E.g. aromatic Boron is written with lowercase letter: b1ccccc1.
The relative stereoconfiguration is stored as "r".
If a reaction contains components with absolute and relative stereo the indexes of the fragments with relative configuration is written.
The absolute stereoconfiguration is the default, which is not marked.
(Absolute stereoconfiguration known also as "Chiral flag" in MDL molfiles. )
Example: "r:2,4,5"
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 are written between "$" characters
each label is separated by ";" characters.
Atom values are written after "$_AV:" separated by
semicolon characters and closed with "$" tag.
Special chacters are escaped.
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.
If atomic coordinates are also exported, then UP bonds are written
after "wU:"
DOWN bonds are written after "wD:" in a similar way to
wiggly bond export.
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 TRANS double bond indexes are written after "t:",
the double bond indexes with UNSPEC flag are written after "ctu:".
- Connected groups are separated by ",".
- A connected group is a "." separated list of fragment indices.
Example: "f:0.1,5.6"
Atom indexes with local ODD parity are written after "@:", while atom indexes with local EVEN parity are written after "@@:" characters separated by commas.
For each ligand connected to non-bridgehead atoms of bicyclo-alkanes, if they are in a syn/anti or endo/exo position (ligand is not in the plane of the bridge to which it is connected), their relative position in the ring system is stored by their position in relation to the bridges to which they are not connected. Bridges are identified by the indexes of the contained atoms: higher bridge is the one with the highest atom index, the other is the lower bridge. The ligand's position can be:
- towards higher bridge (THB), if it lies towards the higher bridge regarding the plane of the connected bridge
- towards lower bridge (TLB), if it lies towards the lower bridge regarding the plane of the connected bridge
- towards either bridge (TEB), if its position is not determined, it can lie towards both of the bridges (it is connected by a wiggly bond)
- "THB", followed by ":", than for each THB ligand as follows:
- index of the ligand atom for which bicyclo stereo description is stored, followed by ":"
- index of the ring atom in the bicyclo-alkane to which the ligand is connected (connection atom), followed by ":"
- list of indexes in the lower bridge, separated by "." and followed by ":"
- list of indexes in the higher bridge, separated by "."
- stereo description of separate ligands are separated by ","
- the same lists are present for THB and TEB atoms, separated by ",".
Examples:
| [H][C@]12CCC[C@]([H])(CC(C)C1)C2(S)Cl |r,TLB:13:11:2.4.3:7.10.8,THB:12:11:2.4.3:7.10.8,9:8:11:2.4.3| |  |
| [H][C@]12COC[C@]([H])(C[C@@H](CCCC)C1)[C@@]2(Cl)C1CCCC1 |r,TLB:15:14:2.4.3:7.13.8,THB:16:14:2.4.3:7.13.8,9:8:14:2.4.3| |  |
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:",
- trivalent doublet radical center are written after "^6:",
- trivalent quartet radical center are written after "^7:",
The indexes of the atoms having bond connected lone electron pairs are written after "LP:".
The indexes of the atoms followed by a colon character and the number of
explicit lone electron pairs are written after
"lp:".
(See live example.)
Example: "LP:1,lp:0:1,2:2"
The atom index of the first atom in the coordinate bond is written after
"C:" followed by a dot character and the coordinate bond index.
The coordinate bonds are separated by commas.
In the smiles part of cxsmiles the atom-to-atom coordinate bonds are
represented by single bonds, which are corrected according to the
C information at the extended part.
Hydrogen bonds exported in the same format after "H:".
Hydrogen bond: "CO(C)[H]N1C=CC=C1 |c:5,7,H:3.2| "
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.
Example: "m:0:7.6.5.4.3,2:12.11.10.9.8,C:0.0,2.1"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"
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 redundant 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.
Atomic indexes in the data sgroup are written after
"SgD:" followed by
field name, data value, query operator, unit, tag
and coordinates in parenthesis if necessary, separated by
colon characters. The field values with special characters are escaped. If atomic coordinates are exported (with
c option) (-1) is used in the coordinate field
for data sgroup attached to the atoms.
Example: "SgD:3,2,1,0:name:data:like:unit:t:(-1)"
The R-group attachment point is written explicitly as ANY atom into the SMILES
string.
The order of attachment point is written as alias string
(see above) after "_AP" separated by semicolon characters.
Before version 5.4 only two attachment point type was supported, the
attachment point was not exported to the SMILES string explicitly.
In the extended part the atomic indexes of the attachment points written
after "AP_x:" format was used, where x denoted
attachment type 1, 2 or 3 for attachment points 1, 2 or both.
Example: "C[C@H](N*)C(*)=O |$;;;_AP1;;_AP2;$|", before version 5.4: "C[C@H]([NH])[C]=O |AP_1:2,AP_2:3|"
S-group attachment point informations are not handled by cxsmiles or cxsmarts.
Rgroup information can be exported to extended cxsmiles/cxsmarts. Rgroups in the molecule is exported to ANY atom in the SMILES part, they are described in the alias part as "_Rn". Rgroup descriptions (molecules) are enumerated also in the extended part after "RG" followed by a colon character.
- The Rgroup number is written after "_R" followed by "=" (eg. _R1=)
- The Rgroup description is written as cxsmiles/cxsmarts in braces "{}"
- Members of the same Rgroup are seperated by commas
- Different Rgroups are seperated by commas.
- C1O[*]CO[*]1 |$;;_R2;;;_R1$,RG:_R1={C},{N},_R2={C},{N}|
- Cl[*](Br)I |$;_R1;;$,RG:_R1={*CCCC(C*)CC* |$_AP3;;;;;;_AP2;;;_AP1$|},{*CCCN(C*)CC* |$_AP3;;;;;;_AP2;;;_AP1$|},LO:1:0.2.3|
Ligand order information can be exported to extended cxsmiles/cxsmarts after "LO" followed by a colon character.
- First the center atom's index is exported followed by a colon
- After that all atom's indexes connected to the central atom is written in ligand order sperated by "."
- The different ligand order informations are seperated by comma.
- Eg: LO:centerIdx1:idx1.idx2.idx3,centerIdx2:idx1.idx2...
- Cl[*](Br)I |$;_R1;;$,RG:_R1={*CCCC(C*)CC* |$_AP3;;;;;;_AP2;;;_AP1$|},{*CCCN(C*)CC* |$_AP3;;;;;;_AP2;;;_AP1$|},LO:1:0.2.3|
Pseudo atoms can be exported to extended cxsmiles/cxsmarts.
They are described in the alias part as "pseudo_p",
where pseudo is the value of the pseudo atom.
Example:
CCCC* |$;;;;pseudo_p$| 
Special atoms AH, QH, M, MH, X, XH and Pol, are exported to cxsmiles/cxsmarts as pseudo atoms, i.e. AH_p, QH_p, M_p, MH_p, X_p, XH_p, and Pol_p, respecively. Special atoms Q and star are exported as Q_e and star_e, respectively. Special atom A can be handled by SMILES export, therefore it is not written to the alias part of the cxsmiles/cxsmarts.
Examples:
*C(*)CC(*)CC(*)* |$;;Pol_p;;;Q_e;;;star_e;M_p$| 
*C(*)CC(*)CC(*)* |$Q_e;;AH_p;;;X_p;;;QH_p;XH_p$|
Ring bond count (rb), Substitution count (s) and unstaturated atom (u) are exported in the following form:
rb:atomIndex1:value,atomIndex2:value
s:atomIndex1:value,atomIndex2:value
u:atomIndex1,atomIndex2,atomIndex3
Examples: "rb:1:2,2:*,4:2", "u:3,4,5"
Each Sgroup exported after "Sg:" in fields separated by a colon. Fields are:
- Sgroup type keyword.
Valid keywords are:
Keyword Sgroup Type n SRU mon monomer mer mer co copolymer xl crosslink mod modification mix mixture f formulation any anypolimer gen generic c component grf graft alt alternating copolymer ran random copolymer blk block copolymer - Atom indexes separated with commas.
- Subscript of the Sgroup. If the supscript equals the keyword of the Sgroup this field can be empty. Escaped field.
- Superscript of the Sgroup. In the superscript only connectivity and flip information is allowed. This field can be empty. Escaped field.
- Head crossing bond indexes. The indexes of bonds that share a common bracket in case of ladder-type polymers. This field can be empty.
- Tail crossing bond indexes. The indexes of bonds that share a common bracket in case of ladder-type polymers. This field can be empty.
- If the c export option is present then bracket orientation, bracket type followed by the coordinates (4 pair, separated with commas). Bracket orientation can be s or d (single or double), bracket type can be b,c,r,s for braces, chevrons, round and square, respectively. The brackets are written between parentheses and separated with semicolons.
A colon is needed after the last non-empty field.
If one needs to retain not only the chemically relevant information, but the whole structure (as drawn), then the c export option
should be used.
Examples:
CCCC |Sg:gen:0,1,2:|
CCCC |Sg:n:0,1,2:3-6:eu|
*CC(*)C(*)N* |$star_e;;;star_e;;star_e;;star_e$,Sg:n:6,1,2,4::hh,f:6,0,:4,2,|
C1=CC=CC=C1 |c:0,2,4,(-4.62,1.05,;-3.29,.28,;-3.29,-1.27,;-4.62,-2.04,;-5.95,-1.27,;-5.95,.28,),Sg:mon:0,5,4,3,2,1:::::(d,s,-7.03,2.12,-2.21,2.12,-2.21,-3.11,-7.03,-3.11,)|
Parent-child relationship of the sgroups is described with the "SgH" tag.
The structure of the SgH tag is the following:
SgH:parentSgroupIndex1:childSgroupIndex1.childSgroupIndex2,parentSgroupIndex2:childSgroupIndex1
The indices of the sgroups come from the order in they are written in the cxsmiles string, i.e. the first sgroup has the index 0, the second has 1, and so on. This includes datasgroups and polymer sgroups as well. Examples:
CC(N)C=O |Sg:gen:0::,Sg:mon:1,2,4,0,3::,SgH:1:0| // A monomer sgroup contains all 5 atoms, and it contains the generic sgroup with 1 atom.
C1CCCCC1 |SgD:0,1,2,3,4,5:f:34::::,Sg:mon:0,1,2,3,4,5::,SgH:1:0| // A monomer sgroup contains all the atoms, and it contains the datasgroup too.
C.C |SgD:1::::::,SgD:0,1::::::,SgD:0::::::,SgD:0::::::,Sg:gen:0::,Sg:gen:1::,Sg:gen:1::,SgH:5:6,6:0,2:4.3| // A more difficult example with multiple sgroup relations.
Atom properties are exported to CXSMILES and CXSMARTS after the keyword 'atomProp' at the extended part. Every property is exported separately with the following rule:
- first comes the atom index
- second is the property key (after a dot)
- last is the property value (after a dot)
The properties are separated with colons. The end of the atom property block is marked with a comma. If the atom has a non-string property, an exception is thrown. Example:
CNC |atomprop:0.key1.value1:0.key2.value2:1.key3.value3| // The 0th atom has two properties and the 1 indexed atom has one.
R-logic is exported along with the R-group information. It is indicated by the LOG tag, which includes the list of R-logics for the R-groups. The list items are separated by dots. One item consits of the R-logic properties separated by semicolons: identifier of an other rgroup which is after the 'then' part of the R-logic (e.g. 'if R1>0 then R2'), the restH property ('H' if set, empty if not) and the R-logic range. If there is no R-logic specified for an R-group, then it is not included in the list. Example:
[*]C1CCCCC1[*] |$_R1;;;;;;;_R2$,RG:_R1={CCC},_R2={N},LOG={_R1:;;>0._R2:_R1;H;0,1}|