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VIDA is capable of saving multiple types of files including molecules, grids, surfaces, and state files. The details of the individual formats can be found in the relevant sections below.
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A file can be saved by choosing the ``Save" option the File menu. This will launch a dialog prompting the user to select which objects to save (see Figure 4.2). There are two sets of buttons at the top of this dialog which provide mechanisms for filtering the available options. The three buttons on the top left toggle the display of molecules, surfaces, and grids respectively. The two buttons on the top right provides filters for showing only the Marked and/or Visible objects respectively. Once one or more objects have been selected and the ``OK" button is pressed, a file dialog will appear allowing the user to specify the desired file. The file formats listed in the file dialog filter will reflect which file formats are supported based on the objects selected. Only the OpenEye binary format supports writing multiple object types (molecules, grids, and/or surfaces) to the same file.
This process can be expedited by simplying right-clicking on the desired objects and selecting the ``Save" option. This allows the user to bypass the selection dialog and go directly to the file dialog.
Multiple molecular file formats are supported for writing 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, writes all files according to the standard; however, it does provide a mechanism to allow the user to override the handling of certain formats (SMILES, MDL/SDF, PDB, Mol2, MF, MOPAC, 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.
In addition to changing the flavor of a format, there are a few other advanced options available when writing molecules including aromaticity model specification and conformer splitting. The desired aromaticity model to be applied can be specified in the pulldown menu next to the ``Aromaticity Model" label. For more specific details on the available aromaticity models, please see the OEChem documentation.
It is important to note that because these advanced options are available through the application preferences, they will be remembed by the application and automatically applied in future ``Save" operations unless they are subsequently restored.
Multiple grid formats are supported for writing and include:
Multiple surface formats are supported for writing and include:
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.
With the release of VIDA 3.0, a new state file version was introduced which is significantly smaller in size and faster to load than previous versions. However, this new version, ``OpenEye State Version 2" cannot be read or written by VIDA 2.x. To address that issue, VIDA does provide the functionality to save ``OpenEye State Version 1" files which can be read and written by all versions of VIDA.
The new state version also supports a ``mini" option which only writes out objects that are currently visible or referenced in the display bookmarks. This can provide for an even greater savings in disk size and load time. This mini-state file can be further compressed by selecting the ``Compress grid contour information" option in the General section of the application preferences. Selecting this option zeros all non-contour related positions in the grid which greatly improves its compressibility. This should only be done if there is no expectation that the user loading the resulting state file will want to look at grid contour levels other than those already defined when the file was generated.
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To save a state file, select the ``Save State" option in the File menu and specify the desired state file. The state file version can be selected using the file format filter as seen in Figure 4.3.
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