Structure Menu in MarvinSketch

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.