Attributes may be assigned to structures and patterns. Structure attributes are delimited by angle brackets (<>) and must follow the atom-bond connectivity of the SLN. Each attribute is separated from the previous one by a semicolon. Unlike atom and bond attributes, structure attributes cannot have logical expressions, the semicolon serves only as a separator.

Available structure attributes include:

• Coordinates
• Re-orderable Attributes
• Valued Attributes
• Boolean Attributes

Structure attributes are also used in the Structures and Mixtures.

Coordinates

Coordinates are specified as structure attributes.

Coordinate_type=Coordinate_list

• Coordinate_type--Either coord2d for 2D or coord3d for 3D coordinates.
• Coordinate_list--List of coordinates. There must be a coordinate for each atom in the structure. Coordinates are optionally delimited by an open parenthesis ("(") followed by a comma-separated list of real numbers. For 2D coordinates, there are 2 real numbers in the list (X and Y coordinates), for 3D, there are 3 (X, Y, and Z coordinates). This list is terminated by an optional closing parenthesis (")"). Coordinate sets are separated by commas.

Example:

 
        C[1]H:CH:CH:CH:CH:CH:@1<coord2d=(-0.699,-1.211),\
	 (-1.244,-2.154),(0.699,-1.211),(1.244,-2.154),\
	 (1.398,0.000),2.487,0.000),(0.699,1.211),\
	 (1.244,2.154),(-0.699,1.211),(-1.244,2.154),\
	 (-1.398,0.000),(-2.487,0.000)>

Re-orderable Attributes

It is common practice to use structure attributes to store some information about the structure, usually this takes the form of atom IDs stored in a structure attribute. However, the atom IDs can be made invalid by internal operations that reorder the atoms, bonds, or fragments in the SLN. A re-orderable structure attribute allows the software to maintain the correct values for the IDs.

Attribute_name:=Value:ID_list

• Attribute_name--Name of structure attribute. It is case insensitive, must begin with a letter, and can contain letters, numbers, or underscores.
• :=--Identifies that this is a re-orderable structure attribute.
• Value--Optional attribute value to associate with the list. Value may be a quoted string, a number, or an identifier. The value, if present, must be followed by a colon.
• ID_list--List of atom IDs (comma-separated).

Two predefined re-orderable attributes are the SLASH_BOND and the DATIVE_BOND. In the SLASH_BOND the value is an ID of an atom which can replace a hydrogen attached to one of the atoms whose IDs are in the ID list.

The DATIVE_BOND specifies that an atom is to be bonded to multiple atoms. See Combinatorial Chemistry Support for more details.

Examples

<ATOMS_IN_FLUX:=4,7,9>	Atoms 4, 7, and 9 are all "ATOMS_IN_FLUX".
NH2CH(OH)Cl<wedge_up:=4,1; wedge_down:=4,6>	Two re-orderable structure attributes are used to indicate wedge bonds for use in rendering a 2D drawing of the structure.

Valued Attributes

Attribute_name=attribute_value

• Attribute_name--Name of structure attribute. It is case insensitive, must begin with a letter, or underscore character, and can only contain letters, numbers, underscore characters, and periods.
• attribute_value--Text string containing the value of the attribute.

Tripos has reserved several Valued Attribute names for use in Tripos software:

• regId serves as a place holder for companies' registration identifiers to uniquely identify molecules
• name holds a molecule's name
• RXNID is reserved for the specification of external identification for a reaction. It can be specified for a parent CT or child compounds (for reference to another reaction)
  Example: <RXNID="123-456">CCOH<RXNID="456-321">+\
  CC(=O)OH->CC(=O)OCC

By convention, Tripos software chooses regId first when it looks for unique molecule identifiers. If regId is not found, it uses the name field. The dbtranslate command is an example of this.

Example:

 
        N[+](CH3)(CH3)(CH3)CH3<type="CATION"> 

In the SLN above, the structure has been assigned a structure attribute, "type" whose value is the string "CATION". "TYPE" is a user defined attribute, and will not be used when searching.

Boolean Attributes

Attribute_name

• Attribute_name--Name of structure attribute. It is case insensitive, must begin with a letter, and can contain letters, numbers, or underscore characters.

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