# Optional Parameters¶

## Execute Options¶

-param

The argument for this flag is the name of a file containing control parameters. The control parameter file acts to either replace or augment the command line interface. All parameters necessary for program execution may be provided in the control parameter file, although any command given explicitly on the command line will supersede options found in the parameter file. The application generates a new parameter file containing the full set of execution parameters upon every execution. The name of the parameter file is created by combining the prefix base name with the ‘.param’ extension.

-mpi_np <n>

Specifies the number of processors n when the application is run in MPI mode.

-mpi_hostfile <filename>

Specifies the name of the file containing processors configuration. For every host this file should contain a line host_name slots=n where n is the number of processors on the host.

## File Options¶

-out

File to write conformers generated by OMEGA. Gzipped OEBinary is the recommended output format.

Supported file formats: cdx, cif, dat, ent, json, mdl, mmd, mmod, mol, mol2, mol2h, mopac, oeb, oez, pac, pdb, sd, sdf, syb, xyz, and the corresponding compressed formats (i.e., xx.gz).

-commentEnergy

This flag causes the conformer energy in kcal/mol to be written in the comment field for each conformer. This is particularly useful when writing SD or MOL2 files that will be passed to software that anticipates strain energies written in the comment field. [default = false]

-includeInput

When true this boolean flag will include the input conformer in the output file. This requires that the input file format is a 3D format (eg: SDF, MOL2, OEB, etc.). [default = false]

-log

The argument for this flag specifies the name of the log file. The level of detail for logfile information can be altered using the -verbose flag. Output can be directed to the terminal as well with the -progress log option. Generation of an output log may be disabled by providing ‘nul’ or ‘null’ as an argument. [default = prefix.log]

-prefix

The argument for this flag defines the prefix to be used for various information and data files generated by OMEGA. Most important among these is the ‘oeomega_<mode>.parm’ file which includes a copy of all the parameters used in the OMEGA run. The prefix is also used to generate a default log file name if not explicitly specified with the -log flag. [default = oeomega_<mode>].

-progress

Show progress on screen. Options are ‘none’, ‘dots’, ‘log’ and ‘percent’. The ‘dots’ options will displays dots on screen to show molecules completed. The ‘log’ option will duplicate the log file on screen. The ‘percent’ option will track progress through the input file. [default = none]

-rotorOffsetCompress

This flag controls the behavior of writing the rotor offset compressed flavor of the OEBinary format. Rotor offset compressed files contain the same information as standard Cartesian OEBinary files, but require a small fraction of the storage space. Optimal compression of OMEGA output can be obtained by writing GZip compressed OEBinary files with the -rotorOffsetCompress flag turned on. [default = true]

-sdEnergy

This flag controls the behavior of writing strain energies as SD tags. This flag may be used with either OEBinary or MDL SD files. [default = false]

-verbose

This is a boolean flag that controls the level of detail written to the log file. By default OMEGA will only write minimal information to the log file. Molecule titles and warning messages constitute the bulk of logging at the default level. Verbose logging will cause more information to be written to the log file in order to follow behavior during program execution. In order to have the log shown on the screen, use -progress log. [default = false]

-warts

This boolean flag is used to generate unique titles for conformers that reflect their position in an ensemble of conformations produced by OMEGA. The title given to each conformer will begin with the molecule title taken from the input file, and appended with an underscore and the integer corresponding to the rank order number of the conformer in the final ensemble. [default = true]

## 3D Construction Parameters¶

-addfraglib

[alias: -setfraglib]

The argument that follows this flag is one fragment file, normally generated by MakeFraglib. These fragments will supplement the built-in fragment library.

An enhanced fragment library, omega_fragment_lib_2020.oeb.gz, that improves the performance of conformer generation is available on request from the database downloads page.

-buildff

This flag sets the force field used for constructing fragments that are assembled to build an initial model of the input structure. Consult the description of Force Fields (see Force Fields) for an explanation of appropriate arguments for this flag. [default = mmff94smod_NoEstat]

-canonOrder

This flag can be used to disable the automatic reordering of input molecules to a canonical atom and bond order. In order obtain consistent results from different file formats and different connection table orders, OMEGA reorders the input connection table. This behavior can be turned off using the -canonOrder flag, however, the resultant ensembles will likely be inconsistent in their composition. [default = true]

-deleteFixHydrogens

When a fixfile fragment is specified, all possible mappings (matches) of the fragment and the input molecule are considered for positioning the input molecule. This process begins with a substructure search of the fragment in the input molecule. If hydrogens are included on the fixfile fragment, the number of possible matches will grow exponentially with the number of equivalences. Each geminal hydrogen pair on the fixfile produces a non-productive match multiplied by all other non-productive matches. This flag can be used to prevent the explosion of non-productive matches by deleting hydrogens from the fixfile fragment prior to the substructure search. [default = true]

-fixfile

The argument that follows this flag is a molecule file used to specify the coordinates for a substructure of the input molecules. An initial structure is generated for every input molecule, and then a substructure search is performed using the molecule or fragment provided in the fixfile as a query molecule. Every instance of the fixed substructure found in the input molecule up to a predetermined limit (see maxmatch and umatch) is used to replace the coordinates of the atoms that match the substructure. The input molecule coordinates are aligned relative to the substructure prior to fragment replacement, and then the coordinates are taken from the fixed fragment and assigned to the corresponding atoms of the input molecule. A separate alignment, replacement, and then conformer search is carried out for every matching substructure in the input molecule. Molecules that do not match the fixfile will be sent to the fail file.

-fixrms

Fixfile fragments taken from crystallographic sources may differ in their geometry relative to optimal MMFF94 geometries. OMEGA attempts to superimpose built structures onto fixfile fragments and, if the geometry differs too greatly, OMEGA considers the superposition a poor match and will fail to build a structure using the fixfile. This flag can be used to loosen the default RMS superposition criteria to allow suboptimal superpositions to succeed in spite of the poor geometric complementarity. [default = 0.15]

-fixsmarts

Another way to specify a fixed portion of a molecule. The SMARTS pattern is used to fix a portion of the -fixfile primarily, or fix a portion of the input molecule if -fromCT is set to false secondarily. Molecules that do not match will be sent to the fail file.

-fixmcs

Flag to fix a portion of a molecule based on maximum common subgraph against the -fixfile molecule. Molecules that do not have any common subgraph will fail. [default = False]

-fromCT

This boolean flag determines whether OMEGA should generate an initial set of 3D coordinates using only the connection table of the input molecule. Initial model generation is always necessary for molecule file formats devoid of coordinates (i.e. SMILES). Bond lengths and angles taken from molecule files containing coordinates may be retained by setting this flag to false. -enumNitrogen false must also be set for identical stereochemistry to be guaranteed in the output. [default = true]

-maxmatch

This flag is used to limit the number of fixfile substructure matches in the input molecule. Each match will result in replacement of the matching substructure with coordinates taken from the fixfile fragment. The number of matches may need to be limited using this parameter for a substructure where many matches are possible. [default = 1]

-mcsMinAtoms

This parameter is used to define the limit of mcs based fix using -fixmcs. This is the minimum number of atoms that is required for a MCS based fix. [default = 1]

-strictfrags

This flag sets how OMEGA generates fragments that are not in the fraglib. The default is a faster and less rigorous fragment generation than the makefraglib program, whereas a ‘true’ value will require OMEGA to be identical to the makefraglib program. The most noticeable difference is the time limit for fragment generation, which is increased from 30 seconds to 300 seconds with -strictfrags set to true. [default = false]

-strictatomtyping

Use strict atom typing for MMFF94 or allow ‘close enough’ atom typing. A true setting will fail any molecule that contains an atom type that does not have specified parameters. A false setting will allow parameters from a similar atom type to be used. [default = true]

-umatch

The -umatch boolean flag determines whether only the unique substructure matches of the fixfile are used for coordinate replacement. A unique substructure match is defined as a match that does not cover the identical set of target atoms as any other substructure match in a set. For example, a benzene substructure will match a benzene ring 12 times. Only one substructure match constitutes a unique match, while the other 11 matches are duplicates. If the flag is set to false then all possible substructure matches may be used for coordinate replacement. This behavior is usually unnecessary as non-unique matches will frequently lead to duplication. [default = true]

## Structure Enumeration¶

-enumNitrogen

The -enumNitrogen string flag controls the behavior of OMEGA with respect to enumeration of nonterminal nitrogens. Any nitrogen with pyramidal geometry in the initial model of the input molecule, and having no more than two ring bonds is considered by OMEGA to be ‘invertible’. OMEGA will enumerate all possible puckers if the -enumNitrogen flag is set to true. OMEGA will only enumerate unspecified invertible nitrogens if the flag is set to unspecified. [default = unspecified]

-enumRing

The -enumRing boolean flag controls the behavior of OMEGA with respect to ring conformations. If this flag is set to true, OMEGA will generate all possible combinations of all ring conformations in a molecule. Ring systems with only a single conformation will be replaced with a conformation taken from a fragment file, or generated on the fly by OMEGA. If this flag is set to false then no ring conformer enumeration or replacement will occur. Initial geometries provided in by an input file (see -fromCT) may therefore be preserved by setting -enumRing to false as well. [default = true]

-sampleHydrogens

Sets whether hydrogens will be sampled. This option enables sampling of hydrogen locations for -OH, -SH, and amines. [default = false]

## Torsion Driving Parameters¶

-addtorlib

Takes a filename as a parameter. Torsion rules in the file are placed above any previous torsion rules and therefore are matched first. (see Torsion Library Format)

-erange

The -erange flag sets the energy cutoff used as an accept or reject criteria for conformers depending on the number of rotatable bonds in the structure. Any conformer that has a calculated strain energy less than the sum of the energy window and the energy of the global minimum conformer will be accepted. Conformers with strain energies above this threshold are rejected. The energy range is given as a list of values that correspond to the -rangeIncrement parameter. For example, -erange 5.0 10.0 15.0 20.0 used with -rangeIncrement 3 sets the energy window to 5.0 kcal/mol for structures with zero to two rotatable bonds, 10.0 kcal/mol for structures with three to five rotatable bonds, and so on. The energy window for structures with more rotors than the highest -erange value specified will be taken as the highest specified value.

-ewindow

The -ewindow flag sets the energy window in kcal/mol used as an accept or reject criteria for conformers. Any conformer that has a calculated strain energy less than the sum of the energy window and the energy of the global minimum conformer will be accepted. Conformers with strain energies above this threshold are rejected. [default = 10.0 (classic) or 20.0 (macrocycle)]

-maxConfRange

The -maxConfRange flag allows the user to specify the maximum number of conformers to be output for a structure based on the number of rotatable bonds in the structure. The maximum conformer range is given as a list of values that correspond to the -rangeIncrement parameter. For example, -maxConfRange 100 150 200 250 used with -rangeIncrement 3 sets the maximum number of conformers to 100 for structures with zero to two rotatable bonds, 150 for structures with three to five rotatable bonds, and so on. The number of conformers for structures with more rotors than the highest -maxConfRange value specified will be taken as the highest specified value.

-maxconfs

The -maxconfs flag sets the maximum number of conformations to be generated. Conformers are assembled in energy sorted order. As a special case, setting -maxconfs 0 will result in OMEGA skipping the duplicate removal step and it will write all generated conformers to the output file. Note that this implies -rms 0 is also used. [default = 200]

-maxrot

The -maxrot flag sets the maximum number of rotatable bonds cutoff. Molecules that have equal to or fewer rotors than the -maxrot cutoff will be processed by OMEGA. OMEGA will not search for conformers of molecules that have more rotors than the -maxrot cutoff. By default, OMEGA does not apply a number of rotatable bonds cutoff. Instead, a desired cutoff must be supplied by the user. [default = -1]

-maxtime

This flag limits the amount of time (in seconds) spent generating conformers for each molecule. [default = 120.0]

-rangeIncrement

The -rangeIncrement is used to control the number of rotatable bonds range used with the -maxConfRange, -rmsrange, and -erange flags. The preceding flags are used to control the maximum number of conformers, RMS cutoff, and energy windows used that are dependent on the number of rotors in a given structure. [default = 5]

-rms

The -rms flag sets the minimum Root Mean Square (RMS) Cartesian distance below which two conformers are duplicates. The RMS calculation is performed after superposition such that the true minimum distance between conformers is calculated. Lowering the -rms value may cause OMEGA to generate ensembles that contain more representative conformers of a similar shape. Higher -rms values may result in smaller, yet possibly more shape diverse ensembles. [default = 0.5]

-rmsrange

The -rmsrange flag allows the user to specify the RMS cutoff used for duplicate conformer removal based on the number of rotatable bonds in the structure. The rms range is given as a list of values that correspond to the -rangeIncrement parameter. For example, -rmsrange 0.8 1.0 1.2 1.4 used with -rangeIncrement 3 sets the RMS cutoff value to 0.8 for structures with zero to two rotatable bonds, 1.0 for structures with three to five rotatable bonds, and so on. The RMS cutoff value for structures with more rotors than the highest -rmsrange value specified will be taken as the highest specified value.

-searchff

This flag sets the force field used to calculate strain energies of conformers generated during a torsion search. Consult the description of Force Fields (see Force Fields) for an explanation of appropriate arguments for this flag. [default = mmff94smod_NoEstat]

-settorlib

The -settorlib flag is used to specify the file name of the file containing rules used in resolution control of the torsion driving part of conformer generation. Refer to the section describing the format of the torsion library (see Torsion Library Format).

-torlibtype

The -torlibtype flag is used to specify the type of built-in torsion library. There are two types: original and guba. The original is the classic OMEGA torsion library, and the guba is a new type [Guba-2016] available in OMEGA 3.0 and above. [default = original]

-useGPU

The -useGPU flag is used to engage GPU-Omega to accelerate torsion driving on a GPU if one is available on the system, see GPU-Omega for details. [default = true]

## Stereo Parameters¶

-flipper

Creates an ensemble of stereoisomers before passing the molecules for conformer generation. A value of ‘true’ will flip all unspecified stereo centers and a value of ‘force’ will flip all stereo centers. [default = false]

-flipper_maxcenters

Sets the maximum number of stereocenters than can be flipped exhaustively. The number of molecules generated by enumerating the stereocenters is $$2^N$$, where N is the number of stereocenters. In some instances, this may be larger than is desired. The -flipper_maxcenters parameter indicates the maximum number of stereocenters which will be fully enumerated. If a molecule has more than -flipper_maxcenters stereocenters, OMEGA will randomly enumerate 2^(flipper_maxcenters) instances from the full set of potential isomers. [default = 12]

-flipper_warts

Add wart to title of each stereoisomer. [default = true]

-flipper_enhstereo

Consider enhanced stereo information during stereoenumeration. [default = false]

-strictstereo

Requires all stereo centers to be specified. Molecules sent to conformer generation with unspecified stereo will fail. [default = true]

## General¶

-strict

Convenience flag for setting -strictstereo, -strictatomtyping, and -strictfrags at once. This setting will override any individual settings for these flags.

## Options specific to the macrocycle mode¶

Execute options

-param

A parameter file name.

-mpi_np

Number of MPI processors to launch. If not used job will run on a single processor.

Note

The number of processors should be set to a reasonable number, preferably use the maximum number of CPU cores available.

-mpi_hostfile

Path to hostfile to be used for launching MPI processes.

File options

-in

Input molecular file name. Contrary to oeomega classic, pipe streaming can’t be used.

-molnames

This parameter specifies a text file containing a list of molecule names (one name per line in the file). If this parameter is set then only molecules in the input file(s) (see parameter -in) with names that match those in the text files will be read in.

The general purpose of this flag is to provide an easy mechanism for reading a few specific molecule(s) that are contained in a large database, without having to extract those molecules by hand from the database.

-out

Output molecular file name. The following SD tags will be attached to the output: “Macrocycle Energy”, “Relative Energy”, “Macrocycle Iteration”, “Macrocycle duplicate minima count”, and “RMSD from input structure”. Important note: macrocycle mode does NOT support “-rotorOffsetCompress” option.

-prefix

Prefix used to name output files.

-progress

Show progress on screen. Options are ‘none’, ‘dots’, ‘log’ and ‘percent’. The ‘dots’ options will displays dots on screen to show molecules completed. The ‘log’ option will duplicate the log file on screen. The ‘percent’ option will track progress through the input file. [default = none]

Calculation options

-ewindow

Energy window for output conformers. All conformations with energy higher than energy window will be skipped from the molecular output file.

-iteration_cycle_size

Number of iterations to run before checking if a new minimum was found (run will finish if no new minimum is found). [default = 100] [Aliases: -cycle_size]

-max_iterations

Maximum number of iterations (calculation may converge before reaching this number). Each iteration is a single conformation generation which originates from a unique random atoms (or fragments) placement. [default = 2000] [Aliases: -max_iter]

-ref_tolerance

RMS gradient tolerance for force field refinement. [default = 0.001]

-rms

Deduplication threshold. Default value is 0.5 Å.

-maxconfs

Maximum number of conformations to be saved. [default = 400]