glide_sort Command Help
Command: $SCHRODINGER/utilities/glide_sort
usage: glide_sort [-o OUTPUT_FILE] [-h] [-f FILE_LIST]
[-b BATCH_SIZE] [-use_dscore]
[-use_gscore] [-use_cvdw]
[-use_emodel] [-use_prop PROP]
[-default VAL] [-nosort] [-maxsize N]
[-norecep] [-epv] [-n NREPORT]
[-nbest N] [-ndistinct N_LIGANDS]
[-best] [-best_by_prop PROP]
[-best_by_lignum] [-best_by_title]
[-reset_lignum] [-q]
[-allow_empty_output] [-gscore COEF]
[-cvdw COEF] [-internal COEF]
[-emodel COEF] [-hbond_cut CUTOFF]
[-cvdw_cut CUTOFF]
[-metal_cut CUTOFF]
[-emodel_cut CUTOFF]
[-gscore_cut CUTOFF]
[-dscore_cut CUTOFF] [-nogscore_cut]
[-nodscore_cut] [-nofilter]
[FILE ...]
Re-ranks Glide poses by custom criteria or combines job outputs into one file.
The "best" pose is defined by the property used for sorting. If you set any of
the custom scoring function terms, sorting is done only on this custom function
instead of the standard sorting options.
The input pose files can be in Maestro or SD format, uncompressed (.mae or .sdf)
or compressed (.maegz, .mae.gz, .sdfgz). The same format must be used for all
files, both input and output. You can combine pose-viewer files (_pv.mae[gz])
into ensemble pose-viewer files (_epv.mae[gz]).
positional arguments:
FILE The files to merge and sort.
Modes of Operation (at least one is required):
-o OUTPUT_FILE Write the best-scoring poses to OUTPUT_FILE.
-h, -help Show this message and exit.
File Options:
-f FILE_LIST, -file_list FILE_LIST
Additional method of specifying the Glide pose files,
if listing them on the command line would exceed shell
line length limits. Each line in the FILE_LIST file
should have one filename in it.
-b BATCH_SIZE, -batch BATCH_SIZE
Number of files to merge at a time; equal to the
number of file handles open at once. If this is less
than the number of pose files to merge, then merges
will be done iteratively. Valid only for `glide_merge`
and `glide_sort` in large file mode. (default = 128).
Sorting Options:
-use_dscore This is the default sorting option. It sorts poses
based on the "docking_score" in Glide output poses.
-use_gscore Sort poses based on GlideScore.
-use_cvdw Sort poses based on the Coulomb-vdW energy, E(CvdW).
-use_emodel Sort poses based on Emodel.
-use_prop PROP, -use_prop_a PROP, -use_prop_d PROP
Sort poses based on a user-specified property in
either ascending or descending order. Both `use_prop`
and `use_prop_a` request ascending order while
`use_prop_d` requests descending order. If multiple
`use_prop(_[ad])?` arguments are specified, a multi-
key sort will be used; the first property specified
will be the primary key, the second will be the
secondary key, and so on. Defaults for each property
can be specified after the property name, delimited by
a `:`. E.g., `-use_prop r_i_glide_gscore:10.5` will
use a score of 10.5 if "r_i_glide_gscore" is undefined
for a pose.
-default VAL Global default value to use for missing key properties
(if not specified in one of the `-use_prop(_[ad])?`
flags). If no default is provided, poses missing a key
property are skipped.
-nosort Don't sort the poses.
-maxsize N Maximum amount of memory to use, in bytes. Sizes can
be expressed as bytes or one of the suffixes {K, M, G,
T} can be appended. Zero means unlimited.(default =
3G).
Output Options:
-norecep Don't treat receptors specially. The default is to
write a pose-viewer file if a native Glide sorting
criterion is used and if receptors are found. Native
Glide sorting criteria are those specified by any
`-use` option other than `-use_prop` or by lack of a
`-use` option. Receptors are identified by the
presence of a `b_glide_receptor` property with a value
of 1. In a pose-viewer file, the first structure is a
receptor found as the first structure, followed by
ligands in order of score. Receptors beyond the first
are ignored.
-epv Sort in ensemble pose-viewer mode. In this mode, all
unique receptors are written at the beginning of the
sorted output and there are properties linking each
pose with its receptor.
-n NREPORT, -nreport NREPORT
Retain only the NREPORT lowest-scoring poses. May be
combined with `-nbest` and `-ndistinct`. The total
ligands reported will the lesser of all conditions.
-nbest N Number of poses to report for each ligand. By default,
reports best by (file, ligand number). However, may be
combined with `-best_by_prop`, `-best_by_lignum`, or
`-best_by_title` to override the default. May be
combined with `-nreport` and `-ndistinct`.
-ndistinct N_LIGANDS Retain poses for the N_LIGANDS lowest-scoring distinct
ligands. No more ligands will be reported once this
condition is satisfied. The `-best_by_*` family of
flags is used to determine distinctness. May be
combined with `-nreport` and `-nbest`.
-best Alias for `-nbest 1`.
-best_by_prop PROP Keep only the best pose(s) for each ligand with a
given value to a user-specified property.
-best_by_lignum Synonym for `-best_by_prop "i_i_glide_lignum"`.
-best_by_title Synonym for `-best_by_prop "s_m_title"`.
-reset_lignum Reset the ligand numbers.
-q, -quiet Don't write summary to standard output.
-allow_empty_output Write empty output file when there are no poses.
Custom Scoring Function Options:
Setting any of these custom scoring function terms causes `glide_sort` to use only on the custom scoring function instead of the usual `-use_...` options.
-gscore COEF GlideScore coefficient.
-cvdw COEF E(CvdW) coefficient.
-internal COEF E(internal) coefficient.
-emodel COEF Emodel coefficient.
Filter Options:
-hbond_cut CUTOFF Filter cutoff for H-bond energy. (default = 0.0)
-cvdw_cut CUTOFF Filter cutoff for E(CvdW). (default = 0.0)
-metal_cut CUTOFF Filter cutoff for metal-ligation energy. (default =
10.0)
-emodel_cut CUTOFF Filter cutoff for Emodel energy. (Not used by
default.)
-gscore_cut CUTOFF Filter cutoff for GlideScore. (default = 100.0)
-dscore_cut CUTOFF Filter cutoff for docking score. (default = 100.0)
-nogscore_cut Don't use GlideScore filter.
-nodscore_cut Don't use docking score filter.
-nofilter Don't use _any_ filter cutoffs.