structgen
=========
Performs 3D structure generation for a set of input molecules.
:program:`structgen` is similar to :program:`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
--------
:program:`structgen` [-hVvptASszU] [-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] -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)
- 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)
- 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)
- 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:
4 threads, 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: 80.0000).
-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: 0.0010, 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).