path_finder Command Help

Command: $SCHRODINGER/utilities/path_finder

usage: path_finder [-h]
                                          [-reactions_file REACTIONS_FILE]
                                          [-reagent_classes_file REAGENT_CLASSES_FILE]
                                          [-depth DEPTH] [-write_routes]
                                          [-self_contained] [-plot_routes]
                                          [-prefix PREFIX] [-require REQUIRE]
                                          [-exclude EXCLUDE]
                                          [-max_tier MAX_TIER] [-no_dedup]
                                          [-bonds <atom_idx>-<atom_idx>[,...]]
                                          [-bond_reactions <atom_idx>-<atom_idx>:<reaction-name>[,<reaction-name>...]]
                                          [-frozen_atoms <atom_idx>[,...] |
                                          SMARTS] [-available_sm]
                                          [-fpsim_url FPSIM_URL]
                                          [-fpsim_dbnames FPSIM_DBNAMES]
                                          [-debug]
                                          targets [targets ...]

Perform a retrosynthetic analysis on a target and enumerate all possible
routes.

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

options:
  -h, --help            show this help message and exit
  -reactions_file REACTIONS_FILE
                        non-default JSON reactions file
  -reagent_classes_file REAGENT_CLASSES_FILE
                        non-default JSON reagent classes file
  -depth DEPTH          maximum depth of the retrosynthetic analysis
                        (default=1)
  -write_routes         write JSON route files
  -self_contained       write self-contained JSON route files
  -plot_routes          write PNG route files
  -prefix PREFIX        prefix used for constructing route filenames
  -require REQUIRE      tag or reaction name to require. May be supplied
                        multiple times.Reaction names support *, ?, and []
                        wildcards.
  -exclude EXCLUDE      tag or reaction name to exclude. May be supplied
                        multiple times.Reaction names support *, ?, and []
                        wildcards.
  -max_tier MAX_TIER    only use reactions with with tier <= MAX_TIER (default
                        is to use all reactions)
  -no_dedup             write "duplicate" routes (routes consisting of the
                        same reaction path but with different molecules)
  -bonds <atom_idx>-<atom_idx>[,...]
                        only use reactions which break the specified bonds.
  -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.
  -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)
  -available_sm         only save routes for which the starting materials are
                        available in the FPsim-GPU database
  -fpsim_url FPSIM_URL  URL of FPsim-GPU server
  -fpsim_dbnames FPSIM_DBNAMES
                        comma-separated list of FPsim-GPU database names to
                        use
  -debug                very verbose mode