sdconvert Command Help

Command: $SCHRODINGER/utilities/sdconvert

sdconvert [options] -i<format> <input filename> -o<format> <output filename>

 <format> is one of 
  sd  : MDL SDfile format
  mae : Maestro format

 Either the input or output format must be 'sd', but not both.
 Files compressed with gzip ('.gz' files) are supported for both 
 input as well as output. 

 While writing SD files, the V2000 format is used by default.
 Both V2000 and V3000 formats are accepted as input.

 General Options 
  -a              : append structures to the output file
  -n <structs>    : specify a comma delimited series of colon separated
                    ranges and single values to convert, for example:
                    1:10,14  (structures 1 through 10 and 14)
                    2:       (structure 2 through end of file)
                    :5,13:18 (structure 1 through 5, and 13 through 18)
  -cgch_rgroups   : Convert R# atom types to H atoms in that position 
                    and assign the atom-based integer property
                    i_cgch_from_atom to the atom number of the
                    attached atom.
                    This option is mainly intended for CombiGlide core
                    hopping use.
  -all            : convert all structures (synonym for "-n 1:")

  For multiple -n or -all options, right-most range takes precedence.

 Options Only for SD to Maestro Format Conversions 
  -title prop     : define SD property <prop> as the source for assigning
                    the Maestro title field.
                    Do not include the <brackets> when using -title prop.
  -nostereo       : do not record the atom parity info from the input file
                    as atom chirality information in the output file
                    By default stereo information is recorded.
  -norelstereo    : Discard enhanced stereo data. By default enhanced
                    stereo data is retained.
  -noarom         : do not convert aromatic type 4 bonds to single and
                    double bonds as per Maestro and OPLS conventions.
  -nolewis        : do not fix bond orders and formal charges of nitro
                    and carboxylate groups as appropriate for OPLS use.
  -notypes        : import all properties as strings.
  -rawtypes       : decide property types on per structure basis.
  -bad            : dump structures that could not be converted into a
                    separate SD file. The name of this file is:
                    <input-filename>-bad.sdf[.gz]
  -skip_ambiguous : skip structures that contain bonds of orders 5-8
  -noindex: do not update the indexing properties to store the index of
                    file on conversion

 Options Only for Maestro to SD Format Conversions 
  -pKa            : record pKa values in Maestro input files to SD output.
  -v3             : write output SD file in V3000 format.
  -annstereo      : Derive chirality information only from Maestro props