Drawing programs

SymApps converts 2D structures From the ChemWindow drawing program into 3D representations with the help of a modified MM2 force field (see Section 7.2). Besides basic visualization tools such as display styles, perspective views, and light source adjustments, the module additionally provides calculations of bond lengths, angles, etc, Moreover, point groups and character tables can be determined. Animations of spinning movements and symmetry operations can also he created and saved as movie files (. avi). 

First, a quei y must be drawn using the MOL" ISIS/Draw program. By using this reaction query, a eurrent reaction search " can be performed. This type of reaction retrieval compares the starting material and the product of the reaction query with all the reactions in the CIRX database. Both query structures must match exactly, including the implicit hydrogen atoms not shown in the reaction query. In this case, one hit is found in the CIRX databases. 

All chemists use models. Beginning chemistry students use plastic models to help them understand and visualize the structures of molecules. Recently, both students and experienced researchers have begun to use chemical drawing programs for the same purpose. 

The structure of the molecular system to be investigated follows the initial charge and spin multiplicity line in the molecule specification section. The structure may be obtained in a variety of ways from the coordinates generated by or converted from a drawing program (as demonstrated in the Quick Start), by constructing a Z-matrix by hand (see Appendix B), from the experimental literature, from the results of a previous calculation, and so on. 

By converting output from a drawing program and then editing the generated input. 

Testing action conformance at runtime isn t as easy as just inserting a few lines of code to monitor the postconditions. The problem is that nowhere does my user explicitly say to my implementation, Now I want to do a setSum. It s the same with our other examples A user doesn t say to the drawing program, Now I m going to move a shape from one drawing to another. Rather, the user just uses the select, cut, and paste operations. 

Figure 3. Substructure (I and III), ionic structure (II), and molecular structure (IV) produced by structure drawing program.

Like the similarity protocol, the user interface for the Pipeline Pilot SSS protocol supports multiple databases and multiple probes in a single query. The input of the probe molecule(s) is accomplished using a SD file, which can be generated in most standard chemical drawing programs. This file is supplied as one of the inputs in the SSS interface. The use of identification numbers is not as applicable here as it is in the case of the similarity protocol since we are most likely not using existing molecules as substructures. Consequently, textbox input is not an option nor is the upload of a list of numbers in CSV or Excel format. 

For users who prefer to draw in new structures, the later versions of Chem Draw will deliver a SMILES notation which can be used via cut and paste commands, and ISIS Draw delivers a MOLfile which can be automatically converted to a SMILES file. ACD / LogP uses a proprietary drawing program, MolDraw, which is easy to learn and use. Entry by name in ACD is accomplished via a Dictionary with about 48,000 entries. Drawn structures can be saved to a file, but in version beta 0.9 of ACD/LogP there is no method of batch entry from either SMILES files or MDL MOLfiles. 

One of the common character formats or chemical nomenclature of a valence model which is recognizable by a number of 2D-structure drawing programs is SMILES (Weininger, 1988). A full SMILES language tutorial can be accessed at http // www.daylight.com/dayhtml/smiles/. The general rules for biochemical compounds are as follows ... 

For most chemical structure drawing programs, it works best to use the copy-and-paste feature to insert the structure drawing into a Microsoft Word document. However, you should take care that the structure graphic inserted into your text file is of sufficient resolution, that is, 300 ppi minimum, with 600 or 1200 ppi even better. The author bears the responsibility to ensure the appropriate insertion. 

Even though InChl is a relatively new format (the first stable version of the InChl software was published in 2005), it has already gained broad acceptance in the chem-informatics world. It is supported by most of the major chemical drawing programs and is used in such databases as PubChem (http //pubchem.ncbi.nlm.nih.gov/) and NIST Webbook (Linstrom and Mallard 2005). 

Fig. 17. Three-dimensional model of butadiene-1.2 as generated by the structure drawing program on the display screen...

The continuous enoouragement by Professor Ugi is greatly appreciated. Able students -Oliver Dammer, Erika Diener-Weselsky, Peter Jacob, Manfred Oswald, and Josef Thoma — worked on various programming projects our thanks is extended to them. The structure drawing program is based on concepts developed by Dr, Richard Feldmann of NIH and was extensively modified and expanded here by Wolfgang Schubert, and Josef Thoma. Helpful discussions with Josef Friedrich and Wolfgang Schubert are appreciated. 

Search Queries. For all types of chemical representation, there are query representations that can be applied to a database to return a list of structures which match or "fit"the query, or that the query "hits" in the database. The same chemical drawing programs that are used to input structures can commonly be used to input chemical structure queries. These drawing programs currently include several programs in the commercial and public domains (44). A comparison of pop-... 

Exact Match Searching. Here, the chemist has a particular structure (or reaction) that he wishes to find in the database. The structure/reaction is drawn using a drawing program and then passed to a search program. The program submits the query to the... 

A comparison of chemical drawing programs, available online at http //dragon.kite.hu/ " gundat/rajzprogramok/dprog.html, accessed on September 13,2002. 

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