glide_merge Command Help
Command: $SCHRODINGER/utilities/glide_merge
usage: glide_merge [-o OUTPUT_FILE] [-h] [-f FILE_LIST]
[-b BATCH_SIZE] [-k PROPERTY_NAME]
[-default VAL] [-descending]
[-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 ...]
Merges results from a list of pose files (such as from Glide subjobs) into a
single pose file, sorted by the docking score or a specified property. The pose
files must be already sorted by the docking score or the specified property.
The input and output pose files can be in Maestro or SD format, uncompressed
(.mae or .sdf) or compressed (.maegz, .mae.gz, or .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]). When multiple
pose-viewer files are given as input, only the receptor from the first file is
included in the merged output, unless the -epv option is specified.
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).
Merging Options:
-k PROPERTY_NAME Use PROPERTY_NAME as the merge key. (default =
"r_i_docking_score").
-default VAL Default value to use for missing key properties. If
not provided, poses missing a key property are placed
first.
-descending Merge files that have been sorted in descending order.
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_merge` 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.