ring_chain.py Command Help
Command: $SCHRODINGER/jaguar run ring_chain.py
usage: $SCHRODINGER/jaguar run ring_chain.py [-h] [-min_ring_size <N>]
[-max_ring_size <N>]
[-rc_erg_window <X>]
[-initial_tautomers <maefile>]
[-ignore_chains] [-ignore_rings]
[-find_all] [-max_cycles <N>]
[-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 ring-chain tautomers from an input chain-form molecule.
positional arguments:
infile Input structure .mae file (if multiple structures are present in the file, only the first is used).
options:
-h, --help show this help message and exit
-min_ring_size <N> Minimum ring size to form.
-max_ring_size <N> Maximum ring size to form.
-rc_erg_window <X> Energy cutoff used to filter ring-closed structures for tautomer enumeration.
-initial_tautomers <maefile>
Initial tautomers .mae file, will skip running initial AutoConf.
-ignore_chains Only do chain->ring tautomers (i.e. do not include ring->chain or ring->chain->ring).
-ignore_rings Only do ring->chain tautomers (i.e. do not include chain->ring or ring->chain->ring.
-find_all Find all ring-chain tautomers regardless of number of rings formed.
-max_cycles <N> Maximum number of cycles in exhaustive ring-chain search.
Tautomer Enumerator Options:
-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.