Extended SMILES, SMARTS

Codename: cxsmiles,cxsmarts

Extended SMILES, SMARTS format

ChemAxon Extended SMILES/SMARTS is used for storing special features of the molecules after the SMILES string. Any information can be stored after the SMILES string if it is separated by space or tab characters as the SMILES parsers ignore them or use them as comment. The extended features are stored in the following format:
SMILES_String |<feature1>,<feature2>,...|
The extended feature description is economic. If some feature is missing in the molecule, then the corresponding special characters are not written. (Eg: If the atoms of the molecule has no alias strings at all, no "$" and ";" characters are written.) Moreover, if no feature of the molecule to be written, the extended feature field is omitted.

In extended smiles export the following additional features are exported:

Molecule absolute stereoconfiguration
The relative stereoconfiguration is stored as "r". The absolute stereoconfiguration is the default, which is not marked. (Absolute stereoconfiguration known also as "Chiral flag" in MDL molfiles.)
Enhanced stereochemical representation
The following stereochemical group types are stored:
- Absolute stereo group type.
  a:<atomindex>,<atomindex>...
- OR stereo group type.
  o<group>:<atomindex>,< atomindex>...
- AND stereo group type.
  &<group>:<atomindex>,< atomindex>...
Atom labels / aliases
Atom labels / aliases are written between "$" characters each label is separated by ";" characters.
Single "Up or Down" (Wiggly) bonds
Atom indexes relating to wiggly bonds are written after "w:" followed by a dot character and the wiggly bond index. The wiggly bonds are separated by commas.
CIS, TRANS, UNSPEC bond info for double bonds in rings
Bond indexes of the double bonds in SSSR are written.
The bond stereo information is generated as the following: the double bond has the representation a1-a2=a3-a4, where
- a1 is the smallest atom index of the generated smiles connected to a2
- a2 is the double bond smaller atom index in the generated smiles
- a3 is the double bond larger atom index in the generated smiles
- a4 is the smallest atom index of the generated smiles connected to a3
The CIS double bond indexes are written after "c:",
the TRANS double bond indexes are written after "t:",
the double bond indexes with UNSPEC flag are written after "u:".
Fragment level grouping of reactant, agent and product fragments Grouped fragment indexes are written after "f:" in the following format:
- Connected groups are separated by ",".
- A connected group is a "." separated list of fragment indices.
Example: "f:0.1,5.6"
Local parity information
Atom indexes with local ODD parity are written after "@:", while atom indexes with local EVEN parity are written after "@@:" characters separated by commas.
Radical numbers
Atom indexes with
- monovalent radical center are written after "^1:",
- divalent radical center are written after "^2:",
- divalent singlet radical center are written after "^3:",
- divalent triplet radical center are written after "^4:",
- trivalent radical center are written after "^5:",
characters separated by commas.
Lone electron pairs
The indexes of the atoms having lone electron pairs are written after "LP:".
Multicenter SGroups and coordinate bonds
The multicenter atom indexes written after "m:" followed by a colon character and the indexes of the atoms which forms the given SGroup separated by ".". The SGroups are separated by commas.

Atom indexes relating to coordinate bond indexes are written after "COORDINATE:" followed by a dot character and the coordinate bond index. The coordinate bonds are separated by commas.
Example: "m:0:7.6.5.4.3,2:12.11.10.9.8,COORDINATE:0.0,2.1"
Link nodes
The link node atom indexes are written after "LN:" followed by a colon character, the minimum repetitions, maximum repetitions, the node first and second outer atom indexes separated by ".". If the link node has only two connections, then the first and second outer atom indexes are obvious, so they are omitted. The link nodes separated by commas.
Example: "LN:1:1.5.3.0,6:1.2.7.5,9:1.10.10.8"
Atomic coordinates
The atomic coordinates are written between parentheses. Each atomic coordinate triplet (x, y, z) is separated by semicolon, and the x y z coordinates are separated by commas. Zero coordinates are omitted.
Note: The CIS/TRANS information is rednundant in this case. It is specified in the SMILES string and also in the atomic coordinates. The atomic coordinates has priority over the SMILES string.

Import options

See SMILES import options

Export options

Export options can be specified in the format string. The format descriptor and the options are separated by a colon. All options have default values (see below). Using the "+" or "-" sign the default export values can be changed to "true" or "false" respectively. If the option is given without "+" or "-" modifier than the default values are not used and only the specific feature is exported.
Examples:
"cxsmiles:" writes all default features (absolute stereoconfiguration, enhanced stereo features, atom labels, wiggly bond indexes, ring stereo bond info and reaction fragment level grouping),
"cxsmiles:lc" writes the atom labels and the atomic coordinates only,
"cxsmiles:+c" writes writes all default features and the atomic coordinates,
"cxsmiles:-le" writes absolute stereoconfiguration, enhanced stereo features, ring stereo bond info and reaction fragment level grouping but not atom labels and wiggly bond indexes.

e Write relative stereo configuration and enhanced stereo features. Default value: true.

l Write atom labels / aliases. Default value: true.

w Write wiggly bond indexes. Default value: true.

d Write CIS, TRANS ring bond indexes. Default value: true.

f Reaction fragment level grouping. Default value: true.

p Write local parities. Default value: true.

R Write radical numbers. Default value: true.

L Write lone electron pairs. Default value: true.

m Write multicenter SGroups and coordinate bonds. Default value: true.

N Write link nodes. Default value: true.

cp Write atomic coordinates. p can specify the coordinate precision optionally. If p is not specified, the default value 2 is used. Default value: false.

Extended SMILES, SMARTS

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