Clean 2D > Clean in 2D

Calculates new 2D coordinates for the molecule.

Clean 2D > Clean Wedge Bonds

Arranges the wedge bonds of the molecule in 2D.

Clean 3D > Clean in 3D

Calculates new 3D coordinates for the molecule. Clean3D builds up conformers of fragments from which the best, i.e. the lowest energy conformer is given back. The quality of the structures is measured by a simple energy function (Dreiding type molecular mechanics).

Clean 3D > Cleaning Method > Fine Build

Fine Clean3D builds up conformers of fragments to find low energy conformer. Leaves failed fragments intact.

Clean 3D > Cleaning Method > Fine with Hydrogenize

The build process always adds explicit Hydrogens to the structures which are removed if not present in the original molecule. This option prevents the removal of extra Hydrogen atoms, otherwise gives the same results than Fine build.

Clean 3D > Cleaning Method > Fast Build

Fast clean, which if fails, performs fine clean. It accepts any generated structure, and it is the default behavior of the Clean3D function.

Clean 3D > Cleaning Method > Build or Optimize

Builds 3D structure for non-3D molecules and just optimizes the 3D molecules with the Dreiding force field.

Clean 3D > Cleaning Method > Gradient Optimize

Optimizes with the Dreiding force field using the actual structure as starting geometry.

Clean 3D > Display Stored Conformers

Allows you to choose one of the possible conformer structures which were calculated via the Conformers plugin.

Add > Add Explicit H Atoms

Adds explicit H atoms instead of the current implicit ones. Explicit hydrogens are displayed with atoms joining its neighbor while implicit hydrogens are displayed by atom symbols only.

Remove > Remove H Atoms

Removes explicit H atoms and increases the number of implicit hydrogens.

Aromatic Form > Convert to Aromatic Form

Transforms the molecule to aromatic representation using the transformation method set.

Aromatic Form > Conversion Method > Basic

Basic aromatization method is described here.

Aromatic Form > Conversion Method > General

General aromatization method is described here.

Aromatic Form > Conversion Method > Loose

Loose aromatization method is described here.

Aromatic Form > Convert to Kekulé Form

Transforms the molecule to non-aromatic representation.

Group > Contract Group

Contracts all groups to its abbreviations.

Group > Expand Group

Displays the full structure instead of the abbreviations.

Regenerate Bonds...

Generate bonds for an XYZ structure with a different bond length cut-off.