genfraglib

Creates, updates or merges fragment libraries for conformer generation with CONFORGE.

Synopsis

genfraglib [-hVvptsb] [-c arg] [-l arg] [-m arg] [-I arg] [-F arg] [-r arg] [-T arg] [-n arg] [-e arg] [-g arg] [-f arg] [-D arg] [-E arg] -i arg [arg]… -o arg

Mandatory options

-i [ –input ] arg

When operating in CREATE or UPDATE mode, specifies one or more input file(s) with molecules whose fragments shall be stored in the created fragment library.

Supported Input 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)

  • 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 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)

  • CDPL Conformer Generator Fragment Library Format (.cfl, .cdf)

In MERGE mode, specifies multiple existing fragment libraries in CDF format.

-o [ –output ] arg

Output fragment library 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

Processing mode (CREATE, UPDATE, MERGE default: CREATE).

-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).

-F [ –preset ] arg

Fragment conformer generation preset to use (FAST, THROUGH, default: THOROUGH).

-r [ –rmsd ] arg

Minimum RMSD of two small ring system conformations to be considered dissimilar (default: 0.1, must be >= 0).

-T [ –timeout ] arg

Time in seconds after which fragment conformer generation will be stopped (default: 1800s, must be >= 0, 0 disables timeout).

-n [ –max-lib-size ] arg

Maximum number of output fragments (default: 0, must be >= 0, 0 disables limit, only valid in CREATE mode).

-e [ –e-window ] arg

Energy window for small ring system conformers (default: 8.0, must be >= 0).

-g [ –small-rsys-sampling-factor ] arg

Small ring system conformer sampling factor (default: 20, must be > 1).

-f [ –force-field ] arg

Build force field (MMFF94, MMFF94_NO_ESTAT, MMFF94S, MMFF94S_XOOP, MMFF94S_RTOR, MMFF94S_RTOR_XOOP, MMFF94S_NO_ESTAT, MMFF94S_XOOP_NO_ESTAT, MMFF94S_RTOR_NO_ESTAT, MMFF94S_RTOR_XOOP_NO_ESTAT, default: MMFF94S_RTOR_NO_ESTAT).

-s [ –strict-param ] [=arg(=1)]

Perform strict MMFF94 parameterization (default: true).

-D [ –dielectric-const ] arg

Dielectric constant used for the calculation of electrostatic interaction energies (default: 1.0).

-E [ –dist-exponent ] arg

Distance exponent used for the calculation of electrostatic interaction energies (default: 1.0).

-b [ –pres-bonding-geom ] [=arg(=1)]

Preserve input bond lengths and angles (default: false).