Molecule Editors

A molecule editor can draw a chemical structure and save it, for example as a Molfile. Although it is possible to include stereochemical properties in the drawing as wedges and hashed bonds, or even to assign a stereocenter/stereogroup with its identifiers R/S or E/Z), the connection table of the Molfile only represents the constitution (topology) of the molecule. 

Tools Chemical Structure Drawing Software - Molecule Editors and Viewers... 

The CACTVS molecule editor is a graphical input tool for molecular structures and is free of charge for non-profit use. It can be used as a stand-alone or as a dependent remote program of the CACTVS computation workbench. The software is available for aU platforms (excluding Macintosh systems). 

JChemPaint is a chemical structure drawing applet. The noteworthy characteristic of this 2D molecule editor is that it is an open source program [208]. This means that the software and the source code of the program are freely available. Every programmer or interested person can participate and enter individual special requests for further development of the application. 

Molecule editors represent only two-dimensional chemical structures (thus also could be considered as 2D viewers), the third dimension is visualized by 3D viewers, mainly user-interactive. 

Chcm3D is much more than a molecule viewer. This autonomous software module from the ChemOffice package provides simple molecule editor tools to create structures, but is mainly used as a molecular modeling tool. 

Table 2-10. Overview of molecule editors and their features. w s...

Thus, if the user wants to look for literature including requested chemicals or reactions, it is possible to query the database by the first option Chemical Substance or Reaction , The compound can be entered as a query in three different ways drawing the chemical structure in a molecule editor (Chemical Structure) searching by names or identification number, such as the CAS Number (Structure Identifier) and searching by molecular formula (Figure 5-12). 

As already mentioned (Section 5.3), the stored structure information in this type of database makes it possible to search for chemical structures in several ways. One method is to draw a structure (via a molecule editor) and to perform either a precise structure search (full structure search) or a search containing part of the input structure (substructure search) (see Sections 6.2-6.4). The databases also allow the searching of chemical names and molecular formulas (see Section 6.1). The search results are in most cases displayed in a graphical manner. 

The TcIcSpcc system offens two ways of reading in a query structure. The structure can be input cither directly as a SMILES string (cf. Section 2,3.3) or via a molecule editor which converts the graphical input into the SMILES string. Figure 10.2-10 gives the input form of TeleSpec. 

Figure 10.2-10. Input form of IR Simulator the structures can be entered either as SMILES strings or via a molecule editor.

The structure of a compound including its stereochemistry can be specified with the graphical molecule editor J M E which converts it into a stereochemically unique SMILES string as search item. Figure 10.3-24a shows how I-glutamatc can be input as query,... 

In order to draw a desired target compound WODCA provides a molecule editor which has to be launched. This can be performed by pressing the "New Compound" button in WODCA s button bar, The molecule editor is then started and aftei"wards the target compound can be drawn directly with the mouse. 

The option "Open molecule and process" can be used at any time, whether we are in the Molecules editor or the Processing screen. 

Note If the Select option is activated and you are working in the Molecules editor, none of the drawing options will function, even if the status line shows that one of them is activated. Similarly, working on the Processing screen, it will not be possible to move the synthesis tree nor change the active molecule. The option "Select" must be disactivated before performing any of these activities. 

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