Import Molecules from SMILES or 2D

This import option is found in the toolbar

        Toolbar | Import (Image Next_Folder_16_n_p) | Import Molecules from SMILES or 2D (Image import_molecules_16_n_p)

Using this importer you can import a molecule library where the molecules are given as SMILES strings (.smi file) or where molecule representation is only given in 2D in SDF or Mol2 format. 3D coordinates are generated for the molecules on import. The freely available program Balloon [Vainio and Johnson, 2007] is used for 3D structure generation (see Generation of 3D structure on import).

Prerequisites
The program Balloon should be downloaded from the website http://users.abo.fi/mivainio/balloon/download.php, where it is available for Windows, Mac and a variety of Linux platforms.
In the Preferences settings, found in the Edit menu, the path to the Balloon executable should be specified, for this import option to work (figure 6.7).
Note that the file MMFF94.mff, which is downloaded together with the executable, should be kept in the same folder as the executable.

Image Preferences_Balloon
Figure 6.7: The Preferences settings found in the Edit menu. The Balloon executable specification is seen in the bottom.

The importer will assign a user specified name to molecules that do not have a name in the input. The molecule name consists of a prefix and a number (figure 6.8). The importer can return either the conformation found with lowest energy for each molecule, or an ensemble of low-energy conformations for each molecule (usually one to ten). Especially if the molecules have non-aromatic ring structures, it can be relevant to generate multiple representations, as the rings are kept rigid during docking.

Image ImportFrom2DWizard
Figure 6.8: Specify prefix for molecule names and whether to generate one or more conformations per molecule.