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As mentioned in section 4.1 there are many advanced options available associated with reading molecules. As seen in Figure 4.1, in the ``Advanced" column there is a pulldown menu at the top, a collection of options in the middle, and a Default button at the bottom. The pulldown menu at the top contains a list of all the categories of ``Advanced" options available which include: ``Generic", ``SMILES", ``PDB", ``MOL2", ``XYZ", and ``MMOD". The ``Generic" section contains options that apply to all molecules being read, while the other sections contain options that apply to molecules being read from the associated file formats. The Default button at the bottom of the column will restore all of the ``Advanced" options to their default parameters.
On the ``Generic" page there is a section titled ``Join Conformers" which provides a number of options for conformer testing while reading input. The default option is to ``Keep Separate" which means that all molecules being read in will be treated as independant molecules. The other ``Join Conformers" options will perform comparisons on adjacent molecules in the file to determine if they are actually just different conformers of the same molecule and will be treated as such by the application. For more information on the details of the actual conformer testing, please see the OEChem documentation.
Beneath the ``Join Conformers" section on the ``Generic" is the ``Aromaticity Model" section which allows specification of if and how aromaticity should be perceived on input molecules. The default is ``None" which means that the application will not do any aromaticity perception beyond what is specified in the input file. The other options will result in aromaticity being perceived on reading using the specified model. For more details on aromaticity models, please see the OEChem documentation.
The options on all of the other pages correspond to the Input Flavors associated with the specific file format readers as defined in OEChem.
It is important to note that specified values in the ``Advanced" options are remembered by the application and automatically applied on future ``Open" operations unless they are subsequently changed. These options will also apply to molecules loaded from the ``Recents" menu as well as those specified on the command line.
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