This menu provides chemical functions relating to structures like molecule cleaning, aromatization, reaction-handling, naming, and more.
Menu item | Icon | Description |
---|---|---|
Clean 2D > Clean in 2D | ![]() |
Calculates new 2D coordinates for the molecule. |
Clean 2D > Clean and Arrange in 2D | ![]() |
Cleans structures and positions them to the center of the canvas. |
Clean 2D > Hydrogenize Chiral Center | N/A | Adds an explicit hydrogen atom to a chiral center having no terminal atoms when 2D cleaning is performed. |
Clean 3D | ![]() |
Calculates 3D coordinates for the molecule base on the method set in the Preferences > 3D Options dialog. |
Directed Merge > Assign Atoms | ![]() |
Chooses the atoms of the fragments to be merged. |
Directed Merge > Merge | ![]() |
Merges the fragments at the atoms set. |
Add > Add Explicit Hydrogens | ![]() |
Adds explicit H atoms instead of the current implicit ones. Explicit hydrogens are displayed with atoms joining their neighbor while implicit hydrogens are displayed by atom symbols only. |
Add > Data | ![]() |
Attaches data such as the stoichiometry coefficient to the molecule. |
Add > Absolute Stereo (CHIRAL) | ![]() |
Sets chiral flag for the molecule. |
Add > Multi-Center | N/A | Adds a multi-center attachment point representing a group of atoms. |
Add > Position Variation Bond | ![]() |
Create a variable point of attachment to represent a connection point to a group of atoms. |
Add > No Structure | N/A | Places a No Structure label on the canvas. |
Remove > Explicit Hydrogens | ![]() |
Removes explicit H atoms and increases the number of implicit hydrogens. |
Remove > Data | N/A | Removes the attached data from the molecule. |
Remove > Absolute Stereo (CHIRAL) | ![]() |
Removes the chiral flag of the molecule. |
Edit data | N/A | Changes a previously attached data such as the stoichiometry coefficient of the molecule. |
Edit properties | N/A | Bond properties can be edited from this menu. |
Aromatic Form > Convert to Aromatic Form | ![]() |
Transforms the molecule to aromatic representation using the transformation method set. |
Aromatic Form > Conversion Method > Basic | N/A | The basic aromatization method is described here. |
Aromatic Form > Conversion Method > General | N/A | The general aromatization method is described here. |
Aromatic Form > Conversion Method > Loose | N/A | The loose aromatization method is described here. |
Aromatic Form > Convert to Kekulé Form | ![]() |
Transforms the molecule to non-aromatic representation. |
Group > Group | ![]() |
Creates a custom Substructure Group (S-group). |
Group > Frequency Variation | ![]() |
Creates a Repeating Unit with Repetition Ranges. |
Group > Merge Brackets | N/A | Creates a bracket that crosses two bonds. |
Group > Edit Group | N/A | Modifies the properties of the selected group. |
Group > Contract Group | N/A | Contracts all groups to their abbreviations. |
Group > Expand Group | N/A | Displays the full structure instead of the abbreviations. |
Group > Ungroup | N/A | Removes all abbreviated group associations from the molecule. |
Reaction > Merge Reactants | N/A | Merges the selected fragments to a reactant, product, or agent. |
Reaction > Unmerge Reactants | N/A | Removes selected fragments from a previously merged reactant, product, or agent. |
Mapping > Map Atoms | ![]() |
Inserts map numbers of the selected atoms. |
Mapping > Manual Atom Map | ![]() |
Inserts map numbers manually. |
Mapping > Reaction Mapping Method > Complete | N/A | All atoms in the reaction are mapped. |
Mapping > Reaction Mapping Method > Changing | N/A | Only those atoms are mapped that have changing bond. Either the bond order changes, a new bond is created, or the bond is deleted. Orphan and widow atoms are included. |
Mapping > Reaction Mapping Method > Matching | N/A | Maps all matching atoms in the reaction (Daylight style mapping). A reaction atom is called matching if it is not an orphan/widow atom: it exists on both sides of the reaction. |
Mapping > Unmap Atoms | ![]() |
Removes map numbers of the selected atoms. |
R-Logic | N/A | Allows setting additional R-group conditions such as occurrence, rest H, and if-then expressions to R-groups in the R-logic dialog window. |
Place Analysis Box | N/A | Places the Analysis Box containing the preset calculations. |
Structure to Name | N/A | Generates IUPAC and/or Traditional Name and/or displays CAS Registry Numbers®. |
Name to Structure | N/A | Opens the Source window in IUPAC Name format, and enables you to enter directly an IUPAC Name and convert it to structure. |
Markush Enumeration | N/A | Generates a whole or a subset of the library of a generic Markush Structure. |
Check Structure | ![]() |
Checks and corrects chemical structures. See Structure Checker for more information. |
Auto Check | N/A | Toggles auto checking of structures while drawing. |