MarvinSketch : 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 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 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 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) user has to set the extraBonds parameter to an empty String.
In any other cases, 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		  
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 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 arrow head in Angstroms. It only affects graphical arrows. 0.8
sketchArrowHeadWidth Width of the displayed arrow head 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 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 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