Structure Menu MS
This menu provides chemical functions relating to structures like molecule cleaning, aromatization, reaction-handling, naming and more.
Clean 2D > Clean in 2D |
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Calculates new 2D coordinates for the molecule. |
Clean 2D > Clean and Arrange in 2D |
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Cleans the structure(s) and places them in the center of the canvas. |
Clean 2D > Hydrogenize Chiral Center |
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Adds an explicit hydrogen atom to a chiral center having no terminal atoms when 2D cleaning is performed. |
Clean 2D > Clean Wedge Bonds |
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Arranges the wedge bonds of the molecule in 2D. |
Clean 3D |
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Calculates 3D coordinates for the molecule base on method set in the Preferences < 3D Options dialog. |
Directed Merge > Assign Atoms |
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Chooses the atoms of the fragments to be merged. |
Directed Merge > Merge |
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Merges the fragments at the atoms set. |
Add > Add Explicit Hydrogens |
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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 |
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Attaches data like stoichiometry coefficient to the molecule. |
Add > Absolute Stereo (CHIRAL) |
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Sets chiral flag for the molecule. |
Add > Multi-Center |
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Adds a multi-center attachment point representing a group of atoms. |
Add > Position Variation Bond |
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Create a variable point of attachment to represent a connection point to a group of atoms. |
Add > No Structure |
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Places a No Structure label on the canvas. |
Remove > Explicit Hydrogens |
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Removes explicit H atoms and increases the number of implicit hydrogens. |
Remove > Data |
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Removes attached data from the molecule. |
Remove > Absolute Stereo (CHIRAL) |
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Removes the chiral flag of the molecule. |
Edit data |
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Changes a previously attached data like stoichiometry coefficient of the molecule. |
Edit properties |
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Bond properties can be edited from this menu. |
Aromatic Form > Convert to Aromatic Form |
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Transforms the molecule to aromatic representation using the transformation method set. |
Aromatic Form > Conversion Method > Basic |
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Basic aromatization method is described here. |
Aromatic Form > Conversion Method > General |
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General aromatization method is described here. |
Aromatic Form > Conversion Method > Loose |
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Loose aromatization method is described here. |
Aromatic Form > Convert to Kekulé Form |
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Transforms the molecule to non-aromatic representation. |
Group > Group |
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Creates a custom Substructure Group (S-group) |
Group > Frequency Variation |
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Creates a Repeating Unit with Repetition Ranges. |
Group > Merge Brackets |
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Creates a bracket that crosses two bonds. |
Group > Edit Group |
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Modifies the properties of the selected group |
Group > Contract Group |
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Contracts all groups to its abbreviations. |
Group > Expand Group |
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Displays the full structure instead of the abbreviations. |
Group > Ungroup |
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Removes all abbreviated group associations from the molecule. |
Reaction > Merge Reactants |
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Merges the selected fragments to a reactant, product, or agent. |
Reaction > Unmerge Reactants |
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Removes selected fragments from a previously merged reactant, product, or agent. |
Mapping > Map Atoms |
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Inserts map numbers of the selected atoms. |
Mapping > Manual Atom Map |
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Inserts map numbers manually |
Mapping > Reaction Mapping Method > Complete |
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All atoms in the reaction are mapped. |
Mapping > Reaction Mapping Method > Changing |
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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 |
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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 |
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Removes map numbers of the selected atoms. |
Attribute > R-Logic |
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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 |
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Places the Analysis Box containing the preset calculations. |
Generate Name ... |
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Generates IUPAC or Traditional Name. |
Name to Structure |
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Opens the Source window in IUPAC Name format, and enables you to enter directly a IUPAC Name and convert it to structure. |
Markush Enumeration |
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Generates a whole or a subset of the library of a generic Markush structure. |
Check Structure |
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Checks and corrects chemical structures. See Structure Checker in MarvinSketch for more details. |
Auto Check |
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Toggles auto checking of structures while drawing. |