MIME types

The QCRNA database is viewable and searchable with a web browser on the internet and it is also contained as a MySQL database that is easily incorporated with parameter optimization software to allow for the rapid development of specific reaction parameters. Molecular structures can be viewed with the JMOL [47, 48] or MOLDEN [49, 50] programs as viewers for chemical MIME types. If the web browser is JAVA-enabled, then the JMOL software will automatically load as a web applet. Both programs allow the structure to be manipulated, i.e., rotated, scaled, and translated, and allow for measurement of internal coordinates, e.g., bond lengths, angles, and dihedral angles. Similarly, animations of the vibrational frequencies are available and can be viewed with either program. 

HTML (HyperText Markup Language)is a specific type of information that can be transferred by HTTP [31]. It is transferred in the same way as any other HTTP message its MIME type is text/html . 

The MIME type application/octet-stream is the default HTTP type - it describes messages that are composed of 8-bit bytes (octets) but are otherwise uninterpreted... 

The text/plain example above demonstrates that HTTP networks can support distributed information systems when given appropriate languages, that is, languages that describe abstractions appropriate to that information system. Many other standard MIME types are useful. Most are very specific, for example, image/gif is a specific format for bitmapped images, application/PDF is a page description format and application/tar is a 4.3 BSD archive. Some describe more general abstractions, for example, application/xml . Private (unauthorized) MIME types are also available, for example, chemical/x-pdb and chemical/x-smiles . 

The introduction of this header was a significant step in making it possible for a browser to successfully handle files of any type. There still remains the problem, however, of defining a set of values for the header that can identify the type of any Internet document. Fortunately, a naming scheme for document types was defined in RFC 1521, which describes a mechanism known as Multimedia Internet Mail Extensions (MIME). This proposal set up a central registry of document types for the Internet. This scheme is sufficient for indicating the type of any document transmitted using HTTP, and therefore the Content-lype header of a document is set to its MIME type. An example of a Content-Type header is ... 

A principal aim of the IJC is to provide a means for publishing original research on the development and implementation of Internet resources for chemists. This includes developments of databases and tools to access them, proposals for new MIME types, proposals for file standards, new software for handling Internet data, new visualization tools, development and implementation of VRML tools for chemists, etc. The journal does not intend to set standards or become a clearinghouse for standards, rather it aims to provide an avenue for the publication of proposals, protocols, etc. that may proceed to become standards. 

MIME type File format Typical extension... 

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. 

The MIME type of data sent to remote browsers by HTTP demons is determined by a local set of rules and conventions laid down in the HTTP demon configuration files. Since only the standardized MIME type information is tiansmitted, no details about the local setup need to be exported. 

Gopher servers were organized as a hierarchical file system, but they differed fiom ftp servers in having each file associated with a specific MIME type which served to indicate in at least some measure the type of content encoded in the file. MIME types are sometimes referred to as metainformation about the content of file. 

D coordinates for a small set of molecules are defined using standard modeling techniques, saved in one of the chemical MIME formats, associated with the appropriate MIME type (e.g., chemical/x-mdl-molfile, chemical/x-pdb, chemical/x-xyz) and placed on a Web server. The molfile format in particular carries an atom connection table, which will allow structures encoded in this format to serve as a substructure search query in an appropriate database if necessary. 

At this point, a molecule coordinate file selected by the user needs to be displayed within a frame of the browser window. Generic browsers are capable of displaying only HTML documents, and some image formats, and at this point the MIME mechanism must be invoked for handling other types of media content. If the user has defined a so-called helper program associated with the three possible chemical MIME types represented in the selection list, then this program will be activated and the coordinate files passed to it as data. 

The properties determined from the image coordinates (Scheme 5, line 21) are inserted into the molecule2.htmr (Scheme 6, line 11), thus dynamically creating a new document which reflects fully the peak selection performed by the user. The molecule is defined as an object (using the EMBED syntax) with attributes and a Rasmol script which is passed to, e.g., the Chime plug-in via the appropriate MIME type (in this instance chemical/x-xyz). 

The approach above enables a document to reference chemical data in terms of a small set of chemical MIME types. 

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