shape_screen_gpu run Command Help
Command: $SCHRODINGER/shape_screen_gpu run
usage: $SCHRODINGER/shape_screen_gpu run [-h]
[-shape_data_treatment {copy,remote}]
[-shape <shape>] [-screen <screen>]
[-screen_list <screen_list>]
[-limit <n>] [-atomweights <prop>]
[-norm 1|2|3|4]
[-nosort | -keep <maxhits>] [-osd]
[-ocsv] [-filter <min>] [-best]
[-diverse <fraction>] [-write_report]
[-limit_pdf <n>] [-only_pdf]
[-DRIVERHOST <hostname>]
[-RESTART <state_filename>]
[-HOST <hostname>] [-JOBNAME JOBNAME]
Runs Shape screening on the GPU. To run Shape screening on the CPU, use
$SCHRODINGER/shape_screen.
Screens a Shape data file (.bin) against one or more Shape queries. Each
conformer of a given molecule is aligned to the query in various ways, and a
similarity score is computed based on approximate hard sphere overlapping
volumes. If ligand structures are included in the Shape data file, the conformer
and alignment yielding the highest Shape similarity for a given molecule are
written to the alignments file <jobname>-out.maegz, with the Shape similarity
property r_phase_Shape_Sim. If ligand structures are not included in the Shape
data file, ligand hit titles and max similarities are written to
<jobname>-out.csv.
Similarity scoring and shape assignment are controlled by the options used to
create the Shape data file provided as input. The defaults are to treat each
ligand as a set of Phase pharmacophore spheres, and to count overlap only
between spheres of the same type.
For specific help with each task, see $SCHRODINGER/shape_screen_gpu <task> -h
Copyright Schrodinger LLC, All Rights Reserved.
options:
-h, --help show this help message and exit
-RESTART <state_filename>
Use <state_filename> to restart a failed job. Cannot
be used with any other options.
Shape Data File Treatment Options:
-shape_data_treatment {copy,remote}
Whether to copy a locally accessible Shape data file
(.bin) to the job host or use a Shape data file that
already resides on the job host. The latter is
strongly recommended for large Shape data files to
avoid significant disk I/O and network traffic.
Required Arguments:
-shape <shape> Shape query. May be either a 3D Maestro or SD file
with one or more template structures.
-screen <screen> Shape data file (.bin) created by
$SCHRODINGER/shape_screen_gpu generate. Multiple Shape
data files can be screened in one experiment by
specifying multiple -screen options, one per Shape
data file. If -shape_data_treatment is set to remote,
an absolute path must be provided.
-screen_list <screen_list>
Name of the file that lists Shape data files to be
screened (one per line). If -shape_data_treatment is
set to remote, valid absolute paths at the execution
host must be provided.
Screening Options:
-limit <n> Screen no more than the first <n> conformers.
-atomweights <prop> Weight query overlap by atom real property on [0, 1].
-norm 1|2|3|4 Similarity normalization scheme, computed from query
and screen shape self-overlaps (A and B, respectively)
as 1: max{A,B}; 2: min{A,B}; 3: A; 4: B (default: 1).
Reporting Options:
-nosort Output hits in the order they are screened. The
default is to sort hits by decreasing similarity.
-keep <maxhits> Cap sorted hits at <maxhits> (default: 1000).
-osd Output hits in SD format.
-ocsv Output hit titles and similarities in CSV format.
-filter <min> Filter molecules whose similarities fall below <min>.
The default is to apply no filter.
-best Only report the highest similarity query per ligand.
-diverse <fraction> Retain only the indicated fraction of structurally
diverse hits from each shape data file. For example,
if a maximum of 1000 hits are requested, -diverse 0.1
would retain up to 100 diverse hits per shape query
from each shape data file. Since hits from different
shape data files are combined and capped, the total
number of hits per query could exceed 100 if multiple
shape data files are screened. The supplied fraction
may not exceed 0.2, and this option is not legal in
combination with -nosort or -ocsv.
-write_report Create a shape screen report that consists of a
searchable 3D database of all hits
<jobname>_report.vsdb and a document of annotated 2D
hits <jobname>_report.pdf. The utility
shape_screen_reporter may be used to perform a variety
of tasks with the database, including regeneration of
the PDF file with different settings applied. This
option is legal only when the shape query is a single
structure or a pharmacophore hypothesis.
-limit_pdf <n> Limit on the number of hits written to the PDF file.
By default, only the top 500 hits are output, with
ranking based on pharmacophore shape similarity to the
query structure or hypothesis reference ligand. Take
care when increasing this limit since the resulting
PDF file can be quite large.
-only_pdf Save only the PDF file, not the database. This option
may be appropriate for screens that produce a very
large number of hits since the database file is
typically about three times the size of the equivalent
compressed Maestro file of hits.
Standard Options:
-DRIVERHOST <hostname>
Run the driver on the specified host. The subjobs are
run on the hosts specified with -HOST.
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-JOBNAME JOBNAME Provide an explicit name for the job.