Links the content of a bracketed group with an external feature. A geometric shape such as an arc, line, or arrow. The PE specification enumerates the following Object types: Objects (aka "Elements") express the high-level features of every CDXML document. The purpose of this article is to fill in some of the blanks. Coupled with the useful, but incomplete PE specification, CDX/ML is not an easy format to understand or use. This broad scope, in which chemically meaningful elements are mixed with visual layout and arbitrary vector graphics, makes CDX/ML one the most complicated file formats in cheminformatics. Likewise, a bracket may surround the repeating unit of a polymer. For example, an arrow may be part of a reaction scheme. Sometimes visual elements can carry chemical meaning. Each individual bond can be colored, and the text on atom labels can bear custom colors, fonts, and layout instructions. For example, a given CDX/ML file may contain a chemical structure together with a TLC plate. ![]() Reading (and Rendering) ChemDraw CDX Files in JavaScriptĬDX/ML is an odd cheminformatics file format in that is mixes a molecular graph encoding system with visual elements and styling.Making Sense of the ChemDraw CDX File Format with CDXHexDumper.Reading and Translating ChemDraw CDX Files with OpenBabel.A Brief Introduction to the ChemDraw CDX File Format.Finally, four previous Depth-First articles discuss the CDX binary format: In a similar vein, Open Babel supports reading ChemDraw files, but incompletely. Although the paper says little about the CDXML format itself, the source code may be helpful as a kind of documentation. Two years ago, a paper describing an open source system capable of reading CDXML files was published ( ChemScanner). Those wanting a complete CDXML specification may need to construct one themselves using reverse engineering techniques.Īside from the official PE specification, not a lot of third party CDXML documentation has been published. Several years ago, I wrote an email to technical support noting this problem, but received no response. For example, details on the Arrow element are not available its hyperlink redirects to the Perkin Elmer homepage. Although this documentation is mostly complete, several items are missing. The PE specification lists 263 attributes and 38 elements. Elements ("Objects") and attributes ("Properties") are both enumerated and individually documented. The authoritative specification from Perkin Elmer (PE) offers a starting point for understanding CDXML. In rare cases (e.g., the Style object), an element may contain text data. Each element stores a key/value dictionary as a set of named attributes. The CDXML documentation refers to elements as "Objects." An XML element consists of a named opening tag and a closing tag wrapped in angle brackets ( ). CDXML in a NutshellĪs an XML format, CDXML encodes information in three ways: This article presents a high-level overview of the ChemDraw CDXML format. Often, CDX/ML makes its way from these embedded environments to the outside world via the system clipboard. Although isolated CDX/ML files may be encountered in the wild, it's more common to find them embedded in Microsoft Office or ChemOffice documents. For this reason, this article will refer to the combined binary and XML ChemDraw format as CDX/ML. With minor differences, both formats share similar semantics. CDX is a binary format, whereas CDXML is an XML-based file format. ![]() On ChemDraw's 30th anniversary, C&EN ran a feature about the software's transformative role in chemistry.ĬhemDraw stores documents in one of two formats: CDX and CDXML. Over the years, ChemDraw's list of features has grown from chemical structure and reaction drawing to other tasks, including: biopolymer drawing physical property calculation name/structure conversion NMR simulation and database integration. It's also one of the formats accepted by the USPTO for patents and patent applications. ChemDraw is the de facto standard for creating graphics for publications and presentations, with every major journal providing settings for authors. Every chemist with experience beyond high school will probably have at least heard of it. An Introduction to the ChemDraw CDXML FormatĪlthough it receives relatively little attention in cheminformatics, ChemDraw may be the most important piece of software in chemistry.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |