OMEGA - 3D Conformer Ensemble Generation¶
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Product-based/OMEGA
Role-based/Computational Chemist
Task-based/Library Prep & Design/Conformer Generation
Solution-based/Small Molecule Lead-opt/Conformer Sampling
Description
OMEGA - 3D Conformer Ensemble Generation generates 3D conformations of molecules. OMEGA uses a torsion driving method for conformer generation, which works best on molecules that do NOT contain large, flexible rings (i.e., macrocycles). As such, OMEGA rejects macrocycle molecules to the failure port.
OMEGA can be used using various pre-set modes that generate conformers suitable for different downstream applications. The minimal input into OMEGA is a dataset of molecules in 1D (SMILES), 2D (SD, mol2) or 3D format.
Along with the generated 3D multi-conformer molecule, the other output from the OMEGA floe is an optionally generated interactive report of the torsional profile of each ensemble.
Promoted Parameters
Title in user interface (promoted name)
OMEGA basic settings
Conformer generation mode (mode): Pre-set mode for generating conformers suitable for specific downstream application
Type: string
Default: Classic
Choices: [‘Classic’, ‘ROCS’, ‘Pose’]
Stereo Behavior (stereo_flag): Specify if stereo centers should be enumerated or randomly chosen, for molecules with unspecified stereo-chemistry.
Type: string
Default: Random
Choices: [‘Enumeration’, ‘Random’]
Maximum number of conformers (max_confs): (Optional) Maximum number of conformations to generate. If provided, this will override the default maximum number of conformers for the selected mode, which is 200 for ‘Classic’, 50 for ‘ROCS’, and 800 for ‘Pose’
Type: integer
Generate Torsion Depictions (make_depictions): Whether or not to generate torsion depiction for each conformational ensemble
Required
Type: boolean
Default: False
Choices: [True, False]
OMEGA advanced settings
Energy Window (ewindow): Energy window for conformer selection.
Type: decimal
Default: 10.0
RMS Threshold (rms): RMS threshold for duplicate conformer removal
Type: decimal
Default: 0.5
Clear Fragments Library (clear_frag_lib): Flag indicating if internal fragments library should not be used
Type: boolean
Default: False
Choices: [True, False]
Fragments library file (in_frag_file_field):
Type: file_in
Torsion Library Type (torlib_type): Specify the type of torsion library.
Type: string
Default: Original
Choices: [‘Original’, ‘Guba’]
Normalize pKa switch (pka_norm_switch): Whether or not to modify molecule to the most energetically favorable ionization state for pH=7.4
Required
Type: boolean
Default: False
Choices: [True, False]
Initial Builder settings
Enumerate Nitrogen (enum_nitrogen): If conformers should be enumerated for invertible Nitrogen stereo
Type: string
Default: unspecified
Choices: [‘unspecified’, ‘all’, ‘off’]
Ignore Stereo (ignore_stereo): If failure to respect stereo should be ignored
Type: boolean
Default: False
Choices: [True, False]
Sample Hydrogen (sample_hydrogen): If hydrogen sampling should be done on conformers
Type: boolean
Default: False
Choices: [True, False]
Fix related settings
Fix Molecule (fix_mol_in): (Optional) Dataset containing a molecule to specify the coordinates for a substructure of the input molecules. The floe will fail if multiple molecules are supplied.
Type: data_source
Fix Smarts (fix_smarts): (Optional) Set a string for SMARTS pattern matching to fix a portion of the fix molecule primarily or the input molecule secondarily. Molecules that do not match will be sent to the fail output. When the fix molecule is not provided, the input molecule has to be 3D and Stereo Behavior has to be Random.
Type: string
Default:
Fix MCS (fix_mcs): If MCS should be used to fix part of molecule
Type: boolean
Default: False
Choices: [True, False]