File Format Exchange

molconvert smiles caffeine.mol (printing the SMILES string of a molecule in a molfile) 

molconvert smiles -a -s clcccccl (dearomatizing an aromatic molecule) 

molconvert smiles a a5 -s CN1C=NC2=CIC(=0)N(C)C(=0)N2C (aromatizing a molecirle using the basic algorithm) 

molconvert mol caffeine.smiles -o caffeine.mol (converting a SMILES file to MDL Molfile) 

molconvert query-encoding. sdf (printing the encodings of SDfiles in the working directory) 

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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. 

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... 

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

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. 

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

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 ... 

The following examples show proper Neutral Data Exchange File formats. 

Other structure-encoding schemas are developed by software vendors and academia such as Daylight Smiles, CambridgeSoft ChemDraw Exchange (CDX), and Chemical Markup Language (CML), and they all have advantages and disadvantages. The MDL CT File Format is the only one that is supported by almost all chemical informatics software vendors. 

A second way of looking at chemical representation is to consider the manner in which the chemical structure data is organized and exchanged, either in some file format or in a database. The most common ways of representing structures and reactions include the following. 

GENERAL NOTE This table is composed of the applicable fields from Appendix Q, ANSI/API 610, Centrifugal Pumps for Petroleum, Heavy-Duty Chemical and Gas Industry Services, with the addition of data fields from the Process Industry Practices (PIP) specification that completely define necessary data for the electronic exchange of ASME B73 pump data. See Appendix Q, API 610 for complete information on the neutral data exchange file format. 

Connection tables are the predominant form of internal representation of chemical structures in computer memory. That is, they form the data structures to which various processing algorithms can be applied. Many external connection table file formats also exist for disk storage and exchange of structure representations. 

It can be seen from the reaction scheme in Fig. 10.3 that an exchange of H" " and 804 ions, and H2O flows (signified by Njj+, Nsq2- and Nh o) is needed between the reaction layer and the bulk of electrolyte for the reactions to proceed. Let us assume that file water exchange is very rapid and does not control the processes in file reaction layer. The flows of H and 804 ions may enter or leave the reaction layer, depending on phase composition of the paste, current density, electrolyte pH, etc. [6]. The process of formation will advance in the direction where the H" " and 8O4 ion flows move at the highest rate. 

H atoms In the SD file exported by Beilstein structures are coded without H atoms. H atoms are, however, requited for calculating some indices and for calculating 3D molecular models. H atoms were thus added according to the valences of all non-H atoms. (The MDL SD file format is a popular exchange format for molecular structures, see [53]. 

In fact, suitable interfaces are necessary for software communication, since the disciplines involved use different applications. Besides, neutral data formats such as STEP AP 214 (ISO 10303) are required due to the fact that the different software components involved often create proprietary file formats. A neutral file format can ease information exchange between many applications, because it helps avoiding bidirectional conversions. 

A useful aspect of many software products is the ability to share information among programs. In this section, we will illustrate how Mathcad can exchange information with other software, focusing on Microsoft Excel and Word. While Microsoft Office is not designed as a mathematical tool, it is used commonly to write reports. The user may receive information in Word and want to transfer it into Mathcad or vice versa. Please note that for Mathcad 14, the user will need to save Excel files in Excel 2003 (.xls). Mathcad 15 supports the new Excel file format (.xlsx). 

The standard file formats can be extended by each discipline participating in order to meet particular requirements. Compatibility can still be guaranteed at different levels (e.g. XML, XDF for data files). Data can be exchanged on the base of a common denominator. 

SMD format " is a computer file format which is being proposed as a standard for the exchange of chemical structure information between different organisations and computer programs. 

The layout editor may have an internal data format that is used to store the layout, and it should also be able to generate output data files in the formats that are commonly used by foundries. These include GIF (Caltech Intermediate Format) and GDSII (Graphic Data System). Some tools do not support these formats, but it may be possible to find eon-verters from one file format, such as DXF (Drawing Exchange Format), to the required format, such as GDSII. Typically the user will transfer the data file to the foundries mask data folder using an FTP (file transfer protocol) command. In some cases the foundry may require the user to submit checksum data to ensure that the file transferred eorrectly. 

A number of file formats exist which serve different purposes in the area of textual data exchange. The simplest of them is of course plain 7-bit ASCII, and also ISO 8859-x text exchange is quite portable. The shortcomings of these text formats are that they neither support stylistic attributes nor content-based markup. 

There are many file formats used to store chemistry-specific information. Most have evolved from historical applications without going through a proper design process. They often started as private formats of some program and were reused in other projects. Unfortunately, some of the most established structure exchange formats are also those which lack most in the areas of flexibility and clear coding syntax and are consequently those which are most heavily abused. Some of the major formats are as follows. 

Efforts are currently being undertaken to standardize the MIME types of a number of popular structure and spectral information exchange file formats. Even without the official blessing of the standardization organizations, the proposed chemical MIME data types are already used in a consensual fashion. This topic is continued in Internet-based Computational Chemistry Tools. The article includes an extensive table of the important chemical MIME format identifiers and their corresponding file formats and typical extensions. 

Most in-house systems permit links to other database management software, in particular to relational database systems such as ORACLE, in order to integrate large amounts of textual or numeric data that already exist there with reaction databases. As many of the reaction retrieval systems mentioned here are able to import and export files in MolFile or RxnFile formats (originally proprietary file formats of MDL, later published), or in the SMD format, even exchange of reaction databases between different retrieval systems is often possible. ... 

The exchange file format MIF (molecular information file, see below) can code stereochemistry using stereovertex lists like those discussed above. 

For transmi.ssion and exchange of chemical structure representations, appropriate Internet protocols will become increasingly important, though basic connection table file formats (and for large databases, where compactness will remain important, modem line notations) will retain significant u.se for some time to come, and will indeed remain important aspects of the Internet protocols, albeit hidden from all but the programmers. 

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