structgen

Performs 3D structure generation for a set of input molecules.

structgen is similar to confgen but has been designed for use-cases where a single reasonable low-energy 3D struture of a molecule is sufficient (which can be generated much faster than a diverse conformer ensemble).

Synopsis

structgen [-hVvptASszxUa^] [-c arg] [-l arg] [-f arg] [-m arg] [-d arg] [-q arg] [-D arg] [-E arg] [-T arg] [-Z arg] [-P arg] [-w arg] [-k arg] [-K arg] [-B arg] [-g arg] [-G arg] [-I arg] [-O arg] [-F arg] [-j arg] [-J arg] [-~ arg] [-Q arg] -i arg [arg]… -o arg

Mandatory options

-i [ –input ] arg

Specifies one or more input file(s) with molecules for which conformers have to be generated.

Supported Input Formats:

  • JME Molecular Editor String (.jme)

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

  • MDL Molfile (.mol)

  • Daylight SMILES String (.smi)

  • 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)

-o [ –output ] arg

Specifies the output file where the generated structures will be stored.

Supported Output 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)

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).

-f [ –failed ] arg

Specifies the output file for molecules where structure generation failed.

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)

  • 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)

-t [ –num-threads ] [=arg(=4)]

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

-m [ –mode ] arg

Structure generation method to use (AUTO, DG, FRAGMENT, default: AUTO).

-A [ –tol-range-sampling ] [=arg(=1)]

Additionally generate conformers for angles at the boundaries of the first torsion angle tolerance range (only effective for fragment-based structure generation, default: true).

-S [ –from-scratch ] [=arg(=1)]

Discard input 3D-coordinates and generate structures from scratch (default: true).

-d [ –frag-force-field ] arg

Force field used for fragment-based structure generation (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).

-q [ –dg-force-field ] arg

Force field used for DG-based structure generation (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).

-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: 80.0).

-E [ –dist-exponent ] arg

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

-T [ –timeout ] arg

Time in seconds after which structure generation will be stopped (default: 1200 s, must be >= 0, 0 disables timeout).

-Z [ –mc-rot-bond-count-thresh ] arg

Number of rotatable bonds in a ring above which DG-based structure generation will be performed(only effective in generation mode AUTO, default: 10, must be > 0).

-P [ –ref-tol ] arg

Energy tolerance at which force field structure refinement stops (only effective in DG-based structure generation, default: 0.001, must be >= 0, 0 results in refinement until convergence).

-w [ –max-ref-iter ] arg

Maximum number of force field structure refinement iterations (only effective in DG-based structure generation, default: 0, must be >= 0, 0 disables limit).

-k [ –add-tor-lib ] arg

Torsion library to be used in addition to the built-in library (only effective for fragment-based structure generation).

-K [ –set-tor-lib ] arg

Torsion library used as a replacement for the built-in library (only effective for fragment-based structure generation).

-B [ –frag-build-preset ] arg

Fragment build preset to use (FAST, THOROUGH, only effective for fragment-based structure generation, default: FAST).

-g [ –add-frag-lib ] arg

Fragment library to be used in addition to the built-in library (only effective for fragment-based structure generation).

-G [ –set-frag-lib ] arg

Fragment library used as a replacement for the built-in library (only effective for fragment-based structure generation).

-z [ –canonicalize ] [=arg(=1)]

Canonicalize input molecules (default: false).

-U [ –hard-timeout ] [=arg(=1)]

Specifies that exceeding the time limit shall be considered as an error and cause structure generation to fail (default: false).

-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).

-O [ –output-format ] arg

Allows to explicitly specify the output 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). Note that only storage formats make sense that allow to store atom 3D-coordinates!

-F [ –failed-format ] arg

Allows to explicitly specify the output 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).

-j [ –fixed-substr ] arg

Fixed substructure template molecule file. The given molecule can serve as source for fixed substructure atom 3D coordinates and also as query for finding fixed substructure matches in the processed input molecules if a SMARTS pattern has not been specified by option –fixed-substr-ptn. If the template molecule file does not provide atom 3D coordinates then the coordinates of matched input molecule atoms will be used (if 3D coordinates are not provided either way an error will be reported). [since V1.1]

-J [ –fixed-substr-ptn ] arg

SMARTS pattern for finding fixed substructure matches in the processed input molecules. If a template molecule file has been specified by option –fixed-substr then matching atoms of that molecule will serve as primary source for fixed atom 3D coordinates. Otherwise, the coordinates of matched input molecule atoms will be used (if 3D coordinates are not provided either way an error will be reported). [since V1.1]

-U [ –fixed-substr-mcss ] [=arg(=1)]

Use maximum common substructure search to find fixed substructure matches (default: false, using reqular substructure searching). [since V1.1]

-a [ –fixed-substr-align ] [=arg(=1)]

Align generated 3D structure on fixed substructure input atom positions (default: false). [since V1.1]

-~ [ –fixed-substr-min-atoms ] arg

The minimum required number of matched atoms when using maximum common substructure searching to find fixed substructure matches (default: 2). [since V1.1]

-Q [ –fixed-substr-max-matches ] arg

The maximum number of considered fixed substructure matches (default: 1, 0 disables limit). [since V1.1]

-^ [ –fixed-substr-ignore-h ] [=arg(=1)]

Ignore hydrogens that are present in the specified fixed substructure template molecule file (default: false). [since V1.1]