Marvin Documents (MRV)

Codename: mrv

An mrv file may contain four elements,cml, MDocument, molecule, reaction, all of which has complex type. The elements of the complex types are shown as list items, while its attributes are written with italic under the name of the corresponding complex type name.

Element: cml

version

Version information (file format version number and generation version number).

  • MHead: Header containing global properties. (optional)

    • MarvinGUI: Description of Marvin GUI properties

      • mprop: Marvin GUI property type.

        dataType

        Type name of marvin GUI dat

        name

        Name tag of the marvin GUI properties.

        value

        Value of Marvin GUI property

  • MDocument: Main marvin document element containing molecules, graphical objects, reactions, etc.

  • molecule: Element containing the description of a molecule.

  • reaction: Element containing the description of a reaction.

Element: MDocument

atomSetFont

Font type of atom sets.

atomSetRGB

Atom 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).

bondSetLineThickness

Thickness of bonds in the bond sets.

bondSetRGB

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).

extraLabelSetRGB

Color setting of the extra label.

multipageBottom

Bottom margin of a page in multipage molecular document. Its value is "d" where d is a floating point number.

multipageColumnCount

Number of columns in multipage molecular document. Its value is "k" where k is a positive integer.

multipageEnabled

Enables the multipage molecular document. Its value is "true" or "false".

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 margin of a page in multipage molecular document. Its value is "d" where d is a floating point number.

multipageRowCount

Number of rows in multipage molecular document. Its value is "k" where k is a positive integer.

multipageSelectedPage

The selected page in multipage molecular document. Its value is "k" where k is a positive integer.

multipageTop

Top margin of a page in multipage molecular document. Its value is "d" where d is a floating point number.

multipageWidth

Width of a page in multipage molecular document. Its value is "d" where d is a floating point number.

  • propertyList: List containing Marvin GUI attributes.

    • property: Marvin document properties.

      dictRef

      Key of the properties related to the document.

      title

      Title of a Marvin document.

      • scalar: Scalar Marvin document property: it contains a single data value.

        dataType

        Data type of the scalar tag value.

      • array: Array Marvin document property: it contains an array of double values.

        dataType

        Data type of the array tag values.

        size

        Size of the array.

  • MChemicalStruct: Description of a chemical Structure.

    • molecule: Element containing the description of a molecule.

    • reaction: Element containing the description of a reaction.

    • Rgroup: Element containing the definition of an R-group.

      restH

      It is a condition for an R-group: If it is set for an R-group, the hit molecules do not contain ligands on that atom other than hydrogen or those specified as R-group. If RestH condition is false, then R-group sites can contain any additional non-hydrogen ligands as well.

      rgroupID

      ID of the R-group.

      rlogicRange

      It shows that the given R-group how many times can occur in the target. (For example: 1-3,6 means the R-group can occur one, two three or six time in the target.).

      thenR

      It is a condition for an R-group:R-group has to be satisfied only when conditions of another R-group are satisfied.

      • molecule: Element containing the description of a molecule.

    • RgroupBridge: Element containing the metadata of an R-group bridge.

      rgroupBridgeId

      The IDs of the two R-groups.

      rgroupIndex

      The index of the representing R-group.

  • MMoleculeMovie: Animation of a chemical process.

    • MChemicalStruct: Element containing the description of a chemical structure.

      • molecule: Element containing the description of a molecule.

      • reaction: Element containing the description of a reaction.

      • Rgroup: Element containing the definition of an R-group.

        restH

        It is a condition for an R-group: If it is set for an R-group, the hit molecules do not contain ligands on that atom other than hydrogen or those specified as R-group. If RestH condition is false, then R-group sites can contain any additional non-hydrogen ligands as well.

        rgroupID

        ID of the R-group.

        rlogicRange

        It shows that the given R-group how many times can occur in the target. (For example: 1-3,6 means the R-group can occur one, two three or six time in the target.).

        thenR

        It is a condition for an R-group:R-group has to be satisfied only when conditions of another R-group are satisfied.

        • molecule: Element containing the description of a molecule.

      • RgroupBridge: Element containing the metadata of an R-group bridge.

        rgroupBridgeId

        The IDs of the two R-groups.

        rgroupIndex

        The index of the representing R-group.

  • MBracket: Bracket graphical object.

    orientation

    Determines whether bracket is in pairs or a standalone bracket. "Single" means that the bracket can be moved or resized alone, "double" means that the pair of brackets are treated as one entity, can be moved and resiyed only together.

    tcenter

    Geometric center of the object for transformations like rotation. Identifies corners and middle-points with points of the compass, e.g. NW (North West) identifies the top right corner. Possible values are the eight points of the compass or center.

    toption

    It shows that the object can be rotated or not.

    type

    Type of the bracket.

    • MPoint:

      x

      X coordinate.

      y

      Y coordinate.

      z

      Z coordinate.

  • MEFlow: Curved electron flow arrow. MEFlow is a subclass of MPolyline thus it has the same attributes, but it can only contain two points.

    arcAngle

    Angle of the electron flow arrow arc.

    baseElectronContainerIndex

    Describes which electroncontainer holds electron.

    baseElectronIndexInContainer

    Describes which electron is base electron.

    • MEFlowBasePoint: Starting point of the electron flow arrow if the source is an atom.

      atomRef

    • MAtomSetPoint: It represents an atom or atom pair (bond or incipient bond).

      atomRefs

      weights

    • MAtomSetPoint: It represents an atom or atom pair (bond or incipient bond).

      atomRefs

      weights

  • MEllipse: Ellipse graphical object, it is derived from MRectangle, inheriting its attributes.

    background

    Background color.

    tcenter

    Geometric center of the object for transformations like rotation. Identifies corners and middle-points with points of the compass, e.g. NW (North West) identifies the top right corner. Possible values are the eight points of the compass or center.

    toption

    It shows that the object can be rotated or not.

    • MPoint: Basic point of a polyline object.

      x

      X coordinate.

      y

      Y coordinate.

      z

      Z coordinate.

  • MElectron: Represents the electrons of the atom, it has an atom reference, and a location difference to the location of the referenced atom.

    atomRef

    difLoc

  • MElectronContainer: This element holds information about electrons of atom, this know whether the electron is free, or occiupied with an MEflowArrow.

    occupation

    radical

  • MPolyline: Line, arc, polyline and/or graphical arrow.

    arcAngle

    Angle of arc.

    • MPoint: Basic Point of a polyline object.

      x

      X coordinate.

      y

      Y coordinate.

      z

      Z coordinate.

    • MRectanglePoint: Point of an object connected to a point of another graphical object which is a polyline.

      pos

      Identifies to which point of a rectangle this point is connected.

      rectRef

      Reference name of the rectangle to which this point of the object is connected.

    • MMidPoint: Point of an object connected to a middle point of another graphical object which is a polyline.

      pos

      Identifies to which point of a polyline this point is connected.

      lineRef

      Reference name of the line to which this point of the object is connected.

    • MAtomSetPoint: It represents an atom or atom pair (bond or incipient bond).

      atomRefs

      weights

  • MRectangle: Rectangle graphical Object.

    background

    Background color.

    tcenter

    Geometric center of the object for transformations like rotation. Identifies corners and middle-points with points of the compass, e.g. NW (North West) identifies the top right corner. Possible values are the eight points of the compass or center.

    toption

    It shows that the object can be rotated or not.

    • MPoint: Basic point of a polyline object.

      x

      X coordinate.

      y

      Y coordinate.

      z

      Z coordinate.

  • MRoundedRectangle: Rounded cornered rectangle graphical object.

    arcHeight

    The height of the arc of the rounded corner.

    arcWidth

    The width of the arc of the rounded corner.

  • MTextBox: Text box.

    autoSize

    It aranges the text box size to the size automatically.

    background

    Background color.

    color

    Color.

    fontScale

    The size of the font.

    halign

    Horizontal alignment of the text box.

    tcenter

    Geometric center of the object for transformations like rotation. Identifies corners and middle-points with points of the compass, e.g. NW (North West) identifies the top right corner. Possible values are the eight points of the compass or center.

    toption

    It shows that the object can be rotated or not.

    valign

    Vertical alignment of the text Box.

    • Field: Element containing the text of the text box.

      name

      Name of the text field, usually has value "text".

    • MPoint: Basic Point of a polyline object.

      x

      X coordinate.

      y

      Y coordinate.

      z

      Z coordinate.

  • MNameTextBox: Text object that contains molecule name; it is derived from MTextBox, thus it inherits its attributes.

    autoAlign

    It shows that auto alignment function of the textbox is on or off.

    autoResize

    It shows that auto resize function of the textbox is on or off.

    preferredWidth

    The prefered width of the name text box.

  • NoStructure: A label representing a NoStructure element.

    x

    X coordinate

    y

    Y coordinate

    z

    Z coordinate

    isSelected

    Boolean type variable which shows that the object is selected or not.

    molRef

    ID number of the molecule in the MRV file.

Element: molecule

absStereo

It shows that absolute stereo label is on or off.

id

ID of the molecule in CML format.

molID

ID number of the molecule in the MRV file.

title

Title of the molecule.

oneLetterName

One letter name of an amino acid.

threeLetterName

Three letter name of an amino acid.

  • name: Name of the molecule.

  • propertyList: Property list of the molecule.

    • property: Molecule property type.

      dictRef

      Key of the properties related to the document.

      title

      • scalar: Scalar type molecular property.

        dataType

        Scalar data types

      • array: Array type molecular property.

        delimiter

        Delimiter string of molecule array properties.

  • atomArray: Array of atoms according to their label.

    atomID

    This argument is a space separated list of atoms.

    attachmentOrder

    Attachment point order value in the case of R-group attachment point.

    attachmentPoint

    List of attachment points.

    elementType

    Element in the Periodic Table.

    formalCharge

    It is the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond are shared equally between atoms, regardless of relative electronegativity.

    hydrogenCount

    Number of implicit hydrogen if needed. In the cases of 5-6 membered aromatic rings containing nitrogen atoms, it is not obvious which N atoms have implicit hydrogens.

    isSelected

    Boolean type variable which shows that the object is selected or not.

    isotope

    Atomic mass number.

    lonePair

    Number of lone pairs.

    mrvAlias

    Atom alias.

    mrvExtraLabel

    List of Atom extra labels.

    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.

    mrvLinkNodeRep

    Number of repetitions for a link node in format " n " (maximum number of repetitions) or " m - n " (minimum and maximum).

    mrvMap

    The map corresponding to the given atom mapping .

    mrvPseudo

    List of pseudoatom names.

    mrvQueryProps

    List of query atom properties

    mrvSetExtraLabelSeq

    Atom set extra label numbers.

    mrvSetSeq

    Atom set sequence number.

    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.

    mrvStereoGroup

    MDL enchanced stereo group representation.

    mrvValence

    Valence list.

    radical

    List of the radicals.

    reactionStereo

    List of reaction stereo properties.

    residueAtomName

    PDB atom name.

    residueId

    List of residue Ids.

    residueType

    List of residue types.

    rgroupRef

    List of R-group reference values.

    sgroupAttachmentPoint

    List of attachment points.

    sgroupRef

    List of S-group references.

    x2

    X coordinates in two-dimensional representation.

    x3

    X coordinates in three-dimensional representation.

    y2

    Y coordinates in two-dimensional representation.

    y3

    Y coordinates in three-dimensional representation.

    z3

    Z coordinates in three-dimensional representation.

    • atom: Atom type.

      attachmentOrder

      Attachment point order value in the case of R-group attachment point.

      attachmentPoint

      Attachment point value.

      elementType

      Element in the Periodic Table.

      formalCharge

      It is the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond are shared equally between atoms, regardless of relative electronegativity.

      hydrogenCount

      Number of implicit hydrogen if needed. In the cases of 5-6 membered aromatic rings containing nitrogen atoms, it is not obvious which N atoms have implicit hydrogens.

      id

      Atom ID.

      isotope

      Atomic mass number.

      isSelected

      Boolean type variable which shows that the object is selected or not.

      ligandOrder

      Order of ligands connected to an R-group atom: list of atom identifiers.

      lonePair

      Number of lone pairs.

      mrvAlias

      Atom alias.

      mrvExtraLabel

      Atom extra label.

      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.

      mrvLinkNodeRep

      Number of repetitions for a link node in format " n " (maximum number of repetitions) or " m - n " (minimum and maximum).

      mrvMap

      The map corresponding to the given atom mapping.

      mrvPseudo

      Pseudoatom name.

      mrvQueryProps

      Query atom properties.

      mrvSetExtraLabelSeq

      Atom set extra label numbers.

      mrvSetSeq

      Atom set sequence number.

      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.

      mrvStereoGroup

      MDL enchanced stereo group representation.

      mrvValence

      Valence.

      radical

      Name of the radical center.

      reactionStereo

      Reaction stereo value.

      residueAtomName

      PDB atom name.

      residueId

      Name of residue ID.

      residueType

      Name of residue type

      rgroupRef

      R-group reference value.

      sgroupAttachmentPoint

      S-group attachment point: "1", (on first site) "2" (on second site) or "both" (on both sites).

      sgroupRef

      S-group reference name.

      x2

      X coordinates in two-dimensional representation.

      y2

      Y coordinates in two-dimensional representation.

      x3

      X coordinates in three-dimensional representation.

      y3

      Y coordinates in three-dimensional representation.

      z3

      Z coordinates in three-dimensional representation.

      • atomParity: Atom parity.

        atomRefs4

        Represents the parity value of the stereocenter according to the given four atom reference frame.

      • scalar: List of the atom special scalar properties.

        convention

        Name of the convention where the property is being interpeted.

        dataType

        Type of the property.

        id

        ID of the atom property.

        title

        String usually same as string.

      • atomBicycloStereo: Bicyclostereo (endo- exo-) information of the atom. Possible values: If the ligand is oriented towards the bridge that contains the higer atomic index, it gets the THB (Towards Higher Bridge) label; if it's oriented towards the other bridge it gets the TLB (Towards Lower Bridge) label; if the position is undefined, it gets either value.

        connectionAtom

        The ID of the connecting atom.

        highBridge

        The atom reference list of the high bridge.

        lowBridge

        The atom reference list of the low bridge.

  • bondArray: Array of bonds according to bond tags.

    • bond:

      id

      The id of the bond.

      atomRefs2

      List containing two atom references (a1,a2).

      convention

      A number referring the MDL stereo type of the bond or "cxn:coord" in case of coordinative bond, "cxn:hydrogen" in case of hydrogen bond.

      mrvBold

      Bold bond attribute.

      mrvHashed

      Hashed bond attribute.

      mrvQueryProps

      Query bond properties.

      mrvReactingCenter

      Reacting center bond query feature . Possible values: -1: not center, 1: center, 4: make or break, 8: change, 12: make and change.

      mrvReactionCenter

      mrvSetSeq

      Atom set sequence number.

      order

      Name of bond order (e.g., single, double, triple, aromatic etc.).

      queryType

      Name of query bond type.

      topology

      Defines that the bond is a part of a ring or a chain.

      • bondStereo:

        convention

        Stereo representation framework type.

        conventionValue

        Stereo Convention Value: It can be MDLStereoValue or ChemAxonStereoValue.

      • scalar: List of the bond special scalar properties.

        convention

        Name of the convention where the property is being interpeted.

        dataType

        Type of the property.

        id

        ID of the bond property.

        title

        String usually same as string.

  • molecule: Submolecule (S-groups).

    atomRefs

    Reference to the atoms in the S-Groups.

    bondList

    List of bonds

    center

    Atom reference of center atom

    charge

    Place of the charge. It's value can be "onAtoms" or "onBracket"

    connect

    Type of monomer connection in case of copolymers.

    context

    Context of the data field.

    correspondence

    S-group correspondence

    dataDetached

    Boolean type variable showing if the data is detached or not.

    displayedChars

    Number of characters displayed per line

    displayedLines

    Number of the lines displayed

    fieldData

    First field of the data.

    fieldData1

    Second field of the data

    fieldData2

    Third field of the data

    fieldData3

    Fourth field of the data

    fieldData4

    Fifth field of the data

    fieldData5

    Sixth field of the data

    fieldData6

    Seventh field of the data

    fieldData7

    Eighth field of the data

    fieldData8

    Ninth field of the data

    fieldData9

    Tenth field of the data

    fieldName

    Name of the field in Data S-Groups.

    fieldType

    Type of the field

    id

    ID number of the S-group

    labelCenter

    Defines the atom of the S-group to which the bond points, if flipping effect is not used.

    leftName

    Alternative name of the abbreviated group when flipping effect is used, and the name group is on the left hand side of the molecule. (e.g. the leftName of "COOH" is HOOC).

    molID

    ID number of the molecule in the MRV file.

    placement

    Defines if the placement of the data is absolute or relative in data S-groups.

    pos

    Identifies to which point of a rectangle this point is connected.

    queryOp

    Query operator in data S-groups.

    queryType

    Name of the query bond type.

    rightName

    Alternative name of the abbreviated group when flipping effect is used, and the name group is on the right hand side of the molecule (e.g. the rightName of "MeO" is OMe).

    role

    Name of the Sgroup type (e.g. SRU).

    tag

    Tag of the fieldData.

    title

    Title of the S-group. That is the string written in the subscript.

    units

    Unit of the data in Data S-group.

    unitsDisplayed

    Shows if the unit of data is displayed in data S-group.

    x

    X coordinate.

    y

    Y coordinate.

    oneLetterName

    One letter name of an amino acid.

    threeLetterName

    Three letter name of an amino acid.

    • propertyList: List of molecule property attributes.

      • property: Molecule property type.

        dictRef

        Key of the properties related to the document.

        title

        • scalar: Scalar type molecular property.

          dataType

          Scalar data types

        • array: Array type molecular property.

          delimiter

          Delimiter string of molecule array properties.

    • atomArray: List of atoms in the S-group.

      atomID

      This argument is a space separated list of atoms.

      attachmentOrder

      Attachment point order value in the case of R-group attachment point.

      attachmentPoint

      List of attachment points.

      elementType

      Element in the Periodic Table.

      formalCharge

      It is the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond are shared equally between atoms, regardless of relative electronegativity.

      hydrogenCount

      Number of implicit hydrogen if needed. In the cases of 5-6 membered aromatic rings containing nitrogen atoms, it is not obvious which N atoms have implicit hydrogens.

      isSelected

      Boolean type variable which shows that the object is selected or not.

      isotope

      Atomic mass number.

      lonePair

      Number of lone pairs.

      mrvAlias

      Atom alias.

      mrvExtraLabel

      List of Atom extra labels.

      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.

      mrvLinkNodeRep

      Number of repetitions for a link node in format " n " (maximum number of repetitions) or " m - n " (minimum and maximum).

      mrvMap

      The map corresponding to the given atom mapping .

      mrvPseudo

      List of pseudoatom names.

      mrvQueryProps

      List of query atom properties

      mrvSetExtraLabelSeq

      Atom set extra label numbers.

      mrvSetSeq

      Atom set sequence number.

      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.

      mrvStereoGroup

      MDL enchanced stereo group representation.

      mrvValence

      Valence list.

      radical

      List of the radicals.

      reactionStereo

      List of reaction stereo properties.

      residueAtomName

      PDB atom name.

      residueId

      List of residue Ids.

      residueType

      List of residue types.

      rgroupRef

      List of R-group reference values.

      sgroupAttachmentPoint

      List of attachment points.

      sgroupRef

      List of S-group references.

      x2

      X coordinates in two-dimensional representation.

      x3

      X coordinates in three-dimensional representation.

      y2

      Y coordinates in two-dimensional representation.

      y3

      Y coordinates in three-dimensional representation.

      z3

      Z coordinates in three-dimensional representation.

      • atom: Atom type.

        attachmentOrder

        Attachment point order value in the case of R-group attachment point.

        attachmentPoint

        Attachment point value.

        elementType

        Element in the Periodic Table.

        formalCharge

        It is the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond are shared equally between atoms, regardless of relative electronegativity.

        hydrogenCount

        Number of implicit hydrogen if needed. In the cases of 5-6 membered aromatic rings containing nitrogen atoms, it is not obvious which N atoms have implicit hydrogens.

        id

        Atom ID.

        isotope

        Atomic mass number.

        isSelected

        Boolean type variable which shows that the object is selected or not.

        ligandOrder

        Order of ligands connected to an R-group atom: list of atom identifiers.

        lonePair

        Number of lone pairs.

        mrvAlias

        Atom alias.

        mrvExtraLabel

        Atom extra label.

        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.

        mrvLinkNodeRep

        Number of repetitions for a link node in format " n " (maximum number of repetitions) or " m - n " (minimum and maximum).

        mrvMap

        The map corresponding to the given atom mapping.

        mrvPseudo

        Pseudoatom name.

        mrvQueryProps

        Query atom properties.

        mrvSetExtraLabelSeq

        Atom set extra label numbers.

        mrvSetSeq

        Atom set sequence number.

        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.

        mrvStereoGroup

        MDL enchanced stereo group representation.

        mrvValence

        Valence.

        radical

        Name of the radical center.

        reactionStereo

        Reaction stereo value.

        residueAtomName

        PDB atom name.

        residueId

        Name of residue ID.

        residueType

        Name of residue type

        rgroupRef

        R-group reference value.

        sgroupAttachmentPoint

        S-group attachment point: "1", (on first site) "2" (on second site) or "both" (on both sites).

        sgroupRef

        S-group reference name.

        x2

        X coordinates in two-dimensional representation.

        y2

        Y coordinates in two-dimensional representation.

        x3

        X coordinates in three-dimensional representation.

        y3

        Y coordinates in three-dimensional representation.

        z3

        Z coordinates in three-dimensional representation.

        • atomParity: Atom parity.

          atomRefs4

          Represents the parity value of the stereocenter according to the given four atom reference frame.

        • scalar: List of the atom special scalar properties.

          convention

          Name of the convention where the property is being interpeted.

          dataType

          Type of the property.

          id

          ID of the atom property.

          title

          String usually same as string.

        • atomBicycloStereo: Bicyclostereo (endo- exo-) information of the atom. Possible values: If the ligand is oriented towards the bridge that contains the higer atomic index, it gets the THB (Towards Higher Bridge) label; if it's oriented towards the other bridge it gets the TLB (Towards Lower Bridge) label; if the position is undefined, it gets either value.

          connectionAtom

          The ID of the connecting atom.

          highBridge

          The atom reference list of the high bridge.

          lowBridge

          The atom reference list of the low bridge.

    • bondArray: List of bonds in the S-group.

      • bond:

        id

        The id of the bond.

        atomRefs2

        List containing two atom references (a1,a2).

        convention

        A number referring the MDL stereo type of the bond or "cxn:coord" in case of coordinative bond, "cxn:hydrogen" in case of hydrogen bond.

        mrvBold

        Bold bond attribute.

        mrvHashed

        Hashed bond attribute.

        mrvQueryProps

        Query bond properties.

        mrvReactingCenter

        Reacting center bond query feature . Possible values: -1: not center, 1: center, 4: make or break, 8: change, 12: make and change.

        mrvReactionCenter

        mrvSetSeq

        Atom set sequence number.

        order

        Name of bond order (e.g., single, double, triple, aromatic etc.).

        queryType

        Name of query bond type.

        topology

        Defines that the bond is a part of a ring or a chain.

        • bondStereo:

          convention

          Stereo representation framework type.

          conventionValue

          Stereo Convention Value: It can be MDLStereoValue or ChemAxonStereoValue.

        • scalar: List of the bond special scalar properties.

          convention

          Name of the convention where the property is being interpeted.

          dataType

          Type of the property.

          id

          ID of the bond property.

          title

          String usually same as string.

    • SgroupAtom: Properties of the SuperatomSgroup's SgroupAtom containing colouring, font size and atomic properties.

      mrvSetSeq

      Atom set sequence number.

      • scalar: List of the atom special scalar properties.

        convention

        Name of the convention where the property is being interpeted.

        dataType

        Type of the property.

        id

        ID of the atom property.

        title

        String usually same as string.

    • AttachmentPointArray: Array of the attachment points of the superatom S-group in the multiple attachment point representation.

      • attachmentPoint: AttachmentPoint of the Superatom S-group.

        atom

        The atom on which the attachment point is placed.

        order

        The order of the attachment point.

        bond

        The crossing bond of the attachment point.

        crossingBondType

        The type of the crossing bond.

    • MBracket: Bracket object.

      isSelected

      Boolean type variable which shows that the object is selected or not.

      lineColor

      Line color.

      orientation

      Determines whether bracket is in pairs or a standalone bracket. "Single" means that the bracket can be moved or resized alone, "double" means that the pair of brackets are treated as one entity, can be moved and resiyed only together.

      tcenter

      Geometric center of the object for transformations like rotation. Identifies corners and middle-points with points of the compass, e.g. NW (North West) identifies the top right corner. Possible values are the eight points of the compass or center.

      thickness

      Thickness.

      toption

      It shows that the object can be rotated or not.

      type

      Type of the bracket.

      • MPoint: Basic Point of a polyline object.

        x

        X coordinate.

        y

        Y coordinate.

        z

        Z coordinate.

Element: reaction

absStereo

It shows that absolute stereo label is on or off.

title

Title.

  • arrow: Reaction arrow type.

    type

    Type of reaction arrow. E.g., EQUILIBRIUM.

    x1

    The X coordinate of the staring point of the reaction arrow.

    x2

    The X coordinate of the endpoint of the reaction arrow.

    y1

    The Y coordinate of the staring point of the reaction arrow.

    y2

    The Y coordinate of the endpoint of the reaction arrow.

    z1

    The Z coordinate of the staring point of the reaction arrow.

    z2

    The Z coordinate of the endpoint of the reaction arrow.

  • propertyList: Property list.

    • property: Molecule property type.

      dictRef

      Key of the properties related to the document.

      title

      • scalar: Scalar type molecular property.

        dataType

        Scalar data types

      • array: Array type molecular property.

        delimiter

        Delimiter string of molecule array properties.

  • reactantList: List of reactants in the reaction.

    • molecule: Element containing the description of a molecule.

  • agentList: List of agents in the reaction.

    • molecule: Element containing the description of a molecule.

  • productList: List of products in the reaction.

    • molecule: Element containing the description of a molecule.

Escape characters

Special value of an element or attribute is escaped as follows:

    null

    "0"

    0

    "zero" (character string)

    no value

    "."

    "."

    &#n;, n is the character code