Display Parameters

Parameter

Meaning

Default

addRemoveHatomsEnabled

Add/Remove Explicit Hydrogens is enabled or disabled in the Structure menu. It will be disabled if this parameter is false.

true

atomStrings

A comma-separated list of string type atom properties to be enabled.

  • alias - atom aliases

  • pseudo - pseudoatoms

  • smarts - SMARTS query atom string

  • value - atom values

Example: "smarts".

autoscale

How to display a loaded molecule:

  • "true" - fit to the applet's window

  • "false" - use default scaling

false

bondDraggedAlong

Bond in hand is visible (true) or not (false). This option can also be set on the Edit/Preferences/MarvinSketch panel.

true

customizationEnabled

Specifies whether an end-user can customize the user interface. Setting this parameter to false disables the View/Customize dialog and the View/Configurations menu.

true

dispQuality

Display quality.

  • 0 - low quality, faster rendering

  • 1 - high quality (antialiasing), slower rendering

1

elements

A comma-separated list of allowed elements (H, He, Li, ...). All elements in an atomic number interval can be specified with the short X-Y notation.
Example: "B-F,P-Cl". Here B-F is equivalent to B,C,N,O,F.

H-Ha

extraBonds

A comma-separated list of extra bond types.
By default (if extraBonds parameter is not set) all the bond types are displayed.
To switch off all the bonds except the defaults (Single, Double, Triple) the user has to set the extraBonds parameter to an empty String.
In any other case, all the bond types to be displayed have to be listed in the extraBonds parameter besides the default bond types.

  • bold_single - Bold single bond

  • arom - Aromatic bond

  • any - Any bond

  • 1or2 - "Single or Double" query bond

  • aromany - "Single or Aromatic" and "Double or Aromatic" query bond types

  • topology - "Chain" and "Ring" bonds (in molfiles)

  • wedge - Up and Down stereo wedge bonds

  • either - "Up or Down" and "Cis or Trans"

  • ctu - "Cis or Unspecified" and "Trans or Unspecified"

  • coordinate - Coordinate bond

Example: "arom,wedge".
See also: Query Properties in Molecule File Formats

marginSize

width of margin in pt

0.8

molbg

Molecule background color in hexadecimal value. Sets the background color of the molecule canvas.

#ffffff

moreEnabled

Enable/disable the Periodic System also called More button.

true

queryAtoms

A comma-separated list of query atoms and properties.

  • any - any atom ("A" in molfile, "*" in SMARTS),

  • arom - aliphatic and aromatic, ("a" and "A" in SMARTS),

  • conn - total number of connections, ("X" in SMARTS),

  • H - total number of hydrogens, ("H" in SMARTS),

  • hetero - heteroatom ("Q" in molfile, "[!C!H]" in SMARTS),

  • list - atom list,

  • notlist - atom 'NOT' list,

  • Rgroup - Rgroups,

  • rings - "R" in SMARTS,

  • srs - smallest ring size, "r" in SMARTS,

  • val - valence, "v" in SMARTS,

Example: "list,notlist".
See also: Query Properties in Molecule File Formats

reactionSupport

Enables/disables reaction arrow drawing.

true

simpView

Visibility of the currently used bond at the mouse cursor.

sketchArrowHeadLength

Length of the displayed arrowhead in Angstroms. It only affects graphical arrows.

0.8

sketchArrowHeadWidth

Width of the displayed arrowhead in Angstroms. It only affects graphical arrows.

0.5

sketchArrowTailLength

Length of the displayed arrow tail in Angstroms. It only affects graphical arrows.

0.8

sketchArrowTailWidth

Width of the displayed arrow tail in Angstroms. It only affects graphical arrows.

0.5

statusBar

Enable the status bar.

false

tmpls0
tmpls1
tmpls2
...

The format of this parameter is :name:file, where name is the template set name, file is the sdf or cssdf file containing the template structures.
The file can be optionally compressed with GZIP (Java >= 1.1). A template molecule is automatically converted to 2D if the mol2dcmd field contains one of the following values:

  • z=0 - for trivial conversion,

  • clean - for sophisticated 2D cleaning.

For automatic 3D conversion, the value of the mol3dcmd field must be

  • clean - for sophisticated 3D cleaning.

Templates may have abbreviations if the abbreviation fields are specified.

Click here

ttmpls0
ttmpls1
ttmpls2
...

Templates to be displayed on the template toolbar. Same as tmpls but these template groups will also appear on the template toolbar by default.

Click here

template.2d

Enables (true) or disables (false) to change the visible template groups on the Advanced Templates Toolbar.
When enabled, the visibility of all template groups can be altered using the Template Library.

true

templateToolbarCustomizable

Enables (true) or disables (false) to change the visible template groups on the Advanced Templates Toolbar.
When enabled, the visibility of all template groups can be altered using the Template Library.

true

isMyTemplatesEnabled

To avoid the lookup for marvin.mytemplates file and disable the usability of the My templates on template toolbar set this property to false.

true

transferButtonIcon

Sets the location of a custom icon for the Transfer action.

transferButtonText

Sets the custom text for the Transfer action.

transferButtonVisible

Makes the Transfer button visible on the General Toolbar.

false

viewonly

Visualization mode: hide editing buttons; "true" or "false".

false

verticalbar

Deprecated.

xtmpls

The file containing extra templates. Extra templates are placed beside the normal templates and they appear on the template toolbar by default. (see tmpls).

2dviewerEnabled

Enable (true) or disable(false) 2D viewer

true

3dviewerEnabled

Enable (true) or disable(false) 3D viewer

true