CLI Reference
Documentation for the protein-detective script.
$ protein-detective --help
usage: protein-detective [-h]
[--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
[--version]
{search,retrieve,density-filter,prune-pdbs,powerfit} ...
Protein Detective CLI
positional arguments:
{search,retrieve,density-filter,prune-pdbs,powerfit}
search Search UniProt for structures
retrieve Retrieve structures
density-filter Filter AlphaFoldDB structures based on density
confidence
prune-pdbs Prune PDBe files to keep only the first chain and
rename it to A
powerfit PowerFit related commands
options:
-h, --help show this help message and exit
--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
--version show program's version number and exit
search
$ protein-detective search --help
usage: protein-detective search [-h] [--taxon-id TAXON_ID]
[--reviewed | --no-reviewed]
[--subcellular-location-uniprot SUBCELLULAR_LOCATION_UNIPROT]
[--subcellular-location-go SUBCELLULAR_LOCATION_GO]
[--molecular-function-go MOLECULAR_FUNCTION_GO]
[--limit LIMIT]
session_dir
positional arguments:
session_dir Session directory to store results
options:
-h, --help show this help message and exit
--taxon-id TAXON_ID NCBI Taxon ID
--reviewed, --no-reviewed
Reviewed=swissprot, no-reviewed=trembl. Default is
uniprot=swissprot+trembl.
--subcellular-location-uniprot SUBCELLULAR_LOCATION_UNIPROT
Subcellular location (UniProt)
--subcellular-location-go SUBCELLULAR_LOCATION_GO
Subcellular location (GO term, e.g. GO:0005737)
--molecular-function-go MOLECULAR_FUNCTION_GO
Molecular function (GO term, e.g. GO:0003677)
--limit LIMIT Limit number of results
retrieve
$ protein-detective retrieve --help
usage: protein-detective retrieve [-h] [--what {alphafold,pdbe}]
[--what-af-formats {amAnnotations,amAnnotationsHg19,amAnnotationsHg38,bcif,cif,paeDoc,paeImage,pdb}]
session_dir
positional arguments:
session_dir Session directory to store results
options:
-h, --help show this help message and exit
--what {alphafold,pdbe}
What to retrieve. Can be specified multiple times.
Default is pdbe and alphafold.
--what-af-formats {amAnnotations,amAnnotationsHg19,amAnnotationsHg38,bcif,cif,paeDoc,paeImage,pdb}
AlphaFold formats to retrieve. Can be specified
multiple times. Default is 'pdb'.
density-filter
$ protein-detective density-filter --help
usage: protein-detective density-filter [-h]
[--confidence-threshold CONFIDENCE_THRESHOLD]
[--min-residues MIN_RESIDUES]
[--max-residues MAX_RESIDUES]
session_dir
positional arguments:
session_dir Session directory for input and output
options:
-h, --help show this help message and exit
--confidence-threshold CONFIDENCE_THRESHOLD
pLDDT confidence threshold (0-100)
--min-residues MIN_RESIDUES
Minimum number of residues above confidence threshold
--max-residues MAX_RESIDUES
Maximum number of residues above confidence threshold.
prune-pdbs
$ protein-detective prune-pdbs --help
usage: protein-detective prune-pdbs [-h] session_dir
positional arguments:
session_dir Session directory containing PDB files
options:
-h, --help show this help message and exit
powerfit
$ protein-detective powerfit --help
usage: protein-detective powerfit [-h]
{commands,run,report,fit-models,list-runs,list-lcc} ...
positional arguments:
{commands,run,report,fit-models,list-runs,list-lcc}
commands Generate PowerFit commands for PDB files in the
session directory
run Run PowerFit on PDB files in the session directory
report Generate a report of the best PowerFit solutions.
fit-models Fit models based on PowerFit solutions
list-runs List all PowerFit runs in the session directory
list-lcc List Local Cross Validation (lcc.mrc) files for
PowerFit runs
options:
-h, --help show this help message and exit
powerfit commands
$ protein-detective powerfit commands --help
usage: protein-detective powerfit commands [-h] [-a <float>] [-l] [-cw] [-nr]
[-rr <float>] [-nt] [-tc <float>]
[-p <int>] [-g] [--output OUTPUT]
target resolution session_dir
positional arguments:
target Target density map to fit the model in. Data should
either be in CCP4 or MRC format
resolution Resolution of map in angstrom
session_dir Session directory for input and output
options:
-h, --help show this help message and exit
-a, --angle <float> Rotational sampling density in degree. Increasing this
number by a factor of 2 results in approximately 8
times more rotations sampled.
-l, --laplace Use the Laplace pre-filter density data. Can be
combined with the core-weighted local cross-
correlation.
-cw, --core-weighted Use core-weighted local cross-correlation score. Can
be combined with the Laplace pre-filter.
-nr, --no-resampling Do not resample the density map.
-rr, --resampling-rate <float>
Resampling rate compared to Nyquist.
-nt, --no-trimming Do not trim the density map.
-tc, --trimming-cutoff <float>
Intensity cutoff to which the map will be trimmed.
Default is 10 percent of maximum intensity.
-p, --nproc <int> Number of processors used during search. The number
will be capped at the total number of available
processors on your machine.
-g, --gpu Off-load the intensive calculations to the GPU.
--output OUTPUT Output file for powerfit commands. If set to '-'
(default) will print to stdout.
powerfit run
$ protein-detective powerfit run --help
usage: protein-detective powerfit run [-h] [-a <float>] [-l] [-cw] [-nr]
[-rr <float>] [-nt] [-tc <float>]
[-p <int>] [-g]
target resolution session_dir
Run PowerFit on PDB files in the session directory and store results.
positional arguments:
target Target density map to fit the model in. Data should
either be in CCP4 or MRC format
resolution Resolution of map in angstrom
session_dir Session directory containing PDB files
options:
-h, --help show this help message and exit
-a, --angle <float> Rotational sampling density in degree. Increasing this
number by a factor of 2 results in approximately 8
times more rotations sampled.
-l, --laplace Use the Laplace pre-filter density data. Can be
combined with the core-weighted local cross-
correlation.
-cw, --core-weighted Use core-weighted local cross-correlation score. Can
be combined with the Laplace pre-filter.
-nr, --no-resampling Do not resample the density map.
-rr, --resampling-rate <float>
Resampling rate compared to Nyquist.
-nt, --no-trimming Do not trim the density map.
-tc, --trimming-cutoff <float>
Intensity cutoff to which the map will be trimmed.
Default is 10 percent of maximum intensity.
-p, --nproc <int> Number of processors used during search. The number
will be capped at the total number of available
processors on your machine.
-g, --gpu Off-load the intensive calculations to the GPU.
powerfit report
$ protein-detective powerfit report --help
usage: protein-detective powerfit report [-h]
[--powerfit_run_id POWERFIT_RUN_ID]
[--top TOP] [--output OUTPUT]
session_dir
positional arguments:
session_dir Session directory containing PowerFit results
options:
-h, --help show this help message and exit
--powerfit_run_id POWERFIT_RUN_ID
ID of the PowerFit run to report on
--top TOP Number of top solutions to report
--output OUTPUT Output file for solutions table. If set to '-'
(default) will print to stdout.
powerfit fit-models
$ protein-detective powerfit fit-models --help
usage: protein-detective powerfit fit-models [-h]
[--powerfit_run_id POWERFIT_RUN_ID]
[--top TOP] [--output OUTPUT]
session_dir
positional arguments:
session_dir Session directory containing PowerFit results
options:
-h, --help show this help message and exit
--powerfit_run_id POWERFIT_RUN_ID
ID of the PowerFit run to report on. If not provided,
will use the all runs.
--top TOP Number of top solutions to fit models for
--output OUTPUT Output file for fitted model table. If set to '-'
(default) will print to stdout.
powerfit list-runs
$ protein-detective powerfit list-runs --help
usage: protein-detective powerfit list-runs [-h] session_dir
positional arguments:
session_dir Session directory containing PowerFit results
options:
-h, --help show this help message and exit
powerfit list-lcc
$ protein-detective powerfit list-lcc --help
usage: protein-detective powerfit list-lcc [-h] session_dir
positional arguments:
session_dir Session directory containing PowerFit results
options:
-h, --help show this help message and exit