Marvin Documents - MRV

    Code: 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 occupied 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.

        chargeAngle

        The angle of charge assigned to an atom.

        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.

          chargeAngle

          The angle of charge assigned to an atom.

          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