Import Molecules from SMILES or 2D
This import option is found in the toolbar
Toolbar | Import (
) | Import Molecules from SMILES or 2D (
)
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).
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Prerequisites
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Figure 6.8: The Preferences settings found in the Edit menu. The Balloon executable specification is seen in the bottom.
The importer has three options (see figure 6.9).
- 3D structure generator settings:
Molecule Name
In SDF files, the first line for each molecule is the molecule name. In Mol2 files, the second line for each molecule is the molecule name. If the molecules do not have a name specified in the input file, the importer will assign a user specified name. The molecule name then consists of the prefix, specified in the import wizard, and a number.
Molecule Conformations
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.
- Filter settings: If an import issue (Import issues) is encountered for a molecule during import, there is an option to exclude this molecule from the imported Molecule Table.
- Subset selection: You can choose only to import a specific subset of the molecules from the input file.
Figure 6.9: Options when importing molecules with coordinates in 2D, or from SMILES.