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Import options


Fix chiral flag from cxsmiles input.
By default the molecule absolute stereoconfiguration (relative or absolute chirality - chiral flag) is specified at the extended part of the cxsmiles string. If it is missing it is assumed to be absolute by default (see Molecule absolute stereoconfiguration above). Using the 's' option the molecule's absolute stereoconfiguration is tried to be figured out.

  • molconvert cxsmiles -s 'C[C@H]1CC[C@@H](C)CC1{cxsmiles}' results C[C@H]1CC[C@@H](C)CC1
  • molconvert cxsmiles -s 'C[C@H]1CC[C@@H](C)CC1{cxsmiles:s}' results C[C@H]1CC[C@@H](C)CC1 |r|

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.


  • "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.



Write unique cxsmiles output. (Includes unique smiles string.)
Enhanced stereo information are also stored in unique format.
Default value: false.
eWrite relative stereo configuration and enhanced stereo features. Default value: true.
lWrite atom labels / aliases / values. Default value: true.
wWrite wiggly and in case of atomic coordinate export also UP and DOWN bond indexes. Default value: true.
dWrite CIS, TRANS ring bond indexes. Default value: true.
fReaction fragment level grouping. Default value: true.
pWrite local parities. Default value: true.
RWrite radical numbers. Default value: true.
LWrite lone electron pairs. Default value: true.
mWrite multicenter SGroups and coordinate bonds. Default value: true.
NWrite 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.
DWrite Data Sgroup information. Default value: true.
BOMWrite the UTF-8 byte order mark (BOM), if the given or the system's encoding is UTF-8. Default value: false.
qWrite MDL query features. Default value: true.
PWrite polymer Sgroups. Default value: true.
bWrite local bicyclo-alkane stereo information. Default value: true.
BWrite Hydrogen bonds. Default value: true.


Write atom properties. Default value: true.