FreeForm Pose

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/Analysis

  • Task-based/Ligand Posing & Analysis

  • Product-based/SZYBKI

Description

Computes the FreeForm delta G of the conformers of the molecule sent to the cube. The floe does not change the input conformers.

The delta G is computed by running FreeForm on a copy of the input molecule and then assigning the delta G of each input conformer to be the delta G of the freeform conformation with the closest RMSD. The energy and RMSD are attached as conformer data in the output record, and additionally lowest delta G of any input conformer is attached directly to the output record.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input Dataset (input_dataset): Dataset with poses or conformers to estimate the freeform delta g of. The structure of the outputted molecule will remain unchanged.

  • Required

  • Type: data_source

Outputs

Output Dataset (output_dataset): Output dataset with the FreeForm Delta G attached to the molecules conformer data.

  • Required

  • Type: dataset_out

  • Default: FreeForm Pose

Failure Dataset (failure_dataset): Dataset for records that failed the FreeForm calculation.

  • Required

  • Type: dataset_out

  • Default: Failed FreeForm Pose

Options

Single Conformer/Pose Input (single_conformerpose_input): Set this to ‘Off’ if the input molecule(s) each have multiple conformers/poses, and ‘On’ if all the input molecules have a single conformer/pose. If ‘On’ the floe will assumed that the input molecules are single conformer/pose and place the calculated FreeForm data on the top level records directly, rather than in child conformer records. If ‘Off’ the floe assume the input molecules are multi-conformer/pose and place the result for each conformer/pose on the corresponding child conformer records. If multi conformer molecules are passed to this floe with this option ‘On’ the floe will use the active conformer of the molecule and place the result on the top level records.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Absolute Delta G Limit (absolute_delta_g_limit): If specified conformers with a delta G value greater than this value will be removed from the output molecules. If all poses of a molecule are removed in this fashion record with the molecule will not be outputted.

  • Type: decimal

Relative Delta G Limit (relative_delta_g_limit): If specified conformers with a delta G value greater than this value plus the lowest delta G of any conformer will be removed from the output molecules. If all poses of a molecule are removed in this fashion record with the molecule will not be outputted.

  • Type: decimal

Sort Output Conformers By Delta G (sort_output_conformers_by_delta_g): If ‘On’ the outputted conformers will be sorted by delta G

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Input Fields

Input Molecule Field (input_molecule_field): Field on the input records to use in the FreeForm calculation. If not specified the primary (i.e., default) molecule field will be used

  • Type: field_parameter::mol

Output Fields

Output Molecule Field (output_molecule_field): Field on the output records the molecule with FreeForm conformer data will be placed. If not specified the primary (i.e., default) molecule field will be used

  • Type: field_parameter::mol

Delta G Field (delta_g_field): Float field to place the computed FreeForm Delta G

  • Type: field_parameter::float

  • Default: FreeForm Pose Delta G

RMSD Field (rmsd_field): If specified the RMSD of the nearest FreeForm conformer will be attached

  • Type: field_parameter::float

  • Default: FreeForm Pose RMSD

Development

Enable cube timing report (time_all_cubes): If true this cube will emit timing information to the timing_data port.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Catch exceptions (catch_exceptions): If Off exception handling will be disabled for this cube.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Catch exceptions (parallel_catch_exception_methods): Specifies which methods of a parallel cube an exception will be caught and emitted to the exception port if the port is connected. If the exception port is connected to an exception handler this will stop the floe

  • Type: string

  • Default: [‘begin’]

  • Choices: [‘begin’, ‘process’, ‘end’]