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.
This floe is used in the FastROCS Plus with Freeform Analysis tutorial.
Title : FreeForm PoseTags : Large Scale Floes freeform AnalysisPython Name : #07_freeform_pose
- Input Dataset Dataset with poses or conformers to estimate the freeform delta g of. The structure of the outputted molecule will remain unchanged.Type : data_sourceRequired : TruePython Name : input_dataset
- Output Dataset Output dataset with the FreeForm Delta G attached to the molecules conformer data.Type : dataset_outRequired : TrueDefault : FreeForm PosePython Name : output_dataset
- Failure Dataset Dataset for records that failed the FreeForm calculation.Type : dataset_outRequired : TrueDefault : Failed FreeForm PosePython Name : failure_dataset
- Single Conformer/Pose 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 : booleanRequired : FalseDefault : TrueChoices :True, FalsePython Name : single_conformerpose_input
- 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 : decimalRequired : FalseMin Value : 0.0Python Name : absolute_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 : decimalRequired : FalseMin Value : 0.0Python Name : relative_delta_g_limit
- Sort Output Conformers By Delta G If ‘On’ the outputted conformers will be sorted by delta GType : booleanRequired : FalseDefault : FalseChoices :True, FalsePython Name : sort_output_conformers_by_delta_g
These parameters specify the fields on the input datasets and/or collections these floes read data from. Note that parameters identifying a molecule field are special. If left empty the floe will read the molecule from the primary (i.e., default) molecule field on the input record. The primary molecule of a dataset can be identified in the UI by looking for star on its field badge.
- 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 usedType : field_parameter::molRequired : FalsePython Name : input_molecule_field
These parameters allow the user to change the default output fields this floe creates in the output datasets and/or collections. Note that parameters identifying a molecule field are special. If a molecule field is left empty the floe writes the molecule to the primary (i.e., default) molecule field of the record. The primary molecule of a dataset can be identified in the UI by looking for star on its field badge. CAUTION: If these parameters are modified the modifications must also be applied to the input fields of downstream floes that read fields written by this floe. If the downstream floe does not support specifying the input field then they may not work properly with the output of this floe if these settings are modified.
- 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 usedType : field_parameter::molRequired : FalsePython Name : output_molecule_field
- Delta G Field Float field to place the computed FreeForm Delta GType : field_parameter::floatRequired : FalseDefault : FreeForm Pose Delta GPython Name : delta_g_field
- RMSD Field If specified the RMSD of the nearest FreeForm conformer will be attachedType : field_parameter::floatRequired : FalseDefault : FreeForm Pose RMSDPython Name : rmsd_field