AutoTSReaction Command Help

Command: $SCHRODINGER/utilities/AutoTSReaction

usage: AutoTSReaction [-h] [-jobname JOBNAME]
                                             [-reactant_file [REACTANT_FILE ...]]
                                             [-file_mode {TUPLES,PRODUCTS}]
                                             [-autots_input_template AUTOTS_INPUT_TEMPLATE]
                                             [-reaction_type REACTION_TYPE [REACTION_TYPE ...]]
                                             [-reaction_file REACTION_FILE]
                                             [-dump_reactions] [-debug]
                                             [-skip_minimization]
                                             [-enumerate_equivalent_hydrogens]
                                             [-enumerate_stereoisomers]

Generate product molecules by performing a specified
chemical transformation to a set of reactants

No output MAESTRO files will be generated for reactants that don't
match the reaction type.

Any stereocenters that are created in the reaction whose chirality
are not explicitly specified by the reaction SMARTS will
have arbitrarily determined stereochemistry unless all possible
stereochemistries are requested.

options:
  -h, --help            show this help message and exit
  -jobname JOBNAME      Base name for output files mae files
  -reactant_file [REACTANT_FILE ...]
                        The names of MAESTRO file(s) which define Reactant molecule(s), given as a
                        space separated list.
                        
                        IMPORTANT: Each file corresponds to a different reactant TYPE in the reaction.
                        For a reaction A + B -> C, one file contains candidates for reactant A,
                        and another file contains candidates for reactant B. Multiple structures
                        within a single file are treated as alternative candidates for that reactant type.
                        If you have multiple structures of the SAME reactant type, put them all
                        in a single file. A default reactant will be used for any reactant types
                        not specified.
                        
                        Example: For a Michael addition (nucleophile + electrophile -> product):
                          - One file: nucleophiles.mae (each nucleophile + default electrophile)
                          - One file: electrophiles.mae (each electrophile + default nucleophile)
                          - Two files: nucleophiles.mae electrophiles.mae (all pairs of nucleophile + electrophile)
                        
  -file_mode {TUPLES,PRODUCTS}
                        Strategy used to couple reactants together 
                        in order to make the left hand side of a reaction.
                        The TUPLES mode pairs structures in each file 
                        and will generate at most the number of structures
                        in the smallest file or one if no reactant files are specified.
                        The PRODUCTS mode makes a cartesian product
                        of the structures and will generate at most, the product of
                        the number of structures in each file.
  -autots_input_template AUTOTS_INPUT_TEMPLATE
                        Name of a template AutoTS input file.  This file
                        will be used to define AutoTS and Jaguar parameters
                        which will be used to write input files accompanying
                        reactant and product structure files.
                        If this file is not provided input files will not be written.
  -reaction_type REACTION_TYPE [REACTION_TYPE ...]
                        Choice of pre-defined reaction type. 
  -reaction_file REACTION_FILE
                        User defined json Reaction file
  -dump_reactions       Print information about all known reaction types and exit
  -debug                Print additional debugging information
  -skip_minimization    Skip minimization of generated structures
  -enumerate_equivalent_hydrogens
                        Enumerate abstraction of all hydrogen atoms instead of only
                        topologically distinct ones.  This setting only applies to
                        hydrogen abstraction reactions.
  -enumerate_stereoisomers
                        Enumerate all stereoisomers of unassigned stereocenters.
                        Otherwise, choose one arbitrarily