Parameter Meaning Default autoscale
How to display a loaded molecule:
"true"
- fit to the applet's window"false"
- use default scalingfalse
viewonly
Visualization mode: hide editing buttons; "true"
or"false"
.false
verticalbarDeprecated.
statusBar
Enable the status bar. false
dispQuality
Display quality.
0
- low quality, faster rendering1
- high quality (antialiasing), slower rendering1
implicitH
How to display H labels.
off
hetero
- on heteroatomsheteroterm
- on hetero or terminal atomsall
- all atomsheteroterm
explicitH
Show explicit hydrogens. true
chiralitySupport
When to show atom chirality (R/S).
off
- neverselected
- if chiral flag is set for the molecule or the atom's enhanced stereo type is absoluteall
- alwaysoff
ezVisible
Show ( true
) or hide (false
) E/Z labels.false
backgroundDeprecated. molbg
Molecule background color in hexa. Sets the background color of the molecule canvas. See also: background colorScheme
Color scheme.
mono
- monochromecpk
- Corey-Pauling-Kultunshapely
- shapely (residue types)group
- residue sequence numberscpk
rendering
Rendering style.
wireframe
- wireframewireknobs
- wireframe with knobssticks
- 3D sticksballstick
- ball & stickspacefill
- ballswireframe
wireThickness
Line thickness for "wireframe" and "wireknobs" rendering modes, in Angstroms. 0.064 stickThickness
3D stick diameter for "sticks" and "ballstick" rendering modes, in Angstroms. 0.1 ballRadius
Ball radius for "ballstick" rendering mode, in units of covalent radius. 0.5 scale
Magnification. A 1.54 Å long C-C bond is magnified to scale pixels. 26.4 atomFont
Atom symbol/label font: Serif
,SansSerif
orMonospaced
SansSerif
atomsize
Atom symbol font size in C-C bond length units:
atomsize*1.54 Å = atomsize*scale points 0.4 bondSpacing
Double bond spacing in C-C bond length units:
spacing*1.54 Å = spacing*scale pixels 0.18 stickdst
Stick distance of atoms in C-C bond length units. 0.3 mergedst
Merge distance of atoms in C-C bond length units. 0.1 downWedge
Wedge bond display convention. Down wedge points downward in MDL's convention ( mdl
), upward (at the chiral center) in Daylight's (daylight
).mdl
importConv
Conversion(s) after molecule loading. Currently the following options are implemented:
"a" or "+a" General aromatization "a_bas" or "+a_bas" Basic aromatization "-a" dearomatization "H" or "+H" add explicit H atoms "-H" remove explicit H atoms "c" automatic cleaning cleanOpts
Options for 2D or 3D cleaning.
cleanOpts
accepts the same parameter values as clean2dOpts or clean3dOpts depending on the cleaning dimension (cleanDim).clean2dOpts
Options for 2D cleaning (0D->2D) See base 2D cleaning options clean3dOpts
Options for 3D cleaning (0D->3D) See base 3D cleaning options cleanDim
Number of space dimensions for cleaning. See also: cleanOpts, importConv.
2
- two-dimensional cleaning3
- three-dimensional cleaning2
showSets
Show the specified atom sets only. Comma separated list of set sequence numbers (0, ..., 63). setColoringEnabled
Atom/bond set coloring. true
atomSetColor0
atomSetColor1
...
atomSetColor63Atom set color in hexa. bondSetColor1
...
bondSetColor63Bond set color in hexa. undo
Maximum number of undo operations. 50 moreEnabled
Enable/disable the More button. true
elements
Comma-separated list of allowed elements ( H
,He
,Li
, ...). All elements in an atomic number interval can be specified with the shortX-Y
notation.
Example:"B-F,P-Cl"
. HereB-F
is equivalent toB,C,N,O,F
.
H-Ha queryAtoms
Comma-separated list of query atoms and properties. Example:
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,"list,notlist"
.
See also: Query properties in file formats.atomStrings
Comma-separated list of string type atom properties. Example:
alias
- atom aliasespseudo
- pseudoatomssmarts
- SMARTS query atom string"smarts"
.extraBonds
Comma-separated list of extra bond types. Example:
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"."arom,wedge"
.
See also: Query properties in file formats.reactionSupport
Enables/disables reaction arrow drawing. true
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 and the option - defines a separator line over the template name in the menu. 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:
For automatic 3D conversion, the value of the mol3dcmd field must be
z=0
- for trivial conversion,clean
- for sophisticated 2D cleaning.Template buttons may have a title if the abbreviation fields are specified. A button is rotatable if the rotation.unit field is specified (the unit rotation angle in degrees). For template tables, endrow=
clean
- for sophisticated 3D cleaning.E
can be specified for molecules in the last column. If it is not set for any molecule, then the best number of columns and rows are calculated automatically.
click here ttmpls0
ttmpls1
ttmpls2
...Templates for the toolbar. Same as tmpls but these template tables must contain only one row to fit in the toolbar. click here xtmpls
File containing extra templates. Extra templates are left to the normal templates (see tmpls) in the template panel. 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
abbrevgroups
File containing the abbreviated groups. chemaxon/marvin
/templates
/default.abbrevgroupmolFormat
Default file format: mol
,csmol
,smiles
,cxsmiles
,cml
,pdb
,pov
,sybyl
, orxyz
.mol
bondDraggedAlong
Bond in hand is visible ( true
) or not (false
). This option can also be set from the Edit/Preferences/Sketching menu.true
debug
Debug mode. Possible values: 0, 1, 2. 0 bondLengthVisible
Shows bond length labels
true
- displayfalse
- do not displayfalse
atomSymbolsVisible
Shows atom symbols
true
- displayfalse
- do not displaytrue
atomNumbersVisible
Show atom numbers
true
- displayfalse
- do not displayfalse
atomMappingVisible
Show atom mapping
true
- displayfalse
- do not displaytrue
atomPropertiesVisible
Show atom properties
true
- displayfalse
- do not displaytrue
lonePairsVisible
Show lone pairs
true
- displayfalse
- do not displayfalse
valenceErrorVisible
Highlight (by underlining) the labels of those atoms with valence errors. This option can also be set from the Edit/Preferences/Sketching menu.
true
- display errorsfalse
- do not display errorstrue
reactionErrorVisible
Highlight invalid reactions with a red rectangle around the reaction arrow. You can also change its value from Edit/Preferences/Sketching menu.
true
- display rectanglefalse
- do not display rectangletrue
grinvVisible
Set visibility of graph invariants.
true
- show graph invariantsfalse
- hide themfalse
sketchHelp
Sketcher help contents. chemaxon/marvin/help
/sketch-index.htmlsketchQuickHelp
Sketcher quick help. chemaxon/marvin/help
/sketch.htmlviewHelp
Viewer help contents. chemaxon/marvin/help
/view-index.htmlviewQuickHelp
Viewer quick help. chemaxon/marvin/help
/view.htmladdRemoveHatomsEnabled
Add/Remove -> Explicit Hydrogens is enabled or disabled in the Edit menu. It will be disabled if this parameter is false. true 2dviewerEnabled
2D viewer is allowed or not.
true
- enabledfalse
- disabledtrue 3dviewerEnabled
3D viewer is allowed or not.
true
- enabledfalse
- disabledtrue copyOpts
Output formats for the copy command. To specify more formats, enumerate them in a comma separated list.
text
- Copy As Textbitmap
- Copy As Bitmap Imageemf
- Copy As Vector Graphical Image (EMF)platform dependent defaultSaveFormat
Determines the default chemical file format in the Save As dialog. mrv sketchAnyBond
How to draw any bond in sketcher.
auto
- dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).dashed
- draw dashed linesolid
- draw solid lineauto viewAnyBond
How to draw any bond in viewer.
auto
- dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).dashed
- draw dashed linesolid
- draw solid lineauto rgroupsVisible
Show (true) or hide (false) R-group definitions. true terminalBondDeletionStyle
If set to "withAtom", the default operation of the eraser tool when clicking on a terminal bond is to delete the bond, and the terminal atom. With the ALT modifier key it is possible to delete only the bond. The default behaviour and the behaviour with the ALT key can be switched if this is being set to "withoutAtom". There is also a possibility to set this on the Preferences dialog. withAtom disablePluginsLookup
Set this to true if you want to disable the lookup for plugins.properties. To load plugins.properties form a location to enable the Tools menu, define the location of the file with toolfiles parameter. false
defaultDatatransferPolicy
Set this to true if you want to disable the search of datatransfer.properties in the codebase, and use the default configuration (mostly suitable for every use case). false