Package chemaxon.marvin.common

Class UserSettings

  • All Implemented Interfaces:
    chemaxon.marvin.services.ServicesConfigURLProvider
    @PublicAPI
public class UserSettings
extends Object
implements chemaxon.marvin.services.ServicesConfigURLProvider
    Represents the settings of the MarvinSketch and MarvinView applications. Loads the default configuration, and the configuration properties that are stored in the configuration file that is given. The default constructor uses the marvin.properties file. The class loads files from the Chemaxon configuration directory in the home directory of the user.

    This class uses different containers to store the properties, one for the default settings one for the settings that are different from the default and has to be stored between two session, they called as the persistent properties, and a temporary store for the properties that are required only for the actual session of the application.

    The class gives specific getters and setters for the persistent properties but developers can use the setPersistentProperty and getPersistentProperty to define properties that has to be stored. The very default properites can be found in this file: chemaxon/marvin/common/UserSettings_defaultprops.properties The persistent properties are stored in the %USER_HOME%/chemaxon/marvin.properties or in the ~/.chemaxon/marvin.properties file, or in this directories, but the given filename, if constructing the object with a filename.

    Since:
    Marvin 3.0, 12/16/2002

    • Field Detail

      • PROPERTY_TYPE_TRANSIENT

        public static final String PROPERTY_TYPE_TRANSIENT
        Constant to use as the type parameter of getPropertyMap(String) method to get the properties that are being stored temporary, and will not be saved to the properties file.
        Since:
        Marvin 5.4
        See Also:
        Constant Field Values

      • MAX_RECENT_FILE_LIST_SIZE

        public static final int MAX_RECENT_FILE_LIST_SIZE
        The maximum size of sketchRecentFileList
        Since:
        Marvin 5.4
        See Also:
        Constant Field Values

      • MIN_RECENT_FILE_LIST_SIZE

        public static final int MIN_RECENT_FILE_LIST_SIZE
        The minimum size of sketchRecentFileList
        Since:
        Marvin 5.4
        See Also:
        Constant Field Values

    • Constructor Detail

      • UserSettings

        public UserSettings()
        Construct a UserSettings object based on the default configuration, and the marvin.properties file stored in the chemaxon settings directory in the home directory of the user.

      • UserSettings

        public UserSettings​(String configFileName)
        Construct a UserSettings object based on the default configuration, and the file stored in the chemaxon settings directory in the home of the user.
        Parameters:
        configFileName - the name of the config file name in the chemaxon settings directory.
        Since:
        Marvin 5.4

      • UserSettings

        public UserSettings​(InputStream input)

      • UserSettings

        public UserSettings​(UserSettings settings)
        Copy consturctor. Creates a new UserSettings object based on the one given as a parameter. It copies every property from the given UserSettings object one by one.
        Parameters:
        settings - the object to copy.
        Since:
        Marvin 5.4

    • Method Detail

      • getPropertyMap

        public Map<String,​String> getPropertyMap()
        Shortcut to getPropertyMap(UserSettings.PROPERTY_TYPE_ALL)
        Returns:
        all properties that are stored in this object as a map.
        Since:
        Marvin 5.4

      • save

        public void save​(String comment)
          throws IOException
        Save the persistent properties to the config file set by the constructor.
        Parameters:
        comment - comment at the beginning of file
        Throws:
        IOException - error occurred while saving

      • save

        public void save​(String fileName,
                 String comment)
          throws IOException
        Save the persistent properties to the file given as the first parameter. The config file will be placed into the chemaxon settings directory in the home directory of the user.
        Parameters:
        fileName - the name of the config file.
        comment - the comment that will be place to the beginning of the saved file
        Throws:
        IOException - if the file cannot be written.

      • addOwner

        public void addOwner​(PropertyChangeListener o)
        Adds an owner, that should be notified about the changes in the properties. One UserSettings object can have more owners.
        Parameters:
        o - the owner

      • removeOwner

        public void removeOwner​(PropertyChangeListener o)
        Removes an owner.
        Parameters:
        o - the owner

      • getOwnerCount

        public int getOwnerCount()
        Gets the current number of owners.
        Returns:
        the number of owners of this UserSettings object

      • addPropertyChangeListener

        public void addPropertyChangeListener​(PropertyChangeListener l)
        Add a property change listener
        Parameters:
        l - the property change listener

      • removePropertyChangeListener

        public void removePropertyChangeListener​(PropertyChangeListener l)
        Remove a property change listener
        Parameters:
        l - the property change listener

      • getDefaultProperty

        public String getDefaultProperty​(String key)
        Gets the value of the given key in the default configuration or null if the key does not exist.
        Parameters:
        key - the key of the value that has to be returned.
        Returns:
        the default value of the property or null
        Since:
        Marvin 5.4

      • getProperty

        public String getProperty​(String key)
        Returns the value for the given key. If the key is not found in the persistent properties, then returns the value from the transient properties. If it did not find the key, then returns null.
        Parameters:
        key - the key of the value that has to be returned.
        Returns:
        the property value or null
        Since:
        Marvin 5.4

      • setProperty

        public void setProperty​(String key,
                        String value)
        Sets a property for the given key with the given value. Properties are stored in the config file, if the value is different from the default value.
        Parameters:
        key - the key for the property.
        value - the value of the property.
        Since:
        Marvin 5.4

      • setProperty

        public void setProperty​(String key,
                        String value,
                        boolean isPersistent)
        Sets a property for the given key with the given value. Properties are stored in the config file, if the value is different from the default value and isPersistent is true.
        Parameters:
        key - the key for the property.
        value - the value of the property.
        isPersistent - if set to false, and persistent properties not contains the given key, then stores the value in a temporary storage, and the property will not be saved into the config file. If true, then the method does the same as the setProperty(String, String) method.
        Since:
        Marvin 5.4

      • removeAllProperty

        public void removeAllProperty()
        Removes all property that are stored in this UserSettings object. It does not hurt the default values.

      • setTerminalBondDeletionStyle

        public void setTerminalBondDeletionStyle​(String style)
        Sets the bond deletion style. Meaningful values: "withAtom", "withoutAtom" If either is set, the terminal bond is being deleted with the eraser tool with or without the atom by default, and the opposite if the ALT button is pressed while clicking.
        Parameters:
        style - the default operation style

      • getTerminalBondDeletionStyle

        public String getTerminalBondDeletionStyle()
        Gets the terminal bon deletion style.
        Returns:
        the bond deletion style.

      • setAutoCheckStructure

        public void setAutoCheckStructure​(boolean b)
        Turn on automatic Structure checking
        Parameters:
        b - true (on) / false (off)

      • isAutoCheckStructure

        public boolean isAutoCheckStructure()
        Tells whether the automatic structure checking is enabled or not
        Returns:
        true if enabled false otherwise.

      • getViewColorScheme

        public String getViewColorScheme()
        Gets the viewer's default color scheme.
        Returns:
        the color scheme

      • setViewColorScheme

        public void setViewColorScheme​(String c)
        Sets the viewer's default color scheme.
        Parameters:
        c - the color scheme. (See the colorScheme parameter.)

      • getSketchColorScheme

        public String getSketchColorScheme()
        Gets the sketcher's default color scheme.
        Returns:
        the color scheme

      • setSketchColorScheme

        public void setSketchColorScheme​(String c)
        Sets the sketcher's default color scheme.
        Parameters:
        c - the color scheme. (See the colorScheme parameter.)

      • getSketchMolbg2d

        public Color getSketchMolbg2d()
        Gets the sketcher's default 2D molecule background color.
        Returns:
        the color
        Since:
        Marvin 4.1, 01/26/2006

      • setSketchMolbg2d

        public void setSketchMolbg2d​(Color c)
        Sets the sketcher's default 2D molecule background color.
        Parameters:
        c - the color
        Since:
        Marvin 4.1, 01/26/2006

      • getSketchMolbg3d

        public Color getSketchMolbg3d()
        Gets the sketcher's default 3D molecule background color.
        Returns:
        the color
        Since:
        Marvin 4.1, 01/26/2006

      • setSketchMolbg3d

        public void setSketchMolbg3d​(Color c)
        Sets the sketcher's default 3D molecule background color.
        Parameters:
        c - the color
        Since:
        Marvin 4.1, 01/26/2006

      • getViewMolbg2d

        public Color getViewMolbg2d()
        Gets the viewer's default molecule background color for 2D.
        Returns:
        the color
        Since:
        Marvin 3.1.3

      • setViewMolbg2d

        public void setViewMolbg2d​(Color c)
        Sets the default molecule background color for the 2D viewer.
        Parameters:
        c - the color
        Since:
        Marvin 3.1.3

      • getViewMolbg3d

        public Color getViewMolbg3d()
        Gets the viewer's default molecule background color for 3D.
        Returns:
        the color
        Since:
        Marvin 3.1.3

      • setViewMolbg3d

        public void setViewMolbg3d​(Color c)
        Sets the default molecule background color for the 3D viewer.
        Parameters:
        c - the color
        Since:
        Marvin 3.1.3

      • getSketchImplicitH

        public String getSketchImplicitH()
        Gets the display method of implicit hydrogens for the sketcher.
        Returns:
        the method

      • setSketchImplicitH

        public void setSketchImplicitH​(String s)
        Sets the display method of implicit hydrogens for the sketcher.
        Parameters:
        s - the method. (See the implicitH parameter.)

      • getViewImplicitH

        public String getViewImplicitH()
        Gets the display method of implicit hydrogens for the viewer.
        Returns:
        the method

      • setViewImplicitH

        public void setViewImplicitH​(String s)
        Sets the display method of implicit hydrogens for the viewer.
        Parameters:
        s - the method. (See the implicitH parameter.)

      • getViewAnyBond

        public String getViewAnyBond()
        Gets the default any bond drawing style in the viewer.
        Returns:
        "auto", "dashed" or "solid"

      • setViewAnyBond

        public void setViewAnyBond​(String v)
        Sets the default any bond drawing style in the viewer.
        Parameters:
        v - "auto", "dashed" or "solid"

      • getSketchAnyBond

        public String getSketchAnyBond()
        Gets the default any bond drawing style in the sketcher.
        Returns:
        "auto", "dashed" or "solid"

      • setSketchAnyBond

        public void setSketchAnyBond​(String v)
        Sets the default any bond drawing style in the sketcher.
        Parameters:
        v - "auto", "dashed" or "solid"

      • getDownWedge

        public String getDownWedge()
        Gets the wedge bond display convention. Down wedge points downward in MDL's convention, upward (at the chiral center) in Daylight's.
        Returns:
        "mdl" or "daylight"

      • setDownWedge

        public void setDownWedge​(String s)
        Sets the convention to use for displaying a down wedge.
        Parameters:
        s - "mdl" or "daylight"

      • getCoordinateBondStyle

        public String getCoordinateBondStyle()
        Gets the "coordinative" bond line style when both atoms are single.
        Returns:
        "solid" or "arrow"

      • setCoordinateBondStyle

        public void setCoordinateBondStyle​(String s)
        Sets the "coordinative" bond line style when both atoms are single.
        Parameters:
        s - "solid" or "arrow"

      • getCoordinateBondStyleAtMulticenter

        public String getCoordinateBondStyleAtMulticenter()
        Gets the "coordinative" bond line style when one of the atoms is multicenter.
        Returns:
        "solid" or "hashed"

      • setCoordinateBondStyleAtMulticenter

        public void setCoordinateBondStyleAtMulticenter​(String s)
        Sets the "coordinative" bond line style when one of the atoms is multicenter.
        Parameters:
        s - "solid" or "hashed"

      • isBondDraggedAlong

        public boolean isBondDraggedAlong()
        Is the currently used bond shown at the mouse cursor?
        Returns:
        true if the bond is dragged along by the mouse cursor, false otherwise
        Since:
        Marvin 3.5, 09/30/2004

      • setBondDraggedAlong

        public void setBondDraggedAlong​(boolean v)
        Sets the visibility of the currently used bond at the mouse cursor.
        Parameters:
        v - true to drag along the bond by the mouse cursor, false to hide it
        Since:
        Marvin 3.5, 09/30/2004

      • getCopyAsFormat

        public String getCopyAsFormat()
        Gets the selected format from the Copy As dialog.
        Returns:
        the selected format
        Since:
        5.0 10/05/2007

      • setCopyAsFormat

        public void setCopyAsFormat​(String fmt)
        Sets the selected format in the Copy As dialog.
        Parameters:
        fmt - copy as format to select
        Since:
        5.0 10/05/2007

      • getDefaultSaveFormat

        public String getDefaultSaveFormat()
        Gets the default molecule format in the "Save As" dialog.
        Returns:
        the format string
        Since:
        Marvin 4.1.19 07/06/2007

      • setDefaultSaveFormat

        public void setDefaultSaveFormat​(String s)
        Sets the default molecule format in the "Save As" dialog. If the user saves a structure into a new file, "mrv" is the selected output format, in default. Use this method to change it. Example: To select "MDL SDfile" in "Files of Type" combo of the save dialog, set "sdf" as default save format. 
         settings.setDefaultSaveFormat("sdf");
        Parameters:
        s - the format
        Since:
        Marvin 4.1.19 07/06/2007
        See Also:
        MarvinPane.setFormat(String)

      • isValenceErrorVisibleInView

        public boolean isValenceErrorVisibleInView()
        Are valence errors visible in MarvinView?
        Returns:
        True, if valence errors are shown
        Since:
        Marvin 5.0.1

      • setValenceErrorVisibleInView

        public void setValenceErrorVisibleInView​(boolean v)
        Show or hide valence errors in MarvinView
        Parameters:
        v - underline valence errors if true
        Since:
        Marvin 5.0.1

      • isvalidateSgroupsAtCreation

        public boolean isvalidateSgroupsAtCreation()
        Is the validation of the possible sgroups and allow only the chemically correct ones on sgroups creation and edit dialog.
        Returns:
        true if validation is on, false otherwise.

      • setvalidateSgroupsAtCreation

        public void setvalidateSgroupsAtCreation​(boolean b)
        Set the validation of the possible sgroups and allow only the chemically correct ones on sgroups creation and edit dialog.
        Parameters:
        b - true means validate, false means not validate

      • isValenceErrorVisible

        public boolean isValenceErrorVisible()
        Are valence errors visible?
        Returns:
        True, if valence errors are shown

      • setValenceErrorVisible

        public void setValenceErrorVisible​(boolean v)
        Show or hide valence errors
        Parameters:
        v - underline valence errors if true

      • isEZVisible

        public boolean isEZVisible()
        Are E/Z labels visible?
        Returns:
        True, if E/Z labels are shown

      • setEZVisible

        public void setEZVisible​(boolean v)
        Show or hide E/Z labels
        Parameters:
        v - show E/Z labels if true

      • getAbsoluteLabelVisible

        public String getAbsoluteLabelVisible()
        Are Absolute labels visible?
        Returns:
        True, if Absolute labels are shown

      • setAbsoluteLabelVisible

        public void setAbsoluteLabelVisible​(String v)
        Show or hide Abolute labels
        Parameters:
        v - show Absolute labels if true

      • isLonePairAutoCalc

        public boolean isLonePairAutoCalc()
        Returns the state of the automatic lone pair calculation.
        Returns:
        true if lone pairs are calculated automatically

      • setLonePairAutoCalc

        public void setLonePairAutoCalc​(boolean v)
        Sets the state of the automatic lone pair calculation. In case of automatic calculation on, the visibility of lone pairs should also be set to have the results displayed properly.
        Parameters:
        v - true if lone pairs should be calculated automatically

      • getSketchRendering2d

        public String getSketchRendering2d()
        Gets the rendering style for the 2D sketcher.
        Returns:
        the style
        Since:
        Marvin 4.1, 01/26/2006

      • setSketchRendering2d

        public void setSketchRendering2d​(String s)
        Sets the rendering style for the 2D sketcher.
        Parameters:
        s - the style. (See the rendering parameter.)
        Since:
        Marvin 4.1, 01/26/2006

      • getSketchRendering3d

        public String getSketchRendering3d()
        Gets the rendering style for the 3D sketcher.
        Returns:
        the style
        Since:
        Marvin 4.1, 01/26/2006

      • setSketchRendering3d

        public void setSketchRendering3d​(String s)
        Sets the rendering style for the 3D sketcher.
        Parameters:
        s - the style. (See the rendering parameter.)
        Since:
        Marvin 4.1, 01/26/2006

      • getViewRendering2d

        public String getViewRendering2d()
        Gets the rendering style for the 2D viewer.
        Returns:
        the style
        Since:
        Marvin 3.1.3

      • setViewRendering2d

        public void setViewRendering2d​(String s)
        Sets the rendering style for the 2D viewer.
        Parameters:
        s - the style. (See the rendering parameter.)
        Since:
        Marvin 3.1.3

      • getViewRendering3d

        public String getViewRendering3d()
        Gets the rendering style for the 3D viewer.
        Returns:
        the style
        Since:
        Marvin 3.1.3

      • setViewRendering3d

        public void setViewRendering3d​(String s)
        Sets the rendering style for the 3D viewer.
        Parameters:
        s - the style. (See the rendering parameter.)
        Since:
        Marvin 3.1.3

      • getViewNavmode2d

        public String getViewNavmode2d()
        Gets the navigation mode for the 2D viewer.
        Returns:
        the navigation mode
        Since:
        Marvin 3.1.3

      • setViewNavmode2d

        public void setViewNavmode2d​(String s)
        Sets the navigation mode for the 2D viewer.
        Parameters:
        s - the navigation mode. (See the navmode parameter.)
        Since:
        Marvin 3.1.3

      • getViewNavmode3d

        public String getViewNavmode3d()
        Gets the navigation mode for the 3D viewer.
        Returns:
        the navigation mode
        Since:
        Marvin 3.1.3

      • setViewNavmode3d

        public void setViewNavmode3d​(String s)
        Sets the navigation mode for the 3D viewer.
        Parameters:
        s - the navigation mode. (See the navmode parameter.)
        Since:
        Marvin 3.1.3

      • getClean2dOpts

        public String getClean2dOpts()
        Gets the 2D cleaning options.
        Returns:
        the cleaning options
        Since:
        Marvin 3.1.3

      • setClean2dOpts

        public void setClean2dOpts​(String s)
        Sets the 2D cleaning options.
        Parameters:
        s - the cleaning options. (See the clean2dOpts parameter.)
        Since:
        Marvin 3.1.3

      • isCleanHOptionEnabled

        public boolean isCleanHOptionEnabled()
        Returns true if the H option for cleaning is enabled.
        Returns:
        true if an explicit hydrogen atom is added to chiral centers having no terminal atoms
        Since:
        Marvin 5.1.5

      • setCleanHOptionEnabled

        public void setCleanHOptionEnabled​(boolean b)
        Sets to add an explicit hydrogen atom to chiral centers having no terminal atoms when 2D cleaning is performed.
        Parameters:
        b - true to add Hydrogen atoms
        Since:
        Marvin 5.4

      • isViewAtomMarkEnabled

        public boolean isViewAtomMarkEnabled()
        Returns true if atom mark and highlight is enabled in View.
        Returns:
        true if atom mark and highlight is enabled in View.
        Since:
        Marvin 5.8

      • setViewAtomMarkEnabled

        public void setViewAtomMarkEnabled​(boolean b)
        Sets atom mark and highlight visibility in Marvin View.
        Parameters:
        b - true to add Hydrogen atoms
        Since:
        Marvin 5.8

      • setCleanHOption

        @Deprecated
public void setCleanHOption​(boolean b)
        Deprecated.
        As of release 5.4, replaced by setCleanHOptionEnabled(boolean)
        Sets to add an explicit hydrogen atom to chiral centers having no terminal atoms when 2D cleaning is performed.
        Parameters:
        b - true to add Hydrogen atoms
        Since:
        Marvin 5.1.5, 20/12/2008

      • getClean3dOpts

        public String getClean3dOpts()
        Gets the 3D cleaning options.
        Returns:
        the cleaning options
        Since:
        Marvin 3.1.3

      • setClean3dOpts

        public void setClean3dOpts​(String s)
        Sets the 3D cleaning options.
        Parameters:
        s - the cleaning options. (See the clean2dOpts parameter.)
        Since:
        Marvin 3.1.3

      • getAtomMappingMethod

        public int getAtomMappingMethod()
        Gets the atom mapping method.
        Returns:
        MolEditor.MAPATOMS_CHANGING or MolEditor.MAPATOMS_COMPLETE or MolEditor.MAPATOMS_MATCHING
        Since:
        Marvin 5.0, 09/26/2007

      • setAtomMappingMethod

        public void setAtomMappingMethod​(int method)
        Sets the atom mapping method.
        Parameters:
        method - MolEditor.MAPATOMS_CHANGING or MolEditor.MAPATOMS_COMPLETE or MolEditor.MAPATOMS_MATCHING
        Since:
        Marvin 5.0, 09/26/2007

      • getAtomNumberingType

        public int getAtomNumberingType()
        Gets the atom numbering type.
        Returns:
        0 for no numbering, 1 for atom numbers and 2 for IUPAC numbering.

      • setAtomNumberingType

        public void setAtomNumberingType​(int type)
        Sets the atom numbering type.
        Parameters:
        type - 0 for no numbering, 1 for atom numbers and 2 for IUPAC numbering.

      • getAtomFont

        public Font getAtomFont()
        Gets the atom symbol font name.
        Returns:
        the font name
        Since:
        Marvin 3.4, 06/16/2004

      • setAtomFont

        public void setAtomFont​(Font f)
        Sets the atom symbol font name.
        Parameters:
        f - the font name
        Since:
        Marvin 3.4, 06/16/2004

      • getAtomSize

        public double getAtomSize()
        Gets the atom size in C-C bond length units.
        Returns:
        the atom size
        Since:
        Marvin 3.4, 06/16/2004

      • setAtomSize

        public void setAtomSize​(double r)
        Sets the atom size in C-C bond length units.
        Parameters:
        r - the atom size. (See the atomsize parameter.)
        Since:
        Marvin 3.4, 06/16/2004

      • getBoldBondWidth

        public double getBoldBondWidth()
        Gets the bold bond width in pt.
        Returns:
        the bond length of C-C bond length in pt units.

      • setBoldBondWidth

        public void setBoldBondWidth​(double w)
        Sets the bold bond width in pt.
        Parameters:
        w - the bold bond width of C-C bond bonds in pt units.
        Since:
        Marvin 15.2.16, 2/13/2015

      • getBondLength

        public double getBondLength()
        Gets the bond length in pt.
        Returns:
        the bond length of C-C bond length in pt units.

      • setBondLength

        public void setBondLength​(double w)
        Sets the bond length in pt.
        Parameters:
        w - the bond length of C-C bond bonds in pt units.
        Since:
        Marvin 4.1, 10/19/2005

      • getBondSpacing

        public double getBondSpacing()
        Gets the double bond spacing.
        Returns:
        the bond spacing in C-C bond length units.
        Since:
        Marvin 4.1, 10/19/2005

      • setBondSpacing

        public void setBondSpacing​(double w)
        Sets the double bond spacing.

        width = w*1.54 Å = w*scale pixels

        Parameters:
        w - the bond spacing in C-C bond length units.
        Since:
        Marvin 4.1, 10/19/2005

      • getBondHashSpacing

        public double getBondHashSpacing()
        Gets the bond hash spacing.
        Returns:
        the bond hash spacing in C-C bond length units.
        Since:
        Marvin 4.1, 10/19/2005

      • setBondHashSpacing

        public void setBondHashSpacing​(double w)
        Sets the bond hash spacing.
        Parameters:
        w - the bond hash spacing in C-C bond length units.
        Since:
        Marvin 4.1, 10/19/2005

      • getFogFactor

        public int getFogFactor()
        Gets the fog factor.
        Returns:
        the fog factor in a range from MolPainterCommon.NO_FOG to MolPainterCommon.STRONG_FOG.

      • setFogFactor

        public void setFogFactor​(int w)
        Sets the fog factor.
        Parameters:
        w - the fog factor in a range from MolPainterCommon.NO_FOG to MolPainterCommon.STRONG_FOG.

      • isAutomaticFogEnabled

        public boolean isAutomaticFogEnabled()
        Gets the state of automatic fog calculation mode.
        Returns:
        true if the fog is automatically calculated, false if the custom fog is applied.

      • isAutomaticReactionEnabled

        public boolean isAutomaticReactionEnabled()
        Gets the state of automatic reaction calculation mode.
        Returns:
        true if the reactions are automatically calculated, false otherwise.

      • setAutomaticFogEnabled

        public void setAutomaticFogEnabled​(boolean enable)
        Sets the fog to automatic calculation mode.
        Parameters:
        enable - True to enable automatic fog calculation. False to enable custom fog and disable automatic fog calculation.

      • setAutomaticReactionEnabled

        public void setAutomaticReactionEnabled​(boolean enable)
        Sets the calculation of reaction plus signs to automatic.
        Parameters:
        enable - True to enable automatic fog calculation. False to enable custom fog and disable automatic fog calculation.

      • setPeptideDisplayType

        public void setPeptideDisplayType​(String type)
        Sets the peptide displaying tpye. Valid values are "1-letter" and "3-letter"
        Parameters:
        type - the peptide display type

      • getPeptideDisplayType

        public String getPeptideDisplayType()
        Gets the current peptide display type
        Returns:
        the peptide display type

      • getWireThickness

        public double getWireThickness()
        Gets the bond thickness in wireframe mode.
        Returns:
        the bond thickness
        Since:
        Marvin 3.4, 06/16/2004

      • setWireThickness

        public void setWireThickness​(double d)
        Sets the bond thickness in wireframe mode.
        Parameters:
        d - the bond thickness
        Since:
        Marvin 3.4, 06/16/2004

      • getStickThickness

        public double getStickThickness()
        Gets the stick diameter for ball and stick mode.
        Returns:
        the stick thickness
        Since:
        Marvin 3.4, 06/16/2004

      • setStickThickness

        public void setStickThickness​(double d)
        Sets the stick diameter for ball and stick mode.
        Parameters:
        d - the stick thickness
        Since:
        Marvin 3.4, 06/16/2004

      • getBallRadius

        public double getBallRadius()
        Gets the ball radius for ball and stick mode.
        Returns:
        the ball radius
        Since:
        Marvin 3.4, 06/16/2004

      • setBallRadius

        public void setBallRadius​(double r)
        Sets the ball radius for ball and stick mode.
        Parameters:
        r - the ball radius
        Since:
        Marvin 3.4, 06/16/2004

      • getSketchArrowHeadLength

        public double getSketchArrowHeadLength()
        Gets the current arrow head length.
        Returns:
        the arrow head length
        Since:
        Marvin 3.5, 07/01/2004

      • setSketchArrowHeadLength

        public void setSketchArrowHeadLength​(double d)
        Sets the arrow head length.
        Parameters:
        d - the arrow head length
        Since:
        Marvin 3.5, 07/01/2004

      • getSketchArrowHeadWidth

        public double getSketchArrowHeadWidth()
        Gets the current arrow head width.
        Returns:
        the arrow head width
        Since:
        Marvin 3.5, 07/01/2004

      • setSketchArrowHeadWidth

        public void setSketchArrowHeadWidth​(double d)
        Sets the arrow head width.
        Parameters:
        d - the arrow head width
        Since:
        Marvin 3.5, 07/01/2004

      • getSketchArrowTailLength

        public double getSketchArrowTailLength()
        Gets the current arrow tail length.
        Returns:
        the arrow tail length
        Since:
        Marvin 3.5, 07/01/2004

      • setSketchArrowTailLength

        public void setSketchArrowTailLength​(double d)
        Sets the arrow tail length.
        Parameters:
        d - the arrow tail length
        Since:
        Marvin 3.5, 07/01/2004

      • getSketchArrowTailWidth

        public double getSketchArrowTailWidth()
        Gets the current arrow tail width.
        Returns:
        the arrow tail width
        Since:
        Marvin 3.5, 07/01/2004

      • setSketchArrowTailWidth

        public void setSketchArrowTailWidth​(double d)
        Sets the arrow tail width.
        Parameters:
        d - the arrow tail width
        Since:
        Marvin 3.5, 07/01/2004

      • getViewRecentFileList

        public List<String> getViewRecentFileList()
        Gets the recent files' list in MarvinView, the last item is the most recent. The list has a maximum of getViewRecentFileListSize() element.
        Returns:
        List recentFiles - List of recently used files' path
        Since:
        Marvin 5.0.1

      • addToViewRecentFileList

        public void addToViewRecentFileList​(File f)
        Add an element to marvinview's recent file list
        Parameters:
        f - the File which has to be added to the List
        Since:
        Marvin 5.0.1

      • getViewRecentFileListSize

        public int getViewRecentFileListSize()
        Gets the recent file list requested size, based on a preferences setting
        Returns:
        the recent file list size.
        Since:
        Marvin 5.1

      • setViewRecentFileListSize

        public void setViewRecentFileListSize​(int size)
        Sets the recent file list requested size, if it is smaller than zero, then the size will be zero, if it is more than 10 then the size will be 10.
        Parameters:
        size - the requested size.
        Since:
        Marvin 5.1

      • removeViewRecentFile

        public void removeViewRecentFile​(File f)
        Remove a file from marvinview's recent file list
        Parameters:
        f - the File which has to remove from the list

      • getSketchRecentFileList

        public List<String> getSketchRecentFileList()
        Gets the recent files' list at marvinsketch, the last item is the most recent. The list has a maximum of SKETCH_RECENT_FILE_LIST_SIZE element.
        Returns:
        List recentFiles - List of recently used files' paths'
        Since:
        Marvin 5.0.1

      • addToSketchRecentFileList

        public void addToSketchRecentFileList​(File f)
        Add an element to marvinsketch's recent file list
        Parameters:
        f - the File which has to be added to the List
        Since:
        Marvin 5.0.1

      • removeSketchRecentFile

        public void removeSketchRecentFile​(File f)
        Remove a file from marvinsketch's recent file list
        Parameters:
        f - the File which has to remove from the list

      • getSketchRecentFileListSize

        public int getSketchRecentFileListSize()
        Gets the recent file list requested size, based on a preferences setting
        Returns:
        the recent file list size.
        Since:
        Marvin 5.1

      • setSketchRecentFileListSize

        public void setSketchRecentFileListSize​(int size)
        Sets the recent file list requested size, if it is smaller than zero, then the size will be zero, if it is more than MAX_RECENT_FILE_LIST_SIZE then the size will be the value of MAX_RECENT_FILE_LIST_SIZE
        Parameters:
        size - the requested size.
        Since:
        Marvin 5.1

      • getLoadSaveLocation

        public String getLoadSaveLocation()
        Gets the load/save filechooser working directory selection method names, based on the preferences dialog. This method names: saveLastLocation, saveStartupLocation, and saveCustomLocation. If the $HOME/[.]chemaxon/marvin.properties contains other value, the function will defaults to saveLastLocation.
        Returns:
        the setting for load and save location based on preferences.

      • setLoadSaveLocation

        public void setLoadSaveLocation​(String s)
        Sets the load/save filechooser working directory selection method names, based on the preferences dialog. This method names: saveLastLocation, saveStartupLocation, and saveCustomLocation. If the String parameter is null then the setting will be deleted from userprops
        Parameters:
        s - the selection method name (case sensitive).

      • getLoadWorkingDir

        public File getLoadWorkingDir()
        Gets the filechooser's default working directory, if it is set, and the filechooser working directory selection method is saveCustomLocation. Otherwise return null.
        Returns:
        null, or the default filechooser working directory set on the preferences dialog.

      • setLoadWorkingDir

        public void setLoadWorkingDir​(String s)
        Sets the filechooser's default working directory, if the filechooser working directory selection method is saveCustomLocation. Does nothing otherwise If the parameter is null, then the setting will deleted from userprops.
        Parameters:
        s - the path of the directory which has to been set.

      • setMarginSize

        public void setMarginSize​(double size)
        Sets the documents margin size.
        Parameters:
        size - the size of the margin
        Since:
        Marvin 15.2.23, 2/16/2015

      • getMarginSize

        public double getMarginSize()
        Gets the documents margin size.
        Returns:
        the margin size
        Since:
        Marvin 15.2.23, 2/16/2015

      • getViewLoadWorkingDir

        public File getViewLoadWorkingDir()
        Based on the preferences this funtion returns the proper working directory for the MarvinView application's load filechooser.
        • If set on the preferences panel the startup directory, then returns the value in the user.dir system property or null if it can't be reached.
        • If set on the preferences panel the last used directory, then returns the value of the last used directory for loading, and it remembers the earlier runnings. If in the $HOME/[.]chemaxon/marvin.properties there is nothing about the last used directory, then returns the user.home system property, or null if it can't be reached.
        • If set on the preferences panel the custom directory, then returns the value which is set on the preferences panel. Or if only the custom directroy using is set, but no directory for use the function returns null
        Returns:
        the working directory for the load filechooser in MarvinView application
        Since:
        Marvin 5.0.1

      • setViewLoadWorkingDir

        public void setViewLoadWorkingDir​(String s)
        Sets the load working directory for MarvinView load filechooser. This value is stored in $HOME/[.]chemaxon/marvin.properties file The value is taking effect when on the preferences the user set either the last directory or the startup directory usage for loading. If the String parameter is null then the setting will be deleted from userprops
        Parameters:
        s - the absolute path of the directory.
        Since:
        Marvin 5.0.1

      • getViewSaveWorkingDir

        public File getViewSaveWorkingDir()
        Not implemented yet, don't use it.
        Since:
        Marvin 5.0.1

      • setViewSaveWorkingDir

        public void setViewSaveWorkingDir​(String s)
        Not implemented, don't use it.
        Parameters:
        s - the absolut path of the directory.
        Since:
        Marvin 5.0.1

      • getSketchLoadWorkingDir

        public File getSketchLoadWorkingDir()
        Based on the preferences this funtion returns the proper working directory for the MarvinSketch application's load filechooser.
        • If set on the preferences panel the startup directory, then returns the value in the user.dir system property or null if it can't be reached.
        • If set on the preferences panel the last used directory, then returns the value of the last used directory for loading, and it remembers the earlier runnings. If in the $HOME/[.]chemaxon/marvin.properties there is nothing about the last used directory, then returns the user.home system property, or null if it can't be reached.
        • If set on the preferences panel the custom directory, then returns the value which is set on the preferences panel. Or if only the custom directroy using is set, but no directory for use the function returns null
        Returns:
        the working directory for the load filechooser in MarvinSketch application
        Since:
        Marvin 5.0.1

      • setSketchLoadWorkingDir

        public void setSketchLoadWorkingDir​(String s)
        Sets the load working directory for MarvinSketch load filechooser. This value is stored in $HOME/[.]chemaxon/marvin.properties file The value is taking effect when on the preferences the user set either the last directory or the startup directory usage for loading. If the String parameter is null then the setting will be deleted from userprops
        Parameters:
        s - the absolute path of the directory.
        Since:
        Marvin 5.0.1

      • getSketchSaveWorkingDir

        public File getSketchSaveWorkingDir()
        Not implemented yet don't use it.
        Since:
        Marvin 5.0.1

      • setSketchSaveWorkingDir

        public void setSketchSaveWorkingDir​(String s)
        Not implemented yet, don't use it.
        Parameters:
        s - the absolut path of the directory.
        Since:
        Marvin 5.0.1

      • setSaveLoadZoomFactorToMRV

        public void setSaveLoadZoomFactorToMRV​(boolean b)
        Tells wether to save the zoom factor information to mrv files or not.
        Parameters:
        b - if true, marvin will save the zoom factor.

      • getSaveLoadZoomFactorToMRV

        public boolean getSaveLoadZoomFactorToMRV()
        Tells if marvin save the zoom factor to mrv or not.
        Returns:
        true if the zoom factor saving is on.

      • setSaveGUIPropertiesInMRV

        public void setSaveGUIPropertiesInMRV​(boolean flag)
        Sets whether the GUI properties should be saved when saving as a Marvin file
        Parameters:
        flag - if true, many GUI properties will be saved within the tag
        Since:
        Marvin 5.0

      • getSaveGUIPropertiesInMRV

        public boolean getSaveGUIPropertiesInMRV()
        Returns:
        true if we want to save GUI properties in the Marvin file
        Since:
        Marvin 5.0

      • getViewCarbonVisibility

        public String getViewCarbonVisibility()
        Gets the default carbon displaying style in the viewer.
        Returns:
        the style

      • setViewCarbonVisibility

        public void setViewCarbonVisibility​(String v)
        Sets the default carbon visibility style in the viewer.
        Parameters:
        v - the style

      • getViewLigandOrderVisibility

        public String getViewLigandOrderVisibility()
        Gets the default ligand order displaying style in the viewer.
        Returns:
        the style

      • setViewLigandOrderVisibility

        public void setViewLigandOrderVisibility​(String v)
        Sets the default ligand order visibility style in the viewer.
        Parameters:
        v - the style

      • getSketchCarbonVisibility

        public String getSketchCarbonVisibility()
        Gets the default carbon displaying style in the sketcher.
        Returns:
        the style

      • setSketchCarbonVisibility

        public void setSketchCarbonVisibility​(String v)
        Sets the default carbon visibility style in the sketcher.
        Parameters:
        v - the style

      • getSketchLigandOrderVisibility

        public String getSketchLigandOrderVisibility()
        Gets the default ligand order displaying style in the sketcher.
        Returns:
        the style

      • setSketchLigandOrderVisibility

        public void setSketchLigandOrderVisibility​(String v)
        Sets the default ligand order visibility style in the sketcher.
        Parameters:
        v - the style

      • isTransformationEnabled

        public boolean isTransformationEnabled()
        Gets the transformation enabled/disabled.
        Returns:
        true if on

      • setTransformationEnabled

        public void setTransformationEnabled​(boolean v)
        Enable/disable transformation
        Parameters:
        v - enabled if true

      • getViewLayout

        public int getViewLayout()
        Gets the table layout of the Viewer.
        Returns:
        the MarvinView layout identifier.

      • getRLogicVisible

        public String getRLogicVisible()
        Tells whether the R-logic is visible if exists
        Returns:
        on/off

      • setRLogicVisible

        public void setRLogicVisible​(String v)
        Sets R-logic visibility
        Parameters:
        v - (visible)/off(invisible)

      • isAtomPropertiesVisible

        public boolean isAtomPropertiesVisible()
        Tells wheter the atom properties are visible or not if exist.
        Returns:
        true/false

      • setAtomPropertiesVisible

        public void setAtomPropertiesVisible​(boolean v)
        Sets atom properties visibility.
        Parameters:
        v - true(visible)/false(invisible)

      • getCheckerConfigFileName

        @Deprecated
public String getCheckerConfigFileName()
        Deprecated.
        Use getCheckerConfigURL() instead. Deprecated in 5.12.
        Returns:
        the name of the configuration file for StructureChecker in marvin Sketch
        Since:
        5.4

      • setCheckerConfigFileName

        @Deprecated
public void setCheckerConfigFileName​(String checkerConfigFileName)
        Deprecated.
        Use setCheckerConfigURL(String) instead. Deprecated in 5.12 Sets the name of the configuration file for StructureChecker in marvin sketch
        Parameters:
        checkerConfigFileName - the name of the configuration file
        Since:
        5.4

      • getServicesConfigURL

        public String getServicesConfigURL()
        Returns the URL of configuration for Services in marvin sketch
        Specified by:
        getServicesConfigURL in interface chemaxon.marvin.services.ServicesConfigURLProvider
        Returns:
        the URL of configuration for Services in marvin sketch
        Since:
        5.6

      • setServicesConfigURL

        public void setServicesConfigURL​(String servicesConfigURL)
        Sets the URL of the configuration for Services in marvin
        Parameters:
        servicesConfigURL - the configuration URL
        Since:
        5.6

      • getCheckerConfigURL

        public String getCheckerConfigURL()
        Returns the URL of configuration for Checkers in marvin sketch.
        Returns:
        the URL of configuration for Checkers in marvin sketch
        Since:
        5.12

      • setCheckerConfigURL

        public void setCheckerConfigURL​(String checkerConfigURL)
        Sets the URL of the configuration for Checkers in marvin sketch.
        Parameters:
        checkerConfigURL - the configuration URL
        Since:
        5.12

      • getExternalCheckerConfigURL

        public String getExternalCheckerConfigURL()
        Returns the URL of the configuration file containing the list of external Checkers in marvin sketch.
        Returns:
        the URL of the configuration file containing the list of external Checkers in marvin sketch.
        Since:
        6.1

      • setExternalCheckerConfigURL

        public void setExternalCheckerConfigURL​(String checkerConfigURL)
        Sets the URL of the configuration file containing the list of external Checkers in marvin sketch.
        Parameters:
        checkerConfigURL - the URL of the configuration file containing the list of external Checkers in marvin sketch.
        Since:
        6.1

      • isValencePropertyVisible

        public boolean isValencePropertyVisible()
        Tells wheter the atom valence property is visible or not.
        Returns:
        true/false

      • setValencePropertyVisible

        public void setValencePropertyVisible​(boolean v)
        Sets atom valence property visibility.
        Parameters:
        v - true(visible)/false(invisible)

      • isLigandErrorVisible

        public boolean isLigandErrorVisible()
        Tells wheter the bond's ligand error is visible or not.
        Returns:
        true/false

      • setLigandErrorVisible

        public void setLigandErrorVisible​(boolean v)
        Show or hide ligand errors
        Parameters:
        v - show ligand errors by coloring to red if true

      • setShowMultiMoleculeOnEditSource

        public void setShowMultiMoleculeOnEditSource​(boolean show)

      • isShowMultiMoleculeOnEditSource

        public boolean isShowMultiMoleculeOnEditSource()

      • getImageImportServiceURL

        public String getImageImportServiceURL()

      • setImageImportServiceURL

        public void setImageImportServiceURL​(String url)

      • getNameIOServiceURL

        public String getNameIOServiceURL()

      • setNameIOServiceURL

        public void setNameIOServiceURL​(String url)

      • getPageFormat

        public PageFormat getPageFormat​(String s)
        Gets the specified PageFormat
        Parameters:
        s - panelType (sketch / view)
        Returns:
        the loaded PageFormat

      • setPageFormat

        public void setPageFormat​(PageFormat pageFormat,
                          String s)
        Parameters:
        pageFormat -
        s - panelType (sketch / view)

      • isDisplayLonePairsAsLine

        public boolean isDisplayLonePairsAsLine()

      • setDisplayLonePairsAsLine

        public void setDisplayLonePairsAsLine​(boolean value)

      • isDisplayChargeWithCircle

        public boolean isDisplayChargeWithCircle()

      • setDisplayChargeWithCircle

        public void setDisplayChargeWithCircle​(boolean value)

      • setDocumentStyleName

        public void setDocumentStyleName​(String name)

      • setDocumentStyleName

        public void setDocumentStyleName​(String name,
                                 boolean valuesAlreadySet)

      • getDocumentStyleName

        public String getDocumentStyleName()

      • isAminoAcidBondColoringEnabled

        public boolean isAminoAcidBondColoringEnabled()
        Gets wether the user uses peptide bridge coloring or not.
        Returns:
        true, if user uses peptide bridge coloring.

      • setAminoAcidBondColoringEnabled

        public void setAminoAcidBondColoringEnabled​(boolean b)
        Sets wether the user uses peptide bridge coloring or not.
        Parameters:
        b - if false, than we won't use peptide bridge coloring.

      • isAdvancedSave

        public boolean isAdvancedSave()
        Gets wether the useres uses advanced save or not.
        Returns:
        true, if user uses advanced save options.

      • setAdvancedSave

        public void setAdvancedSave​(boolean advanced)
        Sets wether the user prefers advanced svae or not.
        Parameters:
        advanced - if false, than we won't use advanced save.

      • isStartupSelectorShown

        public boolean isStartupSelectorShown()

      • setStartupSelectorShown

        public void setStartupSelectorShown​(boolean shown)

      • isZoomToScaffoldOnLoad

        public boolean isZoomToScaffoldOnLoad()

      • setZoomToScaffoldOnLoad

        public void setZoomToScaffoldOnLoad​(boolean zoomToScaffoldOnLoad)

      • isMPVisible

        public boolean isMPVisible()

      • setMPVisible

        public void setMPVisible​(boolean b)

      • getLastSketchFrameSize

        public Dimension getLastSketchFrameSize()

      • setLastSketchFrameSize

        public void setLastSketchFrameSize​(Dimension d)

      • getAnalysisBoxTerms

        public String getAnalysisBoxTerms()

      • setAnalysisBoxTerms

        public void setAnalysisBoxTerms​(String terms)

      • needsAnalysisBoxWarning

        public boolean needsAnalysisBoxWarning()

      • setAnalysisBoxWarning

        public void setAnalysisBoxWarning()

      • setAllowExperimentalFeatures

        public void setAllowExperimentalFeatures​(boolean b)

      • isExperimentalFeaturesAreAllowed

        public boolean isExperimentalFeaturesAreAllowed()

      • setSaveBOM

        public void setSaveBOM​(boolean b)

      • isSaveBOM

        public boolean isSaveBOM()

      • getLastViewFrameSize

        public Dimension getLastViewFrameSize()

      • setLastViewFrameSize

        public void setLastViewFrameSize​(Dimension d)

      • isGridVisible

        public boolean isGridVisible()

      • setGridVisible

        public void setGridVisible​(boolean gridVisible)

      • getDataCollectionConsent

        public chemaxon.marvin.collecting.Consent getDataCollectionConsent()

      • getOrCreateUUID

        public String getOrCreateUUID()

      • setDataCollectionConsent

        public void setDataCollectionConsent​(chemaxon.marvin.collecting.Consent consent)

      • getLastLicense

        public chemaxon.marvin.collecting.LastLicense getLastLicense()

      • setLastLicense

        public void setLastLicense​(chemaxon.marvin.collecting.LastLicense lastLicense)

      • getDataCollectionServer

        public String getDataCollectionServer()