simbad-database options¶

usage: simbad-database [-h] {lattice,contaminant,morda,custom,validate} ...

Sub-commands:¶

lattice¶

lattice database

simbad-database lattice [-h] [-debug_lvl DEBUG_LVL] [-latt_db LATT_DB]

Named Arguments¶

-debug_lvl

Default: “info”

-latt_db

Path to local copy of the lattice database

Default: “/empty/path/share/simbad/static/niggli_database.npz”

contaminant¶

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]

Named Arguments¶

`-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

Cluster queue submission options¶

-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¶

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

Positional Arguments¶

simbad_db

Path to local copy of the SIMBAD database

Named Arguments¶

-chunk_size

Max jobs to submit at any given time [disk space dependent

Default: 5000

-debug_lvl

Default: “info”

Cluster queue submission options¶

-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¶

custom database

simbad-database custom [-h] [-debug_lvl DEBUG_LVL] custom_db input_db

Positional Arguments¶

`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

Named Arguments¶

-debug_lvl

Default: “info”

validate¶

validate database

simbad-database validate [-h] [-debug_lvl DEBUG_LVL] database

Positional Arguments¶

database

The database to validate

Named Arguments¶

-debug_lvl

Default: “info”