Query atoms

The query atom A (Any atoms) is added in phenyl, naphthyl, etc. aromatic cycles to allow finding any hetero-aromatic cycles. 

Query atoms can be defined either as single atoms or as atom lists. Atom lists are represented in brackets, such as [C,N,0,P], In this case, the atoms in the list are allowed at the corresponding position. Query atom lists can be negated (NOT [N,0]) to exclude atom types at certain positions. It is possible to define multiple query atom lists at several positions. 

During the following steps, the procedure is trying to match query atom 6, connected to query atom 3, onto a target atom that is connected to target atom e and that has not been matched to any other query atoms so far. However, this exercise... 

Partition criteria Query atom sets Target atom sets Set no. 

The brute force approach of trying every possible correspondence between the query atoms and the file structure atoms is clearly a non-starter, at least on conventional computer architecture. Beyond this, the simplest approach is backtracking, which was first used by Ray and Kirsch in 1957. ... 

Set reduction involves the successive elimination of candidate structure atoms from sets corresponding to each pattern atom on the basis of an analysis of neighbourhood and connectivity information. The technique has been widely used as a component of 2-D substructure searching systems and we have developed a modification of the technique which can be used for geometric searching. The first stage of the algorithm involves the creation of a distance table. The NQ pattern atoms are labelled from 1 to NQ and for each of the NQ(NQ-l)/2 distinct interatomic distances in the pattern (or less if not all of the query distances are specified for the search), a list of pairs of atoms from the structure is produced. The distance between the atoms in these pairs is equal to that between the pattern atoms (to within any specified tolerances), and the atom type of the first atom corresponds with the type of the first query atom (and similarly for the second atom). 

Match search query atoms to atoms in the candidate, using a rapidly calculable approximation of the 3D screens described previously. Rather than using a complete systematic comformational analysis to determine the attainable atom pair distances, the technique used here determines values for the upper and lower distances possible between a given atom pair. The procedure is illustrated in Figure 4. 

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. 

A limitation of the scope of the method is that each equation is structure-class specific. In real-world examples that do not readily fall into a previously studied class, model selection is a problem. Two methods have been described. In one approach, all the unique atom-based fragments obtained from all structure classes studied are projected into n-dimensional space (six and seven dimensions) based on topological environment vectors. A vector is then calculated for each carbon atom in the query compound. That model equation which corresponds to the atom fragment in n-dimensional space which is closest to the query atom fragment (Euclidean distance) is selected for predicting its chemical shift. Alternatively, a neural network is trained to relate the chemical environment of the set of carbon... 

Most query atoms are normal atoms. That is, they are not special atoms, they have no unspecified bonds and their valance is not zero. It is required that they match file atoms. The file structure must contain one identical atom for each normal atom in the query. If the query atom is in a ring a flag is set in the atom descriptor word and the file atom must also be in a ring. However, if the query atom is not in a ring, the file atom need not be in a ring, but it is allowed to be. For example ... 

If you wish to force a query atom to be matched only by a file atom which is a ring member, the query atom must be in a ring. 

If the query cannot be written in such a way as to include the particular query atom in a ring, ring members may perhaps be specified with a special atom. 

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