psdcreate

Creates a pharmacophore-screening database file from one or more molecule input files (see psdscreen).

Synopsis

psdcreate [-hVvpdts] [-c arg] [-l arg] [-m arg] [-I arg] [-T arg] -i arg [arg]… -o arg

Mandatory options

-i [ –input ] arg

Specifies one or more input file(s) with molecules that shall be stored in the created database.

Supported Input Formats:

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

  • MDL Molfile (.mol)

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

  • Native CDPL-Format (.cdf)

  • Tripos Sybyl MOL2 File (.mol2)

  • Atomic Coordinates XYZ File (.xyz)

  • 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 Tripos Sybyl MOL2 File (.mol2.gz)

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

  • Pharmacophore Screening Database (.psd)

-o [ –output ] arg

Output database file.

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

Database creation mode (CREATE, APPEND, UPDATE, default: CREATE).

-d [ –drop-duplicates ] [=arg(=1)]

Drop duplicate molecules (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).

-I [ –input-format ] arg

Allows to explicitly specify the format of the input file(s) 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(s) (because missing, misleading or not supported). Note that only storage formats make sense that allow to store atom 3D-coordinates!

-T [ –tmp-file-dir ] arg

Temporary file directory (default: ‘/tmp’)

-s [ –add-src-file-prop ] [=arg(=1)]

Add a source-file property to output molecules (default: false).