Extended Connection Table

The first line of the connection table, called the counts line (see Figure 2-21), specifies how many atoms constitute the molecule represented by this file, how many bonds arc within the molecule, whether this molecule is chiral (1 in the chiral flag entry) or not, etc. The last-but-onc entry (number of additional properties) is no longer supported and is always set to 999. The last entry specifics the version of the Ctab format used in the current file. In the ease analyzed it is V2000". There is also a newer V3000 format, called the Extended Connection Table, which uses a different syntax for describing atoms and bonds [50. Because it is still not widely used, it is not covered here. 

Barnard, J. M., M. F. Lynch, and S. M. Welford. 1982. Computer storage and retrieval of generic structures in chemical patents. 4. An extended connection table representation for generic structures. J. Chem. Inf. Comput. Sci. 22(3) 160-164. 

Extended Connection Table Representation molecular graph... 

Barnard, J.M. Lynch, M.F. Welford, S.M. Computer Storage and Retrieval of Generic Chemical Structures in Patents, Part 4, An Extended Connection Table Representation for Generic Structures. J. Chem. Inf. Comput. Sci. 1982, 22, 160-164. 

The internal representation of GENSAL is called ECTR (Extended Connection Table Representation). It was described first by Barnard, Welford and Lynch in... 

Extended Connection Table Representation (ECTR) Example ... 

Both tables, the atom and the bond lists, are linked through the atom indices. An alternative coimection table in the form of a redundant CT is shown in Figure 2-21. There, the first two columns give the index of an atom and the corresponding element symbol. The bond list is integrated into a tabular form in which the atoms are defined. Thus, the bond list extends the table behind the first two columns of the atom list. An atom can be bonded to several other atoms the atom with index 1 is connected to the atoms 2, 4, 5, and 6. These can also be written on one line. Then, a given row contains a focused atom in the atom list, followed by the indices of all the atoms to which this atom is bonded. Additionally, the bond orders are inserted directly following the atom in-... 

A connection table can be extended by adding otlier lists, such as lists of tbe free electrons and/or with the charges on the atoms of the molecule. Thus, in effect, all the information in a BE-matrix can also be stored in a connection table [40]. 

The results shown in Table 15.1.5 indicate that a considerable proportion of bond cleavage occurs at the extender connection, and also that the extender influences the thermal stability of the polymer. Regarding the decomposition of the heterocyclic moiety, the ether bond between the two isoindolino[2,1-a]benzimidazol-11-one units and the C(0)-N bond from the pyrrolydin-2-one ring are likely to cleave more easily than other parts of the molecule. 

The molecular structure entry is performed by sketching the compounds on a graphics terminal, and then storing them as connection tables. The geometries are optimized using adapt s molecular mechanics routine, MM2 [4], the semiempirical molecular orbital program (MOPAC) [5], or a newly developed extended Huckel method [6]. 

There are several ways in which molecular descriptors can be classified. The majority of descriptors are atom-based rather than field-based. The bulk of this review is focused on a discussion of atom-based descriptors. As the name implies, atom-based descriptors are based on individual atoms, with the description extending outward to incorporate information about the atom s environment. The descriptors are typically generated by analysis of 2D or 3D connection tables, and can include ID, 2D, or 3D information about the molecule. Atom-based descriptors include individual atoms, feature counts, substructural fragments, topological indices, atomic properties, pharmacophores (see Chapters 17 and 18 of this book), and calculated physicochemical properties. 

Connection tables can be easily extended in their rows, for example, by having information about alternating bonds, cyclic and noncyclic bonds, stereochemistry or by description of variable positions or generic groups in a molecule. Generic groups are represented by Markush structures. 

HIV-1 potencies of the two groups of reverse transcriptase inhibitors whose base structure is shown in Fig. 8 and hsted in Table 13, commonly known as TIBO and HEPT derivatives. The activities are measured by the concentration of compound required to achieve 50% protection for MT-4 cells against the virus for modeling reasons it is expressed as log(10 C5o). In the present analysis, both types of graphs based on HFG and GAO are used, including the Morgan-extended connectivities °ECfc, EC, and EC introduced previously. The flexible variable is deflned as ... 

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