CXSMILES and CXSMARTS import and export options
Import options
Codename |
Explanation |
s |
Fix chiral flag from cxsmiles input.
|
See also 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 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 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.
Codename |
Explanation |
u |
Write unique cxsmiles output. (Includes unique smiles string.) |
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. |
BOM |
Write the UTF-8 byte order mark (BOM), if the given or the system's encoding is UTF-8. Default value: false. |
q |
Write MDL query features. Default value: true. |
P |
Write polymer Sgroups. Default value: true. |
b |
Write local bicyclo-alkane stereo information. Default value: true. |
B |
Write Hydrogen bonds. Default value: true. |
A |
Write atom properties. Default value: true. |
See also SMILES export options and basic export options.