Chemical structures, graphical input

The compact textual coding requires no graphical input and additionally permits a fast transmission. These are important advantages of using SMILES in chemical applications via the Internet and in online services. SMILES is also used for the input of structures in the Daylight Toolkit [22]. 

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. 

Free patent information is provided by the website http //www.freepatentsonline.com/, covering U.S., EP, and PCT patents/applications and Japanese patent abstracts. In addition to the usual text-based searches in various search fields, this site also enables graphically input chemical structure searches to be performed on over 9 million compounds (including prophetic compounds) using exact structure, substructure, or chemical similarity searches. Chemistry searches using SMILES strings or chemical names are also possible. Full patent documents may be viewed in text or PDF format. 

Tel. 800-232-2224, 203-335-0906, fax 203-336-2481 Display and manipulation of 3D models using keyboard input. Molecular Animator for creating and displaying 3D models. Molecular Graphics for display and manipulation of atomic coordinate data. ChemFile II for creating databases of 2D chemical structures with associated text. PCs and Macintosh. 

Entry of Structures and Substructures. The main data input to the ADAPT system is chemical structures along with the relevant biological or physicochemical property. Structures are entered by sketching on the CRT screen of a graphics display terminal. 

Tel. 212-460-1622, e-mail griepke spint.compuserve.com Structure building. Stick and dot surface display. Geometry optimization dynamics by AMBER parameters. MNDO and AMI semiempirical calculations. AUTONOM for computerized assignment of chemical nomenclature to structures from graphical input. Beilstein and Brookhaven chemical databases in CD-ROM format. PC. 

The US National Cancer Institute needed a method for easily and quickly entering large numbers of chemical structures into a database. Command-driven systems and Teletype systems driven by keyboard input had been tried, but these systems were judged to be clumsy, difficult to learn, and slower than a graphics system should be. The result was the design and development of a microcomputer-oriented program which has evolved into a product known today as Superstructure. This paper discusses the design criteria and the development decisions which resulted in a fast and easy-to-learn chemical structure editor. 

The first major graphics application for an ACS publication automated the input and composition of structures in CA. Later, this structure input method was modified and added to the Messenger software for use in STN International as the basis for the STRUCTURE command that builds queries for substructure searching. After a search, structure images can be displayed on certain graphics terminals. Chemical structures are also produced by Messenger batch software on STN International off-line prints. 

A problem CAS intends to address is that different software is now used to handle chemical structures for different purposes. Ideally, one set of software would handle chemical structure input and storage serving the multiple purposes of substance registration, publication in ACS services and in STN International, and structure query input to STN International. The emerging graphics standards and advances in graphics tools will help CAS solve the problem. 

Conventions have therefore been established to ensure uniformity in the representations of chemical structures forming the graphics database, and to define methods for handling structures such as those with pi bonds which cannot be input directly. In arriving at these conventions Derwent s aims have been ... 

The structure of the chemical compounds under investigation influences all aspect of its chemistry, particularly spectroscopy. Therefore, the handling of chemical structures is one of the basic features that have to accompany the library search. For the input of chemical structures into a computer, flexible online editing of chemical graphics is required. 

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