usage: simbad-database [-h] {lattice,contaminant,morda,custom,validate} ...
lattice database
simbad-database lattice [-h] [-debug_lvl DEBUG_LVL] [-latt_db LATT_DB]
-debug_lvl | The console verbosity level < notset | info | debug | warning | error | critical > Default: “info” |
-latt_db | Path to local copy of the lattice database Default: “/empty/path/share/simbad/static/niggli_database.npz” |
Contaminant database
simbad-database contaminant [-h] [-nproc NPROC] [-submit_qtype {local,sge}]
[-submit_queue SUBMIT_QUEUE]
[-debug_lvl DEBUG_LVL] [-cont_db CONT_DB]
[--add_morda_domains]
-debug_lvl | The console verbosity level < notset | info | debug | warning | error | critical > Default: “info” |
-cont_db | Path to local copy of the contaminant database Default: “/empty/path/share/simbad/static/contaminants” |
--add_morda_domains | |
Retrospectively add morda domains to an updated contaminant database Default: False |
-nproc | Number of processors. For local, serial runs the jobs will be split across nproc processors. For cluster submission, this should be the number of processors on a node. Default: 1 |
-submit_qtype | Possible choices: local, sge The job submission queue type Default: “local” |
-submit_queue | The queue to submit to on the cluster. |
morda database
simbad-database morda [-h] [-nproc NPROC] [-submit_qtype {local,sge}]
[-submit_queue SUBMIT_QUEUE] [-chunk_size CHUNK_SIZE]
[-debug_lvl DEBUG_LVL]
simbad_db
simbad_db | Path to local copy of the SIMBAD database |
-chunk_size | Max jobs to submit at any given time [disk space dependent Default: 5000 |
-debug_lvl | The console verbosity level < notset | info | debug | warning | error | critical > Default: “info” |
-nproc | Number of processors. For local, serial runs the jobs will be split across nproc processors. For cluster submission, this should be the number of processors on a node. Default: 1 |
-submit_qtype | Possible choices: local, sge The job submission queue type Default: “local” |
-submit_queue | The queue to submit to on the cluster. |
custom database
simbad-database custom [-h] [-debug_lvl DEBUG_LVL] custom_db input_db
custom_db | Path to local copy of the custom database of PDB files in SIMBAD format |
input_db | Path to local copy of the custom database of PDB files |
-debug_lvl | The console verbosity level < notset | info | debug | warning | error | critical > Default: “info” |