Molecular structure external representation

As with all data in an RDBMS, there is an external and internal representation of data. This was discussed in an earlier chapter for standard data types, such as text and numeric. For molecular structures, there is of course no SQL standard. When building a database containing molecular structures, a decision should first be made which internal representation will be used and which external representation. 

The external representation of molecular structure is a less rigorous definition. For example, there are many programs available that can convert to and from SMILES and molfiles. These can be used when a molfile (the external representation) needs to be imported as a SMILES (the internal representation) into the database. Similarly, a SMILES can be easily exported as a SMILES or converted to a molfile or other file format. It is useful to have these conversion functions as SQL extensions. 

The molfile or sdf file format is a very common way to store molecular structures. This can be considered as an external representation of a molecular structure data type. There are many other common file formats in use and only the essential features common to all of them will be considered here. The essential aspects of molecular structure contained in these files are atomic number or atomic symbol, formal atomic charge, bonded atom pairs, and bond orders. These are the minimum attributes necessary to define an unambiguous valence bond molecular structure. Other atom properties, such as atom types might also occur in these files, but these are specific to particular modeling programs and will not be discussed here. Sometimes molecular properties are also stored in these files. A way to store these properties in relational tables is discussed. 

Figure 13.8 Schematic operation of a two-station rotaxane as a controllable molecular shuttle, and idealized representation of the potential energy of the system as a function of the position of the ring relative to the axle upon switching off and on station A. The number of dots in each position reflects the relative population of the corresponding coconformation in a statistically significant ensemble. Structures (a) and (c) correspond to equilibrium states, whereas (b) and (d) are metastable states. An alternative approach would be to modify station through an external stimulus in order to make it a stronger recognition site compared to station A.

Fig. 2.3. Diagrammatic representation of the molecular organisation of the tegument plasma membrane (based on the fluid mosaic model of membrane structure of Singer Nicolson (1972)). The carbohydrate moieties of the membrane glycoproteins and glycolipids are exposed on the external face as the glycocalyx. (After Smyth Halton, 1983.)...

Structure and data storage is shown on the right. A structure table contains the structures, their internal identifiers, and their external identifiers, if any. The structures are stored in a compact binary representation that includes the connection table, the coordinates, the ring information, and any stereochemical, valence, isomer, isotope, or bond information. Certain types of structure-specific information such as polymer or component designations are stored here, whereas other types of structure-specific information (atom- or bond-specific data, and more verbose text data) are stored in their own tables, referenced by the internal identifier, and the atom or bond numbers to which the data correspond. A formula table contains the molecular formula and various atom and atom-type indexes to enhance formula searching and sorting. 

The similarity tool should encode different similarity indexes, and since the similarity indexes make use of molecular descriptors, the tool should also be able to derive the numerical representation from the given structure or to upload it from an external file. As for all the tools included in the DSS, the use of the chemical similarity tool should lead to results (e.g., category... 

AIA = Analytical Instruments Association AFFN = ASCII free format numeric API = application programming interface ASDF = ASCII squeezed difference form ASMS = American Society of Mass Spectrometry ASTM = American Society for Testing and Materials CCDB = Committee on Chemical Databases CDF = common data form CPEP = Committee on Printed and Electronic Publications CS = chemical structure EPA = United States Environmental Protection Agency lUPAC = International Union of Pure and Applied Chemistry JCAMP-DX = Joint Committee on Atomic and Molecular Physical Data - Data Exchange LDR = labeled data record netCDF = network common data form SMD = standardized molecular data UCAR = University Corporation for Atmospheric Research XDR = external data representation. 

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