Starting from August 2016
- Added Abbvie MPS score and BBB Gupta score using ChemAxon calculators.
- Added Enumerate charges using DimorphiteDL.
- Alternative rDock docking allowing filtering relative to reference ligand.
- Open3DAlign now allows to include Crippen descriptors.
- Fix problem with export of large SD files.
- Fix problem with CDK writing SD files with aromatic bonds.
- Added ability to export datasets to CSV and TSV formats.
- Fix pKa calculation for CNS MPO cell (now uses basic pKa not acidic pKa)
- Fix for ChemAxon solubility predictor not working
- Fix for range cell when no default value was specified
- RDKit MaxMin Picker cell for a scaleable approach to picking diverse subsets
- Image viewer cell for viewing generated PNG format images
- TmaxCmax Simulation cell for simulating bioavailability profiles
- [RDKit Butina clustering»doc:Cell Directory.Data.RDKit Butina Clustering]] and RDKit Diverse Subset Picker cells have options for how to handle multi-fragment molecules. You will need to re-create the cell to see these new options.
- rDock docking cell improved, and execution parallelised.
- ChemAxon services updated to version 17.15.0.
- eMolecules Plus database removed - replaced with separate Screening compounds and Building Blocks databases.
- Chemical databases updated. Addition versions of ChEMBL added. Ligands from PDB added.
- Improved database connection management
- MolAlignAssemblies cell for performing 3D overlays
- Fixed problem with built in services such as Dataset Merge
- Notebook list can now be filtered. Term is applied to notebook name or owner in a case insensitive manner
- SMoG2016 cell for docking pose scoring
- PLI scoring cell now accepts score threshold
- Constrained conformer generator cell now includes UUID and StructureNum fields for the source molecule
- NGLViewer cell for 3D structure visualisation
- Results viewer for Scatter plot and Parallel coordinate plot cells
- PLI docking scoring cell
- Diverse subset picker cell
- XChem reaction smarts filter cell
- XChem reaction maker cell
- Molecules from field cell
- molecule display uses CDK for depiction
- Disconnect cell by dragging endpoint to empty area of canvas, bindings popup removed as no longer needed
- Whole page not reloaded when cells are connected or disconnected
- Selection propagation between visual cells - selection from one cell can be used to filter or mark values in different cell
- Smiles reader cell
- SMARTCyp metabolism prediction cell
- Atom highlighting, illustrated by SMARTCyp results
- Improvement to layout of results viewer
- Sorting of rows and columns in heatmap cell
- Record index can be used as axis in scatter plot
- LogD, LogS and pKa calculator cells from ChemAxon.
- New menu at top left of cells. Some actions moved from main toolbar to here.
- Editable cell description that can be shown or hidden.
- Main content panel can be hidden for some types of cell.
- Currently focussed cell is always on top.
- More efficient rendering of scatter plot.
- Field names in alphabetical order in cell options.
- Small cleanup of some UI aspects.
- Filters have a “Number of violations” option allowing filter to be tuned
- Dataset sorter cell - a simple way to sort data
- Various new structure filters:
- Lipinski calculator converted to a filter (RDKit, ChemAxon)
- Drug like filter behaves like other filters (ChemAxon)
- Ghose filter (RDKit, ChemAxon)
- Rule of 3 filter (RDkit,ChemAxon)
- REOS filter added using ChemAxon (RDKit version was already present)
- Fixed connection leak related to results viewer
- Lipinski calculators and ChemAxon drug like filter have been modified. Old versions will still appear and can be used, but it’s probably simplest to remove them and replace with new ones.
- Selected area in scatter plot is retained when cell reloads
- Selections and axes settings in parallel coordinate plot is retained when cell reloads
- Some cells made wider to allow better display of text
- History panel hidden by default
- Cells at top of notebook to not relocate to 0,0 when reloaded
- SDF/CSV filename added to metadata for file upload cells
- Results viewer allowing a ‘quick look’ at a cell’s output (including the extensive metadata), and to export those results to files.
- Potions - a simple language for data transforms
- Metadata can handle arbitrary field properties, allowing better recording of history
- Cell cannot be positioned above the top of the notebook
- Notebooks with range fields (e.g. REOS filter cell) will not load correctly and will need to be rebuilt
- Range fields for cells that have min and max ranges e.g. REOS filter
- Parallel coordinate plot cell
- Heatmap cell
- Support for Python scripts
- Better resizing of viz cells (but some improvements still needed)