ionizer Command Help

Command: $SCHRODINGER/utilities/ionizer

usage: ionizer [-h] [-i INFILE] [-o OUTFILE]
                                      [-b BADFILE] [-l LOGFILE] [-adjust]
                                      [-retain] [-retain_lab] [-s SPECFILE]
                                      [-sm] [-sf] [-ss] [-ll {0,1,2}]
                                      [-mi MAXIONS] [-mq MAXABSTOTQ]
                                      [-mg MAXGROUPS] [-mo <limit>] [-ph PH]
                                      [-pht <maxdiff>] [-pkt PKTHRESH] [-kp]
                                      [-rw RETITLE_WITH] [-strict]
                                      [-j JOBNAME] [-v]

options:
  -h, --help            show this help message and exit
  -i INFILE, -in INFILE, -infile INFILE
                        Input ligand file (required).
  -o OUTFILE, -out OUTFILE, -outfile OUTFILE
                        Ouput ligand file (required).
  -b BADFILE, -bad BADFILE, -badfile BADFILE
                        File to write failed ligand to (required, unless
                        -strict is specified).
  -l LOGFILE, -log LOGFILE, -logfile LOGFILE
                        Redirect output from the script to this file
                        (deprecated)
  -adjust               Retain only the most favorable structure in the output
                        file.
  -retain               Retain the input structure in the output file.
  -retain_lab           Retain the input structure with the orig_ion_str
                        property.
  -s SPECFILE, -spec SPECFILE, -specfile SPECFILE
                        Use non-standard patterns spec file.
  -sm, -showmatches     Show substructure pattern matches.
  -sf, -showfinal       Show final ionization candidate list
  -ss, -showskips       Show skipped state generations. Augments log level 1
                        and up. Log levels > 1 give skip reasons.
  -ll {0,1,2}, -loglevel {0,1,2}
                        Expansion report log level -- Use 0 for quietest
                        (default) -- Use 1 to log state generations -- Use 2
                        to log ion frag fusions too
  -mi MAXIONS, -maxions MAXIONS
                        Max num of ionizations (default 4).
  -mq MAXABSTOTQ, -maxabstotq MAXABSTOTQ
                        Max abs total charge (default 2). Options -mi|-maxions
                        and -mq|-maxabstotq apply only to runs in the pK-
                        threshold mode. They are ignored for runs in default
                        pH mode.
  -mg MAXGROUPS, -maxgroups MAXGROUPS
                        Max ion groups to handle (default 15). Any input CT
                        with more ion groups will pass into output,
                        unexpanded. Specified limit cannot exceed 31
  -mo <limit>, -maxoutcts <limit>
                        Max output CTs per input CT (default 512). "-mo -1" to
                        set highest limit.
  -ph PH                Effective pH of active site (default 7.0)
  -pht <maxdiff>, -phthresh <maxdiff>
                        pH threshold (default 2.0). For pH-based ion state
                        rejections. De/protonated |pKa-pH| diff limit
  -pkt PKTHRESH, -pkthresh PKTHRESH
                        Strong/weak pK threshold (no default). Overrides pH-
                        based rejection mode. Reject on pKa values only (no
                        pH). Limit on de/protonated pKa diffs
  -kp, -keep_props      Retain all properties in output CTs. Absent this
                        option, connectivity-dependent properties are cleared.
  -rw RETITLE_WITH, -retitle_with RETITLE_WITH
                        Re-title CTs by appending this prefix followed by the
                        ion state number. By default, CTs are not retitled.
                        Examples of retitling: If the original CT title is
                        "TITLE", and the output CT is for ionization state 3,
                        then specifying -rw _ will give output CT title
                        "TITLE_3"; specifying -rw " Ion_state_num=" will give
                        output title "TITLE Ion_state_num=3".
  -strict               Terminate run if any input CT is bad (-badfile option
                        is ignored).
  -j JOBNAME, -job JOBNAME, -jobname JOBNAME
                        If specified, essential file names are derived from
                        this prefix (deprecated).
  -v, -ver, -version    Show the mmshare python version number and exit.

For complete documentation on the Ionizer, please read:
$SCHRODINGER/mmshare-v#####/doc/README.ionizer