Added a 1D/2D molecule input dialog which supports SMILES, names, and interactive building.
Added a 3D editing mode which enables significant modification of the current molecule including in-vacuo minimization with MMFF94.
Added support for DNA/RNA ribbon style visualization
Added support for displaying and controlling alternate residue conformations (turn on ALL flavor when reading PDB files to enable this) as well as a number of coloring schemes associated with alternate residues
2D depiction in 3D display is now selectable
Add object-type specific tool buttons to the bottom display which provide context sensitive operations such as coloring and style options.
Added the ability to import all of OpenEye’s Python toolkits for use within VIDA, provided that the user has a license for those toolkits.
Added the ability to transfer molecules, grids, and surfaces between the main application and the bundled OpenEye Python toolkits.
Added support for PythonQt scripting within VIDA.
Added support for PyQt scripting with VIDA (separate license required from Riverbank computing).
Added interactive protein depictions in the spreadsheet.
Added many new atom properties to the atom spreadsheet.
Added a residue spreadsheet which is capable of controlling alternate residue conformations.
Added the ability to load molecules directly from the PDB ( “File > Open Special > From PDB” )
Added the following command line arguments:
-e- Runs the associated file through the Python interpreter and populates the sys.argv variable with the remaining command line arguments
-eonview- Loads the associated files and processes them using the built in EON view
-fredview- Loads the associated files and processes them using the built in FRED view
-rocsview- Loads the associated files and processes them using the built in ROCS view
-import- Loads the associated files and immediately launches the spreadsheet import dialog
PICTO application now ships with VIDA. PICTO requires a valid VIDA license.
Significantly increased the speed of searches performed within VIDA.
Significantly improved and expanded the scripting examples that come with the distribution.
Significantly optimized the loading of OEB molecule files which contain attached grids.
When displaying Marked molecules, now only the carbon atoms (as opposed to all) are colored using the Marked color unless the non-carbon atoms are specifically Marked themselves.
Optimized the AtomDataGet function when working with multi-conformer molecules.
Vastly improved the display and usability of the embedded 3D toolbars
Major Bug Fixes¶
Fixed rendering problems associated with having multiple overlapping transparent surfaces displayed simultaneously.
Fixed the handling of triple-quoted strings in the VIDA interpreter.
Fixed a bug which was preventing scripts from being aborted while running.
Fixed a problem where SD data was being lost on read if one or more conformers in a multiconformer molecule did not have the same SD data fields as the rest.
Minor Bug Fixes¶
Fixed a number of erroneous tooltips.
Fixed a few spelling errors in prompts and widgets.
Fixed the behavior of the drop-down selections in the constraints and extra molecule buttons in the FRED View controller.
Fixed the hybridization, isotope, and symmetry atom labels.
Fixed a bug where the ColorSetScoped function did not color selected atoms if SelectedScope was explicitly specified as opposed to BestScope.
Fixed the MoleculeMergeScoped function to ensure that residue information is not lost when two molecules are merged together.
Fixed the standard deviation function in the spreadsheet.
The “Create Spreadsheet” option for list entries in the list windows now works as expected.
Fixed the coordinates returned in the AtomData class by the AtomDataGet function when working with multi-conformer molecules.
Silenced a large number of annoying and unnecessary warnings that would appear in the scripting window