structurebased_adme permeability Command Help

Command: $SCHRODINGER/structurebased_adme permeability

usage: 
$SCHRODINGER/structurebased_adme permeability [<options>] <struct_file>

Calculate ligand membrane permeabilities by comparing their optimized conformations in low and high dielectric environments.

positional arguments:
  struct_file           Input ligands in Maestro format

options:
  -h, --help            show this help message and exit
  -v                    show program's version number and exit
  -jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
                        Set the base name of outputs

Membrane Permeability Options:
  -protocol {standard, macrocycle, auto, thorough, HT}
                        Specify sampling algorithm to use. Choices are:
                          'standard': Prime ligand sampling
                          'macrocycle': Prime macrocycle sampling
                          'auto' (default): Automatic selection; uses 'macrocycle' if ligand contains a ring larger
                                than 9 atoms, otherwise uses 'standard'
                          'thorough': Similar to 'auto', but with extended sampling parameters
                          'HT': High-throughput mode; skips sampling and instead uses the input conformation directly
                                to calculate permeability values. Use '-treat_neutral asis' to prevent the neutralizer
                                from perturbing the input structures
  -force_field FORCE_FIELD
                        Set the force field to be used; default = OPLS_2005
  -sort_conformers_by MP_SORT_BY
                        Specify the property used to determine the output structure for the
                        Membrane Permeability calculation; default is 'r_adme_Membrane_dG_Insert'
                        Conformers will be sorted in ascending order based on the specified property;
                        the conformer with the lowest value will be selected as the output.
                        Use the '-num_output_structures' option, to increase the number of output structures
  -penalize {zero,user,state,epikx,ionization}
                        Select which quantity represents the neutralization penalty. Choices are:
                          'state' (default): Use the tautomerization + neutralization penalty calculated by Epik Classic
                          'ionization': Use only the neutralization penalty calculated by Epik Classic
                          'zero': Do not apply any penalty
                          'user': Use the value of the structure property 'r_user_adme_penalty'
                          'epikx': Similar to 'state', but calculated by Epik instead
  -treat_neutral {all,first,asis}
                        Specify behavior when multiple neutral states are available:
                          'all': Sample all neutral states
                          'first' (default): Use only the first neutral form
                          'asis': Use the input form as-is; do not run neutralizer
  -num_output_structures NUM_OUTPUT_STRUCTURES
                        Number of output conformations to return for each input ligand; default = 1
  -include_qikprop_in_csv
                        Include QikProp properties of output structures in CSV file
  -treat_bad_torsions {raise,fix,ignore}, --treat_bad_torsions {raise,fix,ignore}
                        Choose method for handling bad torsions in macrocyclic input structures;
                        used only with Prime Macrocycle sampling
                          'raise': raise an error and exit the program if torsion violations found
                          'fix': automatically fix the torsions violations
                          'ignore' (default): ignore the torsion violations

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.
  -NOJOBID              Run the job directly, without Job Control layer.

Standard Options:
  -NJOBS NJOBS          Divide the overall job into NJOBS subjobs.
  -RETRIES RETRIES      If a subjob fails for any reason, it will be retried RETRIES times. (Default: 2)
  -NOLAUNCH             Set up subjob inputs, but don't run the jobs.

Restart Options:
  -restart_file RESTART_FILES
                        Output of a partially completed subjob; keyword may be used multiple times, once per partial subjob
  -RESTART              Run 'restart_file' automatically by guessing the names of the files to use