epikx Command Help

Command: $SCHRODINGER/epikx

usage: epikx [-h] [-add_hydrogen_coords] [-batch_size BATCH_SIZE]
             [-best_neutral] [-best_neutral_zwit] [-cm CUSTOM_MODEL] [-gpu]
             [-highest_pka HIGHEST_PKA] [-lowest_pka LOWEST_PKA]
             [--match_exp MATCH_EXP] [-ma MAX_NUM_ATOMS]
             [-mapka MAX_NUM_ATOMS_PKA] [-mb] [-ms MAX_NUM_STRUCTS]
             [-norefine] [-nt] [-p P] [-ph PH] [-pht PHT] [-q_hi Q_HI]
             [-q_lo Q_LO] [--query] [-R] [-r] [-retain_i] [-t]
             [-tn MAX_NUM_TAUTS] [-sm] [-HOST <hostname>] [-WAIT] [-D] [-SAVE]
             [infile] [outfile]

Epik

positional arguments:
  infile                Input file name (.sdf, .mae, .smi, or .csv).
  outfile               Output file name (.sdf, .mae, .smi, or .csv).

options:
  -h, --help            show this help message and exit
  -add_hydrogen_coords  Add coordinates to non-polar hydrogens.
  -batch_size BATCH_SIZE
                        Number of ligands to process at once. Including more
                        than 1,000 may lead to memory issues. (default =
                        1000).
  -best_neutral         Provide the most populated neutral tautomer. (default
                        = False)
  -best_neutral_zwit    Provide the most populated neutral tautomer and
                        optionally a low energy neutral zwitterion if one is
                        identified. (default = False)
  -cm CUSTOM_MODEL, --custom_model CUSTOM_MODEL
                        Custom model path (default = None).
  -gpu                  Run with GPGPU acceleration (if available).
  -highest_pka HIGHEST_PKA
                        Set the highest pKa that will be displayed. (default =
                        14).
  -lowest_pka LOWEST_PKA
                        Set the lowest pKa that will be displayed. (default =
                        0).
  --match_exp MATCH_EXP
                        Property label of the experimental pKa value for which
                        to find the best protonated state (default = None).
  -ma MAX_NUM_ATOMS, --max_num_atoms MAX_NUM_ATOMS
                        Structures containing more than this many atoms will
                        not have their states enumerated and scored. (default
                        = 200).
  -mapka MAX_NUM_ATOMS_PKA, --max_num_atoms_pka MAX_NUM_ATOMS_PKA
                        Structures containing more than this many atoms will
                        be skipped. (default = 500).
  -mb, --metal_binding  Generate states appropriate for interacting with metal
                        ions in protein binding pockets.
  -ms MAX_NUM_STRUCTS, --max_num_structs MAX_NUM_STRUCTS
                        Maximum number of returned structures per input.
                        (default = 16)
  -norefine             Do not refine prioritization step to remove unwanted
                        states. (default = False)
  -nt                   Do not tautomerize. (Warning: state penalties,
                        populations, and macro-pKa values will be inaccurate
                        with this option.)
  -p P                  State population cutoff. (default = 0.01)
  -ph PH                Query pH (default = 7.40)
  -pht PHT              pH tolerance for generated structures. (default = 2.0)
  -q_hi Q_HI            Upper bound for the charge level window. (default = 2)
  -q_lo Q_LO            Lower bound for the charge level window. (default =
                        -2)
  --query               Query pKas only; do not predict states. (default =
                        False)
  -R, --racemize        Enumerate and score individual racemers. (default =
                        False)
  -r, --report          Generate pKa report for predict states mode (one
                        structure only) (default = False)
  -retain_i             Ensure that the ionization and tautomerization state
                        of the input structure is retained in the output.
  -t, --taut_only       Tautomerize only. Do not evaluate pKas. (default =
                        False)
  -tn MAX_NUM_TAUTS, --max_num_tauts MAX_NUM_TAUTS
                        Maximum number of tautomers. (default = 8)
  -sm, --single_model   Use single best model instead of ensemble (default =
                        False)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
  -WAIT                 Do not return a prompt until the job completes.
  -D, -DEBUG            Show details of Job Control operation.
  -SAVE                 Return zip archive of job directory at job completion.