Prepare Giga Collections
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Product-based/FastROCS
Product-based/Gigadock
Role-based/Computational Chemist
Solution-based/Virtual-screening/DB Preparation
Task-based/Library Prep & Design/Conformer Generation
Description
Constructs GigaDocking and FastROCS collections from input files or collections.
This floe filters the input molecules and generates conformers for the Gigadock and FastROCS collections, with a maximum of 200 and 10 conformers per molecule, respectively. The filtering is configurable (see the ‘Filtering: Basic Properties’, ‘Filtering: SMARTS’ and ‘Filtering: OEFilter’ parameter groups). Use the Dry Run switch to examine, at negligible cost, the contents of the input files (see the Floe Report) and see how many molecules pass each filter (examine the port counts) without generating conformers or creating any collections.
The input molecules are expected to come from a collection outputted by one of the generative design floes, or more commonly an input file. Supported file formats are: can, can.gz, csv, csv.bz2, csv.gz, cxsmiles, cxsmiles.gz, ism, ism.gz, isosmi, isosmi.gz, mol2, mol2.gz, oeb, oeb.gz, oedb, oez, sd, sd.gz, sdf, sdf.gz, smi, smi.gz, syb, syb.gz, tar, tar.bz2, tar.gz, tgz, tsv, tsv.bz2, tsv.gz, usm, usm.gz, zip. Comma- and tab-separated files (i.e., .csv and .tsv) are expected to have SMILES representations of molecules in one of the columns. For archive formats (e.g., .tar and .zip), this floe will read molecules from files in the archive that are of a supported format.
IMPORTANT: For comma and tab separated files (i.e., .csv and .tsv), this floe cannot automatically identify molecule titles from the file, and will by default create molecules with no titles that will be filtered out (i.e., the floe will read in no molecules). When working with CSV/TSV input files you should run the floe once with ‘Options -> Dry Run’ and ‘Options -> Allow Empty Titles’ both on. A floe report will be created where you can examine the column/field titles in the CSV/TSV file. In subsequent runs, you can then specify the column/field you want to use (must be a string field) as the molecule title using the ‘Format Specific Settings -> Mol Title Field’ parameters. If the file doesn’t have any appropriate title columns/fields, you can leave ‘Options -> Allow Empty Titles’ in subsequent runs.
Disk Space Considerations: With file input, there is a limitation on the size of the file. The disk space available for a file is specified by the ‘Hardware->Disk Space’ parameter. For non-archive files, this is that maximum size input file. For archive files (e.g., tar and zip), each file is extracted from the archive processed and then cleaned up before extracting and processing the next file in the archive. The disk space required is thus the size of the archive file plus the size of the largest single file in the archive when it is extracted from the archive.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Input File(s) (input_file): One or more input files to convert into docking and FastROCS collections.
Type: file_in
Inputs : Alternate
Input Dataset(s) (input_datasets): One or more input datasets to convert into Gigadock and FastROCS collections.
Type: data_source
Input Collection(s) (input_collection): One of more input collections to convert into docking and FastROCS collections. These collections are expected to be from the output of the reaction enumeration floes.
Type: collection_source
Outputs
Giga Docking Collection Name (docked_collection_name): Name of the collection to create
Required
Type: collection_sink
Default: GigaDock Collection
FastROCS Collection Name (rocs_collection_name): Name of the collection to create
Required
Type: collection_sink
Default: FastROCS Collection
Temporary Collection Name (temp_collection_name): This collection is used to store temporary data during the run of the floe and is automatically deleted when the floe completes. If you cancel the floe, you should delete the collection manually.
Required
Type: collection_sink
Default: Prepare Giga Collections Temporary Collection
Options
Dry Run (dry_run_switch): If On, molecules will be read and passed through the filtering cubes normally but will not be passed to the Omega conformer generation and collection creation cubes. This makes the floe very inexpensive to run, however, no output collections will be generated. With this switch On, you can see how many molecules will be read from your input files/collections and how many will pass the filters (examine the filtering cube port counts) that have been configured, and make adjustments without incurring significant expense. Once the best filtering settings are determined, you can run the floe with those settings and this option turned Off to generate the collections.
Required
Type: boolean
Default: False
Choices: [True, False]
Allow Empty Titles (allow_no_title_switch): If On, molecules without titles will be allowed. If Off, molecules without titles will be filtered out. If your input is a comma- or tab-separated file, you can use the ‘Format Specific Settings -> Mol Title Field’ parameter to set the molecule title to a specific string column in the comma- or tab-separated file.
Required
Type: boolean
Default: False
Choices: [True, False]
Keep this fraction (random_retain_probability): Parameter to create collections that contain a random subset of the input molecule when set to less than the default value of 1. This parameter is the fraction of the input molecules that will be retained using a random selection criterion.
Required
Type: decimal
Default: 1.0
pKa
Set Neutral pH on input molecules (set_neutral_ph_on_input_molecules): If turned Off, a neutral pH 7.4 pKa state will not be set on the input molecules. This option should only be turned off if you are certain your input molecule has a correct pKa state set.
Required
Type: boolean
Default: True
Choices: [True, False]
Filtering : Basic Properties
Max molecular weight (mw_max): Molecules with molecular weight greater than this value will be filtered out. If unspecified this cube will not filter out molecules with high molecular weight.
Type: decimal
Default: 500.0
Min molecular weight (mw_min): Molecules with molecular weight less than this value will be filtered out. If unspecified this cube will not filter out molecules with low molecular weight.
Type: decimal
Max rotatable bond count (rot_bond_max): Molecules with rotatable bond count greater than this value will be filtered out. If unspecified this cube will not filter out molecules with high rotatable bond count.
Type: integer
Default: 15
Min rotatable bond count (rot_bond_min): Molecules with rotatable bond count less than this value will be filtered out. If unspecified this cube will not filter out molecules with low rotatable bond count.
Type: integer
Max count undefined atom stereo (atom_stereo_max): Molecules with count undefined atom stereo greater than this value will be filtered out. If unspecified this cube will not filter out molecules with high count undefined atom stereo.
Type: integer
Default: 3
Max count undefined bond stereo (bond_stereo_max): Molecules with count undefined bond stereo greater than this value will be filtered out. If unspecified this cube will not filter out molecules with high count undefined bond stereo.
Type: integer
Default: 3
Max acceptor count (acc_max): Molecules with acceptor count greater than this value will be filtered out. If unspecified this cube will not filter out molecules with high acceptor count.
Type: integer
Min acceptor count (acc_min): Molecules with acceptor count less than this value will be filtered out. If unspecified this cube will not filter out molecules with low acceptor count.
Type: integer
Max donor count (don_max): Molecules with donor count greater than this value will be filtered out. If unspecified this cube will not filter out molecules with high donor count.
Type: integer
Min donor count (don_min): Molecules with donor count less than this value will be filtered out. If unspecified this cube will not filter out molecules with low donor count.
Type: integer
Max topological polar surface area (tpsa_max): Molecules with topological polar surface area greater than this value will be filtered out. If unspecified this cube will not filter out molecules with high topological polar surface area.
Type: decimal
Min topological polar surface area (tpsa_min): Molecules with topological polar surface area less than this value will be filtered out. If unspecified this cube will not filter out molecules with low topological polar surface area.
Type: decimal
Max xlogp (xlogp_max): Molecules with xlogp greater than this value will be filtered out. If unspecified this cube will not filter out molecules with high xlogp.
Type: decimal
Min xlogp (xlogp_min): Molecules with xlogp less than this value will be filtered out. If unspecified this cube will not filter out molecules with low xlogp.
Type: decimal
Max formal charge (charge_max): Molecules with formal charge greater than this value will be filtered out. If unspecified this cube will not filter out molecules with high formal charge.
Type: integer
Min formal charge (charge_min): Molecules with formal charge less than this value will be filtered out. If unspecified this cube will not filter out molecules with low formal charge.
Type: integer
Max aromatic ring count (aro_max): Molecules with aromatic ring count greater than this value will be filtered out. If unspecified this cube will not filter out molecules with high aromatic ring count.
Type: integer
Min aromatic ring count (aro_min): Molecules with aromatic ring count less than this value will be filtered out. If unspecified this cube will not filter out molecules with low aromatic ring count.
Type: integer
Filtering: SMARTS
Required SMARTS (required_smarts): If one or more SMARTS patterns are supplied to this parameter then every molecule passed to this cube must match one of these smarts patterns of it will be filtered. This check is skipped if no SMARTS patterns are supplied to this cube.
Type: string
Excluded SMARTS (excluded_smarts): Every molecule that matched any of the SMARTS patterns supplied to this parameter will be filtered.
Type: string
Filtering: OEFilter
OEFilter Type (oefilter_type):
Required
Type: string
Default: BlockBuster
Choices: [‘BlockBuster’, ‘Lead’, ‘Drug’, ‘PAINS’, ‘None’]
Filter Rules (filter_in): Optional rules to create an OEFilter (see https://docs.eyesopen.com/toolkits/python/molproptk/filter_files.html).
Type: file_in
Filtering: 2D Similarity to Known Molecules
Known Molecules (known_molecules): If this parameter is specified, each molecule being prepared will be assigned a single 2D Tanimoto value equal to the highest 2D Tanimoto of any molecule in this dataset. The prepared molecule will then be filtered by comparing this value to the setting of the ‘Filter Out Tanimotos Higher Than’ and/or ‘Filter Out Tanimotos Lower Than’ parameters. WARNING: A significant filtering compute cost can be incurred, even in ‘Dry Run’ mode, if a large number of molecules are passed to this parameter (For a 1 billion molecule collection and 10 K known molecules, the filtering portion of the cost is typically about $20).
Type: data_source
Filter Out Tanimotos Higher Than (filter_out_tanimotos_higher_than): If specified, molecules with a 2D Tanimoto higher that this value will be filtered out. Use this parameter if you want to remove molecules that are similar in 2D space to any of the known molecules.
Type: decimal
Filter Out Tanimotos Lower Than (filter_out_tanimotos_lower_than): If specified, molecules with a 2D Tanimoto lower than this value will be filtered out. Use this parameter if you want to remove molecules are different in 2D space to any of the known molecules.
Type: decimal
Known Molecules 2D Fingerprint Method (known_molecules_2d_fingerprint_method): The 2D fingerprint method used to compute the Tanimotos for the known molecules filter.
Type: string
Default: Circular
Choices: [‘Circular’, ‘Path’, ‘Tree’]
Use Virtual Screening 2D Fingerprint Variant (use_virtual_screening_2d_fingerprint_variant): If On, the virtual screening variant of the selected 2D fingerprint will be used for the known molecule’s filter. The virtual screening variant treats certain functional groups identically regardless of their pKa state, such as protonated and unprotonated carboxylic acids.
Type: boolean
Default: True
Choices: [True, False]
Known Molecule Tanimoto Field (known_molecule_tanimoto_field): If this parameter is specified, the 2D Tanimoto used for known molecule filtering for each processed molecule will be placed in the output collections in a field of this name. If unspecified, the Tanimoto value will not be stored in the output collections.
Type: field_parameter::float
Maximum Number of Filtering Cubes (maximum_number_of_filtering_cubes): Maximum number of cubes to use for filtering. Increasing this value can improve the runtime in cases where a large number of known molecules are supplied. This value can only be set above the default value of 500 if the number of molecules passed to ‘Filtering: 2D Similarity To Known Molecules -> Known Molecules’ times the setting of ‘Options->Keep This Fraction’ is greater than 10,000.
Type: integer
Default: 500
Stereo Enumeration
Enantiomer Title Field (enantiomer_title_field): This string field will be added to the created collection and contains the title of the input molecule appended by and index number to identify the enantiomer. If unspecified, the field will not be created.
Type: field_parameter::string
Default: Enantiomer Title
Conformer Generation Settings
Use GPU Omega (omega_switch): If this value is set to True, this floe will use the GPU version of Omega. The GPU version of Omega (with this parameter set to True) is typically ~40% more cost efficient than the CPU version (with this parameter set to False). However, the AWS spot instances GPU that Omega requires have been in very high demand on AWS, and running this floe in a high demand period with this flag set to True can result in very long run times and less cost efficiency.
Required
Type: boolean
Default: False
Choices: [True, False]
Torsion Library Type (torsion_library_type): Type of torsion library Omega will use. If Custom is selected, then a torsion library must be supplied to the ‘Conformer Generation Settings -> Torsion Library’ parameter.
Type: string
Default: Original
Choices: [‘Original’, ‘Guba’, ‘Custom’]
Torsion Library (torlib_in): Optional torsion library for Omega. (see https://docs.eyesopen.com/toolkits/python/omegatk/OEConfGenClasses/OETorLib.html ). These torsion rules will be added to the selected torsion library. Select Custom for ‘Torsion Library Type’ if you want to replace rather than add rules.
Type: file_in
GPU Omega Input Shard Size (gpu_omega_input_shard_size): This parameter controls how many molecule must be processed within the Orion 12 hour limit when ‘Use GPU Omega’ is On. With lower values, the conformer generation will not be as cost efficient. In general, there is no need to adjust this parameter unless instructed to do so by OpenEye Support.
Required
Type: integer
Default: 10000
CPU Omega Input Shard Size (cpu_omega_input_shard_size): This parameter controls how many molecules must be processed within the Orion 12 hour limit when ‘Use GPU Omega’ is Off. With lower values, the conformer generation will not be as cost efficient. In general, there is no need to adjust this parameter unless instructed to do so by OpenEye Support.
Required
Type: integer
Default: 5000
Format Specific Settings
Additional CSV Extension (additional_csv_extension): Additional file extensions that will be recognized as comma separated valuesfiles. Do not include the ‘.’ in the extensions. Gzip and Bzip2 variants will also automatically be supported.If a built in extension is specified this format specification willoverride it. The primary purpose of this parameter is to enable specifying formats of files within archives (e.g., tar or zip) which cannot easily be renamed.
Type: string
Additional TSV Extension (additional_tsv_extension): Additional file extensions that will be recognized as tab separated valuesfiles. Do not include the ‘.’ in the extensions. Gzip and Bzip2 variants will also automatically be supported.If a built in extension is specified this format specification willoverride it. The primary purpose of this parameter is to enable specifying formats of files within archives (e.g., tar or zip) which cannot easily be renamed.
Type: string
Additional SMILES Extension (additional_smiles_extension): Additional file extensions that will be recognized as SMILESfiles. Do not include the ‘.’ in the extensions. Gzip and Bzip2 variants will also automatically be supported.If a built in extension is specified this format specification willoverride it. The primary purpose of this parameter is to enable specifying formats of files within archives (e.g., tar or zip) which cannot easily be renamed.
Type: string
Mol Title Field (sv_title_field): When reading tab- or comma-separated files, this parameter specifies the column that should be used as the molecule’s title. When reading tab- or comma-separated files, either this parameter must be set to Off, or ‘Options->Allow Empty Titles’ must be set to On (this is not recommended as the molecules will have no titles). This parameter is ignored if the file being read is not a tab- or comma-separated file.
Type: string
Molecule Field Name for TSV/CSV (molecule_field_name_for_tsvcsv): This parameter specifies the name field the molecule will be stored in. If no value is specified for this parameter, the name will the the column header name from the original CSV/TSV file.
Type: string
Default: Molecule
GPU Hardware
GPU Omega Instance Type (gpu_omega_instance_type): These parameters control the AWS instance type the GPU Omega Cube will use. If specified, the AWS instances specified must have at least 16 CPUs per GPU. There is in general no reason to adjust this unless instructed by OpenEye support.
Type: string
Default: !g4dn.12xlarge,!g5.12xlarge,!g6.12xlarge,!g6e.12xlarge
GPU Omega Max Parallel (gpu_omega_max_parallel): Maximum number of instances the GPU Omega conformer generation will use.
Type: integer
Default: 2000
Hardware
Disk Space (read_disk_space): Disk space in MB for the cube reading the input files. The default value should be sufficient, but if you have a single huge file you may need to increase this value.
Type: decimal
Default: 102400
Input Fields
Known Molecule Field (known_molecule_field): Field on the known molecule’s dataset holding the known molecules. If unspecified, the default primary molecule on the record will be used.
Type: field_parameter::mol
Input Dataset Molecule Field (input_dataset_molecule_field): Field on the input datasets containing the field with molecules to prepare. If unspecified, the primary molecule field will be used.
Type: field_parameter::mol