align_ligands Command Help
Command: $SCHRODINGER/utilities/align_ligands
usage: align_ligands [-h] [-o <outfile>] [-ref <ligand_number>]
[-core {<smarts>,MCS}] [-refine] [-freeze <atomsfile>]
[-input_treatment {keep,replace,auto}]
[-sample {rapid,thorough,rdkit}] [-max <numconfs>]
[-minimize] [-terminal {sample,align}] [-fail_on_bad]
[-ignore_sidechains] [-use_sampled_ref]
[-close_contact <d>] [-verbosity {0,1,2}]
[-HOST <hostname>] [-TMPDIR TMPDIR] [-NOJOBID]
[-JOBNAME JOBNAME]
<infile>
Uses a best practices approach to flexibly align a set of ligands using
common core snapping, least-squares alignment of common cores, or full
shape-based superposition.
Copyright Schrodinger LLC, All Rights Reserved.
positional arguments:
<infile> Input Maestro or SD file with the structures to be
aligned.
options:
-h, --help show this help message and exit
-o <outfile> Output Maestro or SD file for aligned structures.
Defaults to <jobname>_align.maegz, where <jobname> is
derived from the basename of <infile>.
-ref <ligand_number> Use the indicated input ligand (1, 2, etc.) as the
reference structure to which all other ligands should
be aligned. By default, one or more reference
structures are chosen automatically after clustering
by largest common Bemis-Murcko scaffold.
-core {<smarts>,MCS} If a reference structure has been designated, use the
supplied SMARTS string or the MCS between each
structure and the reference as the common core. In the
case of MCS, bond orders and elemental types must
match, ring atoms may match only other ring atoms, and
complete rings must be matched. The default behavior
is to align on the largest shared Bemis-Murcko
scaffold.
-refine Refine alignments by generating additional conformers
with core atoms held fixed, and identifying conformers
which increase the average in-place shape similarity
between all pairs of ligands. Conformers are not
generated for the primary reference structure or a
user-designated reference structure.
-freeze <atomsfile> Refine input alignments directly, holding user-defined
sets of atoms fixed when generating conformers. Each
non-blank line in <atomsfile> must contain a comma-
separated list of 3 or more atom numbers that comprise
a connected substructure in the associated ligand. A
blank line (i.e., one that contains only a newline
character) is interpreted to mean that conformers
should not be generated for that ligand. Note that
when this option is used, structures are not snapped
onto one another, nor is there any concept of a
reference structure. Rather, an attempt is made to
select a conformer for each ligand that maximizes the
average in-place shape similarity over all pairs of
ligands.
-input_treatment {keep,replace,auto}
Input structure treatment when doing direct
refinement: keep = use inputs as a starting point for
refinement; replace = replace all inputs with the
closest sampled conformer and perform refinement on
those conformers; auto = make a pass with "keep"
treatment and follow up with "replace" treatment if no
improvement was achieved in first pass (default:
keep).
-sample {rapid,thorough,rdkit}
Conformational sampling method (default: rapid).
-max <numconfs> Maximum number of conformers to generate (default:
1000).
-minimize Perform energy minimization on each conformer.
-terminal {sample,align}
Whether to conformationally sample rotatable terminal
atoms (e.g., -CH3, -NH2, -OH) if they are part of the
core, or align their closest pairs of hydrogens
(default: align).
-fail_on_bad Fail immediately if any structure contains multiple
disconnected fragments or no rings. These structures
cannot be processed and are quietly skipped by
default.
-ignore_sidechains Do not attempt to snap chemically identical sidechains
onto one another in pairs of structures that share a
common snapped core.
-use_sampled_ref Replace the primary reference structure, which is
chosen automatically or specified via -ref, with a
sampled conformer that yields the best shape-based
superposition to the corresponding input structure.
This can sometimes result in a better consensus
alignment since the primary reference structure is an
actual sampled conformer, and as such may produce
better superpositions with sampled conformers for
other structures.
-close_contact <d> Non-bonded close contact distance. If greater than 0,
a snapped ligand structure is rejected when the act of
snapping brings two non-bonded atoms within this
distance of each other. Flexible least-squares
alignment is done if every mapping of the core results
in the creation of a close contact. A value of 0
disables close contact detection (default: 0.0).
-verbosity {0,1,2} Level of printed output: 0 = none, 1 = informative
messages during the alignment process, 2 = additional
messages triggered by core snapping failures (default:
1).
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-TMPDIR TMPDIR The name of the directory used to store files
temporarily during a job.
-NOJOBID Run the job directly, without Job Control layer.
-JOBNAME JOBNAME Provide an explicit name for the job.