confgen

The program confgen has been published under the name CONFORGE and generates high-quality conformer ensembles for a set of given input molecules. Details regarding the implementation and performance of CONFORGE can be found in [5].

Built-in torsion rules are based on the torsion library jointly developed by the University of Hamburg, Center for Bioinformatics, Hamburg, Germany andF. Hoffmann-La-Roche Ltd., Basel, Switzerland [11][12].

Synopsis

confgen [-hVvptRHAuSszYMW] [-c arg] [-l arg] [-f arg] [-C arg] [-m arg] [-e arg] [-r arg] [-n arg] [-N arg] [-d arg] [-q arg] [-D arg] [-E arg] [-T arg] [-X arg] [-L arg] [-x arg] [-y arg] [-Z arg] [-P arg] [-w arg] [-k arg] [-K arg] [-B 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 conformers 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 conformer 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).

-C [ –conf-gen-preset ] arg

Conformer generation preset to use (SMALL_SET_DIVERSE, MEDIUM_SET_DIVERSE, LARGE_SET_DIVERSE, SMALL_SET_DENSE, MEDIUM_SET_DENSE, LARGE_SET_DENSE, default: MEDIUM_SET_DIVERSE).

-m [ –mode ] arg

Conformer sampling mode (AUTO, STOCHASTIC, SYSTEMATIC, default: AUTO).

-e [ –e-window ] arg

Output energy window for generated conformers (default: 15.000000, must be >= 0).

-r [ –rmsd ] arg

Minimum RMSD for output conformer selection (default: 0.5000, must be >= 0, 0 disables RMSD checking).

-n [ –max-num-out-confs ] arg

Maximum number of output conformers per molecule (default: 100, must be >= 0, 0 disables limit).

-N [ –nitrogen-enum-mode ] arg

Invertible nitrogen enumeration mode (NONE, ALL, UNSPECIFIED, default: UNSPECIFIED).

-R [ –enum-rings ] [=arg(=1)]

Enumerate ring conformers (only effective in systematic sampling mode, default: true).

-H [ –sample-het-hydrogens ] [=arg(=1)]

Perform torsion sampling for hydrogens on hetero atoms (default: false).

-A [ –tol-range-sampling ] [=arg(=1)]

Additionally generate conformers for angles at the boundaries of the first torsion angle tolerance range (only effective in systematic sampling mode, default: false).

-u [ –include-input ] [=arg(=1)]

Add input 3D-structure to output conformer ensemble (default: false).

-S [ –from-scratch ] [=arg(=1)]

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

-d [ –systematic-search-force-field ] arg

Search force field used in systematic sampling (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 [ –stochastic-search-force-field ] arg

Search force field used in stochastic smapling (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).

-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 molecule conformer generation will be stopped (default: 3600 s, must be >= 0, 0 disables timeout).

-X [ –max-num-rot-bonds ] arg

Maximum number of allowed rotatable bonds, exceeding this limit causes molecule conf. generation to fail (default: -1, negative values disable limit).

-L [ –max-pool-size ] arg

Puts an upper limit on the number of generated output conformer candidates (only effective in systematic sampling mode, default: 10000, must be >= 0, 0 disables limit).

-x [ –max-num-sampled-confs ] arg

Maximum number of sampled conformers (only effective in stochastic sampling mode, default: 2000, must be >= 0, 0 disables limit).

-y [ –conv-check-cycle-size ] arg

Minimum number of duplicate conformers that have to be generated in succession to consider convergence to be reached (only effective in stochastic sampling mode, default: 100, must be > 0).

-Z [ –mc-rot-bond-count-thresh ] arg

Number of rotatable bonds in a ring above which stochastic sampling will be performed(only effective in sampling mode AUTO, default: 10, must be > 0).

-P [ –ref-tol ] arg

Energy tolerance at which force field structure refinement stops (only effective in stochastic sampling mode, 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 stochastic sampling mode, 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 in systematic sampling mode).

-K [ –set-tor-lib ] arg

Torsion library used as a replacement for the built-in library (only effective in systematic sampling mode).

-B [ –frag-build-preset ] arg

Fragment build preset to use (FAST, THOROUGH, only effective in systematic sampling mode, default: FAST).

-b [ –build-force-field ] arg

Fragment 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, only effective in systematic sampling mode, default: MMFF94S_RTOR_NO_ESTAT).

-g [ –add-frag-lib ] arg

Fragment library to be used in addition to the built-in library (only effective in systematic sampling mode).

-G [ –set-frag-lib ] arg

Fragment library used as a replacement for the built-in library (only effective in systematic sampling mode).

-z [ –canonicalize ] [=arg(=1)]

Canonicalize input molecules (default: false).

-Y [ –energy-sd-entry ] [=arg(=1)]

Output conformer energy in the structure data section of SD-files (default: false).

-M [ –energy-comment ] [=arg(=1)]

Output conformer energy in the comment field (if supported by output format, default: false).

-W [ –conf-idx-suffix ] [=arg(=1)]

Append conformer index to the title of multiconf. output molecules (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).