pose_filter.py Command Help

Command: $SCHRODINGER/run pose_filter.py

Usage: pose_filter.py -asl <asl> <criterion=id>... <pose_view_file> [<output_pose_view_file>] [<options>]

Evaluates poses to see if they satisfy specified interactions with the
receptor. By default, only poses that meet the criteria will be written to the
output file. If -annotate option is used, then criteria matching properties
are added to the structures and no filtering is performed.

Options:
-v, -version Show the program's version and exit.
-h, -help Show this help message and exit.
-a RECEP_ASL, -asl RECEP_ASL
ASL expression that defines a single receptor
substructure. Multiple substructures may be defined
with multiple separate -asl options. Multiple
substructures are identified by their command line
order. The first -asl on the command line is
<substructure_id> 1, the second -asl on the command
line is <substructure_id> 2, and so on. For example,
"-asl 'res.num 12, 34' -asl 'res.num 56'" will place
receptor residue numbers 12 & 34 in <substructure_id>
1 and residue number 56 in <substructure_id> 2. If an
expression contains spaces, it must be enclosed within
quotes. For example, "res.ptype \'UNK \' AND
sidechain".
-lig_asl LIG_ASL ASL expression for the ligand atoms that can match the
criteria. For example, "-lig_asl 'atom.e N,O'" will
consider only N and O ligand atoms when evaluating the
interactions. Note that the entire ligand is still
considered when determining if an atom is aromatic or
in a ring. If an expression contains spaces, it must
be enclosed within quotes. For example, "res.ptype
\'UNK \' AND atom.e H". Default is "all".
-match MATCH When filtering poses, surviving poses must match
choice of 'all', 'any', or 'none' criteria. Default
is to use the logic defined below and in the -doc
section.
-hbond <substructure_id>
Pose must have a hydrogen bond between the ligand and
receptor <substructure_id>. If <substructure_id> is 0
then the pose must have a hydrogen bond between all
substructures (logical AND). If multiple ids are
provided, they are treated with a logical OR. For
example, "-hbond 1 -hbond 3" means the surviving pose
has a hydrogen bond between the first OR third
receptor substructure.
-halogen_bond <substructure_id>
Pose must have a halogen bond between the ligand and
receptor <substructure_id>. If <substructure_id> is 0
then the pose must have a halogen bond between all
substructures (logical AND). If multiple ids are
provided, they are treated with a logical OR. For
example, "-halogen_bond 1 -halogen_bond 3" means the
surviving pose has a halogen bond between the first OR
third receptor substructure.
-contact <substructure_id>
Pose must have any atom in the ligand within the
cutoff distance of any atom in receptor
<substructure_id>. Multiple ids and boolean
operations are supported as described for -hbond.
-ring <substructure_id>
Pose must have a ring atom in the ligand within the
cutoff distance of any atom in receptor
<substructure_id>. Multiple ids and boolean
operations are supported as described for -hbond.
-aromatic <substructure_id>
Pose must have an aromatic atom in the ligand within
the cutoff distance of any atom in receptor
<substructure_id>. Multiple ids and boolean
operations are supported as described for -hbond.
-hbond_and_ring <substructure_id>
Pose must have a hydrogen bond AND ring atom in the
ligand within the cutoff distance of any atom in
receptor <substructure_id>. Multiple ids and boolean
operations are supported as described for -hbond.
-hbond_or_ring <substructure_id>
Pose must have a hydrogen bond OR ring atom in the
ligand within the cutoff distance of any atom in
receptor <substructure_id>. Multiple ids and boolean
operations are supported as described for -hbond.
-hbond_and_aromatic <substructure_id>
Pose must have a hydrogen bond AND aromatic ring atom
in the ligand within the cutoff distance of any atom
in receptor <substructure_id>. Multiple ids and
boolean operations are supported as described for
-hbond.
-hbond_or_aromatic <substructure_id>
Pose must have a hydrogen bond OR aromatic ring atom
in the ligand within the cutoff distance of any atom
in receptor <substructure_id>. Multiple ids and
boolean operations are supported as described for
-hbond.
-hbond_dist_max HBOND_DIST_MAX
Hydrogen bond distance cutoff, in angstroms. Distance
is measured from the hydrogen to the acceptor atom.
Default is 2.5 angstrom.
-hbond_donor_angle HBOND_DONOR_ANGLE
Hydrogen bond donor angle cutoff, in degrees. Angle
is defined by the D-H~X, the donated hydrogen (H), the
donor (D), and the atom attached to the donor (X).
Default is 90.0 degrees.
-hbond_acceptor_angle HBOND_ACCEPTOR_ANGLE
Hydrogen bond acceptor angle cutoff, in degrees.
Angle is defined H~A-Y, the donated hydrogen (H), the
acceptor atom (A), and the atom attached to the
acceptor (Y). Default=60.0 degrees.
-contact_dist_max CONTACT_DIST_MAX
Maximum distance to consider for a ligand atom -
receptor atom contact. Default is 5.0 angstrom.
-ring_dist_max RING_DIST_MAX
Maximum distance to consider for a ring ligand atom -
receptor atom contact. Default is 5.0 angstrom.
-aromatic_dist_max AROMATIC_DIST_MAX
Maximum distance to consider for an aromatic ligand
atom - receptor atom contact. Default is 5.0
angstrom.
-complex Treat the input structure file as a series of ligand-
receptor complexes instead of a pose view file. For
each complex the ligand's pose will be evaluated
against its cognate receptor.
-complex_lig_asl COMPLEX_LIG_ASL
Use the supplied argument as an ASL string to identify
the ligand within the ligand-receptor complex.
Otherwise, it will be assumed that the ligand is the
last molecule in the structure. Only used if the
"-complex" option is specified.
-doc Print command line examples.
-verbose Increase filtering verbosity.
-annotate Annotate the input structures without filtering.

Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-NOJOBID Run the job directly, without Job Control layer.