Codename: cxsmiles,cxsmarts
SMILES_String |<feature1>,<feature2>,...|In extended smiles export the following additional features are exported:
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. )
The following stereochemical group types are stored:
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.
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
Atom indexes with local ODD parity are written after "@:", while atom indexes with local EVEN parity are written after "@@:" characters separated by commas.
Atom indexes with
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 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
"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.
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. 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)"
Atomic indexes of the attachment points written after
"AP_x:" where x denotes the attachment point type
(1 or 2), separated by commas.
Example: "AP_1:10,AP_2:3 "
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 then 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 / values. Default value: true. w Write wiggly and in case of atomic coordinate export also UP and DOWN 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. c[p] Write atomic coordinates. p can optionally specify the coordinate precision. If p is not specified, the default value 2 is used. Default value: false. D Write Data Sgroup information. Default value: true.
See also SMILES export options and basic export options.