Standard Structure Exchange Formats

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. 

Parallel to that the MDL Molfile format (see the Tutorial in Section 2.4.6) developed at Molecular Design Limited (now MDL Information Systems, Inc.) became a de facto standard file format [50]. 

Besides the MDL Molfile formal, other file formats are often used in chemistry SMILES has already been mentioned in Section 2.3.3. Another one, the PDB file format, is primarily used for storing 3D structure information on biological macromolecules such as proteins and polynucleotides (Tutorial, Section 2.9.7) [52, 53). GIF (Crystallographic Information File) [54, 55] is also a 3D structure information file format with more than three incompatible file versions and is used in crystallography. GIF should not be confused with the Chiron Interchange Formal, which is also extended with. cif. In spectroscopy, JCAMP is apphed as a spectroscopic exchange file format [56]. Here, two modifications can be 

The different internal and external file formats make it necessary to have programs which convert one format into another. One of the first conversion programs for chemical structure information was Babel (around 1992). It supports almost 50 data formats for input and output of chemical structure information [61]. CLIFF is another file format converter based on the CACTVS technology and which supports nearly the same number of file formats [29]. In contrast to Babel, the program is more comprehensive it is able to convert chemical reaction information, and can calculate missing atom coordinates [29]. 

During the process of conversion, a program may drop some information produced by other software because the format conventions cannot handle this additional information. For example, when the J ACMP format is converted to a Molfile, its content is reduced to structural data only, without spectra data. In other cases, a 

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The International Society for Measurement and Control (ISA) has published the S88.02 standard titled Batch Control Part 2 Data Structures and Language Guidelines, which provides standardized data exchange and user interface formats between competing batch systems. 

Using the XML export function, a work process model can be stored in a structured standard format, which is a universal exchange format for a number of software tools. As XML files can be easily rearranged or altered into a user-defined format by means of XSLT Extensible Stylesheet Language Transformations, [602]), the XML export is useful when WOMS models are to be used by other software applications. Some examples are given in the following subsections. 

Gasteiger, J. Hendriks, B.M.P. Hoever, P. Jochum, C. Somberg, H. JCAMP-CS. A Standard Exchange Format for Chemical Structure Information in Computer-Readable Form . Submitted for pubhcation in Appl. Spectrosc. 

Chemical Abstracts Service Information System Electronic Laboratory Notebooks Internet Internet-based Computational Chemistry Tools Laboratory Information Management Systems (LIMS) Online Databases in Chemistry Spectroscopic Databases Standard Exchange Formats for Spectral Data Structure and Substructure Searching. 

Circular Dichroism Electronic Computer Graphics and Molecular Modeling Electronic Laboratory Notebooks Electronic Publishing of Scientific Manuscripts Factual Information Databases Internet Molecular Models Visualization Object-oriented Programming Online Databases in Chemistry Standard Exchange Formats for Spectral Data Structural Similarity Measures for Database Searching. 

Computation Structural Applications Spectroscopic Databases Standard Exchange Formats for Spectral Data Structure Databases Structure Determination by Computer-based Spectrum Interpretation Structure Representation Topological Methods in Chemical Structure and Bonding, ... 

Chemical structure description has been done by following the JCAMP rules too. Today the MDL Information Systems, Inc. software, distributed worldwide, has defined a standard of its own. The Molfile and SDfile or RDfile formats serve as standards for structure exchange and are a more common alternative to the JCAMP format. 

Chemometrics Multivariate View on Chemical Problems Combinatorial Chemistry Factual Information Databases Fuzzy Methods in Chemistry Infrared Data Correlations with Chemical Structure Infrared Spectra Interpretation by the Characteristic Frequency Approach Inorganic Chemistry Databases Inorganic Compound Representation NMR Chemical Shift Computation Ab Initio NMR Chemical Shift Computation Structural Applications NMR Data Correlation with Chemical Structure Online Databases in Chemistry Spectroscopy Computational Methods Standard Exchange Formats for Spectral Data Structure and Substructure Searching Structure Determination by Computer-based Spectrum Interpretation Structure Generators Synthesis Design. 

This format has been developed to cover the core functionality of the first version of SMD using the syntactical structure of JCAMP-DX (see Standard Exchange Formats for Spectral... 

Aspects of the development of exchange formats have been discussed by Baumgras and Rogers who have commented that at this time the Molfile offers the opportunity for a robust and complete means to transmit structures, but noted that the lack of standardization in the Molfiles created by [different programs] makes the Molfile unreliable for representation of many structures these views appear to be widely shared in the industry. 

Recently some other research institutions in the field of computer chemistry exhibited distinct interest in the SMD format (e.g., Fraser Williams, ORAC Ltd, FIZ Chemie Berlin, Sadtler and others) and compatible formats have been designed for special purposes. For example there is the format by the Joint Committee on Atomic and Molecular Physics, JCAMP, for spectroscopic data storage which on one hand has a more limited scope, but on the other hand puts much emphasis on spectroscopically relevant features like stereochemistry. (Gasteiger, J. Hendriks, B.M.P. Hoever, P. Jochum, J. Somberg, H. JCAMP-CS. A Standard Exchange Format for Chemical Structure Information in Computer Readable Form , to be published). 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

The most important feature of editing software is the option to save the structure in standard file formats which contain information about the structure (e,g., Mol-filc. PDB-filc). Most of these file formats arc ASCII text files (which can be viewed in simple text editors) and cover international standardized and normalized specifications of the molecule, such as atom and bond types or connectivities (CT) (see Section 2,4). Thus, with these files, the structure can be exchanged between different programs. Furthermore, they can seiwe as input files to other chemical software, e.g, to calculate 3D structures or molecular properties. 

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