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Executing Omega with no arguments will result in:
prompt> omega2
No argument specified on the command line
Required parameters:
-in : Input filename
-out : Output filename
For more help type:
omega2 --help'
A description of the command line interface can be obtained by executing omega with the -help option.
prompt> omega2 --help
will generate the following output:
Help functions: omega2 --help simple : Get a list of simple parameters omega2 --help all : Get a complete list of parameters omega2 --help defaults : List the defaults for all parameters omega2 --help <parameter> : Get detailed help on a parameter omega2 --help html : Create an html help file for this program
If you desire to see all of the command-line options use -help all.
prompt> omega2 --help all
will generate the following output:
Complete parameter list
File Options
-commentEnergy : Writes conformer energies to the comment field
-in : Input filename
-includeInput : Pass the input structure into output (unmodified)
-log : Override prefix used to name output files
-out : Output filename
-param : Omega control parameter file
-pendingFile : Filename used for pending molecules file
-prefix : Prefix to use to name output files
-rotorOffsetCompress : Output compressed OEBinary
-sdEnergy : Writes conformer energies to the SD tag field
-status : Filename used for status report file
-verbose : Triggers copious logging output
-warts : Add conformer number wart to title of multiconformers
3D Construction Parameters
-addfraglib : File(s) containing fragments used for 3D construction, in
addtion to built-in fraglib.
-buildff : Force field to use for initial structure refinement
-canonOrder : Place atoms/bond in canonical order
-deleteFixHydrogens : Deletes hydrogens from fixfile fragment
-dielectric : Dielectric used for electrostatic calculations
-exponent : Exponent used for electrostatic calculations
-fixfile : File used to specify a user defined fragment
-fixrms : RMS used to identify invalid superpositions onto fixfile
template
-fromCT : Generate structures from connection-table only.
-maxmatch : Maximum number of allowed matches of fixfile fragment
-setfraglib : File(s) containing fragments used for 3D construction.
Replaces built-in fraglib
-umatch : Only use unique matches for fixfile fragment replacement
Structure Enumeration
-enumNitrogen : Enumerate pyramidal invertible nitrogen geometries
-enumRing : Enumerate ring conformers
Torsion Driving Parameters
-erange : Energy window values based on number of rotors
-ewindow : Energy window used for conformer selection
-maxConfRange : Maximum number of conformers based on number of rotors
-maxconfgen : Maximum number of conformations to be generated
-maxconfs : Maximum number of conformations to be saved
-maxrot : Maximum number of rotatable bonds in a molecule
-maxtime : Maximum time (s) allowed for torsion search
-rangeIncrement : Size of rotor groupings for range flags
-rms : RMS threshold used to determine duplicate conformations
-rmsrange : RMS threshold values based on number of rotors
-searchff : Force field to use during torsion search
-torlib : Input name of torsion rules file
PVM Parameters
-pvmconf : A text file specifying a PVM configuration
-pvmdebug : Generate an enormous volume of PVM debug information
-pvmlog : Filename used for PVM log file.
-pvmpass : Number of molecules to pass to a slave at one time
-in
-out
Omega can read and write a variety of molecular file formats. The file format is automatically interpreted from the filename suffix.
| File type | Extension |
| SMILES | .smi .ism .can .smi.gz .ism.gz .can.gz |
| SDF | .sdf .mol .sdf.gz .mol.gz |
| SKC | .skc .skc.gz |
| CDK | .cdk .cdk.gz |
| MOL2 | .mol2 .mol2.gz |
| PDB | .pdb .ent .pdb.gz .ent.gz |
| MacroModel | .mmod .mmod.gz |
| OEBinary v2 | .oeb .oeb.gz |
| Old OEBinary | .bin |
Old OEBinary format can be read but not written by Omega.
Gzipped OEBinary version 2 (.oeb.gz) is the recommended output format.
Omega is also capable of piping formatted input and output.
The simple "-" can be used in place of a file name to indicate
std::cin or std::cout with the default SMILES format.
prompt> omega -in - -out -
This execution will run Omega with std::cin as the
input with SMILES format. It will also open std::cout with
SMILES format as output. However, the use of "-" does not allow control of
the file format.
To control the format of std::cin and std::cout one may use
the file extensions without a preceeding filename.
prompt> omega -in .ism -out .oeb.gz
This executes Omega with the input from std::cin formated
in isomeric SMILES and the output sent to std::cout in gzipped OEBinary
version 2 format.
-fraglib-setfraglib)
-addfraglib
-commentEnergy
-param-prefix) with the '.parm' extension.
-prefix-log) flag. [default = omega2].
-rotorOffsetCompress-rotorOffsetCompress flag turned on. [default = true]
-sdEnergy-sdEnergy 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]
-log-verbose) flag. Output can
be directed to the terminal instead of a file by giving a hyphen '-'
as the argument to the flag instead of a filename. Generation of an
output log may be disabled by providing 'nul' or 'null' as an
arguement. [default = prefix.log]
-verbose
-warts
-includeInput
-buildff-fraglib), except in the positioning of protons attached to
ring systems. Consult the description of Force Fields
(Section 3.2) for an explanation of appropriate
arguments for this flag. [default = mmff94s_NoEstat]
-canonOrder-canonOrder flag, however, the resultant ensembles will
likely be inconsistent in their composition. [default = true]
-deleteFixHydrogens
-dielectric
-exponent
where X is the
argument to the -exponent flag). This flag may only be used
with a version of the search force field that includes the coulomb
term, such as the MMFF94 and MMFF94s variants.
[default = 1.0]
-fixfilemaxmatch 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.
-fixrms
-setfraglib
-addfraglib
-fromCT
-maxmatch-maxmatch 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 need to be limited using this parameter for a substructure
where many matcches are possible. [default = 10]
-umatch-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]
-enumNitrogen-enumNitrogen boolean flag controls
the behavior of Omega with respect to enumeration of non-planar
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 of all invertible nitrogens if the
-enumNitrogens flag is set to true. [default = true]
-enumRing-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 false) may therefore be preserved by setting
-enumRing to false as well. [default = true]
-erange-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 comma separated 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 taken as the highest specified
value.
-ewindow-ewindow flag sets the energy window 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]
-maxconfs-maxconfs flag sets the maximum
number of conformations to be generated. Conformers are assembled
in energy sorted order of the contituent fragments. The default
value in most cases will vastly exceed the number of conformers that
need to be generated in order to select the best possible ensembled
based on the RMS distance and energy criteria. 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 = 400]
-maxConfRange-maxConfRange ``100,200'' used with
-rangeIncrement 5 will cause Omega to output 100 conformers
for structures with zero to 4 rotors, and 200 conformers for all
structures with more than 4 rotors.
-maxconfgen-maxconfgen flag controls the
number of fully constructed conformers that Omega will attempt to
build. [default = 50000]
-maxrot-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 bond cutoff. Instead, a desired cutoff
must be supplied by the user. [default = -1]
-maxtime
-rangeIncrement-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-rms flag sets the minimum Root Mean Square
(RMS) cartesian distance below which two conformers are duplicates.
The RMS ccalculation 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 = 0.8]
-rmsrange-rmsrange ``0.8,1.0'' used with
-rangeIncrement 5 will cause Omega to use an RMS cutoff value of 0.8
for structures with zero to 4 rotors, and an RMS cutoff value of 1.0 for all
structures with more than 4 rotatable bonds.
-searchff
-torlib-torlib 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 ( 3.3). If no torsion library is provided then Omega will use
an internally stored copy of the default torsion library.
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