Standard formats, Chemical Structure

The smoke point corresponds to the maximum possible flame height (without smoke formation) from a standardized lamp (NF M 07-028). The values commonly obtained are between 10 and 40 mm and the specifications for TRO fix a minimum threshold of 25 mm. The smoke point is directly linked to the chemical structure of the fuel it is high, therefore satisfactory, for the linear paraffins, lower for branched paraffins and much lower still for naphthenes and aromatics. 

As many different file formats have been developed since the early 1970s, the need for a standard chemical structure format has been increasingly felt. Various attempts have been made by different groups of the chemical commimity to define and push such a format, but none has achieved unanimous acceptance. 

To demonstrate the use of binary substructure descriptors and Tanimoto indices for cluster analysis of chemical structures we consider the 20 standard amino acids (Figure 6.3) and characterize each molecular structure by eight binary variables describing presence/absence of eight substructures (Figure 6.4). Note that in most practical applications—for instance, evaluation of results from searches in structure databases—more diverse molecular structures have to be handled and usually several hundred different substructures are considered. Table 6.1 contains the binary substructure descriptors (variables) with value 0 if the substructure is absent and 1 if the substructure is present in the amino acid these numbers form the A-matrix. Binary substructure descriptors have been calculated by the software SubMat (Scsibrany and Varmuza 2004), which requires as input the molecular structures in one file and the substructures in another file, all structures are in Molfile format (Gasteiger and Engel 2003) output is an ASCII file with the binary descriptors. 

M D Lmolfile Standardized file format for chemical structures including substructure query features (initially defined by Molecular Design Ltd)... 

CLAIMS BIBLIO includes an abstract and claim in addition to basic bibliographic information for chemical and chemically related U.S. patents from 1950 and for all patents from 1963. All claims are searchable and printable from 1971 claims for many patents are not available from 1971 to 1974. From 1972, many tides have been enhanced with additional keywords to describe the invention more clearly and to indicate the presence of a drawing chemical structures have been converted so that they display in linear format. Many company names have been standardized, and USPTO classification is updated annually to reflect reclassification projects. 

Once the method has been established and validated, it should be described in full detail such that it can be carried out by any other analyst. Besides the numerous experimental details relating to the chemicals, solvents and solutions used and the chromatographic parameters, important observations such as for instance the findings about the stability of standard solutions should be laid down appropriately in the method description as notes or remarks. But potential health risks to the analytical operator should also be addressed, for instance in a warning note at the beginning of the method description. The following structure of a method description, which was agreed upon as a CEN standard format, is a recommended example. 

Cleaning and Transforming Data. When importing data from diverse data sources (files, databases, spreadsheets, LIMS systems, etc.) into a database or data warehouse, the 4 ta usually needs to be standardized, checked, and sometimes transformed to some common format and content. This allows faster search and retrieval, and serves as a check of data integrity. The rules that define the cleaning/trans-formation process are often termed "business rules," and in the case of chemical data, they may include checking and modification of chemical structures. 

Instrumental methods in chemistry have dramatically increased the availability of measurable properties. Any molecule can be characterized by many different kinds of data. Examples are provided by Physical measures, e.g. melting point, boiling point, dipole moment, refractive index structural data, e.g. bond lengths, bond angles, van der Waals radii thermodynamic data, e.g. heat of formation, heat of vaporization, ioniziation energy, standard entropy chemical properties, e.g. pK, lipophilicity (log P), proton affinity, relative rate measurements chromatographic data, e.g. retention in HPLC, GLC, TLC spectroscopic data, e.g. UV, IR, NMR, ESCA. 

This service takes as input a chemical structure and (if sfandardization is possible) oufputs a chemical sfrucfure. Allowed sfructural inpuf and output formats include SMILES, InChl, or SDF file however, fhe input and output formats need not be the same. As with structure search, the standardization service is queued on PubChem servers, meaning a request may not start right away or may not complete immediately. One may also import and export standardization requests to a local XML file to serve as an example for consfrucfing queries for the PUG interface (described in detail later). 

Deposition of substance information is performed using the industry standard SDF format, which may include using the SMILES or InChl formats as the chemical structure. Depositing properly formatted substance data into PubChem is as simple as uploading a file, via HTTP or FTP. 

Many file formats have been designed for connection tables, usually by software developers who need some means to save a chemical structure to a disk file. None of these can be considered ideal, though the de facto industry standard has for many years been the Molfile and its associated formats and variants, developed by MDL (subsequently acquired by Symyx Inc., and now part of Accelrys ) Figure 6.4 shows an example. Most formats are... 

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