tug_align.py Command Help

Command: $SCHRODINGER/run -FROM psp tug_align.py

usage: $SCHRODINGER/run -FROM psp tug_align.py struct_file reference_file [options]

Morphing-based alignment of small molecules.

Given a set of ligands and a reference structure, "tug" the ligands towards
the reference structure in such a way to balance RMSD and strain.

Matching atoms can be provided by the user or automatically determined using
a maximum common substructure search. Aligned output structures report
RMSD, strain and clash statistics as structure-level properties. Strain energy
is most accurately reported when the input structure is pre-minimized with the
OPLS forcefield.

positional arguments:
  struct_file           Structure file containing ligand(s) for alignment.
  reference_file        Structure file containing reference ligand for alignment.

options:
  -h, --help            show this help message and exit
  -forcefield {OPLS5,OPLS_2005,OPLS4}
                        Forcefield to use during alignment. Default is S-OPLS
  -jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
                        Set the base name of outputs
  -v                    show program's version number and exit

Alignment Options:
  -receptor_structure RECEPTOR_STRUCTURE, --receptor_structure RECEPTOR_STRUCTURE
                        Structure file containing a receptor to test for clashes during alignment; alignment trials clashing with any receptor will be rejected.
  -nconfs NCONFS, --nconfs NCONFS
                        Number of aligned conformations per ligand to keep; default = 1.
  -strain_tol STRAIN_TOL, --strain_tol STRAIN_TOL
                        Maximum strain (kcal/mol) to allow for aligned molecule; aligned poses with strain above this tolerance value will be skipped in the final output file; default = 50.0.
  -convergence_strain CONVERGENCE_STRAIN, --convergence_strain CONVERGENCE_STRAIN
                        Maximum strain (kcal/mol) required for alignment convergence; this initial value can be relaxed if many alignment trials are rejected; default = 30.0.
  -convergence_rmsd CONVERGENCE_RMSD, --convergence_rmsd CONVERGENCE_RMSD
                        Minimum RMSD value required for alignment convergence, in Angstrom; this initial value can be relaxed if enough alignment trials are rejected; default = 0.4.
  -num_tries_per_cycle NUM_TRIES_PER_CYCLE, --num_tries_per_cycle NUM_TRIES_PER_CYCLE
                        Number of alignment attempts per ligand before relaxing acceptance criteria; higher numbers can lead to extended run times; default = 400.
  -max_tries MAX_TRIES, --max_tries MAX_TRIES
                        Maximum number of attempts to align each ligand. Together with '-num_tries_per_cycle', controls how many rounds of alignment criteria relaxation are allow; higher numbers can lead to extended run times; default = 10000.
  -smarts SMARTS, --smarts SMARTS
                        SMARTS pattern to define the core region to seed the alignment.  Pattern must define a common core shared by the reference and target ligands.
  --mcs_method {rdkit,canvas}
                        DEPRECATED. Which method to use to generate maximum common substructure (obsolete: always uses rdkit).
  -skip_unmatched_smarts, --skip_unmatched_smarts
                        Skip ligands that do not match the SMARTS provided in '--smarts'.
  -mcs_timeout MCS_TIMEOUT, --mcs_timeout MCS_TIMEOUT
                        Timeout for MCS finding algorithm. Default is 120
  -match_reference_peptide_bonds, --match_reference_peptide_bonds
                        Match cis/trans peptide bond torsions during alignment to the reference structure.
  -keep_initial_peptide_bonds, --keep_initial_peptide_bonds
                        Preserve cis/trans peptide bond torsions in the input structure(s) during alignment.
  -freeze_torsion FREEZE_TORSION, --freeze_torsion FREEZE_TORSION
                        Specify atom indices to preserve a torsion angle in the input structure(s); should be in the format '1,2,3,4' where the numbers are the atom indices. Multiple torsions can be specified by using this option multiple times. If multiple ligands are provided, the same atom indices will be used for all ligands.

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

Standard Options:
  -NJOBS NJOBS          Divide the overall job into NJOBS subjobs.
  -RETRIES RETRIES      If a subjob fails for any reason, it will be retried RETRIES times. (Default: 1)
  -NOLAUNCH             Set up subjob inputs, but don't run the jobs.

Restart Options:
  -restart_file RESTART_FILES
                        Output of a partially completed subjob; keyword may be used multiple times, once per partial subjob
  -RESTART              Run 'restart_file' automatically by guessing the names of the files to use

Examples:

1. Align a set of ligands to a reference structure using the default parameters:

$SCHRODINGER/run -FROM psp tug_align.py ligands.maegz reference.maegz

2. Align a set of ligands to a reference structure using a custom SMARTS pattern:

$SCHRODINGER/run -FROM psp tug_align.py ligands.maegz reference.maegz --smarts '[#6](-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#16]'

3. Align a ligand to a reference structure but keep specific torsions in the ligand fixed during alignment:

$SCHRODINGER/run -FROM psp tug_align.py ligands.maegz reference.maegz --freeze_torsion '1,2,3,4' --freeze_torsion '5,6,7,8'