File formats

ProcGen generates a scaled 3D model of the test specimen geometry, in the form of a faceted boundary representation. This model is made available for use by other software tasks in the system. The STEP file format (the ISO standard for product data exchange) was chosen to provide future compatibility with CAD models produced externally. In particular part 204 (faceted b-rep) of this standard is used. 

File Format A survey of established file formats revealed that none was particularly suitable, and therefore a dedicated CamuS file format was defined. 

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]. 

Table 2-5. The most important File formats for exchange of chemical structure information.

SMILES. smi SMILES the most widely used Unear code and file format nmm.daylight.com 20, 21... 

PDB file. pdb Protein Data Bank file format for 3D stmcture information on proteins and polynucleotides nmm.rcsb.org 53... 

GIF. cif Crystallographic Information File format for 3D structure information on organic molecules umnv.iucr.org/iucr4op/cif/ 55... 

Tabic 2-6 gives an overview on the most common file formats for chemical structure information and their respective possibilities of representing or coding the constitution, the configuration, i.c., the stereochemistry, and the 3D structure or conformation (see also Sections 2..3 and 2.4). Except for the Z-matrix, all the other file formats in Table 2-6 which are able to code 3D structure information arc using Cartesian coordinates to represent a compound in 3D space. 

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. 

An alternative and much more flexible approach is represented hy the STAR file format [L48, 149, which can be used for building self-describing data files. Additionally, special dictionaries can be constructed, which specify more precisely the contents of the eorresponding data files. The two most widely used such dictionaries (and file formats) arc the CIF (Crystallographic Information File) file format [150] - the International Union of Crystallography s standard for representation of small molecules - and mmCIF [151], which is intended as a replacement for the PDB format for the representation of macromolecular structures,... 

This section provides only a very brief overview of the file formats introduced above. Taking into account that the mmClF file format specifications alone already comprise about 1700 different entries [152], a detailed description of these file formats would occupy an entire book. 

PDB files were designed for storage of crystal structures and related experimental information on biological macromolecules, primarily proteins, nucleic acids, and their complexes. Over the years the PDB file format was extended to handle results from other experimental (NM.R, cryoelectron microscopy) and theoretical methods... 

The REMARK 4-999 records contain other optional, but predefined, remarks, As shown above, the "REMARK 4 record specifies that the analyzed file conform fully with, the current (December 2002) version 2.2 of the PDB file format specification. 

As this short example shows. PDB files use different syntax for different records and both writing and reading such files require much effort. Another problem is the extensibility of this format to handle new kinds of information, which further complicates the file structure. The Protein Data Bank has been faced with the consequences - the existing legacy data comply with several different PDB formats, so they are not uniform and they arc more difEcuh to handle (145, 155, 157]. As mentioned in Section 2,9.7.1, there is a much more flexible and general way of representing molecular structure codes and associated information - the STAR file format and the file formats based on it. 

The Self-defining Text Archive and Retrieval (STAR) file format addresses primarily the problem of the inflexibility of the PDB file format, its fixed sets of allowable fields, and their strong dependence on order, To overcome the problems described, both the data. structure and the actual data items within a STAR file arc self-defined, which means that they are preceeded by corresponding names (labels) which identify and describe the data. The data may be of any type and there is no predefined order of the data. STAR files, in contrast to PDB files, are easy to read and write manually. The whole syntax of STAR files is very simple and is defined by only a few rules ... 

There are also a few additional, but less important, syntax rules proposed in Ref [148], Users interested in a detailed specification of the STAR file format should make themselves familiar with the definitive STAR file written specification [149],... 

NMR-STAIi Results of macromolecular NMR measurements, this file format is used to... 

The CIF file format was quickly and widely adopted by the scientific community for at least two reasons [165J it was, and still is, endorsed by the lUCr and submission of data to the journal Acta Ciystallographka, Section C in a form conforming to CI F assures faster processing and hence faster publication of accepted papers. The current CIF file dictionary defines about 1200 data names, but it is still unable to represent all the details of the crystallographic measurements of macromolecules. Thus, yet another STAR-based data format is needed. 

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. 

ChemWindow supports ten (mostly internal) file formats for input and output, but only Moltile as a genuine exchange format. 

---