phase_screen Command Help
Command: $SCHRODINGER/phase_screen
usage: phase_screen [-h] [-distinct | -connect | -stereo] [-title <propname>]
[-isub <subset>] [-dbsites {on,off,auto} | -noindex]
[-flex | -refine] [-sample {rapid,thorough,rdkit}]
[-max <numconfs>] [-force_field {OPLS_2005,OPLS4}] [-nddo]
[-ewin <deltaE>] [-append] [-d <dist> | -usetol]
[-match <minsites>] [-ex] [-t <tlimit>] [-inplace]
[-notol] [-nocnst] [-nomask] [-norules]
[-nosort | -keep <maxhits>] [-osd] [-prehypo]
[-report <n>] [-noqsar] [-noref] [-noxvol] [-noivol]
[-atypes] [-aw <weight>] [-ac <cutoff>] [-hard]
[-ap <penalty>] [-vw <weight>] [-vc <cutoff>]
[-volw <weight>] [-volc <cutoff>] [-ivolw <weight>]
[-ivolc <cutoff>] [-HOST <host>[:<m>]] [-NJOBS <n>]
[-TMPDIR <dir>]
<source> <hypo> <jobname>
Screens one or more structure files or Phase databases with one or more
pharmacophore hypotheses.
Copyright Schrodinger LLC, All Rights Reserved.
positional arguments:
<source> The source of structures to screen. Must be a Maestro
file, SD file, an absolute path to a Phase database
(.phdb), or a list file (.list) that contains the
names of one or more Maestro file, SD files or Phase
databases, with one name per line. A list file that
mixes Maestro/SD files and databases is not permitted.
<hypo> Hypothesis file (.phypo) or a Zip archive (.zip)
containing multiple hypothesis files at the root
level. Each returned hit will contain the property
s_phase_HypoID to indicate the hypothesis it matched.
<jobname> Job name. Hits are returned in <jobname>-hits.maegz.
options:
-h, --help show this help message and exit
File Screening 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.
Database Screening Options:
-isub <subset> Screen only the subset of records in the file
<subset>_phase.inp. Not valid when screening multiple
databases.
-dbsites {on,off,auto}
Controls whether pharmacophore sites should be
generated on-the-fly using the hypothesis feature
definitons: on = always generate sites; off = never
generate sites; auto = generate sites only if the
hypothesis and database feature definitions differ.
Note that the job will fail if the feature definitions
differ and -dbsites off is used. The default is auto,
which allows fast pre-filtering using the 2D/3D index
if the database and hypothesis feature definitions are
the same.
-noindex Do not pre-filter using 2D/3D index. Sites will be
generated on-the-fly if database and hypothesis
feature definitions differ.
Conformer Generation Options:
-flex Generate conformers on-the-fly for each input
structure. Not valid in combination with -distinct,
-connect, -stereo or -refine.
-refine Generate conformers on-the-fly for the highest scoring
match and search for additional matches. May be used
in combination with -distinct, -connect or -stereo,
but not with -flex. Use of -append has no effect.
-sample {rapid,thorough,rdkit}
Conformational sampling method (default: rapid).
-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.
Matching Options:
-d <dist> Intersite distance matching tolerance in angstroms.
The default is 2.0 if neither -d <dist> nor -usetol is
specified.
-usetol Use the sum of the two largest positional tolerances
as the intersite distance matching tolerance. Defaults
back to 2.0 if the hypothesis has no positional
tolerances.
-match <minsites> Minimum number of hypothesis sites to match. The
default is all sites.
-ex Do an exhaustive screen that considers matches to n
sites, n-1 sites,...,<minsites>. By default, if a
molecule yields matches to a given number of sites,
matches to smaller numbers of sites will not be
considered.
-t <tlimit> CPU time limit in seconds for finding matches to each
molecule. Does not include the time to generate
conformers. The default is no time limit.
-inplace Find and score matches without aligning to the
hypothesis. Appropriate only when the structures being
screened are already in the same frame of reference as
the hypothesis, such as docked poses that are being
screened with a receptor-based hypothesis.
-notol Ignore positional tolerances if present in hypothesis.
-nocnst Ignore distance/angle/dihedral constraints if present
in hypothesis.
-nomask Ignore required match conditions if present in
hypothesis.
-norules Ignore feature-matching rules if present in
hypothesis.
Reporting Options:
-nosort Output hits in the order they are screened. The
default is to sort hits by decreasing
PHASE_SCREEN_SCORE.
-keep <maxhits> Cap sorted hits at <maxhits> (default: 1000).
-osd Output hits in SD format.
-prehypo Prepend pharmacophore hypothesis to hit file. Ignored
if -osd is used.
-report <n> Report up to <n> hits per molecule, grouped and sorted
by PHASE_SCREEN_SCORE. The default is 1.
-noqsar Do not apply QSAR model to hits.
Scoring and Filtering Options:
-noref Ignore reference ligand. This turns off vector and
volume scoring.
-noxvol Ignore excluded volumes if present in hypothesis.
-noivol Ignore included volumes if present in hypothesis.
-atypes Use MacroModel atom types when computing volume
scores.
-aw <weight> Alignment score weight. Must be >= 0. The default is
1.0.
-ac <cutoff> Alignment score cutoff. Must be > 0. The default is
1.2.
-hard Apply alignment score cutoff as a hard filter to
eliminate hits with alignment scores that exceed the
cutoff. By default, the alignment score cutoff is used
only as a parameter in the alignment score formula.
-ap <penalty> Partial matching alignment score penalty. Must be >=
0. The default is 1.2.
-vw <weight> Vector score weight. Must be >= 0. The default is 1.0.
-vc <cutoff> Eliminate hits with vector scores below this value.
Must lie on [-1, 1]. The default is -1.0.
-volw <weight> Volume score weight. Must be >= 0. The default is 1.0.
-volc <cutoff> Eliminate hits with volume scores below this value.
Must lie on [0, 1]. The default is 0.0.
-ivolw <weight> Included volume score weight. Must be >= 0. The
default is 1.0.
-ivolc <cutoff> Eliminate hits with included volume scores below this
value. Must lie on [0, 1]. The default is 0.0.
Job Control Options:
-HOST <host>[:<m>] Run job on a remote host. Include ":<m>" to split over
<m> CPUS. Note that a multi-conformer Maestro/SD file
cannot be divided over different CPUs, so <m> will be
reduced accordingly if it exceeds the number of multi-
conformer files. Note also that a Phase database must
be accessible to the job host via the absolute path
specified in <source>. By default, the job will run on
a single CPU on localhost.
-NJOBS <n> Divide work over <n> subjobs, where <n> may be greater
than the number of CPUs requested. Allows finer
granularity of work units and shorter delays when a
failed subjob has to be rerun.
-TMPDIR <dir> Store temporary job files in <dir>.