psdscreen

Performs a pharmacophore-based virtual screening of molecule databases (see psdcreate).

Synopsis

psdscreen [-hVvpxabSICDNPt] [-c arg] [-l arg] [-m arg] [-s arg] [-e arg] [-n arg] [-M arg] [-O arg] [-Q arg] -d arg -q arg -o arg

Mandatory options

-d [ –database ] arg

Screening database file.

-q [ –query ] arg

Specifies the file containing one or more pharmacophore(s) that shall be used as a query for the database search.

Supported Input Formats:

  • Native CDPL-Format (.cdf)

  • LigandScout Pharmaceutical Markup Language (.pml)

  • Pharmacophore Screening Database (.psd)

  • GZip-Compressed Native CDPL-Format (.cdf.gz)

  • BZip2-Compressed Native CDPL-Format (.cdf.bz2)

-o [ –output ] arg

Specifies the output file where database molecules matching the query pharmacophore(s) shall be stored.

Supported Output Formats:

  • JME Molecular Editor String (.jme)

  • MDL Structure-Data File (.sdf, .sd)

  • MDL Molfile (.mol)

  • Daylight SMILES String (.smi)

  • Daylight SMARTS String (.sma)

  • IUPAC International Chemical Identifier (.inchi, .ichi)

  • Native CDPL-Format (.cdf)

  • Tripos Sybyl MOL2 File (.mol2)

  • GZip-Compressed MDL Structure-Data File (.sdf.gz, .sd.gz, .sdz)

  • BZip2-Compressed MDL Structure-Data File (.sdf.bz2, .sd.bz2)

  • GZip-Compressed Native CDPL-Format (.cdf.gz)

  • BZip2-Compressed Native CDPL-Format (.cdf.bz2)

  • GZip-Compressed Daylight SMILES String (.smi.gz)

  • BZip2-Compressed Daylight SMILES String (.smi.bz2)

  • GZip-Compressed Tripos Sybyl MOL2 File (.mol2.gz)

  • BZip2-Compressed Tripos Sybyl MOL2 File (.mol2.bz2)

  • Pharmacophore Screening Database (.psd)

Other options

-h [ –help ] [=arg(=SHORT)]

Print help message and exit (ABOUT, USAGE, SHORT, ALL or ‘name of option’, default: SHORT).

-V [ –version ]

Print version information and exit.

-v [ –verbosity ] [=arg(=VERBOSE)]

Verbosity level of information output (QUIET, ERROR, INFO, VERBOSE, DEBUG, default: INFO).

-c [ –config ] arg

Use file with program options.

-l [ –log-file ] arg

Redirect text-output to file.

-p [ –progress ] [=arg(=1)]

Show progress bar (default: true).

-m [ –mode ] arg

Molecule conformer matching mode (FIRST-MATCH, BEST-MATCH, ALL-MATCHES, default: FIRST-MATCH).

-s [ –start-index ] arg (=0)

Screening start molecule index (zero-based, default: 0).

-e [ –end-index ] arg (=0)

Screening end molecule index (zero-based and not included in the screening run, default: number of molecules in the database).

-n [ –max-num-hits ] arg (=0)

Maxmimum number of hits to report (default: no limit).

-M [ –max-omitted ] arg (=0)

Allowed maximum number of unmatched features.

-x [ –check-xvols ] [=arg(=1)]

Check for exclusion volume clashes (default: true).

-a [ –align-hits ] [=arg(=1)]

Align matching conformations to pharmacophore for output (default: true).

-b [ –best-alignments ] [=arg(=1)]

Seek best alignments with highest score (default: false).

-S [ –output-score ] [=arg(=1)]

Output score property for hit molecule (default: true).

-I [ –output-mol-index ] [=arg(=1)]

Output database molecule index property for hit molecule (default: false).

-C [ –output-conf-index ] [=arg(=1)]

Output conformation index property for hit molecule (default: false).

-D [ –output-db-name ] [=arg(=1)]

Output database name property for hit molecule (default: false).

-N [ –output-pharm-name ] [=arg(=1)]

Output query pharmacophore name property for hit molecule (default: false).

-P [ –output-pharm-index ] [=arg(=1)]

Output query pharmacophore index property for hit molecule (default: false).

-t [ –num-threads ] [=arg(=4)]

Number of parallel execution threads (default: no multithreading, implicit value: number of CPUs, must be >= 0, 0 disables multithreading).

-u [ –unique-hits ] [=arg(=1)]

Report molecules matching multiple query pharmacophores only once (default: false) [since V1.1]

-O [ –output-format ] arg

Allows to explicitly specify the format of the hit molecule output file by providing one of the supported file-extensions (without leading dot!) as argument. This option is useful when the format cannot be auto-detected from the actual extension of the file (because missing, misleading or not supported).

-Q [ –query-format ] arg

Allows to explicitly specify the format of the query pharmacophore file by providing one of the supported file-extensions (without leading dot!) as argument. This option is useful when the format cannot be auto-detected from the actual extension of the file (because missing, misleading or not supported).