Release Notes¶

v0.19.1 August 2020¶

Upgrades to OpenEye-orionplatform==3.0.0 the associated OpenEye Toolkits

New Cubes¶

New Spruce depiction cube which generates multiple interactive depictions of the design unit. The depictions are target-ligand interactions, b-factor visualization, 3) Iridium data visualization, and if electron density data is available, 4) ligand density coverage.
New DesignUnit Type ETL. OEDesignUnit have gotten native support in datarecord as Types.Chem.DesignUnit. This cube converts fields with the old design unit blob type and adds a new field with the native type. For backwards compatibility it currently preserves the existing field.
New Named Dataset Reader, Named File Reader, and Named Collection Reader read dataset, file and collection specified by their names. They allow floe developers to permenently customize their floes to utilize a specific resource.
New Calculate RMSD performs RMSD calculation between a 3D reference molecule and multi-conformation molecules.
New Find ShapeQuery identifies shape query in a record. If a shape query is not found, the cube looks for the primary molecule and creates a shape query from that molecule.
New Convert Shape Query to Record reads a shape query file (.sq) and converts the shape query to a record.
New Single File Reader reads a single file and emits its contents in a stream. It will throw a runtime error if two or more files are used as input.
New Record Splitting By Charges splits records into two streams by whether the molecule is charged.

Cube Updates¶

The Tautomer Enumeration was updated to expose more tautomer options. The enumerated tautomers are now also set to the primary molecule on the output record.
The Merging Conformers was updated to handle missing children failures without raising exceptions.
The Spruce Prep has been updated to incorporate changes in the recently release Spruce Toolkit, as well as added support for loop modeling, which is on by default. Loop modeling can add considerable time.
The Find Protein has been modified so the user optionally can specify, the molecule field to use. If the protein is extracted from a design unit, the user now has the option to get other components of the system along with the protein, e.g. cofactors and/or solvent. The cube now also does a minimal check that the molecule extracted is a protein, based on number of standard protein residues. The logic has changed such that the molecule of interest, is emitted on a new record with the molecule as the primary molecule.
The Find Ligand has been modified so the user optionally can specify, the molecule field to use. The logic has changed such that the molecule of interest, is emitted on a new record with the molecule as the primary molecule.
The Activesite Ligand Minimization and Ligand Minimization no longer throw fatal errors when PB solvent mode is set to PB.
The Convert Conformers to Mols output records that no longer contain all conformer records.
The Assign am1bcc partial charges now generates correct charges.
The Brood Report Cube has been improved to align depictions of hits with the non-changing part of the BROOD query.
The Omega Conformation now supports fix molecule and fix smarts to fix an portion of the input molecule.
Support of Open FF 1.0 has been added to the following cubes. PARSLEY_OPENFF100, PARSLEY_OPENFF111 and PARSLEY_OPENFF120 are added as predefined choices, and an .offxml file that defines a SMIRNOFF force field can also be used as input.
The ROCS, SubROCS, and Best Overlay Transform now take a record of shape query from init port. In order to use a molecule as query, Find ShapeQuery can be used to create a shape query from the molecule.
The Record Splitting By Conformers and Record Splitting By Initializer Conformers have been updated to handle shape query in addition to molecule.

Removed Cubes¶

Removed DUFileToRecords cube which is no longer needed as Orion will automatically, upload and ETL an OEDU file to a record.

v0.18.2 April 2020¶

General Notice¶

Upgrades to OpenEye-orionplatform==2.4.5

New Cubes¶

New Record Counter Switch added that can switch floe path based on the number of records in the initializer port.
New Rotate Surface rotates a surface by a 3x3 matrix specified as a 9-element array in row-major order.
New Transform Surface transforms a surface using a supplied OETrans object.
New Translate Surface translates the surface using the supplied 3-element translation vector.
New cube_OptionalDatasetReaderCube to allow a user to pass an optional reference design unit to use when preparing new structures in Spruce.
New Input PDB/MMCIF/MTZ files, which is a re-work of the older and removed PDBFileToInputRecord. This cube takes a set of input PDB files, optional MTZ files, and optional metadata JSON files and pairs them up as input records for Spruce structure preparation.
New Input PDB codes, which is a re-work of the older and removed PDBCodeToInputRecords. This cube downloads PDB (fall-back to MMCIF) files and any associated MTZ files and puts them into records for Spruce structure preparation.
New Molecule Filtering cube has been added that filters molecules based on a user-defined filter type.
New Uncolor Molecule Graph cube has been added that uncolors molecular graphs i.e. removes certain atom and bond properties.
New Random N Record Selection cube has been added that randomly selects N records.
New Concatenate Records cube has been added that concatenates datasets.
New Classification Based on String Field cube has been added that allows classification of records based an a specified string field.
New String Fields Comparison to Sets of Strings cube has been added that filters out records based on the string data of reference records.

The following cubes have been added to mimic some of the stages of biomolecule preparation being done automatically in Spruce. They all, except the Spruce BioUnit Extract, take a dataset with designunits as input. The editing cubes updates the design units on the record. To be able to use them for downstream cubes or floes, after editing, the design units on the records must be converted to molecules or receptors (see conversion cubes section following this section).

New Spruce BioUnit Extract, which generates biological units from an input asymmetric unit crystal structure.
New Spruce sidechain builder cube, takes a dataset of designunits and builds out partial or missing sidechains.
New Spruce capping cube, takes a dataset of designunits and caps any chain breaks.
New Spruce swamp metal cube, takes a dataset of designunits and converts specified metals, e.g. Zn to Mg.
New Spruce mutation cube, takes a dataset of designunits and attempts to mutate specified residues.
New Spruce residue state cube, takes a dataset of designunits and changes the state of specified titratable residues.
New Spruce rotamers cube, takes a dataset of designunits and returns multiple records per design unit each with different rotamers of a specified residue (non-clashing is default, but optional).
New Spruce subset cube, takes a dataset of designunits and subsets them based on inputs, to remove entire design unit components or remove pieces specified by residue identifiers.
New Spruce subset within cube, takes a dataset of designunits and subsets a component of each design unit, e.g. subset the solvent to include only those within 5A of the protein and ligand components.
New Spruce Superpose, takes a dataset with a reference design unit and a dataset of designunits, and superposes each design unit in the dataset to the reference. Several superposition methods are available.
New Spruce minimize designunit cube, takes a dataset of designunits and minimizes parts of the designunits based on input parameters.

The following cubes have been added that convert design units to molecules or receptors, for use in subsequent cubes or floes.

New Spruce DU to Mol, which converts the design unit to a molecule and optionally splits out the ligand to a separate field. All the content in the design unit is output to the molecule, if less is required, first subset the design unit with the cubes: Spruce subset cube or Spruce subset within cube.
New Spruce DU to Receptor, is a cube split out from the old DUtoReceptorMDRecord, to split the two operations therein. This cube takes a DU and writes a receptor for use in docking.
New DU to MD Ready Record, is a cube split out from the old DUtoReceptorMDRecord, to split the two operations therein. This cube takes a DU and writes an complex (not including the ligand), that can be used in MD floes, e.g. Short Trajectory MD floes.

Cube Updates¶

The cube_DUFileToRecords, has been updated to take multiple input files.
The Spruce Prep, has been updated, to take an optional reference design unit using the initializer port, additional options for preparation have been exposed, and several of the input parameters have been updated to make parameter selection easier.
The MDL Substructure Map now emits unmatched molecules through the failure port.
The Exhaustive Docking (Single Receptor) now exits properly when initialization fails.
The Torsion Scan now has a torsion increment option to change the resolution of the torsion drive. It also fails more gracefully when coordinates cannot be generated or the torsion cannot be identified.
The Splitting Conformers now has the option to move conformer fields to the primary record after splitting.
The Prepare Molecule for 2D Depiction cube now can keep the coordinates of the primary molecule and store the 2D coordinates in a new field specified by a new string parameter.
The following changes have been made for the Move Field cube:
- It now handles cases when the specified field does not exist on the record.
- A new parameter has been added that allows to move records with missing field to the success port.
- A fatal port has been added in order to handle cases when no field was renamed in any of the records.
The following changes have been made for the Structure to SMILES cube:
- Meta.Hints.Chem.SMILES meta data is added to the SMILES field
- It re-perceives all necessary perception upon request.
- It noew generates the following SMILES: non-canonical, non-isomeric-canonical, and isomeric-canonical (default)

Removed Cubes¶

Removed DUtoTgtLigRecords cube which was unused.
The following cubes have been removed and replaced with the new Input PDB codes: GetPDBplusMap, PDBCodeToUrl, UrlToFile, PDBCodeToInputRecord, MultiplePDBCodesToInputRecord.
The following cubes have been removed and replaced with the new Input PDB codes: PDBFileToInputRecord, InputRecordtoDataset.
The following cubes have been removed and replaced with new Spruce DU to Receptor and new DU to MD Ready Record: DUtoReceptorMDRecord, ReceptorMDRecordToDataset, DUtoReceptorMDDataset.

v0.17.2 November 2019¶

General Notice¶

Upgrades to OpenEye-orionplatform==2.2.0
Upgrades to 2019.Oct release of the OpenEye Toolkits

New Cubes¶

New Ligand Energy to combine functionality of the GasPhaseLigandEnergyCube, SheffieldLigandEnergyCube and the PBLigandEnergyCube.
New Ligand Minimization to combine functionality of the GasPhaseLigandMinimizeCube, SheffieldLigandMinimizeCube and the PBLigandMinimizeCube.
New Ligand Restrained Minimization to perform free ligand minimization with an additional harmonic potential restraint on ligand atoms
New Activesite Ligand Restrained Minimization to perform activesite ligand minimization with an additional harmonic potential restraint on ligand atoms
New Ligand Hydrogen Optimization to adjust ligand hydrogen coordinates, while keeping the position of the heavy atoms fixed.
New Find Protein to be able to obtain protein from either a molecule dataset or a design units dataset.
New Find Ligand to be able to obtain ligand molecule from either a molecule dataset or a design units dataset.
New Gameplan Depiction to be able to generate 2D depictions of Gameplan results.
New Gameplan Report Cube.
New Record Splitting By Conformers to be able to sort out single and multi conformer molecule records.
New Record Splitting By Initializer Conformers to be able to redirect records through separate paths based on an initializer molecule record containing a single and multi conformer molecule record.
New 2D Fragment Picker to be able to select a fragment from a 2D sketched molecule.
New 2D Torsion Picker to be able to select a torsion fragment from a 2D sketched molecule.
New MDL Query Editor to be able to sketch an MDL query.
New Brood Fragment Selector to be able to select a Brood fragment in a molecule.
New MDL Substructure Map to be able to find substructures against MDL query.
New Brood Query to build Brood Query from molecule with selected fragment.
New Brood Report Cube to generate a report of successful Brood calculation.

Cube Updates¶

Activesite Ligand Energy have been enriched with the following functionality:
- Ability to optimize in PB solvent. Accordingly, PBProteinLigandEnergyCube has been removed.
- Options for multiple force field choices
- Improved validation and error handling, including the addition of a fatal port for fatal errors.
Activesite Ligand Minimization have been enriched with the following functionality:
- Ability to optimize in PB solvent. Accordingly, PBProteinLigandMinimizeCube has been removed.
- Options for multiple force field choices
- Improved validation and error handling, including the addition of a fatal port for fatal errors.
Ligand Torsions Minimization has been enriched with following functionality:
- Options for multiple force field choices
- Additional flag to turn on/off optimization, to allow single point energy calculation.
- Improved validation and error handling, including the addition of a fatal port for fatal errors.
EON Score has been enriched with following functionality:
- Ability to calculate EON tanimoto combo.
- Sort the input conformers based on tanimoto combo, and return only the highest scoring conformer.
- Improved validation and error handling, including the addition of a fatal port for fatal errors.
Szybki Ligand Prep has been enriched with ability to choose a partial charge model, as well as with improved validation and error handling.
Zap Ligand Prep has been modified to always assign MMFF94 charges, as well as with improved validation and error handling.
ROCS for EON has been modified to restrict its scope to a single conformer query molecule as well as with improved validation and error handling, including the addition of a fatal port for fatal errors.
Posit has been modified to use the capabilities of the newly modified Posit toolkit.
Omega Macrocycle has been re-implemented with the toolkit functionality, and accordingly snowball no longer depends on the Omega App.
To improve usability, cubes Freeform Conf Restriction Energies and Freeform Ligand Strain have been modified to emit restriction energies as separate records through a different port compared to the free energies records.
The following cubes have been modified to improve error handling:
The following cubes have been modified to correct functionality issues:
The following OMEGA cubes have been modified to turn on canonical ordering of atoms by default:
The following cubes have been removed due to their suboptimal usability
- GasPhaseLigandEnergyCube
- SheffieldLigandEnergyCube
- PBLigandEnergyCube
- GasPhaseLigandMinimizeCube
- SheffieldLigandMinimizeCube
- PBLigandMinimizeCube
- PBProteinLigandEnergyCube
- PBProteinLigandMinimizeCube
- ActiveSiteRstrLigandMinimizeCube
- ActiveSiteRigidLigandMinimizeCube
- ActiveSiteFlexLigandMinimizeCube
- FlexProteinDistLigandMinimizeCube
- SingleReceptorPositCube
- FreeformEneStrainCube

v0.16.6 September 2019¶

General Notice¶

Upgrades to OpenEye-orionplatform==1.1.4
Upgrades to OpenEye-floereport==0.1.5
Static variables are no longer used, other than as the parameter variables.

New Cubes¶

New Flipper to either enumerate stereo or not.
New Omega Conformation (Modes) to run omega in predefined mode.
New Floe Failure Report that can produce a report of log information from failed records.
New Exception Handler to handle exceptions from downstream cubes and stop a flow.
New Success Counter to count pass-through records and report floe failure when connected properly to an Exception Handler.
New Find Receptor to find receptors in a record.
New Add Query Style to add viewing style to a query molecule.

Cube Updates¶

The following cubes have been enriched by addition of a fatal port. Any failure during initialization is reported by emitting a record containing failure log information through the fatal port.
- ROCS
- SubROCS
- Best Overlay Transform
- ROCS with Multi-conformer Query
- ROCS with Grid Query
- Exhaustive Docking (Single Receptor)
- SingleReceptorPositCube
- OEStructureBasedLigandDesignCube
The following cubes has an additional flag that allows to control the amount of output results to be produced.
Removed mode option from Omega Conformation, to simplify it as a customizable cube.
OEStructureBasedLigandDesignCube and SingleReceptorPositCube now properly reports the output receptor and the bound ligand.
Conformer Integer Hit List, Conformer Float Hit List, and Conformer String Hit List now works on the molecule record field if molecule has a single conformer and the conformer record does not contain the suggested field value.
DUtoReceptorMDDataset now has a new MD component mask and produces robust datasets for MD applications. Also, a small modification was made in how receptors are stored on the output dataset so that grids and other receptor-specific information can be displayed in the 3D window.
EStructureBasedLigandDesignCube and SingleReceptorPositCube now generate a single pose when relaxation is turned off.

v0.16.0 July 2019¶

General Notice¶

Upgrades to OpenEye-orionplatform==1.0.0

v0.15.0 June 2019¶

General Notice¶

Upgrades to OpenEye-orionplatform==0.3.2

v0.14.0 June 2019¶

General Notice¶

Upgrades to OpenEye-orionplatform==0.2.5 and the 2019.Apr release of the OpenEye Toolkits

New Cubes¶

New Gameplan Report Cube to report Gameplan results and app generated log files.
New Brood Report Cube to report Brood results and app generated log files.
New ROCS with Multi-conformer Query cube that works with a multi conformer query molecule.
New SingleReceptorPositCube specifically for single receptor pose prediction.
New DUtoTgtLigRecords to extract target and ligand DataRecords from OEDesignUnits.
New DatasetReaderOpt to read records with an optional data source.

Cube Updates¶

Exhaustive Docking (Single Receptor) no longer produce docked pose with unusually high docking scores.
ROCS, SubROCS and Best Overlay Transform now works with a single conformer query molecule only and no longer produce a Query Conformer field in the output record.
OEStructureBasedLigandDesignCube now checks for memory limits corresponding to the number of receptors and poser cash size before starting to pose.
Updated Brood documentation.
Updated Gameplan documentation.
Spruce cubes have been updated to use and output OEChem::OEDesignUnit object files (.oedu), which are new to the 2019.Apr release of the OpenEye Toolkits.

v0.13.6 March 2019¶

General Notice¶

Upgrades to OpenEye-orionplatform==0.1.14

New Cubes¶

New Splitting Conformers and Merging Conformers cubes which preserve fields added during calculations on the split conformers.
previous cubes for Splitting and Merging conformers which did not preserve fields have been removed.
New Molecule Title To Field cube to create a field with the title of the molecule in a chosen MolField.
New Gameplan added that performs Gameplan calculations.
New Build conformer using Distance Geometry added that generates molecule conformers using distance geometry.
New Macrocycle Convergence added that along with the Build conformer using Distance Geometry can be used to create an efficient Macrocycle Omega floe that can generate macrocycle conformers in parallel mode.
New Omega Conformation (FastROCS mode) added that generates conformers for FastROCS.
New Align Conformers by RMSD Overlay added that can be used to align all conformers of a molecule based on RMSD.
New Omega Conformation (FastROCS mode) added that generates conformers for FastROCS.
New Copy Record added that can be used to generate multiple copies of a record.
New Torsion Scan that identifies torsions on each input molecule and generates copies of the record with a different torsion labeled by an atom tag on each copy.
New Activesite Ligand Energy added that can be used to calculate intermolecular energies between a ligand and a protein.
New Brood added that performs Brood calculations.

Cube Updates¶

Added new parameters mode and rotor_offset in the Omega Conformation.
Fixed a parameter mismatch issue with the Assign Partial Charges.
The Torsion Scan is updated to use a single tag to identify a torsion, instead of four tags. It also now has options to generate conformations using Omega prior to torsion driving or use a provided conformer ensemble. By default the cube reports both the MMFF/Sheffield energy as well as the MMFF/PB energy for each output conformer.
Fixed Zap Ligand Prep to fail gracefully when it cannot prep a molecule.
The Torsion Scan is updated to use a signle tag to identify a torsion, instead of four tags.
New parameters in_strain_mol_field and out_strain_mol_field added to the FreeformStrainCube and the FreeformEneStrainCube cubes to enable using separate input conformers for freeform free energy and strain calculations.
New parameter use_inp_ens have been added, to enable using user provided conformer ensemble in calculations, to the following freeform cubes:
- FreeformConfEntropyCube
- Freeform Conf Energies
- Freeform Ligand Strain
- FreeformEneStrainCube
- Freeform Conf Prepare Ensemble
- Freeform Conf Initial Optimization
- Freeform Conf Duplicate Removal
- Freeform Conf Optimization
- Freeform Conf Energy Calculation

v0.13.4 November 2018¶

General Notice¶

Upgrades to use OpenEye-orionplatform==0.1.9 and the 2018.Oct release of the OpenEye Toolkits

Cube Updates¶

Minor fix to Omega Conformation to preserve molecule titles.
Speed up fix for many of the FreeFormConf cubes.
Updated the Hermite shape cubes for compatibility with the 2018.Oct release of the OpenEye Toolkits

v0.13.3 September 2018¶

General Notice¶

Upgrades to use OpenEye-orionplatform==0.1.7

New Cubes¶

The following serial cubes have been added to merge fields from two records:
- Join Records
- Merge Records
The following serial logic cubes and their corresponding parallel version have been added to compare on string fields:

Cube Updates¶

CalculateXLogPCube now calculates XLogP on the neutral form of the molecule. A new parameter has been added to the cube, called Keep Neutral Form<cube_param_CalculateXLogPCube_keep_neutral> that controls whether to keep the neutral form of the molecule after the calculation or restore the original input form.

v0.13.0 August 2018¶

General Notice¶

Upgrades to use OpenEye-orionplatform==0.1.0