Page tree
Skip to end of metadata
Go to start of metadata

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 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.
oneLetterNameOne letter name of an amino acid.
threeLetterNameThree 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.
    isotopeAtomic mass number.
    lonePair Number of lone pairs.
    mrvAliasAtom 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.
    mrvValenceValence list.
    radical List of the radicals.
    reactionStereo List of reaction stereo properties.
    residueAtomNamePDB 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.
      idAtom ID.
      isotopeAtomic 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.
      mrvAliasAtom alias.
      mrvExtraLabelAtom 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.
      mrvPseudoPseudoatom 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.
      mrvValenceValence.
      radical Name of the radical center.
      reactionStereo Reaction stereo value.
      residueAtomNamePDB atom name.
      residueIdName 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.
    oneLetterNameOne letter name of an amino acid.
    threeLetterNameThree 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.
      isotopeAtomic mass number.
      lonePair Number of lone pairs.
      mrvAliasAtom 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.
      mrvValenceValence list.
      radical List of the radicals.
      reactionStereo List of reaction stereo properties.
      residueAtomNamePDB 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.
        idAtom ID.
        isotopeAtomic 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.
        mrvAliasAtom alias.
        mrvExtraLabelAtom 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.
        mrvPseudoPseudoatom 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.
        mrvValenceValence.
        radical Name of the radical center.
        reactionStereo Reaction stereo value.
        residueAtomNamePDB atom name.
        residueIdName 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