File formats, standardization

We can create working drawings using Autodesk Inventor file format Standard-idw. Once we have created the drawings, we can place appropriate dimensions and notes on each view. 

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. 

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]. 

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,... 

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. 

When the button "submit smiles is pressed, the SMILES string is sent to the web server of Molsoft, converted to 3D, and the 3D structure is displayed in a java molecule viewer on an automatically created web page (see Figure 2-139). Unfortunately, the Molsoft server does not support downloading of the 3D structures in a standard file format. 

There may he as many basis sets defined for polyatomic calculations as there are cpiantum chemists One would like to define, m advance, the standard basis sets that will he suitable to most users. However, one also wants to allow sophisticated users the capability to modify existing basis sets or define their own basis sets. We have thus defined a IlyperChem basis set file format and included with IlyperChem a number of these. BAS files that define standard basis sets. Users, however, can define as many of their own basis sets as they like using Ih is file formal. The details of th e IlyperChem basis set file formal are described in the IJypcrChcm iie.fe.rm ce m anital. 

Image Files. Only the physical problem of moving or storing files has been discussed herein. The format in which the data is actually stored or transmitted is another part of the process. There are a number of file formats, many of which are proprietary, developed to suit the needs of a particular computer platform or software appHcation. There has been some effort to standardize to a few file types, but many others are in use. A thorough discussion of graphics file formats is available (20). 

There is no standard data format for scattering data. The vast list of supported file formats in the reference manual of FIT2D clearly shows the problem. 

The puipose of this t pendix is to establish a standard ftamat for the storage and transmittal of centrifugal pump data. This standard format is tdso known as the neutral data exchange file format ... 

Of course, there are limitations to this approach that must be kept in mind. First, because we use commercially available components for the data visualization, we are tied to the standard file formats. For the most part these formats are sufficient, but in certain cases they can be limiting. For example, there is no standard for handling multiple entries for a single data field. This becomes an issue when retrieving assay results, because in many cases more than one experiment has been run. Second, this system requires a robust and fast network since many file uploads and downloads to the server are involved. However, in practice we have found these issues to be manageable. 

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

FCS format Flow Cytometry Standard is a file format for flow cytometric data storage. Adherence to this format facilitates the programming for analysis of results. Manufacturers of cytometers have finally begun to embrace this standard. 

Another way to get a structure into the computer is to import (read) a molecule file containing the atomic co-ordinates (and perhaps other atomic and molecular information) into your program. Unfortunately, there is no single standard file format that all programs use. However, some of the commonly encountered formats include those of SYBYL MOL2 files and Protein Data Bank (PDB) files. There are also free programs available for download from the World Wide Web that can interconvert the numerous file formats still in use. 

The next type of standard output is the spreadsheet. These file formats use comma-separated ASCII code, but also add calculation information and addressing information for the columns and rows they occupy. The simplest of these are. DIF files, which originated to allow information transfer between VisiCalc worksheets in the Apple II computer and have been retained as a standard format.. WK files are Lotus-1,2,3 formats and. XLS are Microsoft Excel formats that have become spreadsheet standards, allowing transfer of data, calculations, addresses, and macro programs. 

SAS Transport File Format. We are able to archive data sets in SAS XPORT transport format, also called version 5 SAS transport format. This is an open, published file format developed by SAS Institute. For additional information, see the SAS Institute s Standards for Electronic Submissions and SAS XPORT transport format Web site. 

Standardized and consistent representations of stereoisomers and stereoisomeric mixtures are similarly important for the unique representations of distinct compounds. Recent file formats such as SDF v3000 and ChemAxon Extended SMILES provide clear definition and representation of complex relative and absolute stereochemical configurations. In practice these are not widely used because many commercially available files are represented by established v2000 or SMILES formats and also because HTS compounds are mostly relatively simple low molecular weight structures. 

---