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There are multiple mechanisms by which a file can be loaded in VIDA. The simplest method is to select the ``Open" option in the File menu. This will launch a file selection dialog which prompts the user for the desired files(s) which will subsequently be loaded. A short list of the most recently opened files can also be found in the File menu under the ``Recents" (or ``Open Recents" on Mac OS X) submenu. Selecting an option in this submenu will load the associated file. There is an ``Open All" option at the bottom of the recents menu which will load all of the files listed in the recents submenu. Files can also be loaded by specifying them on the command line when starting VIDA or by dragging the file of interest onto the VIDA desktop icon. By default, there can only be one instance of VIDA running at a time, so if an instance of VIDA is running and a new file is specified on the command line or if a file is dragged onto the desktop icon, that file will be loaded in the currently running instance (instead of loading a new instance). If desired, multiple instances can be enabled by selecting the ``Allow multiple instances" option in the application preferences (see Chapter 11).
In addition to the ``Open" menu item, there is a separate ``Open State" item which filters out all files except VIDA state files. State files can be opened using any of the mechanisms described above, but their special nature warranted their own menu item. For more details on state files see Section 4.1.5.
There is also an ``Open Special" submenu which contains a ``Script" option which like the ``Open State" option filters out all files except for Python scripts. The ``Open Special" submenu also serves as an excellent target area for adding custom open operations via the scripting interface (see Chapter 10).
Multiple molecular file formats are supported for reading and include:
As is often the case with file formats, the meaning and use of certain fields within a format may change over time which can potentially lead to problems interpreting those files. VIDA, using OpenEye's OEChem toolkit, makes its best effort to interpret all files correctly; however, it does provide a mechanism to allow the user to override the handling of certain formats (SMILES, PDB, Mol2, XYZ, and MacroModel). The ability to change the ``flavor" of a specific format can be done in the application preferences as seen in Figure 4.1.
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In addition to changing the flavor of a format, there are a few other advanced options available when reading molecules including aromaticity model specification and conformer joining. The desired aromaticity model to be applied can be specified in the pulldown menu next to the ``Aromaticity Model" label. The ``Join Conformers" checkbox controls whether or not adjacent molecules in an input file will be tested on reading to determine whether they are unique compounds or simply different confomers of the same molecule. The specific test to be performed can be specified in the pulldown menu next to the checkbox. For more specific details on the available aromaticity models and conformer tests, please see the OEChem documentation.
It is important to note that because these advanced options are available through the application preferences, they will be remembered by the application and automatically applied in future ``Open" operations unless they are subsequently restored.
Multiple grid and map formats are supported for reading and include:
Multiple surface formats are supported for reading and include:
VIDA supports reading of Python scripts compatible with Python version 2.3. VIDA supports two additional file extensions for Python scripts (.pyv and .vpy) to enable users to associate those file extensions with VIDA without adversely affecting the association of unrelated Python scripts.
For more details about Python scripting, please see Chapter 10 as well as the associated Python scripting API documentation.
The entire state of a session can be stored in a single file called a ``State File" (.oes). A state file contains all of the molecules, grids, and surfaces that were loaded in VIDA at the time the state file was created. In addition, the state file preserves the actual view, layout, and properties of that session. State files provide an extremely convenient way to save sessions for later work or to share with collaborators. Furthermore, state files are the fastest method of reading and writing large data sets.
To load a state file, choose the ``Open State" option in the File menu and select the desired state file. State files can also be loaded from the commandline. It is important to note that loading a state file during a run will clear the current state before loading the new one. Therefore, be sure to save the current state before loading a new state if keeping the current state is desired. Furthermore, since state files contain the entire state of the application that generated them, loading a state file will overwrite local preferences; however, they will not be saved on exit.
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