Command line interface¶

usage: kripodb [-h] [--version]
               {fingerprints,fragments,similarities,dive,serve,pharmacophores}
               ...

Positional Arguments¶

subcommand

Possible choices: fingerprints, fragments, similarities, dive, serve, pharmacophores

Named Arguments¶

--version

show program’s version number and exit

Sub-commands:¶

fingerprints¶

Fingerprints

kripodb fingerprints [-h]
                     {import,export,meanbitdensity,similar,similarities,merge}
                     ...

Sub-commands:¶

import¶

Add Makebits file to fingerprints db

kripodb fingerprints import [-h] infile [infile ...] outfile

Positional Arguments¶

infile

Name of makebits formatted fingerprint file (.tar.gz or not packed or - for stdin)

outfile

Name of fingerprints db file

Default: “fingerprints.db”

export¶

Dump bitsets in fingerprints db to makebits file

kripodb fingerprints export [-h] infile outfile

Positional Arguments¶

infile

Name of fingerprints db file

Default: “fingerprints.db”

outfile

Name of makebits formatted fingerprint file (or - for stdout)

meanbitdensity¶

Compute mean bit density of fingerprints

kripodb fingerprints meanbitdensity [-h] [--out OUT] fingerprintsdb

Positional Arguments¶

fingerprintsdb

Name of fingerprints db file (default: “fingerprints.db”)

Default: “fingerprints.db”

Named Arguments¶

--out

Output file, default is stdout (default: -)

Default: -

similar¶

Find the fragments closests to query based on fingerprints

kripodb fingerprints similar [-h] [--mean_onbit_density MEAN_ONBIT_DENSITY]
                             [--cutoff CUTOFF] [--memory]
                             fingerprintsdb query out

Positional Arguments¶

fingerprintsdb

Name of fingerprints db file

Default: “fingerprints.db”

query

Query identifier or beginning of it

out

Output file tabdelimited (query, hit, score)

Named Arguments¶

`--mean_onbit_density`
	Mean on bit density (default: 0.01) Default: 0.01
`--cutoff`	Set Tanimoto cutoff (default: 0.55) Default: 0.55
`--memory`	Store bitsets in memory (default: False) Default: False

similarities¶

Output formats: * tsv, tab separated id1,id2, similarity * hdf5, hdf5 file constructed with pytables with a, b and score, but but a and b have been replaced

by numbers and similarity has been converted to scaled int

When input has been split into chunks, use –ignore_upper_triangle flag for computing similarities between same chunk. This prevents storing pair a->b also as b->a.

kripodb fingerprints similarities [-h] [--out_format {tsv,hdf5}]
                                  [--fragmentsdbfn FRAGMENTSDBFN]
                                  [--mean_onbit_density MEAN_ONBIT_DENSITY]
                                  [--cutoff CUTOFF] [--nomemory]
                                  [--ignore_upper_triangle]
                                  fingerprintsfn1 fingerprintsfn2 out_file

Positional Arguments¶

`fingerprintsfn1`
	Name of reference fingerprints db file
`fingerprintsfn2`
	Name of query fingerprints db file
`out_file`	Name of output file (use - for stdout)

Named Arguments¶

`--out_format`	Possible choices: tsv, hdf5 Format of output (default: “hdf5”) Default: “hdf5”
`--fragmentsdbfn`
	Name of fragments db file (only required for hdf5 format)
`--mean_onbit_density`
	Mean on bit density (default: 0.01) Default: 0.01
`--cutoff`	Set Tanimoto cutoff (default: 0.45) Default: 0.45
`--nomemory`	Do not store query fingerprints in memory (default: False) Default: False
`--ignore_upper_triangle`
	Ignore upper triangle (default: False) Default: False

merge¶

Combine fingerprints databases into a single new one

kripodb fingerprints merge [-h] ins [ins ...] out

Positional Arguments¶

`ins`	Input fingerprints database files
`out`	Output fingerprints database file

fragments¶

Fragments

kripodb fragments [-h] {shelve,sdf,pdb,filter,merge,export_sd} ...

Sub-commands:¶

shelve¶

Add fragments from shelve to sqlite

kripodb fragments shelve [-h] [--skipdups] shelvefn fragmentsdb

Positional Arguments¶

shelvefn

fragmentsdb

Name of fragments db file (default: “fragments.db”)

Default: “fragments.db”

Named Arguments¶

--skipdups

Skip duplicates, instead of dieing one first duplicate

Default: False

sdf¶

Add fragments sdf to sqlite

kripodb fragments sdf [-h] sdffns [sdffns ...] fragmentsdb

Positional Arguments¶

sdffns

SDF filename

fragmentsdb

Name of fragments db file (default: “fragments.db”)

Default: “fragments.db”

pdb¶

Add pdb metadata from RCSB PDB website to fragment sqlite db

kripodb fragments pdb [-h] fragmentsdb

Positional Arguments¶

fragmentsdb

Name of fragments db file (default: “fragments.db”)

Default: “fragments.db”

filter¶

Filter fragments database

kripodb fragments filter [-h] [--pdbs PDBS] [--matrix MATRIX] input output

Positional Arguments¶

`input`	Name of fragments db input file
`output`	Name of fragments db output file, will overwrite file if it exists

Named Arguments¶

`--pdbs`	Keep fragments from any of the supplied pdb codes, one pdb code per line, use - for stdin
`--matrix`	Keep fragments which are in similarity matrix file

merge¶

Combine fragments databases into a single new one

kripodb fragments merge [-h] ins [ins ...] out

Positional Arguments¶

`ins`	Input fragments database files
`out`	Output fragments database file

export_sd¶

Export molblocks of all fragments as SDF file

kripodb fragments export_sd [-h] fragmentsdb sdfile

Positional Arguments¶

`fragmentsdb`	Input fragments database file
`sdfile`	Output SDF file

similarities¶

Similarity matrix

kripodb similarities [-h]
                     {similar,merge,export,import,filter,freeze,thaw,fpneigh2tsv,histogram}
                     ...

Sub-commands:¶

similar¶

Find the fragments closets to query based on similarity matrix

kripodb similarities similar [-h] [--out OUT] [--cutoff CUTOFF]
                             pairsdbfn query

Positional Arguments¶

`pairsdbfn`	hdf5 similarity matrix file or base url of kripodb webservice
`query`	Query fragment identifier

Named Arguments¶

--out

Output file tab delimited (query, hit, similarity score)

Default: -

--cutoff

Similarity cutoff (default: 0.55)

Default: 0.55

merge¶

Combine pairs files into a new file

kripodb similarities merge [-h] ins [ins ...] out

Positional Arguments¶

`ins`	Input pair file in hdf5_compact format
`out`	Output pair file in hdf5_compact format

export¶

Export similarity matrix to tab delimited file

kripodb similarities export [-h] [--no_header] [--frag1] [--pdb PDB]
                            simmatrixfn outputfile

Positional Arguments¶

`simmatrixfn`	Compact hdf5 similarity matrix filename
`outputfile`	Tab delimited output file, use - for stdout

Named Arguments¶

--no_header

Output no header (default: False)

Default: False

--frag1

Only output *frag1 fragments (default: False)

Default: False

--pdb

Only output fragments which are from pdb code in file, one pdb code per line (default: None)

import¶

When input has been split into chunks,: use –ignore_upper_triangle flag for similarities between same chunk. This prevents storing pair a->b also as b->a.

kripodb similarities import [-h] [--inputformat {tsv,fpneigh}]
                            [--nrrows NRROWS] [--ignore_upper_triangle]
                            inputfile fragmentsdb simmatrixfn

Positional Arguments¶

inputfile

Input file, use - for stdin

fragmentsdb

Name of fragments db file (default: “fragments.db”)

Default: “fragments.db”

simmatrixfn

Compact hdf5 similarity matrix file, will overwrite file if it exists

Named Arguments¶

`--inputformat`	Possible choices: tsv, fpneigh tab delimited (tsv) or fpneigh formatted input (default: “fpneigh”) Default: “fpneigh”
`--nrrows`	Number of rows in inputfile (default: 65536) Default: 65536
`--ignore_upper_triangle`
	Ignore upper triangle (default: False) Default: False

filter¶

Filter similarity matrix

kripodb similarities filter [-h] [--fragmentsdb FRAGMENTSDB | --skip SKIP]
                            input output

Positional Arguments¶

`input`	Input hdf5 similarity matrix file
`output`	Output hdf5 similarity matrix file, will overwrite file if it exists

Named Arguments¶

`--fragmentsdb`	Name of fragments db file, fragments in it will be kept as well as their pair counter parts.
`--skip`	File with fragment identifiers on each line to skip

freeze¶

Optimize similarity matrix for reading

kripodb similarities freeze [-h] [-f FRAME_SIZE] [-m MEMORY] [-l LIMIT] [-s]
                            in_fn out_fn

Positional Arguments¶

`in_fn`	Input pairs file
`out_fn`	Output array file, file is overwritten

Named Arguments¶

`-f, --frame_size`
	Size of frame (default: 100000000) Default: 100000000
`-m, --memory`	Memory cache in Gigabytes (default: 1) Default: 1
`-l, --limit`	Number of pairs to copy, None for no limit (default: None)
`-s, --single_sided`
	Store half matrix (default: False) Default: False

thaw¶

Optimize similarity matrix for writing

kripodb similarities thaw [-h] [--nonzero_fraction NONZERO_FRACTION]
                          in_fn out_fn

Positional Arguments¶

`in_fn`	Input packed frozen matrix file
`out_fn`	Output pairs file, file is overwritten

Named Arguments¶

--nonzero_fraction

Fraction of pairs which have score above threshold (default: 0.012)

Default: 0.012

fpneigh2tsv¶

Convert fpneigh formatted file to tab delimited file

kripodb similarities fpneigh2tsv [-h] inputfile outputfile

Positional Arguments¶

`inputfile`	Input file, use - for stdin
`outputfile`	Tab delimited output file, use - for stdout

histogram¶

Distribution of similarity scores

kripodb similarities histogram [-h] [-f FRAME_SIZE] [-r] [-l]
                               inputfile outputfile

Positional Arguments¶

`inputfile`	Filename of similarity matrix hdf5 file
`outputfile`	Tab delimited output file, use - for stdout

Named Arguments¶

`-f, --frame_size`
	Size of frame (default: 100000000) Default: 100000000
`-r, --raw_score`
	Return raw score (16 bit integer) instead of fraction score Default: False
`-l, --lower_triangle`
	Return scores from lower triangle else return scores from upper triangle Default: False

dive¶

DiVE visualization utils

kripodb dive [-h] {fragments,dump,export} ...

Sub-commands:¶

fragments¶

Export fragments as DiVE formatted sphere

kripodb dive fragments [-h] [--onlyfrag1] inputfile outputfile

Positional Arguments¶

`inputfile`	Name of fragments db input file
`outputfile`	Name of fragments dive output file, use - for stdout

Named Arguments¶

--onlyfrag1

Only *_frag1 (default: False)

Default: False

dump¶

Dump dense matrix with zeros

kripodb dive dump [-h] [--frag1only] inputfile outputfile

Positional Arguments¶

`inputfile`	Name of dense similarity matrix
`outputfile`	Name of output file, use - for stdout

Named Arguments¶

--frag1only

Only *frag1 (default: False)

Default: False

export¶

Writes props for DiVE visualization

kripodb dive export [-h] [--propnames PROPNAMES] [--props PROPS]
                    [--pdbtags PDBTAGS]
                    fragmentsdb uniprot_annot

Positional Arguments¶

`fragmentsdb`	Name of fragments db input file
`uniprot_annot`	Uniprot download accession 2 gene symbol, family mapping. Fetch “http://www.uniprot.org/uniprot/?query=database:pdb&format=tab&columns=id,genes(PREFERRED),families,database(PDB)”

Named Arguments¶

--propnames

Name of prop names file

Default: kripo.propnames.txt

--props

Name of props file

Default: kripo.props.txt

--pdbtags

Tag pdb in file by filename

serve¶

Serve similarity matrix, fragments db and pharmacophores db as webservice

kripodb serve [-h] [--internal_port INTERNAL_PORT]
              [--external_url EXTERNAL_URL]
              similarities fragments pharmacophores

Positional Arguments¶

`similarities`	Filename of similarity matrix hdf5 file
`fragments`	Filename of fragments sqlite database file
`pharmacophores`	Filename of pharmacophores hdf5 file

Named Arguments¶

--internal_port

TCP port on which to listen (default: 8084)

Default: 8084

--external_url

URL which should be used in Swagger spec (default: “http://localhost:8084/kripo”)

Default: “http://localhost:8084/kripo”

pharmacophores¶

Pharmacophores

kripodb pharmacophores [-h] {add,get,filter,merge,import,sd2phar} ...

Sub-commands:¶

add¶

Add pharmacophores from directory to database

kripodb pharmacophores add [-h] [--nrrows NRROWS] startdir pharmacophoresdb

Positional Arguments¶

`startdir`	Directory to start finding .pphores.sd.gz and .pphores.txt files in
`pharmacophoresdb`
	Name of pharmacophore db file

Named Arguments¶

--nrrows

Number of expected pharmacophores,: only used when database is created (default: 65536)

Default: 65536

get¶

Retrieve pharmacophore of a fragment

kripodb pharmacophores get [-h] [--query QUERY] [--output OUTPUT]
                           pharmacophoresdb

Positional Arguments¶

`pharmacophoresdb`
	Name of pharmacophore db file

Named Arguments¶

--query

Query fragment identifier

--output

Phar formatted text file

Default: -

filter¶

Filter pharmacophores

kripodb pharmacophores filter [-h] [--fragmentsdb FRAGMENTSDB]
                              inputfn outputfn

Positional Arguments¶

`inputfn`	Name of input pharmacophore db file
`outputfn`	Name of output pharmacophore db file

Named Arguments¶

--fragmentsdb

Name of fragments db file, fragments present in db are passed (default: “fragments.db”)

Default: “fragments.db”

merge¶

Merge pharmacophore database files into new one

kripodb pharmacophores merge [-h] ins [ins ...] out

Positional Arguments¶

`ins`	Input pharmacophore database files
`out`	Output pharmacophore database file

import¶

Convert phar formatted file to pharmacophore database file

kripodb pharmacophores import [-h] [--nrrows NRROWS] infile outfile

Positional Arguments¶

`infile`	Input phar formatted file
`outfile`	Output pharmacophore database file

Named Arguments¶

--nrrows

Number of expected pharmacophores,: only used when database is created (default: 65536)

Default: 65536

sd2phar¶

Convert sd formatted pharmacophore file to phar formatted file

kripodb pharmacophores sd2phar [-h] [--frag_id FRAG_ID] infile outfile

Positional Arguments¶

`infile`	Input sd formatted file
`outfile`	Output phar formatted file

Named Arguments¶

--frag_id

Fragment identifier

Default: “frag”