shapescreen

Performs a fast Gaussian shape-based similarity screening of molecule databases.

Synopsis

shapescreen [-hVvpMPyazuWSACENGFBYt] [-c arg] [-l arg] [-o arg] [-r arg] [-m arg] [-s arg] [-b arg] [-n arg] [-x arg] [-X arg] [-g arg] [-f arg] [-R arg] [-T arg] [-Q arg] [-D arg] [-O arg] -q arg -d arg

Mandatory options

-q [ –query ] arg

The query molecule input file.

Supported Input Formats:

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

  • MDL Molfile (.mol)

  • 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)

Note that atom 3D-coordinates are required for shape screening!

-d [ –database ] arg

The screened database input file.

Supported Input Formats:

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

  • MDL Molfile (.mol)

  • 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)

Note that atomic 3D-coordinates are required for shape screening!

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).

-o [ –output ] arg

Hit molecule output file.

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)

-r [ –report ] arg

Report output file.

-m [ –mode ] arg

Screening mode specifying which of the obtained results for the query molecule are of interest (BEST_OVERALL, BEST_PER_QUERY, BEST_PER_QUERY_CONF, default: BEST_PER_QUERY).

-s [ –score ] arg

Primary scoring function that will be in effect for hit identification and ranking operations (TOTAL_OVERLAP_TANIMOTO, SHAPE_TANIMOTO, COLOR_TANIMOTO, TANIMOTO_COMBO, TOTAL_OVERLAP_TVERSKY, SHAPE_TVERSKY, COLOR_TVERSKY, TVERSKY_COMBO, QUERY_TOTAL_OVERLAP_TVERSKY, QUERY_SHAPE_TVERSKY, QUERY_COLOR_TVERSKY, QUERY_TVERSKY_COMBO, DB_TOTAL_OVERLAP_TVERSKY, DB_SHAPE_TVERSKY, DB_COLOR_TVERSKY, DB_TVERSKY_COMBO, default: TANIMOTO_COMBO)

-b [ –best-hits ] arg

Maximum number of best scoring hits to output (default: 1000).

-n [ –max-hits ] arg

Maximum number of found hits at which the search will terminate (overrides the –best- hits option, default: 0 - no limit).

-x [ –cutoff ] arg

Score cutoff value which determines whether a database molecule is considered as a hit (default: 0.0 - no cutoff).

-X [ –shape-tanimoto-cutoff ] arg

Shape tanimoto score cutoff that will be used for hit identifiaction in addition to the value specified by the –cutoff option (default: 0.0 - no cutoff).

-M [ –merge-hits ] [=arg(=1)]

If true, identified hits are merged into a single, combined hit list. If false, a separate hit list for every query molecule will be maintained (default: false).

-P [ –split-output ] [=arg(=1)]

If true, for every query molecule a separate report and hit output file will be generated (default: true).

-y [ –score-only ] [=arg(=1)]

If specified, no shape overlay of the query and database molecules will be performed and the input poses get scored as they are (default: false).

-a [ –opt-overlay ] [=arg(=1)]

Specifies whether or not to perform an overlay optimization of the generated starting poses (only in effect if option –score-only is false, default: true).

-z [ –thorough-overlay-opt ] [=arg(=1)]

Specifies whether or not to perform a thorough overlay optimization of the generated starting poses (note: the screening time will increase significantly, default: false).

-u [ –output-query ] [=arg(=1)]

If specified, query molecules will be written at the beginning of the hit molecule output file (default: true).

-g [ –single-conf-db ] arg

If specified, conformers of the database molecules are treated as individual single conformer molecules (default: false).

-f [ –color-ftr-type ] arg

Specifies which type of color features to generate and score (NONE, EXP_PHARM, IMP_PHARM, default: IMP_PHARM).

-W [ –all-carbon ] [=arg(=1)]

If specified, every heavy atom is interpreted as carbon (default: true).

-S [ –shape-center-starts ] [=arg(=1)]

If specified, principal axes aligned starting poses will be generated where both shape centers are located atorigin the coordinates system (default: true).

-A [ –atom-center-starts ] [=arg(=1)]

If specified, principal axes aligned starting poses will be generated so that the center of the smaller shape is located at all the heavy atom centers of the larger shape (default: false).

-C [ –color-center-starts ] [=arg(=1)]

If specified, principal axes aligned starting poses will be generated so that the center of the smaller shape is located at the color feature centers of the larger shape (default: false).

-R [ –random-starts ] arg

Generates the specified number of principal axes aligned starting poses with randomized shape center displacements (default: 0).

-E [ –score-sd-tags ] [=arg(=1)]

If true, score values will be appended as SD-block entries of the output hit molecules (default: true).

-N [ –query-name-sd-tags ] [=arg(=1)]

If true, the query molecule name will be appended to the SD-block of the output hit molecules (default: false).

-G [ –query-idx-sd-tags ] [=arg(=1)]

If true, the query molecule index will be appended to the SD-block of the output hit molecules (default: false).

-F [ –query-conf-sd-tags ] [=arg(=1)]

If true, the query conformer index will be appended to the SD-block of the output hit molecules (default: true).

-B [ –db-idx-sd-tags ] [=arg(=1)]

If true, the database molecule index will be appended to the SD-block of the output hit molecules (default: false).

-Y [ –db-conf-sd-tags ] [=arg(=1)]

If true, the database conformer index will be appended to the SD-block of the output hit molecules (default: true).

-T [ –hit-name-ptn ] arg

Pattern for composing the names of written hit molecules by variable substitution (supported variables: @Q@ = query molecule name, @D@ = database molecule name, @C@ = query molecule conformer index, @c@ = database molecule conformer index, @I@ = query molecule index and @i@ = database molecule index, default: @D@_@c@_@Q@_@C@).

-t [ –num-threads ] [=arg(=4)]

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

-Q [ –query-format ] arg

Allows to explicitly specify the format of the query molecule 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). Note that atomic 3D-coordinates are required for shape screening!

-D [ –database-format ] arg

Allows to explicitly specify the format of the screening database 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(s) (because missing, misleading or not supported). Note that atomic 3D-coordinates are required for shape screening!

-O [ –output-format ] arg

Allows to explicitly specify the hit molecule output file format 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).