Query structures mapping

Recently, Wipke and Rogers described superstructure searching, which retrieves those molecules that are contained within the query structure, rather than the inverse. The same bit maps are used the difference is that for a substructure search the bit screen of the hit must contain all of the query bits, whereas for a superstructure search the query must contain all of the bits present in the hit. This type of search has applications in computer-aided design of synthetic pathways and in building three-dimensional structures from three-dimensional fragments. ... 

Third, the tautomer information from the normalised BRCT is utilised in the tautomer search option of the Softron S4 search system. Although this is not yet fully implemented, S4 uses the tautomer information to control the mapping of the query structure onto all valid tautomeric forms of candidates in the Beilstein file. 

The iterative search examines the candiSate answers from the screen search in more detail and determines which file structures satisfy the full set of characteristics in the query structure. It is an atom-by-atom matching technique that attempts to find a mapping of the query structure onto the file structure such that at least one of the structures implied in the query structure is present in the file structure, while ensuring that query nodes are not mapped into more than one alternative for any variable in the file structure. 

The other match maps query stereocenter 3 to structure center 3. The ligands of the query atom map to the quadruple (2, 4, 5, H) which cannot be converted to (2, 4, H, 5), the ligand list of the structure, by a tetrahedron permutation (or an even number of interchanges). The match is, therefore, stereochemically invalid. 

Substructure searching is the process of identifying the members of a set of chemical moieties that match a specific query moiety. In most applications, the problem corresponds to mapping a query structure, usually containing free valency sites and variable atom or bond attributes, on to a set of target structures stored in a database. 

The four Build Menus in REACCS are Structure, Query, Top, and HighlightRxn. Structure menu contains the basic drawing commands used to construct the backbone of the structure. Query menu contains the commands used to add flexible structural parameters to the query. Top menu contains commands used to build reactions and to store and retrieve reactions, molecules, and graphic queries. HighlightRxn menu contains commands that apply atom/atom mapping and reaction centers to the current reaction. Atom/atom mapping is used to identify the reaction centers and increase accuracy and efficiency by letting the searcher specify that a particular atom in a reactant must correspond to a particular atom in the product. 

Graph isomorphism algorithms can be nsed for mapping a (query) full structure onto a strncture to determine identity between two structures. 

---