MarvinSketch: parameters and events

Version 14.9.29.0

Parameters
1. Applet and JavaBeans parameters
2. Applet only parameters

1 Parameters

1.1 Applet and JavaBeans parameters

Parameters of the MSketch and JMSketch applets can be set using the <param> HTML tag.

1.1.1 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 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 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

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 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 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`

1.1.2 Structure display parameters

Parameter Meaning Default

aminoAcidBondColoringEnabled Enable (true) or disable (false) peptide bridge coloring true

absLabel Show (true) or hide (false) "Absolute" label

atomFont Atom symbol/label font: Serif, SansSerif or Monospaced SansSerif

atomFontSize Atom symbol/label font's size: 12, 14, 8, etc... 12

atomMappingVisible Show (true) or hide (false) atom mapping true

atomPropertiesVisible Show (true) or hide (false) atom properties true

atomNumbersVisible Deprecated

atomNumberingType Sets the type of atom numbering to Off (0), Atom numbers (1) or IUPAC numbering (2) 0

autoCheckStructure Enables (true) or disables (false) automatic structure check. To take effect, set statusBar parameter to true as well. false

valencePropertyVisible Show (true) or hide (false) valence properties true

atomsize Atom symbol font size in C-C bond length units:
atomsize*1.54 Å = atomsize*scale points 0.4

atomSymbolsVisible Show (true) or hide (false) atom symbols true

automaticFogEnabled Deprecated.

ballRadius Ball radius for "ballstick" rendering mode, in units of covalent radius. 0.5

bondLengthVisible Show (true) or hide (false) bond length labels false

bondSpacing Double bond spacing in C-C bond length units:
spacing*1.54 Å = spacing*scale pixels 0.18

chargeWithCircle Charge label (plus or minus sign) is displayed circled(true) or normal(false) false

chiralitySupport When to show atom chirality (R/S).

off - never

selected - if chiral flag is set for the molecule or the atom's enhanced stereo type is absolute

all - always

off

circledChargeFont Circled charge labels font: any of the fonts installed on the machine SansSerif

circledChargeSize Circled Charge labels font size in C-C bond length units:
circledChargeSize*1.54 Å = circledChargeSize*scale points 0.4

colorScheme Color scheme.

mono - monochrome

cpk - Corey-Pauling-Kultun

shapely - shapely (residue types)

group - residue sequence numbers

cpk

downWedge Wedge bond display convention. Down wedge points downward in MDL's convention (mdl), upward (at the chiral center) in Daylight's (daylight). mdl

explicitH Show (true) or hide (false) explicit hydrogens true

ezVisible Show (true) or hide (false) E/Z labels false

fogFactor Set the custom fog factor in a range from 0 to 100. The value 100 is for the strongest fog and 0 for the weakest (no) fog. 66

grinvVisible Show (true) or hide (false) graph invariants (canonical labels) false

implicitH How to display H labels.

off

hetero - on heteroatoms

heteroterm - on hetero or terminal atoms

all - all atoms

heteroterm

ligandErrorVisible Show (true) or not (false) ligand error by coloring to red true

lonePairsVisible Show (true) or hide (false) lone pairs false

lonePairsAutoCalc Switch on (true) or off (false) automatic calculation of lone pairs. The lonePairsVisible parameter should be set to true to display the result of the automatic calculation. false

maxscale Maximizes the magnification for autoscale to prevent overscaling of small molecules. It is usually set to 28, which is the scale factor for 100% magnification.

peptideDisplayType Show peptide sequences with one letter or three letter abbreviations.
Valid values are "1-letter" and "3-letter" 3-letter

reactionErrorVisible Deprecated. false

rendering Rendering style.

wireframe - wireframe

wireknobs - wireframe with knobs

sticks - 3D sticks

ballstick - ball & stick

spacefill - balls

wireframe

rgroupsVisible Show (true) or hide (false) R-group definitions. true

scale Magnification. A 1.54 Å long C-C bond is magnified to scale pixels. 28

sketchAnyBond Display type of the Any bond in the sketcher:

auto - displayed as dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).

dashed - displayed as dashed line

solid - displayed as solid line

auto

stickdst Stick distance of atoms in C-C bond length units. 0.3

showSets Show the specified atom sets only. Comma separated list of set sequence numbers (0, ..., 63).

sketchCarbonVisibility Display the label of carbon atoms in structures.

on - Always show the atom labels of carbon atoms.

off - Never show the atom labels of carbon atoms.

inChain - Show the atom labels of carbon atoms at straight angles and at implicit Hydrogens.

inChain

sketchLigandOrderVisibility Display the ligand order of R-group atoms in structures.

on - Always show the ligand order of R-group atoms.

off - Never show the ligand order of R-group atoms.

showOnlyWithDefinition - Show the ligand order of R-group atoms only on R-groups with definition.

off

stickThickness 3D stick diameter for "sticks" and "ballstick" rendering modes, in Angstroms. 0.1

valenceErrorVisible Highlight (by underlining) the labels of those atoms with valence errors. This option can also be set on the Edit/Preferences/MarvinSketch panel.

true - display errors

false - do not display errors

true

viewAnyBond Display type of the Any bond in the viewer:

auto - displayed as dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files).

dashed - displayed as dashed line

solid - displayed as solid line

auto

zeroBasedAtomIndexing Starts the atom indexing from zero instead of one:

true - atom indexes are started from zero

false - atom indexes are started from one

false

wireThickness Line thickness for "wireframe" and "wireknobs" rendering modes, in Angstroms. 0.064

Parameter	Meaning	Default
`aminoAcidBondColoringEnabled`	Enable (true) or disable (false) peptide bridge coloring	`true`
`absLabel`	Show (true) or hide (false) "Absolute" label
`atomFont`	Atom symbol/label font: `Serif`, `SansSerif` or `Monospaced`	`SansSerif`
`atomFontSize`	Atom symbol/label font's size: `12`, `14`, `8`, etc...	`12`
`atomMappingVisible`	Show (true) or hide (false) atom mapping	`true`
`atomPropertiesVisible`	Show (true) or hide (false) atom properties	`true`
`atomNumbersVisible`	Deprecated
`atomNumberingType`	Sets the type of atom numbering to Off (0), Atom numbers (1) or IUPAC numbering (2)	`0`
`autoCheckStructure`	Enables (true) or disables (false) automatic structure check. To take effect, set `statusBar` parameter to true as well.	`false`
`valencePropertyVisible`	Show (true) or hide (false) valence properties	`true`
`atomsize`	Atom symbol font size in C-C bond length units: atomsize1.54 Å = atomsize**scale points	`0.4`
`atomSymbolsVisible`	Show (true) or hide (false) atom symbols	`true`
`automaticFogEnabled`	Deprecated.
`ballRadius`	Ball radius for "ballstick" rendering mode, in units of covalent radius.	`0.5`
`bondLengthVisible`	Show (true) or hide (false) bond length labels	`false`
`bondSpacing`	Double bond spacing in C-C bond length units: spacing1.54 Å = spacing**scale pixels	`0.18`
`chargeWithCircle`	Charge label (plus or minus sign) is displayed circled(true) or normal(false)	`false`
`chiralitySupport`	When to show atom chirality (R/S). `off` - never `selected` - if chiral flag is set for the molecule or the atom's enhanced stereo type is absolute `all` - always	`off`
`circledChargeFont`	Circled charge labels font: any of the fonts installed on the machine	`SansSerif`
`circledChargeSize`	Circled Charge labels font size in C-C bond length units: circledChargeSize1.54 Å = circledChargeSize**scale points	`0.4`
`colorScheme`	Color scheme. `mono` - monochrome `cpk` - Corey-Pauling-Kultun `shapely` - shapely (residue types) `group` - residue sequence numbers	`cpk`
`downWedge`	Wedge bond display convention. Down wedge points downward in MDL's convention (`mdl`), upward (at the chiral center) in Daylight's (`daylight`).	`mdl`
`explicitH`	Show (true) or hide (false) explicit hydrogens	`true`
`ezVisible`	Show (true) or hide (false) E/Z labels	`false`
`fogFactor`	Set the custom fog factor in a range from `0` to `100`. The value `100` is for the strongest fog and `0` for the weakest (no) fog.	`66`
`grinvVisible`	Show (true) or hide (false) graph invariants (canonical labels)	`false`
`implicitH`	How to display H labels. `off` `hetero` - on heteroatoms `heteroterm` - on hetero or terminal atoms `all` - all atoms	`heteroterm`
`ligandErrorVisible`	Show (true) or not (false) ligand error by coloring to red	`true`
`lonePairsVisible`	Show (true) or hide (false) lone pairs	`false`
`lonePairsAutoCalc`	Switch on (true) or off (false) automatic calculation of lone pairs. The lonePairsVisible parameter should be set to true to display the result of the automatic calculation.	`false`
`maxscale`	Maximizes the magnification for autoscale to prevent overscaling of small molecules. It is usually set to 28, which is the scale factor for 100% magnification.
`peptideDisplayType`	Show peptide sequences with one letter or three letter abbreviations. Valid values are "1-letter" and "3-letter"	`3-letter`
`reactionErrorVisible`	Deprecated.	`false`
`rendering`	Rendering style. `wireframe` - wireframe `wireknobs` - wireframe with knobs `sticks` - 3D sticks `ballstick` - ball & stick `spacefill` - balls	`wireframe`
`rgroupsVisible`	Show (true) or hide (false) R-group definitions.	`true`
`scale`	Magnification. A 1.54 Å long C-C bond is magnified to scale pixels.	`28`
`sketchAnyBond`	Display type of the Any bond in the sketcher: `auto` - displayed as dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files). `dashed` - displayed as dashed line `solid` - displayed as solid line	`auto`
`stickdst`	Stick distance of atoms in C-C bond length units.	`0.3`
`showSets`	Show the specified atom sets only. Comma separated list of set sequence numbers (0, ..., 63).
`sketchCarbonVisibility`	Display the label of carbon atoms in structures. `on` - Always show the atom labels of carbon atoms. `off` - Never show the atom labels of carbon atoms. `inChain` - Show the atom labels of carbon atoms at straight angles and at implicit Hydrogens.	`inChain`
`sketchLigandOrderVisibility`	Display the ligand order of R-group atoms in structures. `on` - Always show the ligand order of R-group atoms. `off` - Never show the ligand order of R-group atoms. `showOnlyWithDefinition` - Show the ligand order of R-group atoms only on R-groups with definition.	`off`
`stickThickness`	3D stick diameter for "sticks" and "ballstick" rendering modes, in Angstroms.	`0.1`
`valenceErrorVisible`	Highlight (by underlining) the labels of those atoms with valence errors. This option can also be set on the Edit/Preferences/MarvinSketch panel. `true` - display errors `false` - do not display errors	`true`
`viewAnyBond`	Display type of the Any bond in the viewer: `auto` - displayed as dashed line in most cases, solid line only when all bonds are generated from atom coordinates (e.g. XYZ and PDB files). `dashed` - displayed as dashed line `solid` - displayed as solid line	`auto`
`zeroBasedAtomIndexing`	Starts the atom indexing from zero instead of one: `true` - atom indexes are started from zero `false` - atom indexes are started from one	`false`
`wireThickness`	Line thickness for "wireframe" and "wireknobs" rendering modes, in Angstroms.	`0.064`

1.1.3 Structure parameters

Parameter Meaning Default

atomSetColor0 atomSetColor1 ... atomSetColor63 Atom set color as hexadecimal value.

bondSetColor1 ... bondSetColor63 Bond set color as hexadecimal value.

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

cleanDim Number of space dimensions for cleaning.

2 - two-dimensional cleaning

3 - three-dimensional cleaning

See also: cleanOpts, importConv. 2

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

setColoringEnabled Atom/bond set coloring. true

valenceCheckEnabled Check valence errors in molecules on the SketchPanel (true) or not (false). true

1.1.4 Other parameters

Parameter Meaning Default

escapeChar Escape character to use for parsing the value of the mol parameter.

abbrevgroups Replacing the built-in abbreviated group collection with a custom one. The parameter value is the location of the file containing the custom abbreviated groups. The location should be relative to the applet codebase.
Live applet example: MarvinSketch Example - Abbreviated groups chemaxon/marvin /templates /default.abbrevgroup

customAbbrevgroups You can add further abbreviations for the default.abbrevgroup contents with the contets of the files that can be specified with the help of this parameter. The parameter has to contain the path of the file relatively to the codebase.
It is possible to define more than one file, the separator character can be a comma(,) or a pipe(|) character.

abbrevgroupsAllowed Enables/disables the usage of abbreviated groups. If the function is disabled, typing with the keyboard over the canvas will only allow changing atom and bond types.
Live applet example: MarvinSketch Example - Student Examination true

userAbbrevGroupsAllowed Enables/disables the usage of user defined abbreviated groups. true

defaultSaveFormat Sets the default chemical file format in the Save As dialog. mrv

debug Debug mode. Possible values: 0, 1, 2. 0

menuconfig Specifies an alternative menu customization file location instead of the default .chemaxon/{MarvinSketch_version}/customization.xml (Unix) or chemaxon/{MarvinSketch_version}/customziation.xml (Windows) file under the user's home. Please note that if this parameter is used, the customizationEnabled parameter is automatically set to false.
If you use applet, the value of this parameter has to be an URL. It can be relative to the applet codebase (e.g. examples/applets/sketch/myconfig.xml). The applet codebase gives the location of the marvin directory on the server (e.g.: http://www.myserver.com/marvin). Of course, the config file can be located on an other server, in this case you have to give the absolute URL of the config file (e.g.: http://www.otherserver.com/marvin-config/myconfig.xml).

mergedst Merge distance of atoms in C-C bond length units. 0.1

molFormat Default file format: mol, csmol, smiles, cxsmiles, cml, pdb, pov, sybyl, or xyz. mol

shortcuts Specifies an alternative shortcut customization file location instead of the default .chemaxon/{MarvinSketch_version}/shortcuts.xml (Unix) or chemaxon/{MarvinSketch_version}/shortcuts.xml (Windows) file under the user's home. Please note that if this parameter is used, the customizationEnabled parameter is defaults to false.

symbols Comma-separated list of symbols that will be always shown in the Insert Symbol popup. The symbols must be specified as font family name/Unicode code point pairs: fontname:codepoint. Fonts can be physical or logical. The logical fonts supported by the JRE: Serif, SansSerif, Monospaced, Dialog, and DialogInput.
Example (Δ,Å): "SansSerif:U+0394,SanSerif:U+212B"

toolbarFloatable Setting this parameter to false makes the toolbars immovable. true
undo Maximum number of undo operations. 50

viewHelp MarvinView help contents. chemaxon/marvin/help /view-index.html

viewQuickHelp MarvinView quick help. chemaxon/marvin/help /view.html

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

defaultTool Sets the initial editing mode in the sketcher.

atom:atomNumber - Atom drawing mode. Additional flags must be used to specify the element type. Example: "atom:6" (carbon atom)
bond:bondType - Bond drawing mode. Additional flags must be used to specify the bond type. Example: "bond:1" (single bond)
select - Rectangle selection
lassoSelect - Lasso selection
structureSelect - Structure selection
erase - Delete mode
bold - Changes the selected bond to Bold.
chain - Chain drawing mode
electronFlow1 - Electron Flow (with one electron) drawing mode
electronFlow2 - Electron Flow (with two electron) drawing mode
reactionArrow - Reaction Arrow drawing mode
retrosyntheticArrow - Retrosynthetic Arrow drawing mode
resonanceArrow - Resonance Arrow drawing mode
equilibriumArrow - Equilibrium Arrow drawing mode
increaseCharge - Increases the charge of the selected atom
decreaseCharge - Decreases the charge of the selected atom
assignAtom - Assigner tool for selecting atom pairs to enable 3D Directed Merge
switchRadical - Tool for switching the number of radical electrons
radicalOff - Tool for setting the number of radical electrons of the atom to 0
monovalentRadical - Tool for setting the number of radical electrons of the atom to 1
increaseLonePairs - Tool for increasing the number of lone pairs of the atom by one

disabledGroupTypesOnUI Disable the availability of certain S-group types available at Group Creation/Edit Dialog. (Structure>Group menu, or Contextual menu>Group menupoint.)
The parameter should be a comma separated list of group types that should be disabled.
Note: R-groups can not be disabled in this way.

superatomGroup - Superatom (abbreviation)

rangeGroup - Repeating unit with repetition ranges(e.g. 2,4-6)

multipleGroup - Multiple group (e.g. 3)

orderedMixtureGroup - Ordered mixture (f)

unorderedMixtureGroup - Unordered mixture (mix)

merGroup - Mer (mer)

monomerGroup - Monomer (mon)

graftGroup - Graft (grf)

modificationGroup - Modification (mod)

crosslinkGroup - Crosslink (xl)

genericGroup - Generic ()

componentGroup - Component (c)

sruGroup - SRU polymer(n)

copolymerGroup - Copolymer (co)

randomCopolymerGroup - Copolymer, random (ran)

blockCopolymerGroup - Copolymer, block (blk)

alternatingCopolymerGroup - Copolymer, alternating (alt)

anypolymerGroup - Anypolymer (anyp)

disableSpecialNodes Set this to true if you want to disable special nodes on the Advanced tab of the Periodic Table dialog. false

imageImportServiceURL Specifies the URL of an image import service for the Sketch applet to use. empty

namingWebServiceURL Specifies the URL of a name recognition and import service for the name import to use. empty

zoomToScaffoldOnLoad Sketch zooms to the scaffold of RG Molecules. false

Parameter	Meaning	Default
`escapeChar`	Escape character to use for parsing the value of the mol parameter.
`abbrevgroups`	Replacing the built-in abbreviated group collection with a custom one. The parameter value is the location of the file containing the custom abbreviated groups. The location should be relative to the applet codebase. Live applet example: MarvinSketch Example - Abbreviated groups	`chemaxon/marvin /templates /default.abbrevgroup`
`customAbbrevgroups`	You can add further abbreviations for the default.abbrevgroup contents with the contets of the files that can be specified with the help of this parameter. The parameter has to contain the path of the file relatively to the codebase. It is possible to define more than one file, the separator character can be a comma(,) or a pipe(\|) character.
`abbrevgroupsAllowed`	Enables/disables the usage of abbreviated groups. If the function is disabled, typing with the keyboard over the canvas will only allow changing atom and bond types. Live applet example: MarvinSketch Example - Student Examination	`true`
`userAbbrevGroupsAllowed`	Enables/disables the usage of user defined abbreviated groups.	`true`
`defaultSaveFormat`	Sets the default chemical file format in the Save As dialog.	`mrv`
`debug`	Debug mode. Possible values: 0, 1, 2.	`0`
`menuconfig`	Specifies an alternative menu customization file location instead of the default `.chemaxon/{MarvinSketch_version}/customization.xml` (Unix) or `chemaxon/{MarvinSketch_version}/customziation.xml` (Windows) file under the user's home. Please note that if this parameter is used, the customizationEnabled parameter is automatically set to false. If you use applet, the value of this parameter has to be an URL. It can be relative to the applet codebase (e.g. examples/applets/sketch/myconfig.xml). The applet codebase gives the location of the marvin directory on the server (e.g.: http://www.myserver.com/marvin). Of course, the config file can be located on an other server, in this case you have to give the absolute URL of the config file (e.g.: http://www.otherserver.com/marvin-config/myconfig.xml).
`mergedst`	Merge distance of atoms in C-C bond length units.	`0.1`
`molFormat`	Default file format: `mol`, `csmol`, `smiles`, `cxsmiles`, `cml`, `pdb`, `pov`, `sybyl`, or `xyz`.	`mol`
`shortcuts`	Specifies an alternative shortcut customization file location instead of the default `.chemaxon/{MarvinSketch_version}/shortcuts.xml` (Unix) or `chemaxon/{MarvinSketch_version}/shortcuts.xml` (Windows) file under the user's home. Please note that if this parameter is used, the customizationEnabled parameter is defaults to false.
`symbols`	Comma-separated list of symbols that will be always shown in the Insert Symbol popup. The symbols must be specified as font family name/Unicode code point pairs: `fontname:codepoint`. Fonts can be physical or logical. The logical fonts supported by the JRE: `Serif`, `SansSerif`, `Monospaced`, `Dialog`, and `DialogInput`. Example (Δ,Å): `"SansSerif:U+0394,SanSerif:U+212B"`
`toolbarFloatable`	Setting this parameter to `false` makes the toolbars immovable.	`true`
`undo`	Maximum number of undo operations.	`50`
`viewHelp`	MarvinView help contents.	`chemaxon/marvin/help /view-index.html`
`viewQuickHelp`	MarvinView quick help.	`chemaxon/marvin/help /view.html`
`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`
`defaultTool`	Sets the initial editing mode in the sketcher. `atom:atomNumber` - Atom drawing mode. Additional flags must be used to specify the element type. Example: `"atom:6"` (carbon atom) `bond:bondType` - Bond drawing mode. Additional flags must be used to specify the bond type. Example: `"bond:1"` (single bond) `select` - Rectangle selection `lassoSelect` - Lasso selection `structureSelect` - Structure selection `erase` - Delete mode `bold` - Changes the selected bond to Bold. `chain` - Chain drawing mode `electronFlow1` - Electron Flow (with one electron) drawing mode `electronFlow2` - Electron Flow (with two electron) drawing mode `reactionArrow` - Reaction Arrow drawing mode `retrosyntheticArrow` - Retrosynthetic Arrow drawing mode `resonanceArrow` - Resonance Arrow drawing mode `equilibriumArrow` - Equilibrium Arrow drawing mode `increaseCharge` - Increases the charge of the selected atom `decreaseCharge` - Decreases the charge of the selected atom `assignAtom` - Assigner tool for selecting atom pairs to enable 3D Directed Merge `switchRadical` - Tool for switching the number of radical electrons `radicalOff` - Tool for setting the number of radical electrons of the atom to 0 `monovalentRadical` - Tool for setting the number of radical electrons of the atom to 1 `increaseLonePairs` - Tool for increasing the number of lone pairs of the atom by one
`disabledGroupTypesOnUI`	Disable the availability of certain S-group types available at Group Creation/Edit Dialog. (Structure>Group menu, or Contextual menu>Group menupoint.) The parameter should be a comma separated list of group types that should be disabled. Note: R-groups can not be disabled in this way. `superatomGroup` - Superatom (abbreviation) `rangeGroup` - Repeating unit with repetition ranges(e.g. 2,4-6) `multipleGroup` - Multiple group (e.g. 3) `orderedMixtureGroup` - Ordered mixture (f) `unorderedMixtureGroup` - Unordered mixture (mix) `merGroup` - Mer (mer) `monomerGroup` - Monomer (mon) `graftGroup` - Graft (grf) `modificationGroup` - Modification (mod) `crosslinkGroup` - Crosslink (xl) `genericGroup` - Generic () `componentGroup` - Component (c) `sruGroup` - SRU polymer(n) `copolymerGroup` - Copolymer (co) `randomCopolymerGroup` - Copolymer, random (ran) `blockCopolymerGroup` - Copolymer, block (blk) `alternatingCopolymerGroup` - Copolymer, alternating (alt) `anypolymerGroup` - Anypolymer (anyp)
`disableSpecialNodes`	Set this to true if you want to disable special nodes on the Advanced tab of the Periodic Table dialog.	`false`
`imageImportServiceURL`	Specifies the URL of an image import service for the Sketch applet to use.	`empty`
`namingWebServiceURL`	Specifies the URL of a name recognition and import service for the name import to use.	`empty`
`zoomToScaffoldOnLoad`	Sketch zooms to the scaffold of RG Molecules.	`false`

Applet example:

<applet CODE=MSketch WIDTH=480 HEIGHT=400>
<param NAME="background" VALUE="#cccccc>
<param NAME="molbg" VALUE="#ffffff">
<param NAME="implicitH" VALUE="hetero">
</applet>

1.1 Applet only parameters

The following parameters are meaningful only for the applets (MSketch, JMSketch) and not for the JavaBean (MSketchPane).

Parameter Meaning Default

menubar Enable the embedded menubar. true

buttonmenubar Enable menubar in button (/hide) mode if the menubar parameter is true. Combine it with the detach parameter to set the button mode.
True, to allow, false to deny menu bar on the big sketcher button. true

detach Detachment behavior. The value consists of some optional arguments: show/hide size, and maxscale. If more arguments are included, they must be separated by a comma.
To detach the sketcher from the web page and display it in a separate window, set "show".
To detach the sketcher without displaying the separate window, set "hide".
Both settings make the applet on the web page look like a molecule viewer.

The initial size of the sketcher window can be specified with "size=widthxheight"
Examples: "show", "size=500x500", "hide,size=500x500".
In case the maxscale argument is set, it can prevent small molecules to be overscaled on the button.
Example for maximum 100% magnification: "hide,maxscale=28"
Live applet example: MarvinSketch Example - Pure visualization mode size=444x350

undetachByX Sketcher window close (x) behavior.
false: always hide sketcher
true: replace viewer component by sketcher in web browser window if the applet is large enough (>= 400x300) true

mol The molecule file to be loaded at startup, as either a URL or the file itself (inline) in MDL mol, compressed mol, SMILES, SMARTS, etc format.
Newlines occurring in the string must be replaced or preceded by "\n" and backslashes are recommended to be escaped as "\\".
The file format and/or import options can be specified if one of the following forms is used:
"file{options}",
"file{MULTISET,options}",
"file{format:}",
"file{format:options}", or
"file{format:MULTISET,options}".
If the MULTISET option is specified, then a multi-molecule file is read into one molecule object containing multiple atom sets.
Examples: "foo.xyz{f1.4C4}", "foo.xyz.gz{gzip:xyz:MULTISET,f1.4C4}"

preload Deprecated

cacheMols Store loaded molecules in an internal cache (true or false). false

loadMols Comma-separated list of molfiles to preload. Useful for caching molecules in JavaScript "slideshows".

usedJars Comma-separated list of additional jar files that can be used by the applet. The additional files have to be defined with their paths relative to the applet's base.

imageSaveFormat The default file format for image saving. png
molLoaderFinishedEvent
Evaluates a JavaScript code after the loading of the molecule into the editor is finished. This "event" is invoked if molecule is loaded-in into the applet in any of the following cases:

Automaticaly, at applet starting: (using the mol applet parameter)

Calling (J)MSketch.setMol(...) from JavaScript.

Note: If the MAYSCRIPT option is not specified, JavaScript can not be evaluated from the applet. E.g.:
     msketch_mayscript=true;
     msketch_begin("marvin",400,300);
     msketch_param("mol","caffeine.mol");
     msketch_param("molLoaderFinishedEvent","js:alert('Molecule is loaded-in.')");
     msketch_end();
     
listenpropertychange
Switch on/off property change event listener to the applet. If listener is active, the applet will call propertyChange(prop) JavaScript method. If you would like to handle property change events in JavaScript, implement this method in your html source. Note: If the MAYSCRIPT option is not specified, JavaScript can not be evaluated from the applet. E.g.:
     function propertyChange(prop) {
        if(document.textform != null) {
            var s = document.textform.txt.value;
            document.textform.txt.value = s + "\n" + prop;
        }
     }

     msketch_mayscript=true;
     msketch_begin("marvin",400,300);
     msketch_param("listenpropertychange","true");
     msketch_end();
     
If you also specify the "appletid" parameter, its value will appear in the name of the property as prefix (e.g.: "firstapplet.mol").
false
appletid Identify applet in property change event notifications to JavaScript. Use this parameter with listenpropertychange when more than one applet are located on the same web page. It helps to identify which applet sent the notification.

skin Change the component's Look & Feel (only in SWING applet). If you do not specify this parameter, Marvin will use the default LookAndFeel style.
This parameter value is the name of the new LookAndFeel class. javax.swing.plaf .metal .MetalLookAndFeel

splashScreenImage Change the component's splash screen displayed at startup. If you do not specify this parameter, Marvin will use its default splash screen.
This parameter value is the relative path of the image, specify relatively to the CODEBASE
Note: Animated gif files can be displayed badly (flashing, or too fast animation) null

license Sets the contents of a pre-read license file to the license manager to read and validate licenses from.

licenseFile Sets the license file location to the license manager to read and validate licenses from.

onError A string containing a javascript code, that has to be run by the applet, if it has a failure at initialization.
The %s wildcard can be used to include the error message given by the applet inside the javascript code.
If used with alertError also set to true, the alert window will be shown first, and after the user has pressed the OK button on the alert will the given code run.

alertError If this parameter is set to true, the applet will show a javascript alert window with an error message, if there was a problem in the initialization process of the applet.

legacy_lifecycle The "legacy_lifecycle" is a general Java applet parameter. If its value is true, it helps avoid destroying the applet when you leaves the applet page. If you use "marvin.js", it sets its value to true automatically unless you specify its value explicitly. By the way, the default value of this parameter in Java is false. See the discussion about it on the forum.

preload You can specifies modules to load them in advance before startup of the MarvinSketch applet. The value of this parameter is the comman separated list of modules. The order of modules determine which module is loaded earlier and which one is loaded later. You can choose from the following modules.

bgloadPriority You can specify the order of the modules for background loading. After startup of MarvinSketch, modules that are not used yet are started downloading in the background to fast up their initalization of their first usage. The value of this parameter is a comma separated list of modules that get priority for loading. You can choose from the following modules. See also bgloadEnabled.

bgloadEnabled Let or deny loading of rest of modules in a background thread after startup. Set this parameter to true to accept background loading. Set it to false if you would like to reject this functionality. true

sketchHelp MarvinSketch help contents. Accepts relative URL to the applet codebase or any absolute URL. chemaxon/marvin/help /sketch-index.html

sketchQuickHelp MarvinSketch quick help. Accepts relative URL to the applet codebase or any absolute URL. chemaxon/marvin/help /sketch.html

checkerConfigURL Default checker configuration URL. Accepts any absolute URL. local configuration

Parameter	Meaning	Default
`menubar`	Enable the embedded menubar.	`true`
`buttonmenubar`	Enable menubar in button (/hide) mode if the menubar parameter is `true`. Combine it with the detach parameter to set the button mode. `True`, to allow, `false` to deny menu bar on the big sketcher button.	`true`
`detach`	Detachment behavior. The value consists of some optional arguments: `show/hide` `size`, and `maxscale`. If more arguments are included, they must be separated by a comma. To detach the sketcher from the web page and display it in a separate window, set `"show"`. To detach the sketcher without displaying the separate window, set `"hide"`. Both settings make the applet on the web page look like a molecule viewer. The initial size of the sketcher window can be specified with "`size=`width`x`height" Examples: "`show`", "`size=500x500`", "`hide,size=500x500`". In case the `maxscale` argument is set, it can prevent small molecules to be overscaled on the button. Example for maximum 100% magnification: "`hide,maxscale=28`" Live applet example: MarvinSketch Example - Pure visualization mode	`size=444x350`
`undetachByX`	Sketcher window close (x) behavior. `false`: always hide sketcher `true`: replace viewer component by sketcher in web browser window if the applet is large enough (>= 400x300)	`true`
`mol`	The molecule file to be loaded at startup, as either a URL or the file itself (inline) in MDL mol, compressed mol, SMILES, SMARTS, etc format. Newlines occurring in the string must be replaced or preceded by "\n" and backslashes are recommended to be escaped as "\\". The file format and/or import options can be specified if one of the following forms is used: "file{options}", "file{MULTISET,options}", "file{format:}", "file{format:options}", or "file{format:MULTISET,options}". If the MULTISET option is specified, then a multi-molecule file is read into one molecule object containing multiple atom sets. Examples: "foo.xyz{f1.4C4}", "foo.xyz.gz{gzip:xyz:MULTISET,f1.4C4}"
`preload`	Deprecated
`cacheMols`	Store loaded molecules in an internal cache (`true` or `false`).	`false`
`loadMols`	Comma-separated list of molfiles to preload. Useful for caching molecules in JavaScript "slideshows".
`usedJars`	Comma-separated list of additional jar files that can be used by the applet. The additional files have to be defined with their paths relative to the applet's base.
`imageSaveFormat`	The default file format for image saving.	`png`
`molLoaderFinishedEvent`	Evaluates a JavaScript code after the loading of the molecule into the editor is finished. This "event" is invoked if molecule is loaded-in into the applet in any of the following cases: Automaticaly, at applet starting: (using the mol applet parameter) Calling (J)MSketch.setMol(...) from JavaScript. Note: If the MAYSCRIPT option is not specified, JavaScript can not be evaluated from the applet. E.g.: msketch_mayscript=true; msketch_begin("marvin",400,300); msketch_param("mol","caffeine.mol"); msketch_param("molLoaderFinishedEvent","js:alert('Molecule is loaded-in.')"); msketch_end();
`listenpropertychange`	Switch on/off property change event listener to the applet. If listener is active, the applet will call propertyChange(prop) JavaScript method. If you would like to handle property change events in JavaScript, implement this method in your html source. Note: If the MAYSCRIPT option is not specified, JavaScript can not be evaluated from the applet. E.g.: function propertyChange(prop) { if(document.textform != null) { var s = document.textform.txt.value; document.textform.txt.value = s + "\n" + prop; } } msketch_mayscript=true; msketch_begin("marvin",400,300); msketch_param("listenpropertychange","true"); msketch_end(); If you also specify the "appletid" parameter, its value will appear in the name of the property as prefix (e.g.: "firstapplet.mol").	`false`
`appletid`	Identify applet in property change event notifications to JavaScript. Use this parameter with listenpropertychange when more than one applet are located on the same web page. It helps to identify which applet sent the notification.
`skin`	Change the component's Look & Feel (only in SWING applet). If you do not specify this parameter, Marvin will use the default LookAndFeel style. This parameter value is the name of the new LookAndFeel class.	`javax.swing.plaf .metal .MetalLookAndFeel`
`splashScreenImage`	Change the component's splash screen displayed at startup. If you do not specify this parameter, Marvin will use its default splash screen. This parameter value is the relative path of the image, specify relatively to the CODEBASE Note: Animated gif files can be displayed badly (flashing, or too fast animation)	`null`
`license`	Sets the contents of a pre-read license file to the license manager to read and validate licenses from.
`licenseFile`	Sets the license file location to the license manager to read and validate licenses from.
`onError`	A string containing a javascript code, that has to be run by the applet, if it has a failure at initialization. The %s wildcard can be used to include the error message given by the applet inside the javascript code. If used with `alertError` also set to true, the alert window will be shown first, and after the user has pressed the OK button on the alert will the given code run.
`alertError`	If this parameter is set to true, the applet will show a javascript alert window with an error message, if there was a problem in the initialization process of the applet.
`legacy_lifecycle`	The "legacy_lifecycle" is a general Java applet parameter. If its value is true, it helps avoid destroying the applet when you leaves the applet page. If you use "marvin.js", it sets its value to true automatically unless you specify its value explicitly. By the way, the default value of this parameter in Java is false. See the discussion about it on the forum.
`preload`	You can specifies modules to load them in advance before startup of the MarvinSketch applet. The value of this parameter is the comman separated list of modules. The order of modules determine which module is loaded earlier and which one is loaded later. You can choose from the following modules.
`bgloadPriority`	You can specify the order of the modules for background loading. After startup of MarvinSketch, modules that are not used yet are started downloading in the background to fast up their initalization of their first usage. The value of this parameter is a comma separated list of modules that get priority for loading. You can choose from the following modules. See also bgloadEnabled.
`bgloadEnabled`	Let or deny loading of rest of modules in a background thread after startup. Set this parameter to true to accept background loading. Set it to false if you would like to reject this functionality.	true
`sketchHelp`	MarvinSketch help contents. Accepts relative URL to the applet codebase or any absolute URL.	`chemaxon/marvin/help /sketch-index.html`
`sketchQuickHelp`	MarvinSketch quick help. Accepts relative URL to the applet codebase or any absolute URL.	`chemaxon/marvin/help /sketch.html`
`checkerConfigURL`	Default checker configuration URL. Accepts any absolute URL.	`local configuration`