Structure Menu

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.

Generate Name ...


Generates IUPAC or Traditional Name.

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.