Marvin Documents

Codename: mrv

Contents

• Marvin Documents format
• Export options

Marvin Documents format

The following tags are recognized:

• <cml> - root element
  Children:
  • <MDocument>
• <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.
        • rgroupRef - R-group reference value or zero.
        • sgroupRef - S-group reference value or zero.
        • attachmentPoint - R-group attachment point value or zero.
        • 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) or "trivalent4" (quartet).
          • reactionStereo - Reaction stereo: "Inv" (inversion) or "Ret" (retention).
          • rgroupRef - R-group reference. Currently, only positive integer values are accepted.
          • sgroupRef - S-group reference.
          • attachmentPoint - R-group attachment point: "1", (on first site) "2" (on second site) or "both" (on both sites).
          • 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).
          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.
        • <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).
          
      • <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)
      • <propertyList>
      • <property>
    • <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.
  • <MTextBox [text="The text"] [fontScale="fontScale"] - text object.
    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)
    Children:
    • <Field name="text">The text </Field>
    • <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.
  • <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

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