Structure Menu in MarvinSketch

This menu provides chemical functions relating to structures like molecule cleaning, aromatization, reaction-handling, naming and more.

Clean 2D > Clean in 2D		Calculates new 2D coordinates for the molecule.
Clean 2D > Clean and Arrange in 2D		Cleans the structure(s) and places them in the center of the canvas.
Clean 2D > Hydrogenize Chiral Center		Adds an explicit hydrogen atom to a chiral center having no terminal atoms when 2D cleaning is performed.
Clean 2D > Clean Wedge Bonds		Arranges the wedge bonds of the molecule in 2D.
Clean 3D		Calculates 3D coordinates for the molecule base on 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 its neighbor while implicit hydrogens are displayed by atom symbols only.
Add > Data		Attaches data like stoichiometry coefficient to the molecule.
Add > Absolute Stereo (CHIRAL)		Sets chiral flag for the molecule.
Add > Multi-Center		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		Places a No Structure label on the canvas.
Remove > Explicit Hydrogens		Removes explicit H atoms and increases the number of implicit hydrogens.
Remove > Data		Removes attached data from the molecule.
Remove > Absolute Stereo (CHIRAL)		Removes the chiral flag of the molecule.
Edit data		Changes a previously attached data like stoichiometry coefficient of the molecule.
Edit properties		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		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 > Group		Creates a custom Substructure Group (S-group)
Group > Frequency Variation		Creates a Repeating Unit with Repetition Ranges.
Group > Merge Brackets		Creates a bracket that crosses two bonds.
Group > Edit Group		Modifies the properties of the selected group
Group > Contract Group		Contracts all groups to its abbreviations.
Group > Expand Group		Displays the full structure instead of the abbreviations.
Group > Ungroup		Removes all abbreviated group associations from the molecule.
Reaction > Merge Reactants		Merges the selected fragments to a reactant, product, or agent.
Reaction > Unmerge Reactants		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		All atoms in the reaction are mapped.
Mapping > Reaction Mapping Method > Changing		Only those atoms are mapped that have changing bond. Either the bond order changes, or new bond is created, or bond is deleted. Orphan and widow atoms are included.
Mapping > Reaction Mapping Method > Matching		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.
Attribute > R-Logic		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		Places the Analysis Box containing the preset calculations.
Structure to Name ...		Generates IUPAC and/or Traditional Name and/or displays CAS Registry Numbers®
Name to Structure		Opens the Source window in IUPAC Name format, and enables you to enter directly a IUPAC Name and convert it to structure.
Markush Enumeration		Generates a whole or a subset of the library of a generic Markush structure.
Check Structure		Checks and corrects chemical structures. See Structure Checker in MarvinSketch for more details.
Auto Check		Toggles auto checking of structures while drawing.