None
  • MouseState_Left
  • MouseState_Middle
  • MouseState_Right
  • MouseState_Shift
  • MouseState_Control
  • MouseState_Alt

Action parameters are distinct and cannot be added together like state parameters. Valid action parameters are:

  • MouseClick_None

  • MouseClick_Menu - creates a context specific popup menu

  • MouseClick_Select - selects the object that was clicked on and clears the

    previous selection

  • MouseClick_SelectAdd - selects the object that was clicked on, but does not

    clear the previous selection

  • MouseClick_SelectGrow - extends the selection of the object that was

    clicked on: atom -> residue -> chain -> mol and clears the previous selection

  • MouseClick_SelectAddGrow - extends the selection of the object that was

    clicked on: atom -> residue -> chain -> mol and clears the previous selection

  • MouseClick_SelectToggle - toggles the selection of the object that was

    clicked on

  • MouseClick_Label - displays a context specific label corresponding to the

    object that was clicked on

ViewerMouseFunctionGet

unsigned int ViewerMouseFunctionGet()

Returns the current function of the mouse when used in the 3D display. For more details on the different types of functions, please see the documentation for ViewerMouseFunctionSet.

ViewerMouseFunctionNameGet

std::string ViewerMouseFunctionNameGet(unsigned int)

Returns the name of the specified mouse function.

ViewerMouseFunctionSet

void ViewerMouseFunctionSet(unsigned int action)
void ViewerMouseFunctionSet(const std::string &)

Sets the current function of the mouse when used in the 3D display. Valid functions are:

  • MouseClick_None - this tells the mouse to act according to behaviors specified by the current mouse map (this is the default behavior)
  • MouseClick_Label - this mode causes a detailed information label to appear on the screen regarding whatever is currently under the cursor
  • MouseClick_MeasureAngle - this puts the mouse into angle measurement mode
  • MouseClick_MeasureDistance - this puts the mouse into distance measurement mode
  • MouseClick_MeasureTorsion - this puts the mouse into torsion measurement mode

ViewerMouseMap

void ViewerMouseMap(const std::string &map)

This function sets the current mouse mapping. Valid parameters include:

  • vida
  • afitt
  • coot
  • insight
  • moe
  • o
  • quanta
  • rasmol
  • sybyl
  • maestro

ViewerMouseMove

void ViewerMouseMove(unsigned int state, unsigned int action,
                     unsigned int loc=OEGUI::MouseLocation::Both,
                     unsigned int dir=OEGUI::MouseDirection::Both)

This function specifies the desired action that should occur when a mouse movement event is generated with the associated state, in the specified location, and in the specified direction. The state parameter specifies which mouse buttons were clicked as well as whether any modifier keys were depressed at the same time. State parameters can be added together to specify complicated states. Valid state parameters are:

  • MouseState_None
  • MouseState_Left
  • MouseState_Middle
  • MouseState_Right
  • MouseState_Shift
  • MouseState_Control
  • MouseState_Alt

The location parameter specifies whether the mouse was inside or outside a central circular region in the 3D display. The bounds of this region can be displayed using the ViewerShowTrackballGuideSet scripting command. Valid location parameters are:

  • MouseLocation_None
  • MouseLocation_Inside
  • MouseLocation_Outside
  • MouseLocation_Both

The direction parameter specifies which direction of mouse motion should control the action. Valid direction parameters are:

  • MouseDirection_None
  • MouseDirection_X
  • MouseDirection_Y
  • MouseDirection_Both

Action parameters are distinct and cannot be added together like state parameters. Valid action parameters are:

  • MouseMotion_None

  • MouseMotion_RotateX - rotates the display along the X axis

  • MouseMotion_RotateY - rotates the display along the Y axis

  • MouseMotion_RotateZ - rotates the display along the Z axis

  • MouseMotion_Trackball - rotates the display using a trackball motion

  • MouseMotion_TranslateXY - translates the display along the X and Y axes

  • MouseMotion_TranslateX - translates the display along the X axis

  • MouseMotion_TranslateY - translates the display along the Y axis

  • MouseMotion_TranslateZ - translates the display along the Z axis

  • MouseMotion_Zoom - zooms the display

  • MouseMotion_Clip - controls the position of the far and near clipping

    planes in a mirrored fashion

  • MouseMotion_ClipFar - controls the position of the far clipping plane

  • MouseMotion_ClipNear - controls the position of the near clipping plane

  • MouseMotion_DepthcueBegin - controls the position of the start of the

    depthcueing calculation

  • MouseMotion_DepthcueEnd - controls the position of the end of the

    depthcueing calculation

  • MouseMotion_SelectRect - draws a rectangle on the screen and will select

    the entire contents of that rectangle when the mouse button is released while clearing the previous selection

  • MouseMotion_SelectRectAdd - draws a rectangle on the screen and will select

    the entire contents of that rectangle when the mouse button is released while keeping the previous selection

  • MouseMotion_Label - displays a context specific label containing

    information about whatever object is currently beneath the mouse

  • MouseMotion_Contour - adjusts the contour level of the grid contours in the

    current scope

  • MouseMotion_TextScale - adjusts the size of the text displayed in the 3D

    display

ViewerMouseOutsideAwareGet

bool ViewerMouseOutsideAwareGet()

Returns whether or not the display window recognizes mouse motion along the outside edge of the window as a potentially different action from mouse motion in the interior of the window. Ordinarily, this function should not need to be called by the user.

ViewerMouseOutsideAwareSet

bool ViewerMouseOutsideAwareSet(bool aware)

Sets whether or not the display window recognizes mouse motion along the outside edge of the window as a potentially different action from mouse motion in the interior of the window. Ordinarily, this function should not need to be called by the user.

ViewerMouseReset

void ViewerMouseReset()

Clears the current mouse mapping. Ordinarily, this function should not need to be called by the user. Furthermore, calling this function without rebuilding the mouse map will disable all interaction with the 3D window.

ViewerMouseSensitivityGet

float ViewerMouseSensitivityGet()

Returns the sensitivity of mouse event detection in the 3D window.

ViewerMouseSensitivitySet

float ViewerMouseSensitivitySet(float s)

Sets the sensitivity of mouse event detection in the 3D window.

ViewerMouseWheel

void ViewerMouseWheel(unsigned int state, unsigned int action)

This function specifies the desired action that should occur when a mouse wheel event is generated with the associated state. The state parameter specifies whether any modifier keys were depressed at the same time. State parameters can be added together to specify complicated states. Valid state parameters are:

  • MouseState_None
  • MouseState_Shift
  • MouseState_Control
  • MouseState_Alt

Action parameters are distinct and cannot be added together like state parameters. Valid action parameters are:

  • MouseMotion_None

  • MouseMotion_RotateX - rotates the display along the X axis

  • MouseMotion_RotateY - rotates the display along the Y axis

  • MouseMotion_RotateZ - rotates the display along the Z axis

  • MouseMotion_TranslateX - translates the display along the X axis

  • MouseMotion_TranslateY - translates the display along the Y axis

  • MouseMotion_TranslateZ - translates the display along the Z axis

  • MouseMotion_Zoom - zooms the display

  • MouseMotion_Clip - controls the position of the far and near clipping

    planes in a mirrored fashion

  • MouseMotion_ClipFar - controls the position of the far clipping plane

  • MouseMotion_ClipNear - controls the position of the near clipping plane

  • MouseMotion_DepthcueBegin - controls the position of the start of the

    depthcueing calculation

  • MouseMotion_DepthcueEnd - controls the position of the end of the

    depthcueing calculation

  • MouseMotion_Contour - adjusts the contour level of the grid contours in the

    current scope

  • MouseMotion_TextScale - adjusts the size of the text displayed in the 3D

    display

ViewerMove

void ViewerMove(int fxnX, int fxnY, int x, int y, int oldx, int oldy, int w, int h,
                bool first)

This function performs an action in the display window corresponding to a mouse move event in the 3D display window. Ordinarily, this function should not need to be called by the user.

ViewerPickSurfaceTrianglesGet

bool ViewerPickSurfaceTrianglesGet()

Returns whether or not picking on a surface picks individual triangles as opposed to picking the entire surface. Ordinarily, this function should not need to be called by the user.

ViewerPickSurfaceTrianglesSet

bool ViewerPickSurfaceTrianglesSet(bool enable)

Sets whether or not picking on a surface picks individual triangles as opposed to picking the entire surface. Ordinarily, this function should not need to be called by the user.

ViewerProgress

OEGLProgress *ViewerProgress(const std::string &message)

Creates and returns a progress bar display shown in the 3D window. The message parameter specifies the text associated with the progress bar.

ViewerRemoveWidget

void ViewerRemoveWidget(OEGLWidget *widget, bool update)

This function removes the specified widget from the 3D display. The update parameter specifies whether or not all the other widgets in the 3D display need to be updated as a result of this change.

ViewerTextBox

OEGLTextBox *ViewerTextBox(const OEPropDB::OEKey &key, int x=-1, int y=-1,
                           int w=-1, int h=-1)
OEGLTextBox *ViewerTextBox(const std::string &message, int x=-1, int y=-1,
                           int w=-1, int h=-1)

Creates and returns a text display widget to be shown in the 3D display. The parameter message specifies the current text. The position and dimensions of the widget are specified by the parameters x, y, w, and h.

ViewerUseInertiaGet

bool ViewerUseInertiaGet()

Returns whether or not the 3D display window tracks the inertia of mouse movements and uses that to keep the scene spinning after the mouse button is released.

ViewerUseInertiaSet

bool ViewerUseInertiaSet(bool state)

Sets whether or not the 3D display window tracks the inertia of mouse movements and uses that to keep the scene spinning after the mouse button is released.

ViewerUseKeyMapGet

bool ViewerUseKeyMapGet()

Returns whether or not the viewer is using its own internal key bindings. Ordinarily, this function does not need to be called by the user.

ViewerUseKeyMapSet

bool ViewerUseKeyMapSet(bool state)

Sets whether or not the viewer is using its own internal key bindings. Ordinarily, this function does not need to be called by the user.

ViewerWheel

void ViewerWheel(int fxn, int x, int y, int delta)

This function performs an action in the display window corresponding to a mouse wheel event in the 3D display window. Ordinarily, this function should not need to be called by the user.

ViewerWidgetUpdate

void ViewerWidgetUpdate()

Forces an update of all the display widgets in the 3D display.

WaitBegin

void WaitBegin()

This function sets the application in a waiting state. It is used for long operations. Ordinarily this function should not need to be called by the user.

WaitEnd

void WaitEnd()

This function stops the application in a waiting state. It is used for long operations. Ordinarily this function should not need to be called by the user.

WindowEnabledGet

bool WindowEnabledGet(const std::string &windowName)

Returns whether or not the specified window is enabled for use within VIDA.

WindowEnabledSet

void WindowEnabledSet(const std::string &windowName, bool enabled)

Sets whether or not the specified window is enabled for use within VIDA.

WindowMenuUpdate

void WindowMenuUpdate()

Updates the contents of the main Window menu.

WindowRegisterHotkey

void WindowRegisterHotkey(const std::string &windowName,
                          const std::string &keystroke,
                          const std::string &pyCommand)

Registers the specified keystroke with the associated Python command in the specified window. If this keystroke is detected when the specified window has the application focus, the associated command will be run.

WindowVisibleGet

bool WindowVisibleGet(const std::string &windowName)

Returns whether or not the specified window is currently visible.

WindowVisibleSet

bool WindowVisibleSet(const std::string &windowName, bool visible,
                      const std::string &pos="")

Sets whether or not the specified window is currently visible.

Display Functions

The functions detailed in this section enable the customization of how the application itself as well as the currently loaded objects are displayed.

AnnotationGet

std::string AnnotationGet(const OEPropDB::OEKey &key)

Returns the text annotation associated with the object specified by key.

AnnotationHas

bool AnnotationHas(const OEPropDB::OEKey &key)

Returns whether or not the object specified by key has a text annotation.

AnnotationSet

void AnnotationSet(const OEPropDB::OEKey &key, const std::string &txt,
                   bool notify=true)

Sets a text annotation on the object specified by key containing the text specified by txt. If notify is set to True, VIDA will be notified to update the user interface to reflect this change.

AtomClearColorScoped

void AtomClearColorScoped(unsigned int scope = BestScope)

This function restores the default atom coloring to those atoms within the specified scope.

AtomColorPaletteUpdate

void AtomColorPaletteUpdate()

This function updates the default atom coloring palette based on whether or not the application is using a dark or light colored background scheme. This function is called internally and should not be called by the user.

AtomColorReferenceScoped

void AtomColorReferenceScoped(unsigned int scope = BestScope)

This function provides a quick way to mark a molecule (or set of atoms) as a reference structure. The coloring function that is applied colors all carbon atoms the current application ‘reference’ color (default is green). The ‘reference’ color can be changed in the preferences.

AtomColorResidueScoped

void AtomColorResidueScoped(unsigned int scope = BestScope)

This function provides a quick way to color a molecule (or set of atoms) based on associated residue information. The default coloring that is applied uses the ‘Shapely’ color scheme for coloring residues. The residue colors can be changed in the preferences:

* ALA     Medium Green  [140,255,140]
* GLY     White         [255,255,255]
* LEU     Olive Green   [ 69, 94, 69]
* SER     Medium Orange [255,112, 66]
* VAL     Light Purple  [255,140,255]
* THR     Dark Orange   [184, 76,  0]
* LYS     Royal Blue    [ 71, 71,184]
* ASP     Dark Rose     [160,  0, 66]
* ILE     Dark Green    [  0, 76,  0]
* ASN     Light Salmon  [255,124,112]
* GLU     Dark Brown    [102,  0,  0]
* PRO     Dark Grey     [ 82, 82, 82]
* ARG     Dark Blue     [  0,  0,124]
* PHE     Olive Grey    [ 83, 76, 66]
* GLN     Dark Salmon   [255, 76, 76]
* TYR     Medium Brown  [140,112, 76]
* HIS     Medium Blue   [112,112,255]
* CYS     Medium Yellow [255,255,112]
* MET     Light Brown   [184,160, 66]
* TRP     Olive Brown   [ 79, 70,  0]
* ASX     Medium Purple [255,  0,255]
* GLX     Medium Purple [255,  0,255]
* PCA     Medium Purple [255,  0,255]
* HYP     Medium Purple [255,  0,255]
* A       Light Blue    [160,160,255]
* C       Light Orange  [255,140, 75]
* G       Medium Salmon [255,112,112]
* T       Light Green   [160,255,160]
* Default Medium Purple [255,  0,255]

AtomColorSetScoped

void AtomColorSetScoped(const OESystem::OEColor &color,
                        unsigned int scope = BestScope)
void AtomColorSetScoped(unsigned int element, const OESystem::OEColor &color,
                        unsigned int scope = BestScope)

This function sets the color of the atoms in the specified scope to be the specified color.

AtomDarkColorsGet

bool AtomDarkColorsGet()

Returns whether or not the application is using the atom color palette designed for dark colored backgrounds. Otherwise, the application is using the atom color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.

AtomDarkColorsSet

void AtomDarkColorsSet(bool dark)

Sets whether or not the application is using the atom color palette designed for dark colored backgrounds. Otherwise, the application is using the atom color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.

AtomDefaultColorGet

OESystem::OEColor AtomDefaultColorGet()
OESystem::OEColor AtomDefaultColorGet(unsigned int elem)

Returns the current default atom color. The default atom color is applied to every atom that does not have its own specific default color assigned. Calling this function with the elem parameter returns the specific default color associated with the passed element number (e.g. carbon = 6).

AtomDefaultColorSet

void AtomDefaultColorSet(const OESystem::OEColor &color)
void AtomDefaultColorSet(unsigned int elem, const OESystem::OEColor &color)

Sets the current default atom color. The default atom color is applied to every atom that does not have its own specific default color assigned. Calling this function with the elem parameter sets the specific default color associated with the passed element number (e.g. carbon = 6).

AtomHaloRadiusGet

float AtomHaloRadiusGet()

Returns the current radius of atom selection halo. The atom selection halo is a transparent white surface with the specified radius drawn around the current selected set of atoms. If the DistanceControlsVisibility property is set (see DistanceControlsVisibilitySet/Get functions), only atoms falling within this radius will be displayed.

AtomHaloRadiusSet

float AtomHaloRadiusSet(float radius, bool notify=true)

Sets the current radius of atom selection halo. The atom selection halo is a transparent white surface with the specified radius drawn around the current selected set of atoms. If the DistanceControlsVisibility property is set (see DistanceControlsVisibilitySet/Get functions), only atoms falling within this radius will be displayed.

AtomHydrogenStyleGet

unsigned int AtomHydrogenStyleGet()
unsigned int AtomHydrogenStyleGet(const OEPropDB::OEKey &key)

Returns the current default hydrogen display style - 0 for no hydrogens, 1 for polar hydrogens only, and 2 for all hydrogens.

AtomHydrogenStyleSet

void AtomHydrogenStyleSet(unsigned int style)

Sets the current default hydrogen display style. Valid style parameter values are 0 for no hydrogens, 1 for polar hydrogens only, and 2 for all hydrogens.

AtomHydrogenStyleSetScoped

void AtomHydrogenStyleSetScoped(unsigned int style,
                                unsigned int scope = BestScope)

Sets the hydrogen display style for all the molecules in the specified scope. Valid style parameter values are 0 for no hydrogens, 1 for polar hydrogens only, and 2 for all hydrogens.

AtomLabelDefaultGet

std::string AtomLabelDefaultGet()

Returns the default label displayed on atoms. The default is “None”. See the AtomLabelSetScoped function for more information about label types.

AtomLabelDefaultSet

void AtomLabelDefaultSet(const std::string &label)

Sets the default label displayed on atoms. The default is “None”. See the AtomLabelSetScoped function for more information about label types.

AtomLabelGet

std::string AtomLabelGet(const OEPropDB::OEKey &k)

Returns the current label set on the specified atom.

AtomLabelSet

bool AtomLabelSet(const OEPropDB::OEKey &k, const std::string &label)

Sets the label on the specified atom. The parameter label contains the text of the label and the parameter key specifies which atom this label should apply to. See the AtomLabelSetScoped function for more information about label types.

AtomLabelSetScoped

bool AtomLabelSetScoped(const std::string &label,
                        unsigned int scope = BestScope)

Sets the current label displayed on the atoms in the specified scope. Label types include:

* "none"               or ""
* "index"              or "%i"
* "element"            or "%e"
* "name"               or "%n"
* "type"               or "%t"
* "inttype"            or "%it"
* "implicit hcount"    or "%h"
* "formal charge"      or "%f"
* "partial charge"     or "%p"
* "residue info"       or "%r"
* "degree"             or "%d"
* "ischiral"           or "%c"
* "chirality"          or "%chi"
* "hasstereospecified" or "%sts"
* "symmetry class"     or "%sy"
* "isinring"           or "%rng"
* "oechem idx"         or "%oei"
* "map index"          or "%m"
* "read order"         or "%ro"
* "isotope"            or "%iso"
* "hcount"             or "%h"
* "residue info (ca)"  or "%car"
* "bfactor"            or "%cab"
* "degree"             or "%d"
* "hybrid"             or "%hyb"
* "comment"            or "%cm"
* "%gd(x)" - where x specifies the desired piece of generic data to use as the label

AtomStyleGet

std::string AtomStyleGet()

Returns the default atom style. The default is “small”. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleGetScoped

unsigned int AtomStyleGetScoped(unsigned int scope = BestScope)

Returns the style of the atoms in the specified scope. If there are multiple styles present, the return type is “mixed”. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleLargeGet

std::string AtomStyleLargeGet()

Returns the default atom style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is “none”. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleLargeSet

void AtomStyleLargeSet(unsigned int style)
void AtomStyleLargeSet(const std::string &atomStyle)

Sets the default atom style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. This function accepts either a string or an enumerated representation as its parameter. The default is “none”. For more information on this large molecule atom cutoff, see the MoleculeSizeCutoff function. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleNucleicGet

std::string AtomStyleNucleicGet()

Returns the default atom style for nucleic acids. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

AtomStyleNucleicSet

void AtomStyleNucleicSet(unsigned int style)
void AtomStyleNucleicSet(const std::string &atomStyle)

Sets the default atom style for nucleic acids. This function accepts either a string or an enumerated representation as its parameter. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

AtomStyleProteinGet

std::string AtomStyleProteinGet()

Returns the default atom style for proteins. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

AtomStyleProteinSet

void AtomStyleProteinSet(unsigned int style)
void AtomStyleProteinSet(const std::string &atomStyle)

Sets the default atom style for proteins. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

AtomStyleSet

void AtomStyleSet(unsigned int style)
void AtomStyleSet(const std::string &atomStyle)

Sets the default atom style. This function accepts either a string or an enumerated representation as its parameter. The default is “small”. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleSetScoped

void AtomStyleSetScoped(unsigned int style,
                        unsigned int scope = BestScope)
void AtomStyleSetScoped(const std::string &atomStyle,
                        unsigned int scope = BestScope)

Sets the display style for the specified atoms. This function accepts either a string or an enumerated representation as its parameter. Available atom styles include:

* "small"   atoms are drawn as small sized spheres
* "medium"  atoms are drawn as medium sized spheres
* "large"   atoms are drawn as large sized spheres
* "stars"   atoms are drawn as stars
* "radii"   atoms are drawn as spheres with radii equivalent to their VDW radii
* "none"    atoms are not drawn, but are still considered visible and thus selectable
* "hidden"  atoms are not drawn and are not considered visible and thus are not selectable

AtomStyleToEnum

unsigned int AtomStyleToEnum(const std::string &style)

This function returns the enumerated type associated the specified string atoms style representation. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleToText

std::string AtomStyleToText(unsigned int style)

This function returns the text string associated with the specified enumerated atom style representation. See the AtomStyleSetScoped function for more information about atom styles.

BondBallToStickRatioGet

float BondBallToStickRatioGet()

This function is currently a placeholder for future functionality.

BondBallToStickRatioSet

float BondBallToStickRatioSet(float ballStickRatio)

This function is currently a placeholder for future functionality.

BondClearColorScoped

void BondClearColorScoped(unsigned int scope = BestScope)

This function restores the default bond coloring to those bonds within the specified scope.

BondColorSetScoped

void BondColorSetScoped(const OESystem::OEColor &color,
                        unsigned int scope = BestScope)

This function sets the color of the bonds in the specified scope to be the specified color c.

BondDrawAromaticGet

bool BondDrawAromaticGet(unsigned int id)

Returns whether or not aromatic bonds should be drawn as aromatic or instead in Kekule format for the molecule with the specified id.

BondDrawAromaticSet

bool BondDrawAromaticSet(unsigned int id, bool aromatic)

Sets whether or not aromatic bonds should be drawn as aromatic or instead in kekule format for the molecule with the specified id.

BondHideHydrogenGet

bool BondHideHydrogenGet()

Returns the global property which specifies whether or not explicit hydrogens should be displayed.

BondHideHydrogenSet

bool BondHideHydrogenSet(bool hide)

Sets the global property which specifies whether or not explicit hydrogens should be displayed.

BondHideNonbondedGet

bool BondHideNonbondedGet()

Returns the global property which specifies whether or not explicit non-bonded atoms should be displayed.

BondHideNonbondedSet

bool BondHideNonbondedSet(bool hide)

Sets the global property which specifies whether or not explicit non-bonded atoms should be displayed.

BondLabelDefaultGet

std::string BondLabelDefaultGet()

Returns the default label displayed on bonds. The default is “None”. See the BondLabelSetScoped function for more information about label types.

BondLabelDefaultSet

void BondLabelDefaultSet(const std::string &label)

Sets the default label displayed on bonds. The default is “None”. See the BondLabelSetScoped function for more information about label types.

BondLabelGet

std::string BondLabelGet(const OEPropDB::OEKey &k)

Returns the current label on the specified bond.

BondLabelSet

bool BondLabelSet(const OEPropDB::OEKey &k, const std::string &label)

Sets the label on the specified bond. The parameter label contains the text of the label and the parameter key specifies which bond this label should apply to. See the BondLabelSetScoped function for more information about label types.

BondLabelSetScoped

bool BondLabelSetScoped(const std::string &label,
                        unsigned int scope = BestScope)

Sets the current label displayed on the bonds in the specified scope. Label types include:

* "none"               or ""
* "index"              or "%i"
* "order"              or "%o"
* "length"             or "%l"
* "type"               or "%t"
* "inttype"            or "%it"
* "ischiral"           or "%c"
* "chirality"          or "%chi"
* "hasstereospecified" or "%sts"
* "oechem idx"         or "%oei"
* "%gd(x)" - where x specifies the desired piece of generic data to use as the label

BondLineWidthGet

float BondLineWidthGet()

Returns the line width (in pixels) to be used when drawing bonds in “line” or “wireframe” styles.

BondLineWidthSet

float BondLineWidthSet(float width)
bool BondLineWidthSet(const OEPropDB::OEKey &k, float width)

Sets the line width (in pixels) to be used when drawing bonds in “line” or “wireframe” styles.

BondRadiusGet

float BondRadiusGet()

Returns the radius of the cylinders to be used when drawing bonds in “cylinder” style.

BondRadiusSet

float BondRadiusSet(float radius)
bool BondRadiusSet(const OEPropDB::OEKey &k, float radius)

Sets the radius of the cylinders to be used when drawing bonds in “cylinder” style.

BondShowAromaticGet

bool BondShowAromaticGet()

Returns the global property which specifies whether or not aromatic bonds should be drawn as aromatic or instead in kekule format.

BondShowAromaticSet

bool BondShowAromaticSet(bool show)

Sets the global property which specifies whether or not aromatic bonds should be drawn as aromatic or instead in kekule format.

BondShowDipolarGet

bool BondShowDipolarGet()

Returns the global property which specifies whether or not dipolar bonds should be drawn as directed bonds.

BondShowDipolarSet

bool BondShowDipolarSet(bool show)

Sets the global property which specifies whether or not dipolar bonds should be drawn as directed bonds.

BondShowOrdersGet

bool BondShowOrdersGet()

Returns the global property which specifies whether or not bond orders should be displayed.

BondShowOrdersSet

bool BondShowOrdersSet(bool show)

Sets the global property which specifies whether or not bond orders should be displayed.

BondStyleGet

std::string BondStyleGet()

Returns the default bond style. The default is “cylinders”. See the BondStyleSetScoped function for more information about bond styles.

BondStyleGetScoped

unsigned int BondStyleGetScoped(unsigned int scope = BestScope)

Returns the style of the bonds in the specified scope. If there are multiple styles present, the return type is “mixed”. See the BondStyleSetScoped function for more information about bond styles.

BondStyleLargeGet

std::string BondStyleLargeGet()

Returns the default bond style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is “lines”. See the BondStyleSetScoped function for more information about bond styles.

BondStyleLargeSet

void BondStyleLargeSet(unsigned int style)
void BondStyleLargeSet(const std::string &bondstyle)

Sets the default bond style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. This function accepts either a string or an enumerated representation as its parameter. The default is “lines”. For more information on this large molecule atom cutoff, see the MoleculeSizeCutoff function. See the BondStyleSetScoped function for more information about bond styles.

BondStyleNucleicGet

std::string BondStyleNucleicGet()

Returns the default bond style for nucleic acids. The default is to mirror the large molecule bond style. See the BondStyleLargeSet function for more information about large molecules and see the BondStyleSetScoped function for more information about bond styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

BondStyleNucleicSet

void BondStyleNucleicSet(unsigned int style)
void BondStyleNucleicSet(const std::string &bondstyle)

Sets the default bond style for nucleic acids. This function accepts either a string or an enumerated representation as its parameter. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

BondStyleProteinGet

std::string BondStyleProteinGet()

Returns the default bond style for proteins. The default is to mirror the large molecule bond style. See the BondStyleLargeSet function for more information about large molecules and see the BondStyleSetScoped function for more information about bond styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

BondStyleProteinSet

void BondStyleProteinSet(unsigned int style)
void BondStyleProteinSet(const std::string &bondstyle)

Sets the default bond style for proteins. The default is to mirror the large molecule bond style. See the BondStyleLargeSet function for more information about large molecules and see the BondStyleSetScoped function for more information about bond styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

BondStyleSet

void BondStyleSet(unsigned int style)
void BondStyleSet(const std::string &bondstyle)

Sets the default bond style. This function accepts either a string or an enumerated representation as its parameter. The default is “cylinders”. See the BondStyleSetScoped function for more information about bond styles.

BondStyleSetScoped

void BondStyleSetScoped(unsigned int style,
                        unsigned int scope = BestScope)
void BondStyleSetScoped(const std::string &bondstyle,
                        unsigned int scope = BestScope)

Sets the display style for the specified bonds. This function accepts either a string or an enumerated representation as its parameter. Available bonds styles include:

* "lines"     bonds are drawn as lines
* "cylinders" bonds are drawn as cylinders
* "none"      bonds are not drawn, but are still considered visible and thus selectable
* "hidden"    bonds are not drawn and are not considered visible and thus are not selectable

BondStyleToEnum

unsigned int BondStyleToEnum(const std::string &style)

This function returns the enumerated type associated the specified string bond style representation. See the BondStyleSetScoped function for more information about bond styles.

BondStyleToText

std::string BondStyleToText(unsigned int style)

This function returns the text string associated with the specified enumerated bond style representation. See the BondStyleSetScoped function for more information about bond styles.

BookmarkDelete

bool BookmarkDelete(const std::string &name)

Deletes the bookmark specified by name.

BookmarkExists

bool BookmarkExists(const std::string &name)

Returns whether or not the specified bookmark exists.

BookmarkLoad

bool BookmarkLoad(const std::string &name)

Loads the specified bookmark.

BookmarkMoveDown

bool BookmarkMoveDown(const std::string &name)

Moves the specified bookmark down in the order of the current set of bookmarks.

BookmarkMoveUp

bool BookmarkMoveUp(const std::string &name)

Moves the specified bookmark up in the order of the current set of bookmarks.

BookmarkOrganizeDialog

std::string BookmarkOrganizeDialog(bool exec=false)

Launches an interactive dialog which allows the user to delete, rename, and reorder the current set of bookmarks.

PromptBookmarkAnimationTime

int PromptBookmarkAnimationTime( int originalTime )

Launches an interactive dialog which allows the user to specify the animation duration when transitioning to a selected bookmark. Two options are provided:

* "Use calculated animation time"          automatically calculated using limits on speed of rotation, scaling and translation.
* "Specify animation time in milliseconds" specified by the user.

BookmarkRename

bool BookmarkRename(const std::string &oldName, const std::string &newName)

Changes the name of the bookmark specified by oldName to the name specified by newName.

BookmarkSave

bool BookmarkSave(const std::string &name)

Saves the current state of the application to a named bookmark specified by the parameter name.

Bookmarks

std::vector<std::string> Bookmarks()

Returns a list of the current set of bookmarks.

BookmarksClear

void BookmarksClear()

Clears the current list of bookmarks.

BookmarksLastLoaded

unsigned int BookmarksLastLoaded()

Returns the index (in the order of the current set of bookmarks) of the last bookmark that was loaded.

CATraceRadiusGet

float CATraceRadiusGet()

Returns the global property which specifies the width of CA Traces.

CATraceRadiusSet

float CATraceRadiusSet(float radius)

Sets the global property which specifies the width of CA Traces.

CATraceStyleGet

std::string CATraceStyleGet()
std::string CATraceStyleGet(const OEPropDB::OEKey &k)

Returns the global property which specifies the style in which CA Traces are drawn. Available styles include: “lines” and “cylinders”.

CATraceStyleSet

std::string CATraceStyleSet(const std::string &style)
std::string CATraceStyleSet(const OEPropDB::OEKey &k, const std::string &style)

Sets the global property which specifies the style in which CA Traces are drawn. Available styles include: “lines” and “cylinders”.

CATraceStyleSetScoped

std::string CATraceStyleSetScoped(const std::string &str,
                                  unsigned int scope = BestScope)

Sets the property which specifies the style in which CA Traces are drawn. Available styles include: “lines” and “cylinders”.

CenterSet

void CenterSet(const OEPropDB::OEKey &)
void CenterSet(const std::vector<OEPropDB::OEKey> &)

Sets the center of the scene to be at the center of the object(s) referenced by the specified key(s).

CenterSetScoped

void CenterSetScoped(unsigned int scope)

Scoped version of CenterSet.

ColorGet

OESystem::OEColor ColorGet(const OEPropDB::OEKey &)

Returns the color of the object specified by the OEKey parameter key.

ColorSet

void ColorSet(const OEPropDB::OEKey &, const OESystem::OEColor &)

Sets the color of the object specified by the OEKey parameter key to be the specified color.

ColorSetScoped

void ColorSetScoped(const OESystem::OEColor &,
                    unsigned int scope = BestScope)

Sets the color for all of the objects in the specified scope to be the specified color.

ColorUniqueScoped

void ColorUniqueScoped(unsigned int scope = BestScope)

Assigns a “unique” color to each individual object found in the specified scope. For large numbers of objects in the scope, the colors used may eventually repeat.

ContourAutoCenterGet

bool ContourAutoCenterGet(unsigned int id=0)

Returns whether or not reentrant grids are automatically contoured at the center of the scene.

ContourAutoCenterSet

bool ContourAutoCenterSet(unsigned int id, bool center)

Sets whether or not reentrant grids are automatically contoured at the center of the scene. If this is set to true, translating the center of the scene will cause the grids to be recontoured as the scene moves.

ContourAutoContourGet

bool ContourAutoContourGet()

Returns whether or not reentrant grids are automatically recontoured when the center of the scene is changed.

ContourAutoContourRadiusScaleSet

bool ContourAutoContourRadiusScaleSet(float radius, float scale)

Sets the radius and scale parameters used in determining how to contour a reentrant grid around the center of the scene.

ContourAutoContourSet

void ContourAutoContourSet(bool autocontour)

Sets whether or not reentrant grids are automatically recontoured when the center of the scene is changed.

ContourCenter

std::vector<float> ContourCenter(unsigned int id=0)
std::vector<float> ContourCenter(unsigned int id, std::vector<float>)

Returns the scene center position associated with the specified contour.

ContourColorForIndexGet

OESystem::OEColor ContourColorForIndexGet(unsigned int id, unsigned int index)

Return the color of the grid contour specified by the grid id and contour index.

ContourColorForIndexGetScoped

OESystem::OEColor ContourColorForIndexGetScoped(unsigned int index,
                                                unsigned int scope = BestScope)

Returns the color of the grid contours in the specified scope at contour index index. This color is determined by looking at the first contour found in the specified scope.

ContourColorForIndexSet

OESystem::OEColor ContourColorForIndexSet(unsigned int id, unsigned int index,
                                          const OESystem::OEColor &color)

For grid id set the color of contour index to color.

ContourColorForIndexSetScoped

OESystem::OEColor ContourColorForIndexSetScoped(unsigned int index,
                                                const OESystem::OEColor &color,
                                                unsigned int scope = BestScope)

For all grids in scope set the color of contour index to color.

ContourColorSet

void ContourColorSet(const OEPropDB::OEKey &, const OESystem::OEColor &)

This function sets the color of the contour associated with the specified key.

ContourColorSetScoped

void ContourColorSetScoped(const OESystem::OEColor &,
                           unsigned int scope = BestScope)

This function sets the color of the contours in the specified scope.

ContourDrawAsSurfaceGet

bool ContourDrawAsSurfaceGet(unsigned int id=0)

Returns whether or not the contour should be drawn as a solid surface or as a mesh.

ContourDrawAsSurfaceSet

bool ContourDrawAsSurfaceSet(unsigned int id, bool draw)

Sets whether or not the contour should be drawn as a solid surface or as a mesh.

ContourDrawAsSurfaceSetScoped

void ContourDrawAsSurfaceSetScoped(bool draw,
                                   unsigned int scope = BestScope)

Returns the style of contour drawing for the surfaces in scope; essentially it returns the state of the first grid found in scope.

See ContourDrawAsSurfaceGet.

ContourDrawStyleGet

std::string ContourDrawStyleGet(unsigned int id=0)

If “surface” the contours are drawn as a surface, otherwise the contour is drawn as a mesh.

ContourDrawStyleSet

void ContourDrawStyleSet(unsigned int id, const std::string &)

If set to “surface” the contours are drawn as a surface, otherwise the contour is drawn as a mesh.

ContourDrawStyleSetScoped

void ContourDrawStyleSetScoped(const std::string &style,
                               unsigned int scope = BestScope)

Set the drawstyle to all contours in scope.

ContourEntireGridGet

bool ContourEntireGridGet(unsigned int id=0)

Returns True if grid id is contoured over the whole grid. Returns False if only the portion near the center of the scene is contoured.

ContourEntireGridSet

bool ContourEntireGridSet(unsigned int id, bool entire)

If true contour the entire extent of grid id, otherwise only contour the portion near the center of the drawing scene.

ContourHideIndex

void ContourHideIndex(unsigned int index, bool hide)
void ContourHideIndex(unsigned int id, unsigned int index, bool hide)

This function controls the visibility of the contour specified by the grid id and contour index. If the hide parameter is set to true, the contour is hidden, otherwise the contour is shown.

ContourHideIndexGet

bool ContourHideIndexGet(unsigned int id, unsigned int index)

This function returns whether or not the contour specified by the grid id and contour index is hidden or not.

ContourHideIndexSet

void ContourHideIndexSet(unsigned int index, bool hide)
void ContourHideIndexSet(unsigned int id, unsigned int index, bool hide)

This function controls the visibility of the contour specified by the grid id and contour index. If the hide parameter is set to true, the contour is hidden, otherwise the contour is shown.

ContourLineWidthGet

float ContourLineWidthGet(unsigned int id=0)

Returns the line width for drawing mesh contours.

ContourLineWidthSet

float ContourLineWidthSet(unsigned int id, float rad)

Set the line width to width for drawing mesh contours.

ContourPickIsoSurfacesGet

bool ContourPickIsoSurfacesGet()

Returns whether or not contours are selectable by picking.

ContourPickIsoSurfacesSet

void ContourPickIsoSurfacesSet(bool pickable)

Sets whether or not contours are selectable by picking.

ContourTransparencySet

void ContourTransparencySet(const OEPropDB::OEKey &, unsigned int)

Sets the transparency of the contour associated with the specified key. The transparency is determined by the alpha parameter which corresponds to the color alpha value which can range from 0 (completely transparent) to 255 (completely opaque).

DefaultColorLabelGet

OESystem::OEColor DefaultColorLabelGet()

Returns the default color for a label.

DefaultColorLabelSet

OESystem::OEColor DefaultColorLabelSet(const OESystem::OEColor &)

Returns the default color for a label.

DefaultColorMarkedGet

OESystem::OEColor DefaultColorMarkedGet()

Returns the default color used when displaying marked objects.

DefaultColorMarkedSet

OESystem::OEColor DefaultColorMarkedSet(const OESystem::OEColor &)

Sets the default color used when displaying marked objects.

DefaultColorReferenceGet

OESystem::OEColor DefaultColorReferenceGet()

Returns the default reference molecule color.

DefaultColorReferenceSet

OESystem::OEColor DefaultColorReferenceSet(const OESystem::OEColor &)

Sets the default reference molecule color.

DefaultColorSelectedGet

OESystem::OEColor DefaultColorSelectedGet()

Returns the default selection color.

DefaultColorSelectedSet

OESystem::OEColor DefaultColorSelectedSet(const OESystem::OEColor &)

Sets the default selection color.

DefaultColorTitleGet

OESystem::OEColor DefaultColorTitleGet()

Returns the default title color.

DefaultColorTitleSet

OESystem::OEColor DefaultColorTitleSet(const OESystem::OEColor &)

Sets the default title color.

DefaultMonitorColorGet

OESystem::OEColor DefaultMonitorColorGet()

Returns the default monitor color.

DefaultMonitorColorSet

OESystem::OEColor DefaultMonitorColorSet(const OESystem::OEColor &)

Sets the default monitor color.

DistanceControlsVisibilityGet

bool DistanceControlsVisibilityGet()

Returns whether or not an atom’s or bond’s distance from the selected set will affect its visibility. The distance cutoff is specified by the AtomHaloSet function.

DistanceControlsVisibilitySet

void DistanceControlsVisibilitySet(bool state)

Sets whether or not an atom’s or bond’s distance from the selected set will affect its visibility. The distance cutoff is specified by the AtomHaloSet function.

DrawAtomsAndBondsGet

bool DrawAtomsAndBondsGet()

Returns whether or not the application has drawing of atoms and bonds enabled. Ordinarily, this function should not need to be called by the user.

DrawAtomsAndBondsSet

bool DrawAtomsAndBondsSet(bool draw)

Sets whether or not the application has drawing of atoms and bonds enabled. Ordinarily, this function should not need to be called by the user.

DrawAxesGet

bool DrawAxesGet()

Returns whether or not axes should be drawn in the application’s 3D display.

DrawAxesSet

bool DrawAxesSet(bool draw)

Sets whether or not axes should be drawn in the application’s 3D display.

DrawCATracesGet

bool DrawCATracesGet()
bool DrawCATracesGet(const OEPropDB::OEKey &k)

Returns whether or not the application has drawing of CA Traces enabled. Ordinarily, this function should not need to be called by the user.

DrawCATracesSet

bool DrawCATracesSet(bool draw)
bool DrawCATracesSet(const OEPropDB::OEKey &, bool draw)

Sets whether or not the application has drawing of CA Traces enabled. Ordinarily, this function should not need to be called by the user.

DrawCATracesSetScoped

bool DrawCATracesSetScoped(bool, unsigned int scope = BestScope)

Sets whether or not a CA Trace should be drawn the proteins in the specified scope.

DrawContoursGet

bool DrawContoursGet()

Returns true if the contours are being drawn. Returns false if no contours are being drawn.

DrawContoursSet

bool DrawContoursSet(bool draw)

If draw is true, then draw all contours for each visible grid. Otherwise no contours are drawn.

DrawLabelsGet

bool DrawLabelsGet()

Returns whether or not the application has drawing of labels enabled.

DrawLabelsSet

bool DrawLabelsSet(bool draw)

Sets whether or not the application has drawing of labels enabled.

DrawMatrixGet

bool DrawMatrixGet()

Returns whether or not the application has matrix (or tiled) displays enabled.

DrawMatrixSet

bool DrawMatrixSet(bool draw)

Sets whether or not the application has matrix (or tiled) displays enabled.

DrawRibbonsGet

bool DrawRibbonsGet()
bool DrawRibbonsGet(const OEPropDB::OEKey &k)

Returns whether or not the application has drawing of protein ribbons enabled. Ordinarily, this function should not need to be called by the user.

DrawRibbonsSet

bool DrawRibbonsSet(bool draw)
bool DrawRibbonsSet(const OEPropDB::OEKey &k, bool draw)

Sets whether or not the application has drawing of protein ribbons enabled. Ordinarily, this function should not need to be called by the user.

DrawRibbonsSetScoped

bool DrawRibbonsSetScoped(bool draw,
                          unsigned int scope = BestScope)

Sets whether or not a ribbon display should be shown for the proteins in the specified scope.

DrawSurfacesGet

bool DrawSurfacesGet()

Returns true if surfaces are being drawn, false if not.

DrawSurfacesSet

bool DrawSurfacesSet(bool draw)

If parameter draw if false, surface objects are not drawn. If draw is true surfaces are drawn.

DrawSymmetryGet

bool DrawSymmetryGet()

Returns whether or not the application has drawing of symmetry enabled.

DrawSymmetrySet

bool DrawSymmetrySet(bool draw)

Sets whether or not the application has drawing of symmetry enabled.

DrawTitlesGet

bool DrawTitlesGet()

Returns whether or not the application has drawing of titles enabled.

DrawTitlesSet

bool DrawTitlesSet(bool draw)

Sets whether or not the application has drawing of symmetry enabled.

DrawUnitCellGet

bool DrawUnitCellGet()

Returns whether or not the application has drawing of unit cells enabled.

DrawUnitCellSet

bool DrawUnitCellSet(bool draw)

Sets whether or not the application has drawing of symmetry enabled.

GridDefaultContourColorByIndexGet

OESystem::OEColor GridDefaultContourColorByIndexGet(unsigned int gridType,
                                                    unsigned int index)

Returns the default contour color for contour index for grids of type gridType.

GridDefaultContourColorByIndexSet

void GridDefaultContourColorByIndexSet(unsigned int gridType,
                                       unsigned int index,
                                       const OESystem::OEColor &color)

Set the default contour color for contour index for grids of type gridType.

GridDefaultDrawAsSurfaceGet

bool GridDefaultDrawAsSurfaceGet(unsigned int gridType)

Returns the default drawing style for contours of grid with type gridType.

If true, then the surface is drawn as a solid surface, otherwise the surface is drawn as a mesh.

GridDefaultDrawAsSurfaceSet

void GridDefaultDrawAsSurfaceSet(unsigned int gridType, bool asSurf)

Set the default drawing style asSurf for contours of grid with type gridType.

If asSurf is true, then the surface is drawn as a solid surface, otherwise the surface is drawn as a mesh.

GridShowCornersGet

bool GridShowCornersGet()

Returns true if grid corners are being shown false if not.

Grid corners are indicators of the extent of visible grids. They are useful for displaying uncontoured grids and showing whether grid space and molecules intersect.

GridShowCornersSet

void GridShowCornersSet(bool show)

Set show to true to show grid corners, false if not.

Grid corners are indicators of the extent of visible grids. They are useful for displaying uncontoured grids and showing whether grid space and molecules intersect.

GridShowLastMaskedGrid

unsigned int GridShowLastMaskedGrid(bool show=true)

Reserved for internal use.

HBondAddTarget

void HBondAddTarget(const OEPropDB::OEKey &key)

This function adds the molecule corresponding to the specified key to the list of targets to be considered when displaying hydrogen bonds. Calling this function on a molecule will cause hydrogens to be added to that molecule if they are not already present.

HBondAddTargetsScoped

void HBondAddTargetsScoped(unsigned int scope = BestScope)

This function adds of the molecules in the specified scope to the list of targets to be considered when displaying hydrogen bonds. Calling this function on a molecule will cause hydrogens to be added to that molecule if they are not already present.

HBondClearTargets

void HBondClearTargets()

This function clears the list of molecule targets to be considered when displaying hydrogen bonds.

HBondColorGet

OESystem::OEColor HBondColorGet()

Returns the current color being used when drawing hydrogen bonds.

HBondColorSet

void HBondColorSet(const OESystem::OEColor &)

Sets the color to be used when drawing hydrogen bonds.

HBondRemoveTarget

void HBondRemoveTarget(const OEPropDB::OEKey &key)

This function removes the molecule corresponding to the specified key from the list of molecule targets to be considered when displaying hydrogen bonds.

HBondRemoveTargetsScoped

void HBondRemoveTargetsScoped(unsigned int scope = BestScope)

This function removes all of the molecules in the specified scope from the list of molecule targets to be considered when displaying hydrogen bonds.

HBondShowExternalGet

bool HBondShowExternalGet()

Returns whether or not external hydrogen bonds (those between two separate molecules) should be displayed if present.

HBondShowExternalSet

void HBondShowExternalSet(bool show)

Sets whether or not external hydrogen bonds (those between two separate molecules) should be displayed if present.

HBondShowInternalGet

bool HBondShowInternalGet()

Returns whether or not internal hydrogen bonds should be displayed if present.

HBondShowInternalSet

void HBondShowInternalSet(bool show)

Sets whether or not internal hydrogen bonds should be displayed if present.

HaloColorDefaultGet

OESystem::OEColor HaloColorDefaultGet()

Returns the default color to be used when displaying halos.

HaloColorDefaultSet

void HaloColorDefaultSet(const OESystem::OEColor &c)

Sets the default color to be used when displaying halos.

HaloColorGet

OESystem::OEColor HaloColorGet(const OEPropDB::OEKey &)

Returns the color of the halo associated with the specified atom key.

HaloColorSet

void HaloColorSet(const OEPropDB::OEKey &k, const std::string &)
void HaloColorSet(const OEPropDB::OEKey &k, const OESystem::OEColor &c)

Sets the color of the halo associated with the specified atom key.

HaloColorSetScoped

void HaloColorSetScoped(const std::string &,
                        unsigned int scope = BestScope)
void HaloColorSetScoped(const OESystem::OEColor &,
                        unsigned int scope = BestScope)

Sets the color of the halos associated with the atoms in the specified scope.

HaloRadiusGet

float HaloRadiusGet(const OEPropDB::OEKey &)

Returns the radius of the halo associated with the specified atom key.

HaloRadiusSet

void HaloRadiusSet(const OEPropDB::OEKey &, float)
void HaloRadiusSet(const OEPropDB::OEKey &, const std::string &)

Sets the radius of the halo associated with the specified atom key.

HaloRadiusSetScoped

void HaloRadiusSetScoped(float, unsigned int scope = BestScope)
void HaloRadiusSetScoped(const std::string &,
                         unsigned int scope = BestScope)

Sets the radius of the halos associated with the atoms in the specified scope.

HaloScaleGet

float HaloScaleGet(const OEPropDB::OEKey &)

Returns the scaling factor for the size of the halo associated with the specified atom key.

HaloScaleSet

void HaloScaleSet(const OEPropDB::OEKey &, float)
void HaloScaleSet(const OEPropDB::OEKey &, const std::string &)

Sets the scaling factor for the size of the halo associated with the specified atom key.

HaloScaleSetScoped

void HaloScaleSetScoped(float, unsigned int scope = BestScope)
void HaloScaleSetScoped(const std::string &,
                        unsigned int scope = BestScope)

Sets the scaling factor for the size of the halo associated with the atoms in the specified scope.

HideNoneScoped

void HideNoneScoped(unsigned int scope = BestScope)

Makes visible any hidden atoms or bonds on all the molecules in the specified scope.

HideOthers

void HideOthers(const std::vector<OEPropDB::OEKey> &keys, bool value)

Hides everything except the objects specified by list of keys passed as a parameter to this function.

HideScoped

void HideScoped(bool value, unsigned int scope = BestScope)

Hides everything in the specified scope.

LabelClearColorScoped

void LabelClearColorScoped(unsigned int scope = BestScope)

This function restores the default label coloring to those labels within the specified scope.

LabelClearScoped

void LabelClearScoped(unsigned int scope = BestScope)

Clears the labels on all the atoms and bonds in the specified scope.

LabelColorScoped

void LabelColorScoped(const OESystem::OEColor &c,
                      unsigned int scope = BestScope)

This function sets the color of the labels in the specified scope to be the specified color c.

LabelDefaultColorGet

OESystem::OEColor LabelDefaultColorGet()

This function returns the default color for labels.

LabelDefaultColorSet

void LabelDefaultColorSet(const OESystem::OEColor &c)

This function sets the default color for labels.

LabelFixedSizeGet

bool LabelFixedSizeGet()

Returns whether or not labels are drawn using a fixed size on the screen or whether they scale with zooming of the scene.

LabelFixedSizeSet

void LabelFixedSizeSet(bool fixed)

Sets whether or not labels are drawn using a fixed size on the screen or whether they scale with zooming of the scene.

LabelGet

std::string LabelGet(const OEPropDB::OEKey &key, bool full=false,
                     bool coords=true)

Returns a description of the specified object. If the full parameter is True, it will also include information from the parent object (if one exists). The coords parameter specifies whether or not coordinates should be included in the description (primarily for atoms and vertices).

MoleculeAltLocationShow

bool MoleculeAltLocationShow(const OEPropDB::OEKey &, unsigned int, bool)
bool MoleculeAltLocationShow(const OEPropDB::OEKey &, unsigned int, unsigned int,
                             unsigned int)

Sets the visibility of the specified alternate locations for the specified molecule. This function is primarily intended for internal use only.

MoleculeAltLocationVisible

bool MoleculeAltLocationVisible(const OEPropDB::OEKey &, unsigned int)
bool MoleculeAltLocationVisible(const OEPropDB::OEKey &, unsigned int,
                                unsigned int)

Returns whether or the specified alternate locations on the specified molecule are visible. This function is primarily intended for internal use only.

MoleculeAtomBondStyleSetScoped

void MoleculeAtomBondStyleSetScoped(const std::string &atomStyle,
                                    const std::string &bondStyle,
                                    unsigned int scope = BestScope)

Set the combined style for atoms and bonds.

  • atomStyle is the style to set the atom , see AtomStyleSetScoped.
  • bondStyle is the style to set the bond, see BondStyleSetScoped.
  • scope is the default scope to use.

MoleculeColorByScoped

void MoleculeColorByScoped(const std::string &property,
                           const std::string &params="",
                           unsigned int scope = BestScope)

This color colors all the molecules in the specified scope according to the scheme specified by the property parameter. Valid properties include:

* "amino"
* "bfactor"
* "chain"
* "charge"
* "cpk"
* "cpknew"
* "formal charge"
* "group"
* "hbond"
* "hydrophobicity"
* "partial charge"
* "shapely"

If the specified property is hydrophobicity, the specific scale to be used can be specified in the params parameter. Valid scale options include:

* "charifson"
* "eisenberg"
* "kytedolittle"
* "whiteoctanol"

For more details on the specifics of these coloring scheme, please see the user manual.

MoleculeColorsResetScoped

void MoleculeColorsResetScoped(unsigned int scope = BestScope)

This function restores the default atom and bond coloring to those atoms and bonds in the specified scope. It is essentially equivalent to calling AtomClearColorScoped followed by BondClearColorScoped.

MoleculeDarkColorsGet

bool MoleculeDarkColorsGet()

Returns whether or not the application is using either the atom or residue color palette designed for dark colored backgrounds. Otherwise, the application is using the atom color palettes designed for light colored backgrounds. All of these palettes can be edited in the preferences. For more information, see the functions AtomDarkColorsGet and ResidueDarkColorsGet.

MoleculeDarkColorsSet

void MoleculeDarkColorsSet(bool dark)

Sets whether or not the application is using the atom and residue color palettes designed for dark colored backgrounds. Otherwise, the application is using the atom color palettes designed for light colored backgrounds. All of these palettes can be edited in the preferences. For more information, see the functions AtomDarkColorsSet and ResidueDarkColorsSet.

MoleculeShowfAntsyGet

bool MoleculeShowfAntsyGet()

Returns whether or not the application is using the high quality molecule representations as opposed to standard models.

MoleculeShowfAntsySet

bool MoleculeShowfAntsySet(bool show)

Sets whether or not the application is using the high quality molecule representations as opposed to standard models.

MoleculeStyleGet

std::string MoleculeStyleGet()

Returns the default molecule style. The default is “stick”. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleGetScoped

unsigned int
  MoleculeStyleGetScoped(unsigned int scope = BestScope)

Returns the style of the molecules in the specified scope. If there are multiple styles present, the return type is “mixed”. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleLargeGet

std::string MoleculeStyleLargeGet()

Returns the default molecule style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is “wireframe”. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleLargeSet

void MoleculeStyleLargeSet(unsigned int style)
void MoleculeStyleLargeSet(const std::string &style)

Sets the default molecule style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is “wireframe”. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleNucleicGet

std::string MoleculeStyleNucleicGet()

Returns the default molecule style for nucleic acids. The default is to mirror the large molecule style. See the MoleculeStyleLargeSet function for more information about large molecules and see the MoleculeStyleSetScoped function for more information about molecule styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

MoleculeStyleNucleicSet

void MoleculeStyleNucleicSet(unsigned int style)
void MoleculeStyleNucleicSet(const std::string &style)

Sets the default molecule style for nucleic acids. The default is to mirror the large molecule style. See the MoleculeStyleLargeSet function for more information about large molecules and see the MoleculeStyleSetScoped function for more information about molecule styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

MoleculeStyleProteinGet

std::string MoleculeStyleProteinGet()

Returns the default molecule style for proteins. The default is to mirror the large molecule style. See the MoleculeStyleLargeSet function for more information about large molecules and see the MoleculeStyleSetScoped function for more information about molecule styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

MoleculeStyleProteinSet

void MoleculeStyleProteinSet(unsigned int style)
void MoleculeStyleProteinSet(const std::string &style)

Sets the default molecule style for proteins. The default is to mirror the large molecule style. See the MoleculeStyleLargeSet function for more information about large molecules and see the MoleculeStyleSetScoped function for more information about molecule styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

MoleculeStyleSet

void MoleculeStyleSet(unsigned int style)
void MoleculeStyleSet(const std::string &atomStyle)

Sets the default molecule style. This function accepts either a string or an enumerated representation as its parameter. The default is “stick”. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleSetScoped

void MoleculeStyleSetScoped(unsigned int style,
                            unsigned int scope = BestScope)
void MoleculeStyleSetScoped(const std::string &atomStyle,
                            unsigned int scope = BestScope)

Sets the display style for the specified molecules. This function accepts either a string or an enumerated representation as its parameter. Available molecule styles include:

* "ball and stick" molecules are drawn in ball and stick mode
* "cpk"            molecules are drawn in CPK mode
* "stars"          molecules are drawn in star mode
* "stick"          molecules are drawn in stick mode
* "wireframe"      molecules are drawn in wireframe mode
* "none"           molecules are not drawn, but are still considered visible and thus selectable
* "hidden"         molecules are not drawn and are not considered visible and thus are not selectable

MoleculeStyleToEnum

unsigned int MoleculeStyleToEnum(const std::string &style)

This function returns the enumerated type associated the specified string molecule style representation. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleToText

std::string MoleculeStyleToText(unsigned int style)

This function returns the text string associated with the specified enumerated molecule style representation. See the MolStyleSetScoped function for more information about molecule styles.

MonitorAngleCreate

unsigned int MonitorAngleCreate(const OEPropDB::OEKey &key1,
                                const OEPropDB::OEKey &key2,
                                const OEPropDB::OEKey &key3)

Attempts to create an angle monitor between the atoms specified by the parameters key1, key2, and key3.

Returns the ID of the created monitor or 0 if one could not be created.

MonitorAngleDelete

void MonitorAngleDelete(const OEPropDB::OEKey &key1,
                        const OEPropDB::OEKey &key2,
                        const OEPropDB::OEKey &key3)

Deletes the monitor, if any, specified by atom keys: key1, key2, key3.

MonitorAngleExists

unsigned int MonitorAngleExists(const OEPropDB::OEKey &key1,
                                const OEPropDB::OEKey &key2,
                                const OEPropDB::OEKey &key3)

Returns the ID of the angle monitor defined by the specified atom keys or zero if no such monitor exists.

MonitorColorGet

OESystem::OEColor MonitorColorGet(const OEPropDB::OEKey &monitor)

Returns the color of the specified monitor.

MonitorColorSet

void MonitorColorSet(const OEPropDB::OEKey &monitor,
                     const OESystem::OEColor &clr)

Sets the color of the specified monitor.

MonitorDeleteScoped

void MonitorDeleteScoped(unsigned int scope = BestScope)

Deletes all the monitors in the specified scope.

MonitorDistanceCreate

unsigned int MonitorDistanceCreate(const OEPropDB::OEKey &key1,
                                   const OEPropDB::OEKey &key2)

Attempts to create a distance monitor between the two atoms specified by the parameters key1 and key2.

Returns the ID of the created monitor or 0 if one could not be created.

MonitorDistanceDelete

void MonitorDistanceDelete(const OEPropDB::OEKey &key1,
                           const OEPropDB::OEKey &key2)

Deletes the monitor specified by the two atom keys.

MonitorDistanceExists

unsigned int MonitorDistanceExists(const OEPropDB::OEKey &key1,
                                   const OEPropDB::OEKey &key2)

Returns the ID of the distance monitor determined by the two atom keys or zero if no such monitor exists.

MonitorSphereCreate

unsigned int MonitorSphereCreate(const OEPropDB::OEKey &key1,
                                 const std::string &name,
                                 const OESystem::OEColor &clr, float radius=0)
unsigned int MonitorSphereCreate(const OEPropDB::OEKey &parent,
                                 const std::string &name, float x, float y,
                                 float z, float radius,
                                 const OESystem::OEColor &color)

Create a sphere monitor on an atom specified by key1 or at the coordinates specified by x, y, and z. The monitor is only visible when the specified atom key or parent key (in the case of coordinate specification) is visible.

Returns the ID of the newly created monitor or 0 if one could not be created.

MonitorTorsionCreate

unsigned int MonitorTorsionCreate(const OEPropDB::OEKey &key1,
                                  const OEPropDB::OEKey &key2,
                                  const OEPropDB::OEKey &key3,
                                  const OEPropDB::OEKey &key4)

Attempts to create a torsion monitor between the atoms specified by key1, key2, key3, and key4.

Returns the ID of the created monitor or 0 if one could not be created.

MonitorTorsionDelete

void MonitorTorsionDelete(const OEPropDB::OEKey &key1,
                          const OEPropDB::OEKey &key2,
                          const OEPropDB::OEKey &key3,
                          const OEPropDB::OEKey &key4)

Deletes the torsion monitor, if any, specified by the atom keys: key1, key2, key3, key4.

MonitorTorsionExists

unsigned int MonitorTorsionExists(const OEPropDB::OEKey &key1,
                                  const OEPropDB::OEKey &key2,
                                  const OEPropDB::OEKey &key3,
                                  const OEPropDB::OEKey &key4)

Returns the ID of the torsion monitor determined by the specified four atom keys or zero if no such monitor exists.

MonitorsVisible

bool MonitorsVisible()

This function returns whether any monitors are currently visible.

MonitorsVisibleDelete

void MonitorsVisibleDelete()

Deletes all monitors that are currently being displayed.

PaneActivated

void PaneActivated(unsigned int pane)

In matrix (tiled) mode, sets the specified pane to be the active pane in the display. Ordinarily, this function should not need to be called by the user.

ProteinColorByBFactor

void ProteinColorByBFactor(const OEPropDB::OEKey &key)

Colors a protein referenced by key. Atoms with the lowest temperature factors will be colored bright blue, while those with the highest will be colored bright red.

ProteinColorByBFactorScoped

void ProteinColorByBFactorScoped(unsigned int scope, int bins=10)
void ProteinColorByBFactorScoped(unsigned int scope,
                                 const std::vector<BFactorColor> &clrs)
void ProteinColorByBFactorScoped(unsigned int scope, float min, float max,
                                 const OESystem::OEColor &clr)

Scoped versions of ProteinColorByBFactor.

ResidueColorPaletteUpdate

void ResidueColorPaletteUpdate()

This function updates the default residue coloring palette based on whether or not the application is using a dark or light colored background scheme. This function is called internally and should not by called by the user.

ResidueDarkColorsGet

bool ResidueDarkColorsGet()

Returns whether or not the application is using the residue color palette designed for dark colored backgrounds. Otherwise, the application is using the residue color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.

ResidueDarkColorsSet

void ResidueDarkColorsSet(bool dark)

Sets whether or not the application is using the residue color palette designed for dark colored backgrounds. Otherwise, the application is using the residue color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.

ResidueDefaultColorGet

OESystem::OEColor ResidueDefaultColorGet()
OESystem::OEColor ResidueDefaultColorGet(unsigned int res)

Returns the current default residue color. The default residue color is applied to every residue that does not have its own specific default color assigned. Calling this function with the res parameter returns the specific default color associated with the passed residue index.

ResidueDefaultColorSet

void ResidueDefaultColorSet(const OESystem::OEColor &c)
void ResidueDefaultColorSet(unsigned int res, const OESystem::OEColor &c)

Sets the current default residue color. The default residue color is applied to every residue that does not have its own specific default color assigned. Calling this function with the res parameter sets the specific default color associated with the passed residue index.

RibbonClearColorScoped

void RibbonClearColorScoped(unsigned int scope = BestScope)

This function restores the default ribbon coloring to those ribbons within the specified scope.

RibbonColorSetScoped

void RibbonColorSetScoped(const OESystem::OEColor &c,
                          unsigned int scope = BestScope)

This function sets the color of the ribbons in the specified scope to be the specified color c.

RibbonCrossResolutionGet

unsigned int RibbonCrossResolutionGet()

Returns the cross resolution used in calculating protein ribbons.

RibbonCrossResolutionSet

unsigned int RibbonCrossResolutionSet(unsigned int res)

Sets the cross resolution used in calculating protein ribbons.

RibbonGapGet

float RibbonGapGet()

Returns the gap value used in calculating protein ribbons.

RibbonGapSet

float RibbonGapSet(float gap)

Sets the gap value used in calculating protein ribbons.

RibbonHeightScaleGet

float RibbonHeightScaleGet()

Returns the height scale used in calculating protein ribbons.

RibbonHeightScaleSet

float RibbonHeightScaleSet(float scale)

Sets the height scale used in calculating protein ribbons.

RibbonRadiusGet

float RibbonRadiusGet()

Returns the radius used in calculating protein ribbons.

RibbonRadiusSet

float RibbonRadiusSet(float radius)

Sets the radius used in calculating protein ribbons.

RibbonResolutionGet

unsigned int RibbonResolutionGet()

Returns the resolution used in calculating protein ribbons.

RibbonResolutionSet

unsigned int RibbonResolutionSet(unsigned int res)

Sets the resolution used in calculating protein ribbons.

RibbonSplineTypeGet

std::string RibbonSplineTypeGet()

Returns the spline type used in calculating protein ribbons. Available types include: “CubicHermite” and “Beta”.

RibbonSplineTypeSet

std::string RibbonSplineTypeSet(const std::string &type)

Sets the spline type used in calculating protein ribbons. Available types include: “CubicHermite” and “Beta”.

RibbonStyleGet

std::string RibbonStyleGet()

Returns the style used in displaying protein ribbons. Available types include: “Round”, “Lines”, and “Cartoon”. The default is “Cartoon”.

RibbonStyleSet

std::string RibbonStyleSet(const std::string &style)
std::string RibbonStyleSet(const OEPropDB::OEKey &k, const std::string &style)

Sets the style used in displaying protein ribbons. Available types include: “Round”, “Lines”, and “Cartoon”. The default is “Cartoon”.

RibbonStyleSetScoped

std::string RibbonStyleSetScoped(const std::string &style,
                                 unsigned int scope = BestScope)

Sets the style used in displaying ribbons for the proteins in the specified scope. Available types include: “Round”, “Lines”, and “Cartoon”. The default is “Cartoon”.

RibbonWidthScaleGet

float RibbonWidthScaleGet()

Returns the width scale used in calculating protein ribbons.

RibbonWidthScaleSet

float RibbonWidthScaleSet(float scale)

Sets the width scale used in calculating protein ribbons.

SceneDrawActiveBorderGet

bool SceneDrawActiveBorderGet()

Returns whether or not a border is drawn (in matrix mode) around the cell containing the focused object.

SceneDrawActiveBorderSet

void SceneDrawActiveBorderSet(bool draw)

Sets whether or not a border is drawn (in matrix mode) around the cell containing the focused object.

SceneMatrixModeGet

std::string SceneMatrixModeGet()

Returns the display style for the individual cells when the application is in matrix mode. Available styles are: “OnePerView”, “LockedOnAll”, and “LockedPerView”.

SceneMatrixModeSet

std::string SceneMatrixModeSet(std::string mode)

Sets the display style for the individual cells when the application is in matrix mode. Available styles are: “OnePerView”, “LockedOnAll”, and “LockedPerView”.

SelectionColorBlendFactorGet

float SelectionColorBlendFactorGet()

Returns the alpha buffer coloring blending factor for selection colors. The default value is 1.0 which corresponds to zero blending with the selection color being the one displayed. A value of 0.0 also corresponds to zero blending but with the underlying color being the one displayed. A value of 0.5 corresponds to even blending of the underlying color and the selected color.

SelectionColorBlendFactorSet

float SelectionColorBlendFactorSet(float alpha)

Sets the alpha buffer coloring blending factor for selection colors. The default value is 1.0 which corresponds to zero blending with the selection color being the one displayed. A value of 0.0 also corresponds to zero blending but with the underlying color being the one displayed. A value of 0.5 corresponds to even blending of the underlying color and the selected color.

ShowESGridScoped

void ShowESGridScoped(bool show=true,
                      unsigned int scope = BestScope)

If show is true, attach and show electrostatic grids to all molecules in scope.

If show if false, hide all attached electrostatic grids to molecules in scope.

ShowSurface

void ShowSurface(const OEPropDB::OEKey &, const std::string &, bool show)

Sets whether or not a property surface of the specified type is displayed for the molecule associated with the specified key. Valid types are “molecular” and “accessible”.

ShowSurfaceScoped

void ShowSurfaceScoped(const std::string &type, bool show,
                       unsigned int scope = BestScope)

Scoped version of ShowSurface.

SurfaceAlterTransparency

void SurfaceAlterTransparency(unsigned int id, unsigned int alpha)

Sets the transparency of the surface associated with the specified id. The transparency is specified by the alpha parameter which determines the alpha component of the surface color. The alpha values ranges from 0 (completely transparent) to 255 (completely opaque).

SurfaceColorBy

std::string SurfaceColorBy(const std::string &mode="")
void SurfaceColorBy(const OEPropDB::OEKey &key, const std::string &mode,
                    const std::string &params="")

This function colors the surface referenced by the specified key using the specified style. Valid styles include:

  • atom - colors the surface based on the color of the nearest atom to the

    vertex being colored

  • concavity - colors the surface by concavity, red is high concavity.

  • curvature - colors the surface by curvature, green is positive curvature.

  • distance - colors the surface by its distance to the currently selected atoms.

    Each color band represents two angstroms.

  • electrostatics - colors the surface using a red-to-blue scheme based on the

    electrostatic potential observed at the surface.

  • hydrogen bonds - colors the surface by the underlying atom hydrogen-bond

    donor/acceptor properties. Donors are red and acceptors are blue.

  • hydrophobicity - colors the surface using a hydrophobic color scale. There

    are four different hydrophobic scales available: charifson, eisenberg, kytedolittle, and whiteoctanol. The desired scale can be set in the application preferences.

  • potential - colors the surface based using a red-to-blue scheme (low to high)

    over the values in the surface’s potential array. This is not the same as coloring by electrostatics.

SurfaceColorByScoped

void SurfaceColorByScoped(const std::string &colorby,
                          const std::string &params="",
                          unsigned int scope = BestScope)

Scoped version of SurfaceColorBy.

SurfaceColorGet

OESystem::OEColor SurfaceColorGet(unsigned int id)

Returns the color of the specified surface.

SurfaceColorGetScoped

OESystem::OEColor
  SurfaceColorGetScoped(unsigned int scope = BestScope)

Returns the color of the first surface found in the specified scope.

SurfaceColorSet

OESystem::OEColor SurfaceColorSet(unsigned int id,
                                  const OESystem::OEColor &color)

Set the color of the surface id to color.

SurfaceColorSetScoped

void SurfaceColorSetScoped(const OESystem::OEColor &color,
                           unsigned int scope = BestScope)

Set the color of the surfaces in scope to color.

SurfaceGrowTriangle

void SurfaceGrowTriangle(unsigned int oerid, const OEPropDB::OEKey &trikey,
                         bool addtriangle=false)

Grow the surface selection when a triangle is double clicked. Ordinarily this function does not need to be called.

SurfaceLineWidthGet

float SurfaceLineWidthGet(unsigned int id=0)

Returns the line width used when drawing the surface specified by id in mesh mode.

SurfaceLineWidthSet

float SurfaceLineWidthSet(unsigned int id, float width)

Sets the line width used when drawing the surface specified by id in mesh mode.

SurfaceStyleGet

std::string SurfaceStyleGet(unsigned int id)

Returns the default style of surfaces. The style is one of:

  • mesh - the surfaces are drawn as meshes.
  • points - the surfaces are drawn as points.
  • solid - the surfaces are drawn as solid objects.

SurfaceStyleGetScoped

std::string SurfaceStyleGetScoped(unsigned int scope = BestScope)

Return the style for the surfaces in scope. The value returned is from the first surface found in scope and is not indicative of all surfaces.

See SurfaceStyleGet for a list of surface styles.

SurfaceStyleSet

std::string SurfaceStyleSet(unsigned int id, const std::string &style)

Set the surface id to on of the following styles:

  • mesh - the surface is drawn as a mesh.
  • points - the surface is drawn as points.
  • solid - the surface is drawn as a solid object.

SurfaceStyleSetScoped

void SurfaceStyleSetScoped(const std::string &style,
                           unsigned int scope = BestScope)

Scoped version of SurfaceStyleSet.

SurfaceTransparencySet

void SurfaceTransparencySet(unsigned int id, unsigned int alpha)

Set the transparency to all surfaces in scope to transparency.

SurfaceTransparencySetScoped

void SurfaceTransparencySetScoped(unsigned int transparency,
                                  unsigned int scope = BestScope)

Set the transparency to all surfaces in scope to transparency.

SurfaceVertexFloodScoped

int SurfaceVertexFloodScoped(unsigned int scope = BestScope)

Get the surface vertex flood of all surfaces in scope. This is essentially the flood of the focused surface or the surface of the focused or first visible molecule.

SymmetryColorModeGet

unsigned int SymmetryColorModeGet()

SymmetryColorModeSet

unsigned int SymmetryColorModeSet(unsigned int mode)

TitleDefaultColorGet

OESystem::OEColor TitleDefaultColorGet()

Returns the default color for titles.

TitleDefaultColorSet

void TitleDefaultColorSet(const OESystem::OEColor &c)

Sets the default color for titles.

TitlesDrawAboveGet

bool TitlesDrawAboveGet()

Returns whether or not titles are drawn at the top of the scene or the bottom of the scene.

TitlesDrawAboveSet

void TitlesDrawAboveSet(bool top)

Sets whether or not titles are drawn at the top of the scene or the bottom of the scene.

TransparencySet

void TransparencySet(const OEPropDB::OEKey &, unsigned int alpha)

This function sets the transparency of the object associated with the specified key. The transparency is determined by the specified parameter alpha which corresponds to the desired alpha value of the object’s color. Alpha can range from 0 (completely transparent) to 255 (completely opaque).

TransparencySetScoped

void TransparencySetScoped(unsigned int alpha,
                           unsigned int scope = BestScope)

This function sets the transparency of all the objects in the specified scope. The transparency is determined by the specified parameter alpha which corresponds to the desired alpha value of the object’s color. Alpha can range from 0 (completely transparent) to 255 (completely opaque).

ViewerAmbientLightGet

OESystem::OEColor ViewerAmbientLightGet()

Returns the OpenGL ambient light property.

ViewerAmbientLightSet

OESystem::OEColor ViewerAmbientLightSet(const OESystem::OEColor &color)

Sets the OpenGL ambient light property.

ViewerAmbientMaterialGet

OESystem::OEColor ViewerAmbientMaterialGet()

Returns the OpenGL ambient material property.

ViewerAmbientMaterialSet

OESystem::OEColor ViewerAmbientMaterialSet(const OESystem::OEColor &color)

Sets the OpenGL ambient material property.

ViewerAnimate

void ViewerAnimate(const std::vector<float> &centers,
                   const std::vector<float> &look,
                   const std::vector<float> &up,
                   unsigned int              msec,
                   unsigned int              fps)

Reserved for future use.

ViewerAnimateTo

void ViewerAnimateTo( const std::string &bookmark,
                      unsigned int       msec,
                      unsigned int       fps)
void ViewerAnimateTo( const OEPropDB::OEKey &centerKey,
                      const OEPropDB::OEKey &refKey,
                      unsigned int           msec,
                      unsigned int           fps,
                      float                  zoom = 0.0 )
void ViewerAnimateTo( const std::vector<float> &center,
                      const std::vector<float> &look,
                      const std::vector<float> &up,
                      unsigned int              msec,
                      unsigned int              fps,
                      float                     zoom = 0.0 )

Animates the scene from the current position to the specified position. All implementations of this function take an msec and fps parameters. The msec parameter specifies how long it should take the animation to be performed. Please note that this time is only a suggestion, as many factors including CPU speed, GPU speed, and available memory will influence the actual performance of the animation. The fps parameters specifies how many frames per second should be used in the animation.

The first implementation takes a bookmark name as its only other parameter. The second implementation takes two OEKey parameters corresponding to the desired final center and viewing point positions for the scene. The third implementation takes three arrays corresponding to the center coordinates, a vector defining the viewing angle, and a vector defining the up direction for the scene.

ViewerAntialiasGet

bool ViewerAntialiasGet()

Returns whether or not antialiasing is turned on for line drawing.

ViewerAntialiasSet

bool ViewerAntialiasSet(bool state)

Sets whether or not antialiasing is turned on for line drawing.

ViewerAutoCenterGet

bool ViewerAutoCenterGet()

Returns whether or not the scene will automatically be recentered when a change in the scene occurs (e.g. a new object is made active, objects are hidden or shown).

ViewerAutoCenterPanesGet

bool ViewerAutoCenterPanesGet()

Returns whether or not the scene in each pane in multi-pane display mode is automatically centered or whether all panes observe the same center.

ViewerAutoCenterPanesSet

void ViewerAutoCenterPanesSet(bool center)

Sets whether or not the scene in each pane in multi-pane display mode is automatically centered or whether all panes observe the same center.

ViewerAutoCenterSet

bool ViewerAutoCenterSet(bool ac)

Sets whether or not the scene will automatically be recentered when a change in the scene occurs (e.g. a new object is made active, objects are hidden or shown).

ViewerAutoFitGet

bool ViewerAutoFitGet()

Returns whether or not the contents of the scene will automatically be fit to the screen when a scene change occurs.

ViewerAutoFitSet

bool ViewerAutoFitSet(bool af)

Sets whether or not the contents of the scene will automatically be fit to the screen when a scene change occurs.

ViewerBackgroundColorGet

OESystem::OEColor ViewerBackgroundColorGet()

Returns the background color of the 3D display.

ViewerBackgroundColorSet

OESystem::OEColor ViewerBackgroundColorSet(const OESystem::OEColor &color)

Sets the background color of the 3D display.

ViewerBookmarkLoad

bool ViewerBookmarkLoad(std::string bm)

Loads the specified bookmark.

ViewerBookmarksGetAnimated

bool ViewerBookmarksGetAnimated()

Returns whether or not the transition between bookmarks is animated.

ViewerBookmarksGetAnimationTime

unsigned int ViewerBookmarksGetAnimationTime()

Returns the default desired time for how long the transition between bookmarks should take if animated.

ViewerBookmarksSetAnimated

void ViewerBookmarksSetAnimated(bool animated)

Sets whether or not the transition between bookmarks is animated.

ViewerBookmarksSetAnimationTime

void ViewerBookmarksSetAnimationTime(unsigned int msecs)

Sets the default desired time for how long the transition between bookmarks should take if animated.

ViewerCenterAndRadiusGet

std::vector<float> ViewerCenterAndRadiusGet()

Returns the current center and radius of the scene in the 3D display in a four-membered list. The first three values in the list are the x,y,z coordinates of the center. The fourth value is the radius.

ViewerCenterAndRadiusSet

std::vector<float> ViewerCenterAndRadiusSet(float x, float y, float z,
                                            float radius, bool redraw=true)

Sets the current center and radius of the scene in the 3D display. The redraw parameter determines whether or not the scene should be redrawn immediately.

ViewerCenterGet

std::vector<float> ViewerCenterGet()

Returns the current center of the scene as a list of three values corresponding to the x,y,z coordinates. If for some reason the 3D display is invalid, the list returned will be empty.

ViewerCenterSet

std::vector<float> ViewerCenterSet(unsigned int, bool redraw=true)
std::vector<float> ViewerCenterSet(float x, float y, float z, bool redraw=true)

Sets the current center of the scene. The function that takes three floating point parameters explicitly sets the center of the scene to the coordinates specified by the x, y, and z parameters. The redraw parameter specifies whether or not the scene should be immediately redrawn.

The function that takes a single unsigned integer parameter (id) attempts to center the scene based on the geometry of the object corresponding to the id parameter. If for some reason, a center could not be calculated, this function will return an empty list, otherwise it will return the new center.

ViewerCenterSetScoped

std::vector<float>
  ViewerCenterSetScoped(unsigned int scope = BestScope,
                        bool redraw=true)

Sets the current center of the scene based on the geometry of the objects found within the specified scope. The redraw parameter specifies whether or not the scene should be immediately redrawn. If for some reason, a center could not be calculated, this function will return an empty list, otherwise it will return the new center.

ViewerDepthCueFollowsSlab

bool ViewerDepthCueFollowsSlab()
bool ViewerDepthCueFollowsSlab(bool enable)

Sets whether or not the depthcue parameters should be adjusted as the slabbing parameters change to maintain the best possible lighting for the scene.

ViewerDepthcueEndGet

float ViewerDepthcueEndGet()

Returns the spatial end point used in depthcue calculations. Ordinarily, this function should not need to be called by the user.

ViewerDepthcueEndSet

float ViewerDepthcueEndSet(float end, bool redraw=true)

Sets the spatial end point used in depthcue calculations. Ordinarily, this function should not need to be called by the user.

ViewerDepthcueGet

bool ViewerDepthcueGet()

Returns whether or not depthcueing is currently enabled in the 3D display.

ViewerDepthcueSet

bool ViewerDepthcueSet(bool state)

Sets whether or not depthcueing is currently enabled in the 3D display.

ViewerDepthcueStartGet

float ViewerDepthcueStartGet()

Returns the spatial start point used in depthcue calculations. Ordinarily, this function should not need to be called by the user.

ViewerDepthcueStartSet

float ViewerDepthcueStartSet(float start, bool redraw=true)

Sets the spatial start point used in depthcue calculations. Ordinarily, this function should not need to be called by the user.

ViewerDiffuseLightGet

OESystem::OEColor ViewerDiffuseLightGet()

Returns the OpenGL diffuse light property.

ViewerDiffuseLightSet

OESystem::OEColor ViewerDiffuseLightSet(const OESystem::OEColor &color)

Sets the OpenGL diffuse light property.

ViewerDiffuseMaterialGet

OESystem::OEColor ViewerDiffuseMaterialGet()

Returns the OpenGL diffuse material property.

ViewerDiffuseMaterialSet

OESystem::OEColor ViewerDiffuseMaterialSet(const OESystem::OEColor &color)

Set the OpenGL diffuse material property.

ViewerDrawDepictionsGet

bool ViewerDrawDepictionsGet()

Returns whether or not a 2D depiction is drawn in the 3D display for the active molecule.

ViewerDrawDepictionsSet

bool ViewerDrawDepictionsSet(bool show)

Sets whether or not a 2D depiction is drawn in the 3D display for the active molecule.

ViewerFit

void ViewerFit(float buffer=0.0f)
void ViewerFit(const std::vector<OEPropDB::OEKey> &keys, float buffer=0.0f)

This function ensures that the entire contents of the scene fit within the 3D display window. The buffer parameter allows specification of an additional buffer applied to the radius of the scene.

The function that takes a list of keys as a parameter will perform the same function as above, but will only ensure that those objects corresponding to the specified keys will be guaranteed to fit within the 3D display window.

ViewerFontSizeGet

unsigned int ViewerFontSizeGet()

Return the size of the font used for text drawn in the 3D display.

ViewerFontSizeSet

void ViewerFontSizeSet(unsigned int sz)

Sets the size of the font used for text drawn in the 3D display.

ViewerForwardGet

std::vector<float> ViewerForwardGet()

Returns the forward facing vector for the OpenGL camera.

ViewerLODGet

int ViewerLODGet()

Returns the level of display (rendering quality) being used in 3D display window.

ViewerLODSet

int ViewerLODSet(unsigned int lod, bool redraw=true)

Sets the level of display (rendering quality) being used in the 3D display.

ViewerLightPositionGet

std::vector<float> ViewerLightPositionGet()

Returns the position of the OpenGL light source.

ViewerLightPositionSet

std::vector<float> ViewerLightPositionSet(const std::vector<float> &pos)

Sets the position of the OpenGL light source.

ViewerLookAt

void ViewerLookAt(const OEPropDB::OEKey &centerKey,
                  const OEPropDB::OEKey &refKey, bool redraw=true)
void ViewerLookAt(const std::vector<float> &center,
                  const std::vector<float> &look,
                  const std::vector<float> &up, bool redraw=true)

Sets up the display such that the object corresponding to centerKey is at the center of the display with the camera looking down the axis between centerKey and the object corresponding to refKey.

ViewerMirrorSlabsGet

bool ViewerMirrorSlabsGet()

Returns whether or not the position of the front and back clipping planes mirror each other.

ViewerMirrorSlabsSet

bool ViewerMirrorSlabsSet(bool mirror)

Sets whether or not the position of the front and back clipping planes mirror each other.

ViewerNiceFontsGet

bool ViewerNiceFontsGet()

Returns whether or not text is rendered in the 3D display using high-quality fonts versus simple fonts. Some graphics cards cannot properly handle the high-quality fonts and it is recommended in those situations not to use “nice” fonts.

ViewerNiceFontsSet

bool ViewerNiceFontsSet(bool nice)

Sets whether or not text is rendered in the 3D display using high-quality fonts versus simple fonts. Some graphics cards cannot properly handle the high-quality fonts and it is recommended in those situations not to use “nice” fonts.

ViewerOrientationGet

std::vector<float> ViewerOrientationGet()

Returns the OpenGL camera orientation matrix.

ViewerOrientationSet

std::vector<float> ViewerOrientationSet(std::vector<float> orientationMatrix)

Sets the OpenGL camera orientation matrix.

ViewerProjectorModeGet

bool ViewerProjectorModeGet()

Returns whether or not the display is being drawn in “Projector Mode”. “Projector Mode” is a display mode which is designed to improve visibility when the application is projected using an LCD projector by using a lighter background and a different atom coloring scheme.

ViewerProjectorModeSet

void ViewerProjectorModeSet(bool state)

Sets whether or not the display is being drawn in “Projector Mode”. “Projector Mode” is a display mode which is designed to improve visibility when the application is projected using an LCD projector by using a lighter background and a different atom coloring scheme.

ViewerRadiusGet

float ViewerRadiusGet()

Returns the current radius of the scene in the 3D display window.

ViewerRadiusSet

float ViewerRadiusSet(float radius, bool redraw=true)

Sets the current radius of the scene in the 3D display window. The redraw parameter specifies whether or not to immediately redraw the scene.

ViewerRecenter

void ViewerRecenter()

This function recenters the scene based on the geometry of the contents of the scene.

ViewerReprobeStereo

bool ViewerReprobeStereo()

This function rechecks to see whether hardware stereo is supported on the current machine. Ordinarily, this function should not need to be called by the user.

ViewerRotate

void ViewerRotate(const std::string &axis, float angle, bool redraw=true)

This function rotates the display around the specified axis (valid parameters: ‘x’,’y’,’z’ for screen or trackball axis, ‘X’, ‘Y’, ‘Z’ for world axis) by angle degrees. The center of rotation is the world center. The redraw parameter specifies whether or not to immediately redraw the scene.

ViewerScaleGet

float ViewerScaleGet()

Returns the scale of the scene in the 3D display window.

ViewerScaleSet

float ViewerScaleSet(float radius, bool redraw=true)

Sets the scale of the scene in the 3D display window.

ViewerShininessMaterialGet

float ViewerShininessMaterialGet()

Returns the OpenGL material shininess property.

ViewerShininessMaterialSet

float ViewerShininessMaterialSet(float shine)

Sets the OpenGL material shininess property.

ViewerShowActiveBorderGet

bool ViewerShowActiveBorderGet()

Returns whether or not a blue border is drawn around the active pane in multi-pane display mode.

ViewerShowActiveBorderSet

void ViewerShowActiveBorderSet(bool show)

Sets whether or not a blue border is drawn around the active pane in multi-pane display mode.

ViewerShowGridGet

bool ViewerShowGridGet()

Returns whether or not borders are drawn around individual panes in multi-pane display mode.

ViewerShowGridSet

void ViewerShowGridSet(bool show)

Sets whether or not borders are drawn around individual panes in multi-pane display mode.

ViewerShowTrackballGuideSet

void ViewerShowTrackballGuideSet(bool show)

Sets whether or not a trackball guide will be displayed on the 3D display window to help guide what is considered inside and outside with respect to mouse actions. Please see ViewerMouseOutsideAwareGet/Set functions for more details.

ViewerSlabEnableGet

bool ViewerSlabEnableGet()

Returns whether or not slabbing (clipping) of the 3D display is enabled.

ViewerSlabEnableSet

bool ViewerSlabEnableSet(bool enable)

Sets whether or not slabbing (clipping) of the 3D display is enabled. The redraw parameter specifies whether or not the scene should be immediately redrawn.

ViewerSlabFarGet

float ViewerSlabFarGet()

Returns the spatial position of the far clipping plane. Ordinarily, this function should not need to be called by the user.

ViewerSlabFarSet

float ViewerSlabFarSet(float radius, bool redraw=true)

Sets the spatial position of the far clipping plane. The redraw parameter specifies whether or not the scene should be immediately redrawn. Ordinarily, this function should not need to be called by the user.

ViewerSlabNearGet

float ViewerSlabNearGet()

Returns the spatial position of the near clipping plane. Ordinarily, this function should not need to be called by the user.

ViewerSlabNearSet

float ViewerSlabNearSet(float radius, bool redraw=true)

Sets the spatial position of the near clipping plane. The redraw parameter specifies whether or not the scene should be immediately redrawn. Ordinarily, this function should not need to be called by the user.

ViewerSlabWidthGet

float ViewerSlabWidthGet()

Returns the distance between the near and far clipping planes. Ordinarily, this function should not need to be called by the user.

ViewerSlabWidthSet

float ViewerSlabWidthSet(float width, bool redraw=true)

Sets the distance between the near and far clipping planes. The redraw parameter specifies whether or not the scene should be immediately redrawn. Ordinarily, this function should not need to be called by the user.

ViewerSpecularMaterialGet

OESystem::OEColor ViewerSpecularMaterialGet()

Returns the OpenGL specular material property.

ViewerSpecularMaterialSet

OESystem::OEColor ViewerSpecularMaterialSet(const OESystem::OEColor &color)

Sets the OpenGL specular material property.

ViewerStereoAngleGet

float ViewerStereoAngleGet()

Returns the angle used when calculating stereographic display offsets.

ViewerStereoAngleSet

float ViewerStereoAngleSet(float angle)

Sets the angle used when calculating stereographic display offsets.

ViewerStereoCrossEyedGet

bool ViewerStereoCrossEyedGet()

Returns whether or not the stereographic display is in cross-eyed mode.

ViewerStereoCrossEyedSet

bool ViewerStereoCrossEyedSet(bool cross)

Sets whether or not the stereographic display is in cross-eyed mode.

ViewerStereoEnableGet

bool ViewerStereoEnableGet()

Returns whether or not stereographic display is enabled.

ViewerStereoEnableSet

bool ViewerStereoEnableSet(bool enabled)

Sets whether or not stereographic display is enabled.

ViewerStereoHardwareGet

bool ViewerStereoHardwareGet()

Returns whether or not stereo hardware is being used for the stereographic display.

ViewerStereoHardwareSet

bool ViewerStereoHardwareSet(bool hardware)

Sets whether or not stereo hardware is being used for the stereographic display.

ViewerStereoSeparationGet

float ViewerStereoSeparationGet()

Returns the eye separation used in stereographic display mode.

ViewerStereoSeparationSet

float ViewerStereoSeparationSet(float separation)

Sets the eye separation used in stereographic display mode.

ViewerStereoStyleGet

unsigned char ViewerStereoStyleGet()

Sets the stereographic display mode (hardware, splitscreen, or none).

ViewerStereoStyleSet

unsigned char ViewerStereoStyleSet(unsigned char style)

Sets the stereographic display mode (hardware, stencil, splitscreen, or none).

ViewerStyleControlVisibleGet

bool ViewerStyleControlVisibleGet(const std::string &style)

Returns whether or not the specified style control widget is currently visible above the 3D display. Available style widgets include: “color”, “selection”, “style”, “contours”, and “graphics”.

ViewerStyleControlVisibleSet

void ViewerStyleControlVisibleSet(const std::string &style, bool vis)

Sets whether or not the specified style control widget is currently visible above the 3D display. Available style widgets include: “color”, “selection”, “style”, “contours”, and “graphics”.

ViewerSupportsHWStereo

bool ViewerSupportsHWStereo()

Returns whether or not the machine the application is being run on supports the use hardware stereo.

ViewerTextFontGet

std::string ViewerTextFontGet()

Returns the font currently being used when rendering text in the 3D display. This font only applies when using “nice” fonts.

ViewerTextFontSet

void ViewerTextFontSet(const std::string &)

Sets the font currently being used when rendering text in the 3D display. This font only applies when using “nice” fonts.

ViewerTextScaleGet

float ViewerTextScaleGet()

Returns the current global scale for text drawn in the 3D display window.

ViewerTextScaleSet

float ViewerTextScaleSet(float scale, bool redraw=true)

Sets the current global scale for text drawn in the 3D display window.

ViewerToggleRenderFeatures

void ViewerToggleRenderFeatures(unsigned int features, bool on)

Toggles the use of certain advanced visualization features.

ViewerTranslateX

void ViewerTranslateX(float val)

Translates the display along the X axis by the specified amount (in Angstroms).

ViewerTranslateY

void ViewerTranslateY(float val)

Translates the display along the Y axis by the specified amount (in Angstroms).

ViewerTranslateZ

void ViewerTranslateZ(float val)

Translates the display along the Z axis by the specified amount (in Angstroms).

ViewerUpGet

std::vector<float> ViewerUpGet()

Returns the OpenGL camera up vector.

ViewerUseDisplayListGet

bool ViewerUseDisplayListGet()

Returns whether or not the 3D renderer uses a display list to encapsulate the master scene. The default is false. Ordinarily, this function does not need to be called by the user.

ViewerUseDisplayListSet

bool ViewerUseDisplayListSet(bool use)

Sets whether or not the 3D renderer uses a display list to encapsulate the master scene. The default is false. Ordinarily, this function does not need to be called by the user. Setting this property to true may have cause significant negative performance on certain machines.

ViewerUseSystemFontsGet

bool ViewerUseSystemFontsGet()

Returns whether or not the 3D renderer uses system fonts when displaying text.

ViewerUseSystemFontsSet

bool ViewerUseSystemFontsSet(bool state)

Sets whether or not the 3D renderer uses system fonts when display text.

ViewerSetShowObjectToolbar

void ViewerSetShowObjectToolbar(bool state)

Sets whether or not the style & color buttons are shown in the bottom toolbar for the active object

ViewerGetShowObjectToolbar

bool ViewerGetShowObjectToolbar()

Sets whether or not the style & color buttons are shown in the bottom toolbar for the active object

Object Functions

The functions detailed in this section provide a mechanism to add, delete, modify, and organize the many types of objects (e.g. molecules, grids, and surfaces) available in VIDA.

Add

unsigned int Add(OESystem::OEBase &, unsigned int listID = 0)

Adds the specified object to the application and returns a unique ID associated with that object. If the optional listID argument is provided, then the object is added to the specified list. Otherwise, a new list is created and the object is added to it.

AddCSVSmiles

unsigned int AddCSVSmiles( const std::string &smiles,
                           const std::vector<std::string> &headers,
                           const std::vector<std::string> &values,
                           const std::string &filename = "",
                           unsigned int       listid   = 0)

Adds a new molecule from SMILES with the optional associated data. smiles species the SMILES string to parse, headers is a list of column names corresponding to the data specified in values, filename is an optional filename to attribute this molecule to, and listid is the ID of the list to which this molecule will be added. If listid is zero, a new list will be created.

Returns the ID of the list to which the molecule was added.

AddURLMol

unsigned int AddURLMol( const std::string              &url,
                        const std::string              &urlFunc,
                        const std::vector<std::string> &headers,
                        const std::vector<std::string> &values,
                        const std::string              &filename,
                        unsigned int                    listid)

Reserved for future implementation.

AtomDataGet

AtomData AtomDataGet(const OEPropDB::OEKey &key )

Returns an AtomData object populated with information about the atom specified by the parameter key.

CheckIn

bool CheckIn(OESystem::OEBase &)

Checks the specified Python accessible object back into the main VIDA application which will synchronize any changes made to the object in Python with the object in VIDA. The object in question must have been checked out of VIDA prior to being checked back in.

See GridCheckOut, MoleculeCheckOut, and SurfaceCheckOut.

ChildrenGet

std::vector<OEPropDB::OEKey> ChildrenGet(unsigned int id)
std::vector<OEPropDB::OEKey> ChildrenGet(const OEPropDB::OEKey &)

Returns a list of keys corresponding to any child objects associated with the specified object.

ContourCloudJitterDefaultGet

float ContourCloudJitterDefaultGet()

Returns the value (between 0.0 and 1.0) indicated by the Jitter slider on the Contours panel.

ContourCloudJitterGet

float ContourCloudJitterGet(unsigned int id)

Returns the jitter value assigned to grid id. The jitter value is used when the contour is displayed with the “cloud” style, and represents the degree to which the grid vertex positions are to be randomized. Jitter values range from 0.0 (no jitter) to 1.0 (jitter equal to the grid spacing).

ContourCloudJitterSet

float ContourCloudJitterSet(unsigned int id, float jitter)

Sets the jitter value to be used when grid id is displayed with the “cloud” style. Jitter values range from 0.0 (no jitter) to 1.0 (jitter equal to the grid spacing).

ContourCountScoped

int ContourCountScoped(unsigned int scope = BestScope)

Returns the number of contours for all grids in scope.

This returns the number of contours for the focused grid or the first grid found in the given scope.

ContourCreate

void ContourCreate(unsigned int id=0)
void ContourCreate(unsigned int id, float threshold)
void ContourCreate(unsigned int id, float threshold,
                   const OESystem::OEColor &color)

Create a new contour for grid id.

ContourCreateSurface

unsigned int ContourCreateSurface(unsigned int id, unsigned int contourIndex)

Create a contour surface for the surface defined by the repository id id for the contour referenced by contourIndex.

ContourDeleteAll

void ContourDeleteAll(unsigned int id)

Delete all contours for grid id.

ContourDeleteByIndex

void ContourDeleteByIndex(unsigned int id, unsigned int index)

Delete contour index for grid id. All contours with indices greater than index will now be at their current index - 1.

ContourDeleteByThreshold

void ContourDeleteByThreshold(unsigned int id, float threshold)

Delete all contours above threshold for grid id. Contour indices will be reassigned.

ContourExtractIsoSurface

unsigned int ContourExtractIsoSurface(unsigned int id, unsigned int vertex,
                                      bool maskVis=true)

Reserved for internal use.

ContourFixAsSurfaceScoped

std::vector<unsigned int>
  ContourFixAsSurfaceScoped(unsigned int scope = BestScope)

Creates an actual surface object for each contour in the specified scope. Returns a list of IDs corresponding to the generated surfaces.

ContourGetAll

std::vector<float> ContourGetAll(unsigned int id=0)

Get all contour levels from each contour drawn for grid id.

ContourLevelForIndexGet

float ContourLevelForIndexGet(unsigned int id, unsigned int index)

Returns the contour level for grid id at index id.

ContourLevelForIndexGetScoped

float ContourLevelForIndexGetScoped(int index,
                                    unsigned int scope = BestScope)

Returns the contour level for index id for the first grid in scope.

ContourLevelForIndexSet

float ContourLevelForIndexSet(unsigned int id, unsigned int index, float thresh)

Set the level for the contour at index index to thresh for grid id.

ContourLevelForIndexSetScoped

void ContourLevelForIndexSetScoped(unsigned int index, float thresh,
                                   unsigned int gridType=UINT_MAX,
                                   unsigned int scope = BestScope)

Set the level for the contour at index index to thresh for all grids in scope.

ContourLevelNudgeScoped

void ContourLevelNudgeScoped(bool increase,
                             unsigned int scope = BestScope)

This function increases or decreases the contour value for the contours in the specified scope by 0.1 depending on whether the increase parameter is set to true or false.

ContourLevelSetScoped

void ContourLevelSetScoped(float level,
                           unsigned int scope = BestScope)

This function sets the contour level of all the contours in the specified scope to the value specified by the parameter level.

ContourMax

float ContourMax(unsigned int oerid)

Returns the maximum allowable contour threshold for grid id.

ContourMaxScoped

float ContourMaxScoped(unsigned int scope = BestScope)

Returns the maximum allowable contour threshold for the first grid found in scope.

ContourMin

float ContourMin(unsigned int oerid)

Returns the minimum allowable contour threshold for grid id.

ContourMinScoped

float ContourMinScoped(unsigned int scope = BestScope)

Returns the minimum allowable contour threshold for the first grid found in scope.

ContourRadiusGet

float ContourRadiusGet(unsigned int id=0)

Returns the radius used when generating contours for crystallographic grids.

ContourRadiusSet

float ContourRadiusSet(unsigned int id, float rad)

Sets the radius used when generating contours for crystallographic grids.

ContourResolutionGet

float ContourResolutionGet(unsigned int id=0)

Return the contouring resolution for drawing the contours in Angstroms. A lower resolution samples more grid points, but requires more memory.

ContourResolutionSet

float ContourResolutionSet(unsigned int id, float rad)

Set the contouring resolution in Angstroms. Lower values sample more grid points and generate finer visualizations but require more memory.

ContourTypedAddScoped

void ContourTypedAddScoped(unsigned int scope = BestScope)

Add a single contour to all grids of type type in scope.

ContourTypedCountScoped

int ContourTypedCountScoped(unsigned int scope = BestScope)

Return the number of contours of all grids of type type in scope. This essentially returns the number of contours of the first grid found.

ContourTypedMaxScoped

float ContourTypedMaxScoped(unsigned int scope = BestScope)

Returns the maximum allowable threshold for the first grid found of type type in scope.

ContourTypedMinScoped

float ContourTypedMinScoped(unsigned int scope = BestScope)

Returns the minimum allowable threshold for the first grid found of type type in scope.

ContourTypedRemoveScoped

void ContourTypedRemoveScoped(unsigned int scope = BestScope)

Remove the last contour from all grids of type type in scope.

ContourTypedSetLevelForIndexScoped

void ContourTypedSetLevelForIndexScoped(unsigned int index, float thresh,
                                        unsigned int scope = BestScope)

Set the contour level for the contour at index for all grids of type type in scope.

ContourVolume

float ContourVolume(unsigned int id, unsigned int contourIndex)

Return the enclosed volume of Grid id‘s contour at index contourIndex.

Delete

void Delete(unsigned int id)
void Delete(const std::vector<unsigned int> &)
void Delete(const std::vector<OEPropDB::OEKey> &)
void Delete(const OEPropDB::OEKey &, bool all=false)

Deletes the specified object(s) from the current session. It is important to note that this does NOT delete the actual files (or entries within files) associated with the specified objects.

DeleteAll

void DeleteAll(bool force=false)

Clears the application back to a clean state with nothing loaded.

DeleteScoped

void DeleteScoped(unsigned int scope, bool inScope)

Scoped version of Delete but with the additional option to specify whether to delete everything within the scope or everything not within the scope using the inScope parameter.

FindByDataScoped

std::vector<OEPropDB::OEKey> FindByDataScoped(const std::string &query,
                                              unsigned int scope = AllScope)

Reserved for future implementation.

FindByQueryScoped

std::vector<OEPropDB::OEKey> FindByQueryScoped(const OEPropDB::OEKey &query,
                                               unsigned int scope = AllScope)
std::vector<OEPropDB::OEKey> FindByQueryScoped(const OEPropDB::OEKey &query,
                                               unsigned int atoms,
                                               unsigned int bonds,
                                               unsigned int scope = AllScope)

Uses the specified molecule as a query to search the specified scope. Returns a list of keys corresponding to molecules that match the specified query.

FindBySMARTSScoped

std::vector<OEPropDB::OEKey> FindBySMARTSScoped(const std::string &smarts,
                                                unsigned int scope = AllScope)

Uses the specified SMARTS pattern as a query to search the specified scope. Returns a list of keys corresponding to molecules that match the specified SMARTS pattern.

FindBySimilarityScoped

std::vector<OEPropDB::OEKey> FindBySimilarityScoped(const OEPropDB::OEKey &query,
                                                    float similarity,
                                                    unsigned int scope = AllScope)

Searches the specified scope for molecules with a Lingo similarity greater than the specified similarity cutoff with the specified molecule query.

FindByTitleScoped

std::vector<OEPropDB::OEKey> FindByTitleScoped(const std::string &expr,
                                               unsigned int scope = AllScope)

Uses the specified title query as a regular expression to search the specified scope for molecules whose title match the expression.

FindInRepository

void FindInRepository()

This function prompts the user to specify a query to search the contents of the application repository. The user then has the option to select some, none, or all of the hits to be placed in a new list.

FindOnDisk

void FindOnDisk()

This function prompts the user to specify a query to search a specific region of the user’s hard drive for molecules matching the query. The user then has the option to load some, none, or all of the files containing the hits. This function will load the entire file where a hit was discovered as opposed to just the hits in that file.

GridAdd

unsigned int GridAdd(OESystem::OESkewGrid &grd, unsigned int listID = 0)
unsigned int GridAdd(OESystem::OEScalarGrid &grd, unsigned int listID = 0)

Adds the specified Python grid object to VIDA. If the optional listID argument is provided, then the grid is added to the specified list. Otherwise, a new list is created and the grid is added to it.

GridCheckIn

bool GridCheckIn(OESystem::OESkewGrid &grd,
                 unsigned int checkInType = OECheckInType_UnknownChange)
bool GridCheckIn(OESystem::OEScalarGrid &grd,
                 unsigned int checkInType = OECheckInType_UnknownChange)

Checks the specified Python accessible grid back into the main VIDA application which will synchronize any changes made to the grid in Python with the grid in VIDA. The grid in question must have been checked out of VIDA prior to being checked back in.

The checkInType parameter tells VIDA what type of changes were made to the grid in order to optimize the check in process. There are multiple allowable values for this parameter which can be OR’d together if necessary:

  • OECheckInType_ConformerChange
  • OECheckInType_CoordinateChange
  • OECheckInType_DataChange
  • OECheckInType_GraphChange
  • OECheckInType_NoChange
  • OECheckInType_RenderChange
  • OECheckInType_AnnotationChange
  • OECheckInType_UnknownChange

GridCheckOut

bool GridCheckOut(OESystem::OESkewGrid &grd, unsigned int id)
bool GridCheckOut(OESystem::OEScalarGrid &grd, unsigned int id)

Checks out a copy of the grid specified by id into the specified Python grid object (grd). Returns whether or not the check out process succeeded.

The checked out grid can be modified in Python, but those changes will not be applied to the original grid in VIDA until the modified grid is checked back in using the GridCheckIn command.

GridClear

void GridClear(unsigned int id)

Clears the data on the specified grid.

GridCopy

unsigned int GridCopy(unsigned int id)

Creates a copy of the specified grid and returns the ID of the newly created copy.

GridCreateElectrostaticsGrid

unsigned int GridCreateElectrostaticsGrid(OEPropDB::OEKey k,
                                          bool property=false)

Create an electrostatics grid for molecule id.

If property is true, then this grid is attached to id and does not show up in the list window. These grids cannot be saved to disk.

If property is false, then this grid is created as a separate entity from id.

GridCreateGaussian

unsigned int GridCreateGaussian(const OEPropDB::OEKey &k, float res)

Creates a gaussian grid representation for the molecule associated with the specified key at the specified resolution.

GridCreateGaussianProduct

unsigned int GridCreateGaussianProduct(const OEPropDB::OEKey &k, float res)

Creates a gaussian product grid representation for the molecule associated with the specified key at the specified resolution.

GridDefaultContourLevelByIndexGet

float GridDefaultContourLevelByIndexGet(unsigned int gridType,
                                        unsigned int index)

Returns the default contour level for contour index for grids of type gridType.

GridDefaultContourLevelByIndexSet

void GridDefaultContourLevelByIndexSet(unsigned int gridType,
                                       unsigned int index, float thresh)

Set the default contour level thresh for contour index for grids of type gridType.

GridDefaultNumContoursGet

unsigned int GridDefaultNumContoursGet(unsigned int gridType)

Returns the default number of contours for grids of type gridType.

GridDefaultNumContoursSet

void GridDefaultNumContoursSet(unsigned int gridType, unsigned int count)

Set the default number of contours for grids of type gridType to count.

GridInitializeContours

void GridInitializeContours(unsigned int id, bool update=true)

Initialize a grid to its default contours, colors and levels.

GridNormalize

bool GridNormalize(unsigned int id)

Normalizes a grid. This finds the sigma for the grid and divides all grid points by that value.

GridRegularize

unsigned int GridRegularize(unsigned int id)

Regularizes the specified skew grid. Returns the ID of the newly created regular scalar grid.

GridToGaussianGrid

unsigned int GridToGaussianGrid(unsigned int id)

Creates a gaussian grid representation for the specified grid.

GridTypeGet

unsigned int GridTypeGet(unsigned int oerid)

Returns the type of grid for grid id.

GridTypeGetScoped

unsigned int GridTypeGetScoped(unsigned int scope = BestScope)

Returns the type of grid for the first grid found in scope.

GridTypeSet

void GridTypeSet(unsigned int id, unsigned int gridType)

Set the grid type of grid id to gridType.

GridTypeSetScoped

void GridTypeSetScoped(unsigned int gridType,
                       unsigned int scope = BestScope)

Scoped version of GridTypeSet.

GridWorkingGetScoped

unsigned int GridWorkingGetScoped(unsigned int scope = BestScope)

Returns the ID for the “working grid” which is determined in the following order: grid associated with selected contour, grid which is currently focused, grid which is a child object of the currently focused object, or lastly the first grid found in the current default scope.

HasGridChildrenScoped

int HasGridChildrenScoped(unsigned int scope = BestScope)

Returns whether or not any of the molecules in the specified scope have visible grids attached to them. Returns 0 for none of the molecules have visible grids, 1 for all molecules have visible grid, and 2 for at least one has a visible grid.

HasSurfaceChildrenScoped

int HasSurfaceChildrenScoped(const std::string &type,
                             unsigned int scope = BestScope)

Returns whether or not any of the molecules in the specified scope have visible surfaces attached to them. Returns 0 for none of the molecules have visible surfaces, 1 for all molecules have visible surface, and 2 for at least one has a visible surface.

Initialize

void Initialize(unsigned int id)
void Initialize(const OEPropDB::OEKey &)

Initializes the specified object for display. This function is automatically called on objects that are loaded into VIDA and ordinarily should not need to be called by the user.

IsAGrid

bool IsAGrid(unsigned int id)
bool IsAGrid(const OEPropDB::OEKey &k)

Returns whether or not the specified object is a grid.

IsAList

bool IsAList(unsigned int id)

Returns whether or not the specified object is a list.

IsAMolecule

bool IsAMolecule(unsigned int id)
bool IsAMolecule(const OEPropDB::OEKey &k)

Returns whether or not the specified object is a molecule.

IsAReflection

bool IsAReflection(unsigned int id)
bool IsAReflection(const OEPropDB::OEKey &k)

Returns whether or not the specified object is a reflection.

IsASmallMolecule

bool IsASmallMolecule(unsigned int id)
bool IsASmallMolecule(const OEPropDB::OEKey &k)

Returns whether or not the specified object is a small molecule.

IsASurface

bool IsASurface(unsigned int id)
bool IsASurface(const OEPropDB::OEKey &k)

Returns whether or not the specified object is a surface.

KeyGet

OEPropDB::OEKey KeyGet(const OESystem::OEBase &)
OEPropDB::OEKey KeyGet(const OESystem::OEBase &, const OEPropDB::OEKey &pkey)

Returns the key associated with the specified OEBase object. If the object’s parent key is known, that can be passed as a parameter as well to aid the key determination process.

KeyIDGet

unsigned int KeyIDGet(const OEPropDB::OEKey &)

Returns the ID associated with the specified key.

KeyParentIDGet

unsigned int KeyParentIDGet(const OEPropDB::OEKey &)

Returns the ID of the parent object associated with the specified key. This function should be used for child object types such as atoms, bonds, triangles, and vertices.

KeySourceIDGet

unsigned int KeySourceIDGet(const OEPropDB::OEKey &)

Returns the ID of the parent object associated with a specified key. This function should be used for top-level object types such as molecules, grids, and surfaces in situations where these objects have been added as children to another object.

KeyTypeGet

std::string KeyTypeGet(const OEPropDB::OEKey &)

Returns a string representation of the object type associated with the specified key. Return values include:

  • “Atom”
  • “Bond”
  • “Grid”
  • “Mol”
  • “Surface”
  • “Triangle”
  • “Vertex”

KeysGet

std::vector<OEPropDB::OEKey> KeysGet(unsigned int id)

Returns a list of all the keys for the specified ID. For most objects, the list returned will contain a single entry; however, for multi-conformer molecules, the list will include a key for each individual conformer.

ListAddObject

bool ListAddObject(unsigned int listid, unsigned int objectid)

Adds the object specified by objectid to the list specified by listid.

ListAddObjects

bool ListAddObjects(unsigned int listid,
                    const std::vector<unsigned int> &ids)

Adds the objects specified by the list of IDs (ids) to the list specified by listid.

ListGetNames

std::vector<std::string> ListGetNames()

Returns a list of the names of all the current lists.

ListGetObjectLists

std::vector<unsigned int> ListGetObjectLists(unsigned int objectid)

Returns a list of all the lists to which the object specified by objectid belongs.

ListGetObjects

std::vector<unsigned int> ListGetObjects(unsigned int listid)

Returns a list of IDs of all the objects contained within the list specified by listid.

ListMoveObject

bool ListMoveObject(unsigned int srclist, unsigned int dstlist,
                    unsigned int objectid)

Moves the object specified by objectid from the list specified by srclist to the list specified by dstlist.

ListMoveObjects

bool ListMoveObjects(unsigned int srclist, unsigned int dstlist,
                     const std::vector<unsigned int> &ids)

Moves the objects specified by list of IDs (ids) from the list specified by srclist to the list specified by dstlist.

ListNew

unsigned int ListNew(const std::string &name)
unsigned int ListNew(const std::string &name,
                     const std::vector<unsigned int> &ids)
unsigned int ListNew(const std::string &name,
                     const std::vector<OEPropDB::OEKey> &keys)

Creates a new list with the specified name. If a list of IDs or keys is specified with this call, all of the objects corresponding to those IDs or keys will be added to the list.

Returns the ID of the created list.

ListNewAnd

unsigned int ListNewAnd(const std::vector<unsigned int> &ids)

Creates a new list containing all of the objects that each appear in every list specified by the list of IDs (ids).

Returns the ID of the created list.

ListNewMarked

unsigned int ListNewMarked(const std::string &name="")

Creates a new list containing all the currently marked objects. Objects will not be removed from this list if they are subsequently unmarked.

Returns the ID of the created list.

ListNewOr

unsigned int ListNewOr(const std::vector<unsigned int> &ids)

Creates a new list containing all of the objects in all of the lists specified by the list of IDs (ids).

Returns the ID of the created list.

ListNewXor

unsigned int ListNewXor(const std::vector<unsigned int> &ids)

Creates a new list containing all of the objects that each appear only once among all the lists specified by the list of IDs (ids).

Returns the ID of the created list.

ListRemoveObject

bool ListRemoveObject(unsigned int listid, unsigned int objectid)

Removes the object specified by objectid from the list specified by listid.

ListRemoveObjects

bool ListRemoveObjects( unsigned int listid,
                        const std::vector<unsigned int> &ids )

Removes the object(s) specified by the list of IDs (ids) from the list specified by listid.

ListRootList

unsigned int ListRootList()

Returns the ID of the root list.

ListSubsetMarked

unsigned int ListSubsetMarked(unsigned int id, bool match)

Creates a new list containing a subset of the objects contained within the list specified by id. If the match parameter is True, the subset will contain all of the marked objects in the source list, if match is False, the subset will contain all of the non-marked objects in the source list.

Returns the ID of the created list.

ListSubsetQuery

unsigned int ListSubsetQuery(unsigned int id, const std::string &, bool match)

Creates a new list containing a subset of the objects contained within the list specified by id. If the match parameter is True, the subset will contain all of the objects that match the specified query in the source list, if match is Fale, the subset will contain all of the objects which fail to match the specified query in the source list. The query parameter can be specified as a SMARTS, a SMILES, or an IUPAC name.

Returns the ID of the created list.

MoleculeAdd

unsigned int MoleculeAdd(const std::string &, unsigned int listID = 0)
unsigned int MoleculeAdd(OEChem::OEMCMolBase &, unsigned int listID  = 0)

Adds a new molecule to VIDA. There are two implementations of this function. The first implementation expects a hexadecimal encoded OEB string specifying a molecule. The second implementation expects a Python molecule object.

If the optional listID argument is provided, then the molecule is added to the specified list. Otherwise, a new list is created and the molecule is added to it.

Returns the ID assigned to the newly added molecule or zero if the add failed for any reason.

MoleculeCheckIn

bool MoleculeCheckIn(OEChem::OEMCMolBase &mol,
                     unsigned int checkInType = OECheckInType_UnknownChange )

Checks the specified Python accessible molecule back into the main VIDA application which will synchronize any changes made to the molecule in Python with the molecule in VIDA. The molecule in question must have been checked out of VIDA prior to being checked back in.

The checkInType parameter tells VIDA what type of changes were made to the molecule in order to optimize the check in process. There are multiple allowable values for this parameter which can be OR’d together if necessary:

  • OECheckInType_ConformerChange
  • OECheckInType_CoordinateChange
  • OECheckInType_DataChange
  • OECheckInType_GraphChange
  • OECheckInType_NoChange
  • OECheckInType_RenderChange
  • OECheckInType_AnnotationChange
  • OECheckInType_UnknownChange

MoleculeCheckOut

bool MoleculeCheckOut(OEChem::OEMCMolBase &mol, unsigned int id)

Checks out a copy of the molecule specified by id into the specified Python molecule object (mol). Returns whether or not the check out process succeeded.

The checked out molecule can be modified in Python, but those changes will not be applied to the original molecule in VIDA until the modified molecule is checked back in using the MoleculeCheckIn command.

MoleculeComponentNamesGet

std::vector<std::string> MoleculeComponentNamesGet(unsigned int id)

Returns a list of names of the individual components of the molecule specified by id based on PDB related subsets.

MoleculeExamine

bool MoleculeExamine(OEChem::OEMCMolBase &, unsigned int id)
bool MoleculeExamine(OEChem::OEMCMolBase &, const OEPropDB::OEKey &key)

Copies the molecule associated with the specified ID or key into the specified Python molecule object. Returns True if the copy happened successfully. In cases where a script needs read-only access to a molecule, MoleculeExamine provides a much faster way to retrieve molecules than MoleculeCheckOut or MoleculeGet. Molecules retrieved using MoleculeExamine cannot be checked back in using MoleculeCheckIn.

MoleculeGet

bool MoleculeGet(OEChem::OEMCMolBase &, unsigned int id)
bool MoleculeGet(OEChem::OEMCMolBase &, const OEPropDB::OEKey &key)
OEChem::OEMol MoleculeGet(unsigned int id)
OEChem::OEMol MoleculeGet(const OEPropDB::OEKey &key)

Copies the molecule associated with the specified ID or key into the specified Python molecule object. Returns whether or not the copy happened successfully.

MoleculeHasComponents

bool MoleculeHasComponents(unsigned int id)

Returns whether or not the molecule specified by id contains multiple distinct components.

MoleculeMaxResidueGet

int MoleculeMaxResidueGet(unsigned int id)

Returns the largest residue index of all the residues contained within the specified molecule.

MoleculeMergeScoped

unsigned int MoleculeMergeScoped(unsigned int scope = BestScope,
                                 const std::string &name="Merged",
                                 unsigned int listid=0)

Merges all of the molecules in the specified scope into a single new molecule. The name parameter specifies the new molecule’s name and the listid parameter specifies in which list to place this new molecule. If listid is 0, a new list will be created to contain the created molecule.

MoleculeNewSubset

std::vector<unsigned int> MoleculeNewSubset(unsigned int listid,
                                            unsigned int id, bool pdb)
std::vector<unsigned int> MoleculeNewSubset(unsigned int listid,
                                            unsigned int id, unsigned int scope,
                                            bool unmatched)
std::vector<unsigned int> MoleculeNewSubset(unsigned int listid,
                                            unsigned int id,
                                            const std::vector<std::vector<unsigned int> > &parts)

This function creates a series of new molecules from the given molecule based on its internal components determined by OEChem using the OEDetermineComponents function.

MoleculeNewSubsetScoped

std::vector<unsigned int> MoleculeNewSubsetScoped(unsigned int listid,
                                                  unsigned int scope, bool pdb)
std::vector<unsigned int> MoleculeNewSubsetScoped(unsigned int listid,
                                                  unsigned int mscope,
                                                  unsigned int scope,
                                                  bool unmatched)

This function creates a series of new molecules from the given scope based on its internal components determined by OEChem using the OEDetermineComponents function.

MoleculeResidueNameSetScoped

void MoleculeResidueNameSetScoped(const std::string &name,
                                  unsigned int scope = BestScope)

Renames all the residues in the specified scope.

MoleculeResidueSet

int MoleculeResidueSet(unsigned int id, int residueNum,
                       bool incrementPerRes=false)

Sets the residue number of every residue in the specified molecule to the specified value (residueNum). The incrementPerRes parameter is currently reserved for future expansion.

MoleculeSetProperty

void MoleculeSetProperty(const std::vector<OEPropDB::OEKey> &keys,
                         unsigned char action, std::string prop, bool state)

Reserved for internal use.

MoleculeSizeCutoffGet

unsigned int MoleculeSizeCutoffGet()

Returns the atom number cutoff at which point a molecule is considered to be a “large” molecule. The default is 255.

MoleculeSizeCutoffSet

void MoleculeSizeCutoffSet(unsigned int size)

Sets the atom number cutoff at which point a molecule is considered to be a “large” molecule. The default is 255.

MoleculeUpdate

bool MoleculeUpdate(OEChem::OEMCMolBase &)

Updates the original molecule stored in VIDA with any changes that may have been made to the specified Python molecule.

NameGet

std::string NameGet(unsigned int)
std::string NameGet(const OEPropDB::OEKey &)

Returns the name of the object specified by either its ID or key.

NameSet

void NameSet(unsigned int, const std::string &)
void NameSet(const OEPropDB::OEKey &, const std::string &)

Sets the name of the object specified by either its ID or key.

OEFuseKeyGroups

OEKeyGroup OEFuseKeyGroups(const std::vector<OEKeyGroup> &k1,
                           unsigned char type)

Fuses the specified keys groups into a single key group.

OEKeyIterToVector

std::vector<OEPropDB::OEKey>
  OEKeyIterToVector(OESystem::OEIterBase<const OEPropDB::OEKey> *iterbase)

Converts a key iterator into a list of keys.

PropertyTypeGet

unsigned int PropertyTypeGet(const std::string &type)

Returns the integer property type for the string type. See KeyTypeGet for a list of types.

SDDataGet

std::string SDDataGet(unsigned int id, const std::string &tag)
std::string SDDataGet(const OEPropDB::OEKey &key, const std::string &tag)

Returns the SD data associated with the specified tag on the specified object.

SDDataHas

bool SDDataHas(unsigned int id, const std::string &tag)
bool SDDataHas(const OEPropDB::OEKey &key, const std::string &tag)

Returns whether or not the specified object contains SD data with the specified tag.

SDDataSet

void SDDataSet(unsigned int id, const std::string &tag, const std::string &data)
void SDDataSet(const OEPropDB::OEKey &key, const std::string &tag,
               const std::string &data)

Sets the value of the SD data associated with the specified tag on the specified object.

SurfaceAdd

unsigned int SurfaceAdd(OESpicoli::OESurface &surf, unsigned int listID = 0)

Adds a new Python surface object to VIDA. Returns the ID assigned to the newly added surface or zero if the add failed for any reason. If the optional listID argument is provided, then the surface is added to the specified list. Otherwise, a new list is created and the surface is added to it.

SurfaceBestFloodScoped

int SurfaceBestFloodScoped(unsigned int scope = BestScope)

Return the largest flood value for all surfaces in the given scope. A flood value defines the surface being scribed.

SurfaceCheckIn

bool SurfaceCheckIn(OESpicoli::OESurface &surf,
                    unsigned int checkInType = OECheckInType_UnknownChange)

Checks the specified Python accessible surface back into the main VIDA application which will synchronize any changes made to the surface in Python with the surface in VIDA. The surface in question must have been checked out of VIDA prior to being checked back in.

The checkInType parameter tells VIDA what type of changes were made to the surface in order to optimize the check in process. There are multiple allowable values for this parameter which can be OR’d together if necessary:

  • OECheckInType_ConformerChange
  • OECheckInType_CoordinateChange
  • OECheckInType_DataChange
  • OECheckInType_GraphChange
  • OECheckInType_NoChange
  • OECheckInType_RenderChange
  • OECheckInType_AnnotationChange
  • OECheckInType_UnknownChange

SurfaceCheckOut

bool SurfaceCheckOut(OESpicoli::OESurface &surf, unsigned int id)

Checks out a copy of the surface specified by id into the specified Python surface object (surf). Returns whether or not the check out process succeeded.

The checked out surface can be modified in Python, but those changes will not be applied to the original surface in VIDA until the modified surface is checked back in using the SurfaceCheckIn command.

SurfaceCreate

unsigned int SurfaceCreate(const std::string &, const OEPropDB::OEKey &key,
                           bool property=false)

Create a surface of type type based on the molecule represented by key.

If property is true, then make the surface a property surface that is bound to the molecule.

SurfaceCreateScoped

bool SurfaceCreateScoped(const std::string &, bool single_surface=false,
                         unsigned int scope = BestScope)

Create a surface of type type for each molecule in scope.

If property is true, then make the surface a property surface that is bound to the molecule.

SurfaceCropDistance

void SurfaceCropDistance(unsigned int id, float distance)

Retains the section of the surface specified by oerid to a distance dist from the selected set of atoms.

SurfaceCropDistanceFrom

void SurfaceCropDistanceFrom(const OEPropDB::OEKey &s, const OEPropDB::OEKey &,
                             float distance)

Retains the section of the surface specified by s based on its distance to another object. The reference object can be a molecule or another surface. The distance cutoff is measured in Angstroms.

SurfaceCropScribedScoped

void SurfaceCropScribedScoped(unsigned int scope = BestScope)

Retains the section of all surfaces in scope to a distance dist from the selected set of atoms.

SurfaceCropUnscribedScoped

void SurfaceCropUnscribedScoped(unsigned int scope = BestScope)

Remove the scribed sections of all scribed surfaces in scope.

SurfaceDelete

void SurfaceDelete(unsigned int id)

Delete the surface specified by id.

SurfaceGenerateBox

unsigned int SurfaceGenerateBox(float x, float y, float z, float width,
                                float height, float depth)

Creates and returns the id of a surface representing a box as determined by the parameters x, y, z, width, height, and depth.

SurfaceGenerateSphere

unsigned int SurfaceGenerateSphere(float x, float y, float z, float radius,
                                   int level=10)

Creates and returns the id of a surface representing a sphere as determined by the parameters x, y, z, and radius. The level parameter specifies how many iterations should be used in determining the quality of the surface.

SurfaceGenerateSpline

unsigned int SurfaceGenerateSpline(const std::vector<float> &coords,
                                   int splineResolution, int seq_res,
                                   int cross_res, float width, float thick,
                                   int splineType, int style)

Creates and returns the id of a surface representing a spline as determined by the parameters coords, splineResolution, seq_res, cross_res, width, thick, splineType, and style.

SurfacePickTriangle

void SurfacePickTriangle(unsigned int oerid, const OEPropDB::OEKey &trikey,
                         bool addtriangle=false)

Pick a surface triangle specified by trikey. Ordinarily, this function does not need to be called.

SurfaceProbeRadiusGet

float SurfaceProbeRadiusGet()

Get the probe radius used when creating surfaces.

SurfaceProbeRadiusSet

float SurfaceProbeRadiusSet(float radius)

Set the probe radius to radius that is used when creating surfaces.

SurfaceResolutionGet

float SurfaceResolutionGet()

Get the resolution used when creating surfaces.

SurfaceResolutionSet

float SurfaceResolutionSet(float res)

Set the resolution used when creating surfaces. The resolution is set to resolution.

SurfaceRestoreScoped

void SurfaceRestoreScoped(unsigned int scope = BestScope)

Restore all surfaces in scope to their original states.

SurfaceScribeScoped

void SurfaceScribeScoped(int flood,
                         unsigned int scope = BestScope)

Scribe all scribed surfaces in scope to include all portions of the surface that fall within flood. Ordinarily, this function does not need to be called.

SurfaceSetPotentialFromGrid

void SurfaceSetPotentialFromGrid(unsigned int id, unsigned int gridid)

Sets the surface potential for the specified surface using the values in the specified grid.

SurfaceSetPotentialFromGridScoped

void SurfaceSetPotentialFromGridScoped(unsigned int gridid,
                                       unsigned int scope = BestScope)

Sets the surface potential for all the surfaces in the specified scope using the values in the specified grid.

SurfaceVolume

float SurfaceVolume(unsigned int id)

Returns the enclosed volume of surface id.

SymmetryNumOperators

unsigned int SymmetryNumOperators(unsigned int id)

This function returns the number of symmetry operators for the specified id.

SymmetryOperatorEnabledGet

bool SymmetryOperatorEnabledGet(unsigned int id, unsigned int operatorNumber)

SymmetryOperatorEnabledSet

bool SymmetryOperatorEnabledSet(unsigned int id, unsigned int operatorNumber,
                                bool enable)

SymmetryRadiusGet

float SymmetryRadiusGet()

SymmetryRadiusSet

float SymmetryRadiusSet(float r)

SymmetryRealize

unsigned int SymmetryRealize(unsigned int id, bool make_new_mol,
                             std::vector<float> center=std::vector<float>(),
                             float radius=0.0f)

XRayAutoMapCalculationPrefsSet

void XRayAutoMapCalculationPrefsSet()
void XRayAutoMapCalculationPrefsSet(const std::string &map1,
                                                  const std::string &map2="")

Set the map types for maps which should be calculated automatically after reading a reflection file.

XRayCalculateMap

unsigned int XRayCalculateMap(unsigned int map_id,
                              unsigned int refln_id,
                              std::string map_type)
unsigned int XRayCalculateMap(unsigned int map_id,
                              unsigned int refln_id,
                              unsigned int map_type)

This set of overloaded functions calculates a map for the set of reflection data specified by ‘refln_id’. If ‘map_id’ is non-zero, then the map replaces the grid with that ID. Otherwise, an entirely new map is created. The string ‘map_type’ parameter may be one of: Fo, Fc, 2Fo-Fc, Fo-Fc, 3Fo-2Fc, 5Fo-3Fc, Fo*Fo, or Fo*FOM, while the integer version may be one of: 0 Fo, 1 Fc, 2 TwoFoFc, 3 FoFc, 4 ThreeFoTwoFc, 5 FiveFoThreeFc, 8 FoSquared, 9 FoFom.

XRayCalculatePhases

bool XRayCalculatePhases(unsigned int refln_id,
                         unsigned int model_id)

This is experimental, and should not be called by the user.

XRayGetCell

std::vector<float> XRayGetCell(unsigned int id)

Returns the cell constants for the given object in a list, in the order a, b, c, Alpha, Beta, Gamma.

XRayGetSpaceGroup

std::string XRayGetSpaceGroup(unsigned int id)

Returns the spacegroup name for the given object.

XRayMTZColumnNamesCurrentDefaultsGet

std::vector<std::string> XRayMTZColumnNamesCurrentDefaultsGet()

XRayMTZColumnNamesGet

std::vector<std::string> XRayMTZColumnNamesGet()
bool XRayMTZColumnNamesGet(std::vector<std::string> &names)

Fills up the input list/vector with the MTZ file column names as specified by XRayMTZColumnNamesSet. Unless XRayMTZColumnNamesSet was called with the permanent flag, this function will only work once per call to XRayMTZColumnNamesSet.

This function returns True if it successfully filled out the list/vector, or False otherwise.

XRayMTZColumnNamesSet

void XRayMTZColumnNamesSet(const std::vector<std::string> &names,
                           bool permanent=false)

Stores a list of column names for mtz files. The next time an MTZ file is read, instead of prompting the user, the column names are taken from the list/vector passed to this function. The column names are in the order Fo, Phi, Fc, PhiC, Sigma, FOM, RFree. If the permanent flag is set to True, then these values are used instead of prompting until the program exits. If permanent is false, then the values are only used once.

In a script, there’s no reason to call this command instead of pre-specifying the prompt results with PromptResponseVectMulti, as shows up in the journal file. However, if creating a function which will read an MTZ file directly then this command is needed since the PromptResponse commands don’t work in interactive commands.

XRayMTZColumnNamesStandardDefaultsGet

std::vector<std::string> XRayMTZColumnNamesStandardDefaultsGet()

XRaySetCrystalParams

bool XRaySetCrystalParams(unsigned int id,
                          unsigned int from_object_id)
bool XRaySetCrystalParams(unsigned int id,
                          std::vector<float> cell,
                          unsigned int sg)
bool XRaySetCrystalParams(unsigned int id,
                          std::vector<float> cell,
                          const std::string &sgname)
bool XRaySetCrystalParams(unsigned int id, float a, float b,
                          float c, float alpha, float beta,
                          float gamma, unsigned int sg)
bool XRaySetCrystalParams(unsigned int id, float a, float b,
                          float c, float alpha, float beta,
                          float gamma, const std::string &sgname)

Set the crystal parameters for the given reflection. The parameters may be specified in multiple ways, which are obvious from the names of the arguments.

XRayValidMaptypes

std::string XRayValidMaptypes(unsigned int refln_id)

Not all map types are available for every reflection data set, since not all files have all required data for every possible map calculation. For example, a reflection data set without Fc data will not be able to calculate any map types which require Fc. This function returns (as a string), the valid map types for the given reflection data set. The string is a concatenation of all available map types, with each type separated by the ‘|’ character.

Molecule Builder Functions

The functions detailed in this section provide the ability to create new molecules from basic inputs and to modify existing ones.

AtomAddHydrogens

void AtomAddHydrogens(const OEPropDB::OEKey &k, bool polaronly=false)

Adds explicit hydrogens to the specified atom. If polaronly is set to True, this will only add polar hydrogens to the specified atom.

AtomAddHydrogensScoped

void AtomAddHydrogensScoped(bool polaronly=false,
                            unsigned int scope = SelectedScope)

Scoped version of AtomAddHydrogens.

AtomAtomicNumDefaultGet

unsigned int AtomAtomicNumDefaultGet()

Returns the default value of the atomic number to be used when setting the atom