shape_screen_gpu generate Command Help
Command: $SCHRODINGER/shape_screen_gpu generate
usage: $SCHRODINGER/shape_screen_gpu generate [-h]
[-shape_data_treatment {copy,remote}]
[-shape_data_dir <path>] -source
<path>
[-shape_type {pharm,atom_color,atom_no_color}]
[-conformer_format {lossless,compact}]
[-keep_properties]
[-no_compress] [-limit <n>]
[-distinct | -connect | -stereo]
[-title <propname>] [-ligprep]
[-ligprep_options <text>]
[-flex]
[-sample {rapid,thorough,rdkit}]
[-max <numconfs>]
[-force_field {OPLS_2005,OPLS4}]
[-nddo] [-ewin <deltaE>]
[-append] [-isub <subset>]
[-HOST <hostname>] [-D] [-SAVE]
[-JOBNAME JOBNAME]
[-NJOBS NJOBS]
[-NSTRUCTS NSTRUCTS] [-STRICT]
[-RETRIES RETRIES]
Utility to generate Shape data files (.bin) suitable for GPU Shape screening.
Shape data files include representation of molecular shapes along with
the corresponding chemical structures.
options:
-h, --help show this help message and exit
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.
-shape_data_dir <path>
Absolute output directory path. Must be specified for
"remote" shape data treatment.
Required Named Arguments:
-source <path> Source of the structures to generate the shapes for.
Supported formats: compressed and uncompressed SMILES
files, 2D and 3D Maestro and Mol/SDF files, Phase
Database (conformers must be included).
Shape Generation Options:
-shape_type {pharm,atom_color,atom_no_color}
Treat each structure as a set of Phase pharmacophores,
typed atoms, or untyped atoms (default: pharm).
General Options:
-conformer_format {lossless,compact}
Format to be used for the conformers. Default:
compact.
-keep_properties Do not strip structure/atom/bond properties from the
stored structures.
-no_compress Do not compress shape data file.
-limit <n> Store shapes of no more than the first <n> conformers.
Default: 10.
Ligand Preparation and Conformer Perception Options:
-distinct Treat each structure as a distinct molecule (i.e., one
conformer only). By default, consecutive structures
with identical titles and connectivity are treated as
conformers of a single molecule.
-connect Consider connectivities only (not titles) when
perceiving conformers.
-stereo Consider stereochemistry when perceiving conformers.
Consecutive structures with the same connectivity will
be treated as conformers of a single molecule if and
only if they have the same stereochemistry. Titles are
ignored.
-title <propname> Use an alternate property (of string or integer type)
as the source of titles for conformer perception.
-ligprep Process input structures using LigPrep. Required for
SMILES and 2D input or if structures lack Hydrogens.
Recommended for 3D input structures not in a low-
energy ionization/tautomeric state. Not compatible
with -distinct, -connect, -stereo, or -title.
-ligprep_options <text>
Options to pass to the ligprep work flow (JSON-
formatted list of strings. Default: '["-epik", "-pht",
"1.0", "-s", "16"]').
Conformer Generation Options:
-flex Generate conformers on-the-fly for each input
structure. Not valid in combination with -distinct,
-connect or -stereo or when input is a Phase Database.
-sample {rapid,thorough,rdkit}
Conformational sampling method (default: thorough).
-max <numconfs> Maximum number of conformers to generate (default:
100).
-force_field {OPLS_2005,OPLS4}
Use a force field to minimize conformers. Increases
conformer generation time by approximately a factor of
50. The default is no force field minimization.
-nddo Minimize conformers using NDDO CM1A-BCC charge model.
Adds significant time to minimization. Valid only with
-force_field OPLS4. The default is off.
-ewin <deltaE> Conformer energy window in kJ/mol (default: 16.0).
-append Append new conformers to existing conformer(s). The
default is to discard existing conformers.
Phase Database Subset Option:
-isub <subset> Instead of creating shapes for all records in the
input Phase Database, process only the subset defined
in the <subset>_phase.inp file.
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-D, -DEBUG Show details of Job Control operation.
-SAVE Return zip archive of job directory at job completion.
-JOBNAME JOBNAME Provide an explicit name for the job.
Standard Options:
-NJOBS NJOBS Divide the overall job into NJOBS subjobs.
-NSTRUCTS NSTRUCTS Divide the overall job into subjobs with no more than
NSTRUCTS structures.
-STRICT Terminate the job if any subjob dies.
-RETRIES RETRIES If a subjob fails for any reason, it will be retried
RETRIES times. (Default: 2)