Codename: mrv
An XML based format that is capable to store graphics objects (lines, text boxes, etc.) and molecule objects.
The following tags are recognized:
<cml> — root
element
Children:
<MDocument>
- top level container of a record
Attributes:
atomSetRGB, bondSetRGB
— atom/bond set colors.
Comma separated list of entries in
"k:color" format, where k is the set
sequence number and color is the color specification in one
of the following forms: "#RRGGBB" - RGB components as a
6-digit hexadecimal number, "D" - default set color, "N"
- no set color (normal atom/bond coloring is used).
multipageEnabled — enables the multipage molecular document. Its value is "true" or "false".
multipageSelectedPage — the selected page in multipage molecular document. Its value is "k" where k is a non-negativ integer.
multipageColumnCount — number of columns in multipage molecular document. Its value is "k" where k is a non-negativ integer.
multipageRowCount — number of rows in multipage molecular document. Its value is "k" where k is a non-negativ integer.
multipageWidth — width of a page in multipage molecular document. Its value is "d" where d is a floating point number.
multipageHeight — height of a page in multipage molecular document. Its value is "d" where d is a floating point number.
multipageLeft — left margin of a page in multipage molecular document. Its value is "d" where d is a floating point number.
multipageRight — right of a page in multipage molecular document. Its value is "d" where d is a floating point number.
multipageTop — top margin of a page in multipage molecular document. Its value is "d" where d is a floating point number.
multipageBottom — bottom margin of a page in multipage molecular document. Its value is "d" where d is a floating point number.
Children:
<MChemicalStruct>
- chemical structure
Children:
<molecule> — It can contain both CML and Marvin attributes. Currently, there is only one Marvin attribute:
absStereo
Children:
<atomArray> — It can contain both CML and Marvin attributes. Marvin attributes are explained below.
residueType, residueId — residue type/ID value or zero
lonePair — Number of lone pairs.
residueAtomName — PDB atom name or zero.
radical — Radical center value or zero.
reactionStereo — Reaction stereo value or zero.
sgroupRef — S-group reference value or zero:
sgroupAttachmentPoint — S-group attachment point value or zero: "1", (on first site) "2" (on second site) or "both" (on both sites)
rgroupRef — R-group reference value or zero.
attachmentPoint — S-group attachment point value. Exported for backward compatibility, but not imported. Attachment point value is imported from attachmentOrder tag for R-group attachment points, from sgroupAttachmentPoint tag for S-group attachment points since Marvin version 5.4.
attachmentOrder — Attachment point order value in the case of R-group attachment point or zero otherwise.
mrvValence — Valence or `-'.
mrvQueryProps — Query atom properties or zero.
mrvAlias — Atom alias or zero.
mrvExtraLabel — Atom extra label or zero.
mrvPseudo — Pseudoatom name or zero.
mrvStereoGroup, mrvMap
mrvSetSeq — Atom set sequence number.
mrvLinkNodeRep — Number of repetitions for link nodes. A number n in the list is the maximum number of repetitions for the corresponding atom (value 1 means that the atom is not a link node), m-n sets both the minimum and maximum values.
mrvLinkNodeOut — Outer bond references for link nodes. Comma separated numbers in the list defines the indices of bonds (amongst bonds of the link atom) leading to the outer atoms (non-repeating neighbours) of the link nodes, "-" means no outer bonds.
mrvSpecIsotopeSymbolPreferred — Special symbols are preferred for Hydrogen isotopes (D, T) if the value is 1, normal element symbol (H) is used if the value is 0.
Children:
<atom> — It can contain both CML and Marvin attributes. Marvin attributes are explained below.
lonePair — Number of lone pais.
residueType, residueId — They were present in CML1 but removed later.
residueAtomName — PDB atom name.
radical — Radical center: "monovalent" (doublet), "divalent", "divalent1" (singlet), "divalent3" (triplet), "trivalent", "trivalent2" (doublet) "trivalent4" (quartet) or "4" (special incorrect value for student examination).
reactionStereo — Reaction stereo: "Inv" (inversion) or "Ret" (retention).
sgroupRef — S-group reference.
sgroupAttachmentPoint — S-group attachment point: "1", (on first site) "2" (on second site) or "both" (on both sites).
rgroupRef — R-group reference. Currently, only positive integer values are accepted.
attachmentPoint — S-group attachment point value. Exported for backward compatibility, but not imported. Attachment point value is imported from attachmentOrder tag for R-group attachment points, from sgroupAttachmentPoint tag for S-group attachment points since Marvin version 5.4.
attachmentOrder — Attachment point order value in the case of R-group attachment point.
ligandOrder — Order of ligands connected to an R-group atom: list of atom identifiers.
mrvValence — Valence.
mrvQueryProps —
Query atom properties.
Format: [atom Type:][Query
properties][;] [str:query string], where atom
type can be "A" (any atom), "Q"
(heteroatom), "L,element1,..." (inclusive atom
list) or "L!element1!..." (exclusive atom
list). Query properties is a semicolon separated list.
An element of the list starts with prefix:
"H" — total hydrogen count, see SMARTS H,
"h" — implicit hydrogen count, see SMARTS h,
"X" — total connection count, see SMARTS X,
"D" — degree, see SMARTS D,
"R" — SSSR ring count, see SMARTS R,
"r" — smallest ring size in SSSR, see SMARTS r,
"a" — aromatic ("a1") or aliphatic ("a0"), see SMARTS a/A,
"u" — unsaturated atom, see MDL M UNS,
"s" — substitution count, see MDL M SUB,
"rb" — ring bond count), see MDL M RBC.
The following characters may be digits representing an integer value or "*" in case of s and rb query properties. The query string contains properties unknown by Marvin or known properties in a logical relation that cannot be represented by Marvin. Examples: "A:" (any atom), "L!O!S:H1,R1" (atom is not oxygen, not sulfur, 1 hydrogen is connected to it and it is inside a ring).
mrvAlias — Atom alias.
mrvExtraLabel — Atom extra label.
mrvPseudo — Pseudoatom name.
mrvStereoGroup, mrvMap
mrvSetSeq — Atom set sequence number.
mrvLinkNodeRep — Number of repetitions for a link node in format "n" (maximum number of repetitions) or "m-n" (minimum and maximum).
mrvLinkNodeOut — Outer bond references for a link node in comma separated list of bond indices (amongst bonds of the link atom) leading to the outer atoms (non-repeating neighbours) of the link nodes, "-" means no outer bonds.
mrvSpecIsotopeSymbolPreferred — Special symbols are preferred for Hydrogen isotopes (D, T) if the value is 1, normal element symbol (H) is used if the value is 0 (default).
<scalar
id="atomId:propertyId"
title="propertyKey"
convention="marvin:atomprop"
dataType="dataType" value="propertyValue"
/> — General atom property represented by a
propertyKey and propertyValue pair. The atom
reference atomId must be valid atom identifier. The
convention value is marvin:atomprop.
Supported data
types are: "string", "boolean", "integer",
"double", "float". The "null"
value is exported with "unknown" data type.
<atomBicycloStereo connectionAtom="atomId" lowBridge="atomId1 atomId2 ... " highBridge="atomId1 atomId2 ... "> stereoValue </atomBicycloStereo> — The atom reference atomId must be valid atom identifier. Supported stereo values are: "either", "lower", "higher" stereo value types.
An <atom> tag is recognized at import even if the atomArray container is not present.
<bondArray>
<bond atomRefs2="a1
a2" order="order" >
The
atom references a1 and a2 must be valid atom ids.
The order value can be "1", "S"
(single), "2", "D" (double), "3",
"T" (triple) or "A" (aromatic).
The
following attributes can be present, which are not included in
CML:
queryType — Query bond type: "SD" (single or double), "SA" (single or aromatic), "DA" (double or aromatic) or "Any".
mrvQueryProps — Query bond properties. Format: str:query string, where query string contains query bond properties unknown by Marvin or known properties in a logical relation that cannot be represented by Marvin.
mrvSetSeq — Bond set sequence number.
mrvBold — Bold bond attribute.
mrvHashed — Hashed bond attribute.
<bond atomRefs2="a1
a2" convention="convention" >
The
atom references a1 and a2 must be valid atom ids.
The convention value can be "cxn:coord"
(coordinate bond).
<bond atomRefs2="a1
a2" mrvBold="mrvBoldValue">
Describes
the "bold" attribute of the bond. The atom references
a1 and a2 must be valid atom ids. The mrvBoldValue
value can be "true" or "false".
<bond atomRefs2="a1
a2" mrvHashed="mrvHashedValue">
Describes
the "hashed" attribute of the bond. The atom
references a1 and a2 must be valid atom ids. The
mrvHashedValue value can be "true" or "false".
<molecule id="sg1" role="SuperatomSgroup"> — contracted Superatom S-group
<atomArray>
<atom>
<bondArray>
<bond>
<molecule id="sg2" role="SuperatomSgroup" /> — expanded Superatom S-group
<molecule id="sg3" role="MultipleSgroup" atomRefs="a1 a2 ... "/> — Multiple S-group
<molecule id="sg3" role="DataSgroup" fieldName="fieldName" [fieldType="F|N|T"] [units="unit"] [x="x coordinate"] [y="y coordinate"] [dataDisplayed="displayed|not displayed"] [placement="Relative|Absolute"] [unitsDisplayed="Unit displayed|not displayed"] [displayedChars="number of characters displayed per line"] [displayedLines="number of lines to display"] [tag="tag"] [pos="0-9"] [queryType="mQ|IQ|MQ|?Q"] [queryOp="<|>|<>|<=|>=|=|like|between|contains"] [fieldData="first line of data"] [fieldData1="second line of data"]... /> — Data S-group
<molecule id="sg1" role="ComponentSgroup" title="c" charge="onAtoms|onBracket " molID="m1" atomRefs="a1 a2 ... "> — Component S-group
<bracket coordinates="x1 y1 z1 x2 y2 z2"/> — coordinates of left bracket-endpoints
<bracket coordinates="x1 y1 z1 x2 y2 z2"/> — coordinates of right bracket-endpoints
<molecule id="sg1" role="MixtureSgroup" title="mix" molID="m1" atomRefs="a1 a2 ... "> — Mixture (unordered mixture) S-group
<bracket coordinates="x1 y1 z1 x2 y2 z2"/> — coordinates of left bracket-endpoints
<bracket coordinates="x1 y1 z1 x2 y2 z2"/> — coordinates of right bracket-endpoints
<molecule id="sg1" role="FormulationSgroup" title="f" molID="m1" atomRefs="a1 a2 ... "> — Formulation (ordered mixture) S-group
<bracket coordinates="x1 y1 z1 x2 y2 z2"/> — coordinates of left bracket-endpoints
<bracket coordinates="x1 y1 z1 x2 y2 z2"/> — coordinates of right bracket-endpoints
<molecule id="sg1" role="SruSgroup" title="name" molID="m1" atomRefs="a1 a2 ... " correspondence="b1 b2 ... " bondList="b1 b2 ... " connect="hh|ht|eu " > — SRU S-group, where
name is single letter: a-z or A-Z.
for correspondence see MDL M CRS
for bondlist see MDL M SBL
for connect see MDL M SCN
<molecule id="sg1" role="GenericSgroup" charge="onAtoms|onBrackets " molID="m1" atomRefs="a1 a2 ... "> — generic S-group
<molecule id="sg1" role="MerSgroup" title="mer" charge="onAtoms|onBracket " molID="m1" atomRefs="a1 a2 ... "> — mer S-group
<molecule id="sg1" role="MonomerSgroup" title="mon" charge="onAtoms|onBracket " molID="m1" atomRefs="a1 a2 ... "> — monomer S-group
<molecule id="sg1" role="AnyPolymerSgroup" title="any" molID="m1" atomRefs="a1 a2 ... "> — anypolymer S-group
<molecule id="sg1" role="AlternatingCopolymerSgroup" title="alt" molID="m1" atomRefs="a1 a2 ... "> — alternating copolymer S-group
<molecule id="sg1" role="BlockCopolymerSgroup" title="blk" molID="m1" atomRefs="a1 a2 ... "> — block copolymer S-group
<molecule id="sg1" role="RandomCopolymerSgroup" title="ran" molID="m1" atomRefs="a1 a2 ... "> — random S-group
<molecule id="sg1" role="CopolymerSgroup" title="co" molID="m1" atomRefs="a1 a2 ... "> — copolymer S-group
<molecule id="sg1" role="CrosslinkSgroup" title="xl" molID="m1" atomRefs="a1 a2 ... "> — crosslink S-group
<molecule id="sg1" role="GraftSgroup" title="grf" molID="m1" atomRefs="a1 a2 ... "> — grafted S-group
<molecule id="sg1" role="ModificationSgrop" title="mod" molID="m1" atomRefs="a1 a2 ... "> — modification S-group
<molecule id="sg1" role="MulticenterSgroup" molID="m1" atomRefs="a1 a2 ... " center="a " > — multicenter S-group to represent coordination compounds and markush structures (depending on bond type connencting to the center)
<reaction> — It can contain both CML and Marvin attributes. Marvin attributes are explained below. Its children can be the same as it is discussed in the CML as well as new ones that are described below.
absStereo
arrowType — reaction arrow type: "DEFAULT" (->), "RESONANCE" (<->), "RETROSYNTHETIC" (=>), "EQUILIBRIUM" (=)
Children:
<agentList>List of agents in this reaction.
<molecule>
<Rgroup rgroupID="rgroupID"> — R-group.
<molecule> — an R-group member in CML
<MMoleculeMovie>
- animation of a chemical process
Children:
<MChemicalStruct> — a frame of the movie
<MPolyline> - line,
arc, polyline and/or arrow.
Attributes:
headSkip, tailSkip — Distance of (visible) head or tail from the corresponding line end point.
headWidth, tailWidth — Arrow head/tail width.
headLength, tailLength — Arrow head/tail length.
headFlags, tailFlags — Arrow head/tail options.
arcAngle — Arc central angle or 0.
Children:
<MPoint x="x" y="y" [z="z"]> — Represents a location in space
<MAtomSetPoint atomRefs="..." [weights="..."]> — Represents an atom or atom pair (bond or incipient bond). The atomRefs argument is a space separated list of atoms, weights is a space separated list of floating point numbers. The atom set's location is the weighted average of the atom locations.
<MMidPoint
lineRef="lineRef" [pos="position"]>
— Middle point of a line or a section of a
polyline.
Attributes:
lineRef — Reference to the MPolyline object.
position — Polyline section index (0, ..., n-1), default: 0.
<MRectanglePoint
pos="position" rectRef="rectRef">
— A corner of a rectangle or a middle point of one of its
edges.
Attributes:
position — Integer value between 0 and 7. Top left corner=0, top right corner=1, bottom right corner=2, bottom left corner=3, top middle point=4, right middle point=5, bottom middle point=6, left middle point=7.
rectRef — Reference to the MRectangle object.
<MEFlow> —
curved electron flow arrow. MEFlow is a subclass of MPolyline thus
it has the same attributes, but it can only contain two
points.
Children:
<MAtomSetPoint>
<MRectangle
[toption="toption"] [tcenter="tcenter"]>
— rectangle object
Optional attributes:
toption — Transformation option: ALLOW_ALL (default, all transformations are allowed), NOROT (only scaling is allowed, the rectangle is not rotatable).
tcenter — Central point: NW (top left corner), NE (top right corner), SE (bottom right corner), SW (bottom left corner), CENTER (geometrical center), N (top middle point), E (right middle point), S (bottom middle point), W (left middle point).
Children:
<MPoint x="x1" y="y1" [z="z1"] /> — Top left corner.
<MPoint x="x2" y="y2" [z="z2"] /> — Top right corner.
<MPoint x="x3" y="y3" [z="z3"] /> — Bottom right corner.
<MPoint x="x4" y="y4" [z="z4"] /> — Bottom left corner.
<MRoundedRectangle
[toption="toption"] [tcenter="tcenter"]>
— rounded cornered rectangle object
It is derived from
MRectangle, thus it inherits the toption
and tcenter attributes.
Extra
attributes:
arcWidth — double value of corner's arc's width
arcHeight — double value of corner's arc's height
Children:
<MPoint x="x1" y="y1" [z="z1"] /> — Top left corner.
<MPoint x="x2" y="y2" [z="z2"] /> — Top right corner.
<MPoint x="x3" y="y3" [z="z3"] /> — Bottom right corner.
<MPoint x="x4" y="y4" [z="z4"] /> — Bottom left corner.
<MEllipse
[toption="toption"] [tcenter="tcenter"]>
— ellipse object
It is derived from MRectangle, thus it
inherits the toption and tcenter
attributes.
Children:
<MPoint x="x1" y="y1" [z="z1"] /> — Top left corner.
<MPoint x="x2" y="y2" [z="z2"] /> — Top right corner.
<MPoint x="x3" y="y3" [z="z3"] /> — Bottom right corner.
<MPoint x="x4" y="y4" [z="z4"] /> — Bottom left corner.
<MTextBox [text="The
text"] [fontScale="fontScale"]
[halign="LEFT|CENTER|RIGHT"]
[valign="TOP|CENTER|BOTTOM"]
[autoSize="true|false"] — text box.
It is
derived from MRectangle, thus it inherits the toption
and tcenter attributes.
Extra
attributes:
text — The text. This attribute can only be used to define a single text line. In case of multiple lines the <Field name="text"> tag must be used. The string can contain \uXXXX unicode escapes. Backslash characters are always escaped with another backslash.
fontScale — Base font size (default: 10)
autoSize — Whether the box should be resized in order for the text to fit.
Children:
<Field name="text">The text </Field>
<MPoint x="x1" y="y1" [z="z1"] /> — Top left corner. Recalculated is autoSize=true, unless halign="LEFT".
<MPoint x="x2" y="y2" [z="z2"] /> — Top right corner. Recalculated if autoSize=true, unless valign="TOP".
<MPoint x="x3" y="y3" [z="z3"] /> — Bottom right corner. Recalculated if autoSize=true, unless valign="BOTTOM".
<MPoint x="x4" y="y4" [z="z4"] /> — Bottom left corner. Recalculated is autoSize=true, unless halign="RIGHT".
<MNameTextBox
[autoResize="true|false"] [autoAlign="true|false"]
[preferredWidth="preferredWidth"] - text object
that contains molecule name.
It is derived from MTextBox, thus
it inherits its attributes. Extra attributes:
autoResize Defines whether the alignment of the text box is in user set or automatic mode (automatic mode means the box is resized according to the position and size of the molecule). The default value is true.
autoAlign Defines whether the alignment of the text box is in user set or automatic mode. (automatic mode means the box is aligned according to the position and size of the molecule). The default value is true.
preferredWidth the preferred width of the text box in automatic resize mode
The argument of MolConverter, MolExporter and the getMol/getM
functions (of the applets and beans) is the format string. The format
specification ("mrv") is followed by ":" and the
selected option(s) for mrv export.
|
mrv:... |
|
|
mrv:S |
Save selection. If set then the mrv output will contain which atoms and graphical objects are in seleted state. |
|
mrv:P |
Create human readable output: put new xml elements in new lines and indent for embedded elements. |
Example of MRV file exported without options:
<?xml version="1.0"?><cml> <MDocument><MChemicalStruct><molecule title="Ethane" molID="m1"><atomArray atomID="a1 a2" elementType="C C" x2="0.0 0.0" y2="0.0 1.54"></atomArray><bondArray><bond atomRefs2="a1 a2" order="1"></bond></bondArray></molecule></MChemicalStruct><MRectangle id="o2"><MPoint x="-6.599999904632568" y="1.7050000429153442"></MPoint><MPoint x="-2.640000104904175" y="1.7050000429153442"></MPoint><MPoint x="-2.640000104904175" y="-0.16500000655651093"></MPoint><MPoint x="-6.599999904632568" y="-0.16500000655651093"></MPoint></MRectangle></MDocument> </cml>
Example of MRV file exported with option "S":
<?xml version="1.0"?><cml> <MDocument><MChemicalStruct><molecule title="Ethane" molID="m1"><atomArray atomID="a1 a2" elementType="C C" isSelected="true true" x2="0.0 0.0" y2="0.0 1.54"></atomArray><bondArray><bond atomRefs2="a1 a2" order="1"></bond></bondArray></molecule></MChemicalStruct><MRectangle id="o2" isSelected="true"><MPoint x="-6.599999904632568" y="1.7050000429153442"></MPoint><MPoint x="-2.640000104904175" y="1.7050000429153442"></MPoint><MPoint x="-2.640000104904175" y="-0.16500000655651093"></MPoint><MPoint x="-6.599999904632568" y="-0.16500000655651093"></MPoint></MRectangle></MDocument> </cml>
Example of MRV file exported with option "P":
<?xml version="1.0"?>
<cml>
<MDocument>
<MChemicalStruct>
<molecule title="Ethane" molID="m1">
<atomArray atomID="a1 a2" elementType="C C" x2="0.0 0.0" y2="0.0 1.54"/>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
</bondArray>
</molecule>
</MChemicalStruct>
<MRectangle id="o2">
<MPoint x="-6.599999904632568" y="1.7050000429153442"/>
<MPoint x="-2.640000104904175" y="1.7050000429153442"/>
<MPoint x="-2.640000104904175" y="-0.16500000655651093"/>
<MPoint x="-6.599999904632568" y="-0.16500000655651093"/>
</MRectangle>
</MDocument>
</cml>
Example of MRV file exported with options "SP":
<?xml version="1.0"?>
<cml>
<MDocument>
<MChemicalStruct>
<molecule title="Ethane" molID="m1">
<atomArray atomID="a1 a2" elementType="C C" isSelected="true true" x2="0.0 0.0" y2="0.0 1.54"/>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
</bondArray>
</molecule>
</MChemicalStruct>
<MRectangle id="o2" isSelected="true">
<MPoint x="-6.599999904632568" y="1.7050000429153442"/>
<MPoint x="-2.640000104904175" y="1.7050000429153442"/>
<MPoint x="-2.640000104904175" y="-0.16500000655651093"/>
<MPoint x="-6.599999904632568" y="-0.16500000655651093"/>
</MRectangle>
</MDocument>
</cml>