Structure editor

The commercial 2D structure editor. Chemistry 4D-Draw, from Chemlnnovativc Software Inc., includes two additional special modules besides conventional chemical drawing tools. NamExpert provides the interpretation ofa compound name according to the lUPAC nomenclature to create the corresponding chemical structure. The latter can be represented in three different styles the shorthand. Kckulc. or semi-structural formula. In contrast to NamExpert, the Nomenclature module assigns lUPAC names to drawn structures. 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

This tutorial, which is based on the Beilstein update BS0202PR (May, 2002) and on the retrieval program Cro.ssFire Commander V6,. shows. some typical advanced search examples in the Beilstein database. It is assumed that the user already knows some of the basic features of the retrieval program. Moreover, in this tutorial the CrossFire Structure Editor is used instead of the (SIS/Draw Structure Editor. The first example is a combined application of structure aiM fact retrieval, whereas the second example demonstrates reaction retrieval. 

In order to allow any multiple chlorination of the biphenyl skeleton, the user may define an atom list (eonsisting of hydrogen and chlorine atoms) and substitute all H-atoms by this list. One may click on the drop-down selection box behind the element icons, select the options Generics. .set the user-defined atom to A1 and quit by the OK button. As a result this atom selection is active for the subsequent drawing steps. After this atom list is drawn ten times as the ten substituents, its composition has to be defined by clicking the A, icon on the left-hand side of the structure editor and by selecting H and Cl in the periodic table (Figure 5-16). 

Figure 5-16. Structure editor of the CrossFire ComiTiander V6, showing the definition ofan atom list (consisting of hydrogen and chlorine atoms) for polychlorinated biphenyls.

Part of the structure editor screen with dialog windows to specify the attachment 1 user-defined generic groups. 

A literature survey carried out in August 2003 in the Beilstein database BS0302PR (allene with maximum degrees of freedom in the structure editor, inp= in the fact editor) gave 194 hits. After taking into account redundant or wrong entries and several compounds not included in this database,... 

A set of n = 209 polycyclic aromatic compounds (PAC) was used in this example. The chemical structures have been drawn manually by a structure editor software approximate 3D-structures including all H-atoms have been made by software Corina (Corina 2004), and software Dragon, version 5.3 (Dragon 2004), has been applied to compute 1630 molecular descriptors. These descriptors cover a great diversity of chemical structures and therefore many descriptors are irrelevant for a selected class of compounds as the PACs in this example. By a simple variable selection, descriptors which are constant or almost constant (all but a maximum of five values constant), and descriptors with a correlation coefficient >0.95 to another descriptor have been eliminated. The resulting m = 467 descriptors have been used as x-variables. The y-variable to be modeled is the Lee retention index (Lee et al. 1979) which is based on the reference values 200, 300, 400, and 500 for the compounds naphthalene, phenanthrene, chrysene, and picene, respectively. 

The capabilities of Leatherface are best illustrated with examples. While a number of these will be typical of substructural modifications involved in building virtual screening databases, we will also show how a 2-D structure editor can be used to establish relationships between molecules and perform unorthodox substructural searches. 

GlycanBuilder Structure-Editor http //www.eurocarbdb.org/applications/ms-tools/ ... 

Commercially available structure editors provide several tools that allow a query to be defined with specific or general components. The back-end software has to transfer this information to the substructure search module. Transferring the structure and special information is done via standardized molecule file formats that include or are enhanced by special code conventions for the additional information. The substructure search module interprets the special conventions and translates them into an internal substructure representation. Examples for special query information are as follows ... 

Several other options are provided by most of the commercially available structure editors ... 

Figure 6.38 shows schematically how the two-dimensional structure is turned into valuable information. The two-dimensional structure is the common representation of a molecule in the chemical language as it is obtained from structure editor software. This representation does not include explicit information about the spatial arrangement of atoms. Several atoms in this molecule can appear in different spatial orientations leading to different enantiomers. 

The functionality required for an ELN to handle these structures is a specialized structure editor allowing creation and visualization of residues, definition of residues as real structures, and combined search for substructures in both the compound and the residue. Some additional features in the structure viewer help to mark and emphasize residues of the structure, allow overlapping residues, and label residues. A flag indicates whether the residues are displayed in the current context or not. If more than one residue is available, it is possible then to show or hide individual residues of a structure. The structure editor may be independent of a primary editor that is able to handle complete structures that is, structures are created with an external standard editor, whereas residue definitions are performed with an embedded tool. Since most databases are not designed for storing incomplete information, an ELN has to provide an internal format to store incomplete structures. In fact, it stores every complete part of a structure in a conventional database and keeps the additional information about the missing parts. 

Searching for structures or reactions in an external repository is an alternative to entering the structure directly into the scientific document. This is especially helpful if the structure is complex and not easy to author. Another application is the search for structures stored in an external system — for instance, to find already performed identical or similar reactions. The search query is typically entered via commonly used structure editors that provide the required standard file format. The search query can be performed on individual databases or on all connected databases, including the internal one, at the same time. 

Design and Development of an Interactive Chemical Structure Editor... 

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 next version of the structure editor system developed with few major changes in concept The terminal interface was created as a "dumb" terminal emulator with no special formatting capabilities A Tektronix 4010 emulator was created with the ability to emulate only the output features of the 4010 and none of the special input features, such as cross-hairs, since these were never to be used ... 

The structure editor had two modes which differed only slightly the normal mode (used to define structures to be entered into the database system) and a query mode (for entering structures for searching the database) In query mode, some options were disabled (such as attachment points and ill-defined fragments) Multivalued atom nodes and a large list of bond types were allowed in query mode In the same manner, in non-query mode, atoms must be singular valued and bond types could only be single, double, triple, stereo-up, stereo-down, or stereo-unknown ... 

The final structure editor routines would show the user a menu consisting of DRAW, NORMALIZE, LABEL ATOM, LABEL BOND, DELETE ATOM, DELETE BOND, SET CHARGE, SET MASS, DOT DISCONNECT, ATTACHMENT POINT, MOVE MENU, TEMPLATES, PRINT, and SEND as illustrated in Figure 1 Whatever menu option was selected would be "lit by displaying the text in reverse video (light background and dark letters) Once in most modes, the system would stay there until a new mode was selected some modes would return automatically to the DRAW state upon completion of an operation ... 

Figure 1. Structure editor menu with figure, user cursor, and "normalized (automatic) atom placement.

---