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-o fileWrite output to specified file instead of standard output
-mProduce multiple output files
-e charsetSet the input character encoding. The encoding must be supported by Java.
-e [in ]..[ out]Set the input (in) and/or output (out) character encodings. Examples: UTF-8, ASCII, Cp1250 (Windows Eastern European), Cp1252 (Windows Latin 1), ms932 (Windows Japanese).
-s stringRead molecule from specified SMILES, SMARTS or peptide string (try to recognize its format)
-s string { format : options }Read molecule from the string in the specified format (can be omitted), using the specified importoptions (can be omitted)
-f <string>Specify the import format and options
--smiles stringRead molecule from specified SMILES string
--smarts stringRead molecule from specified SMARTS string
--peptide stringRead molecule from specified peptide string
-gContinue with next molecule on error (default: exit on error)
-YRemove explicit H atoms
-I <range>process input molecules with molecule index (1-based) falling into the specified range (e.g. 5-8,15 refers to molecules 5,6,7,8,15)
-Ufuse input molecules and output the union
-R <file>[:<range>]fuse fragments to input molecule(s) from file with specified mol index range range syntax: "-5,10-20,25,26,38-" (e.g. -R frags.mrv:20-)
-R<i> <file>[:<range>]fuse R<i> definition members to input molecule(s) from file in specified index range (e.g. -R1 rdef1.mrv:5-8,19)
-R<i>:<1|2> <file>[:<range>]fuse R<i> definition members to input molecule(s) from file in specified index range, filter molecules having 1 (2, resp.) attachment points (e.g. -R1:2 rdef1.mrv:-3,8-10)
-FRemove small fragments, keep the largest
-c"f1 OP value&f2 OP value..."Filtering by the values of fields in the case of SDF import.
OP may be: =,<,>,<=,>=
--mol-fields-to-recordsConvert molecule type fields to separate records.
-vvVery verbose (print stack trace at error)
-2 [ : options] [ : F<i1><i2>...,<iN>]Calculate 2D coordinates Options for coordinate calculation. 
Performs partial clean with fixed atom coordinates for atoms <i1><i2>...,<iN> (1-based indexes) if the Fparameter is specified.
-3 [ : options]Calculate 3D coordinates
Options for coordinate calculation.
-H3D Help on options for 3D calculations. Detailed list on Clean 3d Options