auto_reaction_enum.py Command Help

Command: $SCHRODINGER/run auto_reaction_enum.py

usage: $SCHRODINGER/run auto_reaction_enum.py [-h] [-NJOBS NJOBS]
                                              [-HOST <hostname>]
                                              [-JOBNAME JOBNAME] [-out OUT]
                                              [-max_products <int>]
                                              [-seed <int>] [-debug]
                                              [-reactions_file <filename>]
                                              [-reagent_classes_file <filename>]
                                              [-libpath LIBPATH]
                                              [-fp_dir FP_DIR]
                                              [-fp_url FP_URL]
                                              [-fp_namespace FP_NAMESPACE]
                                              [-depth <int>]
                                              [-frozen_atoms <atom_idx>[,...]
                                              | SMARTS]
                                              [-bond_reactions <atom_idx>-<atom_idx>:<reaction-name>[,<reaction-name>...]]
                                              [-forward] [-max_routes <int>]
                                              [-max_per_route <int>]
                                              [-no_dedup]
                                              [-product_property_filter <filename>]
                                              [-product_smarts_filter <filename>]
                                              [-ref_mols <filename>]
                                              [-sim_keep_percent <percent> | -sim_discard_percent <percent>]
                                              [-descriptors <descriptor>[,...]]
                                              [-prefilter_reagents <int>]
                                              [-ch_dist_tol <float>]
                                              [-ch_ang_tol <float>]
                                              [-no_core_hopping]
                                              target

Perform a retrosynthetic analysis of a target molecule and then enumerate all
possible routes (up to -max_routes) with random sampling from the standard
reactant libraries.

positional arguments:
  target                target molecule (filename or SMILES string)

options:
  -h, --help            show this help message and exit
  -out OUT              output file
  -debug                very verbose mode

Standard Options:
  -NJOBS NJOBS          Divide the overall job into NJOBS subjobs.

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
  -JOBNAME JOBNAME      Provide an explicit name for the job.

Sampling Options:
  -max_products <int>, -max <int>
                        maximum number of products to report (default: 10000)
  -seed <int>           seed for random number generator (default: 42). If
                        zero, a random seed will be generated automatically.
  -max_routes <int>     maximum number of routes to sample (default: 100)
  -max_per_route <int>  maximum number of products per route (default: 1000)
  -no_dedup             don't exclude duplicate products

Data Files:
  -reactions_file <filename>
                        non-default JSON reactions file
  -reagent_classes_file <filename>
                        non-default JSON reagent classes file
  -libpath LIBPATH, -L LIBPATH
                        path to directory containing reagent files (may be
                        used more than once)
  -fp_dir FP_DIR        path to directory containing reagent fingerprint files
  -fp_url FP_URL        URL of server with reagent fingerprint files
  -fp_namespace FP_NAMESPACE
                        Namespace to use for fingerprint files (i.e.,
                        subdirectory of -fp_dir and -fp_url)

Analysis Options:
  -depth <int>          maximum depth of the retrosynthetic analysis (if not
                        provided, depths up to 5 will be explored until enough
                        routes have been generated). If in '-forward' mode,
                        its default is set to 1.
  -frozen_atoms <atom_idx>[,...] | SMARTS
                        only use reactions which don't break any bonds among
                        the specified atoms, which may be either a list of
                        atom indices or a SMARTS (all matching atoms are used)
  -bond_reactions <atom_idx>-<atom_idx>:<reaction-name>[,<reaction-name>...]
                        only use the listed reaction for breaking the
                        specified bond.May be supplied multiple times.
  -forward              forward analysis mode: look for reactions that can be
                        applied to the input molecule to create derivatives.

Filtering Options:
  -product_property_filter <filename>
                        propfilter or JSON file to be applied to each product
  -product_smarts_filter <filename>
                        canvasSearch filter file to be applied to each product
  -ref_mols <filename>  reference molecules for RDKit fingerprint-based
                        similarity calculations
  -sim_keep_percent <percent>
                        keep the top <percent>% products most similar to the
                        first reference molecule
  -sim_discard_percent <percent>
                        discard the top <percent>% products most similar to
                        the first reference molecule
  -descriptors <descriptor>[,...]
                        RDKit descriptors to compute for the products (comma-
                        separated list; default: "MolLogP,MolWt,NumChiralCente
                        rs,NumHAcceptors,NumHDonors,TPSA")
  -prefilter_reagents <int>
                        number of reagents to keep from each reagent class
                        after sorting by similarity to reference molecule

Core-hopping Filtering Options:
  -ch_dist_tol <float>  distance tolerance in Angstroms (default: 1.0)
  -ch_ang_tol <float>   angle tolerance in degrees (default: 15.0)
  -no_core_hopping      don't apply special core-hopping rules to targets
                        where a variable region is connected to more than one
                        frozen region