tautomer_enumerator.py Command Help
Command: $SCHRODINGER/jaguar run tautomer_enumerator.py
usage: $SCHRODINGER/jaguar run tautomer_enumerator.py [-h] [-charge <N>]
[-disable_std_pka]
[-disable_fast_pka]
[-disable_epikx]
[-do_charge_filtering]
[-do_pka_delta_filtering <X> <X>]
[-active_atoms <N> [<N> ...]]
[-use_depth_one]
[-max_proton_jumps <N>]
[-add_stereoisomers]
[-chiral_atoms <N> [<N> ...]]
[-enable_fast3d]
[-disable_FF_geopt]
[-fast_pka_min <X>]
[-fast_pka_max <X>]
[-WAIT] [-DEBUG]
[-jobname <name>]
[-subdir] [-recover]
[-no_subjob_files]
[-scr <absolute path>]
[-PARALLEL <N>]
[-max_threads <T>]
[-procs_per_node <N>]
[-use_one_node | -use_multiple_nodes]
[-HOST <host>:<M>]
[-SUBHOST <host>:<M>]
[-SAVE] [-NOJOBID]
[-OPLSDIR <oplsdir>]
infile
Generate all possible prototropic tautomers for the combinatorial distribution of
protons among a given set of sites which either donate protons (acidic) or
accept protons (basic). The sites (and labile protons) are detected
automatically. At each site at most one proton is added or removed.
This algorithm expects one input structure.
positional arguments:
infile input .mae file containing one structure.
options:
-h, --help show this help message and exit
-charge <N> Charge of output tautomers relative to input.
-disable_std_pka Disable Jaguar-pKa-based active atom classification.
-disable_fast_pka Disable fast-pKa for active atom classification.
-disable_epikx Disable EpikX-based active atom classification.
-do_charge_filtering Enable filtering of tautomers with many separated charges.
-do_pka_delta_filtering <X> <X>
Enable filtering of tautomers using fast-pKa delta values.
-active_atoms <N> [<N> ...]
Atom indices of tautomeric active atoms to add to automatically determined set.
-use_depth_one Use depth-1 algorithm for thorough tautomer search.
-max_proton_jumps <N>
Maximum number of proton jumps relative to input structure.
-add_stereoisomers Add R/S, E/Z and some other stereoisomers.
-chiral_atoms <N> [<N> ...]
Atom indices for chiral centers to racemize.
-enable_fast3d Enable using Fast3D to clean up geometries.
-disable_FF_geopt Disable final FF minimization to clean up geometries.
-fast_pka_min <X> Lower bound for fast-pKa active atom classification
-fast_pka_max <X> Upper bound for fast-pKa active atom classification
other options:
-WAIT Wait for job to finish before returning prompt.
-DEBUG, -D Print detailed information about job launch.
-jobname <name> Set the job name.
-subdir Run Jaguar in a sub-directory.
-recover Manually re-run a job using the recover mechanism. NOTE this option is not recommended for default recovery jobs.
Use "jaguar run <filename>.recover" instead (see documentation for more details).
-no_subjob_files Do not return subjob output files to launch directory.
-scr <absolute path> Specify a scratch directory (must not already exist). Directory must be given as an absolute path.
Note this will be used by the Fortran backend and is independent of the specification of -TMPDIR.
-PARALLEL <N> Use up to <N> CPUs simultaneously for the whole workflow, automatically allocated among subjobs, including threaded subjobs.
-max_threads <T> Use no more than <T> OpenMP threads for each Jaguar subjob. Default 8.
-procs_per_node <N> Use no more than <N> CPUs per node. Default is taken from the schrodinger.hosts file; if undefined 8.
-use_one_node Force CPU resources to be requested upfront on one node.
This pool of CPUs will be used for the duration of the job instead of resubmitting to the queue.
-use_multiple_nodes Force CPU resources to be requested dynamically from the queue (if available) instead of upfront on one node.
commonly used Schrodinger Suite options:
-HOST <host>:<M> Run job remotely on host <hostname>. The optional :<M> defines the maximum number of simultaneous subjobs.
May be combined with -PARALLEL <N>.
-SUBHOST <host>:<M> Run any subjobs remotely on subhost <hostname>. The optional :<M> defines the maximum number of simultaneous subjobs.
May be combined with -PARALLEL <N>.
-SAVE Return .zip file of scratch directory.
-NOJOBID Run Jaguar interactively without jobserver (not available with python workflows).
-OPLSDIR <oplsdir> Use custom FF parameters from specified directory for workflows which support it.