Chemoffice 2012

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About four years ago I speculated that JavaScript may be capable of filling some important holes in chemistry software. Since then, a number of important events have taken place to move JavaScript onto center stage as a programming language, including the release of Chrome with its huge JavaScript performance increases and rocket trajectory to overtake IE as the most popular browser, the runaway success of iOS as a computing platform free of browser plugins, the renaissance of server-side JavaScript through Node.js and other frameworks, and a dazzling array of languages like CoffeeScript that compile to JavaScript.

JavaScript for cheminformatics has started to look a lot less improbable as well. In late 2010, my company began distributing the first copies of its chemical structure editor ChemWriter - a complete rewrite of the original Java applet in JavaScript. Following this, we released the plugin- and server-free chemical structure rendering package ChemVector. Other companies now offer products in this space as well, with indications that big players are now starting to take notice.

This article highlights a small part of some work I'm now doing that demonstrates the readiness of JavaScript to solve difficult cheminformatics problems.

Demo: Read a ChemDraw File

Given an arbitrary binary ChemDraw CDX file, it's now possible to print out the encoded object graph in a JavaScript console. For example, this file generates this output:

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For background, see previous D-F articles on the ChemDraw CDX file format and the CDX HexDumper utility.

ChemDraw JS is a web version of ChemDraw, ready to be embedded into your web application to make them 'ChemDraw Smart'. Site Subscription Gallery. Site Subscriptions are a convenient, affordable way to access or distribute the application throughout your. Reading (and Rendering) ChemDraw CDX Files in JavaScript 2012-06-01T00:00:00.000Z. About four years ago I speculated that JavaScript may be capable of filling some important holes in chemistry software. ChemOffice+ Cloud. ChemOffice+ Cloud is the Suite that transforms your chemical drawings into chemical knowledge. It builds on the foundations of ChemDraw Professional and adds access to a broad set of powerful scientific tools. to enable scientific research. ChemOffice 15.1 is the latest release of the ChemOffice suite of personal productivity tools for chemists and biologists. ChemOffice helps scientists efficiently capture and share their work, visualize and gain a deeper understanding of their results, and correlate biological activity and other properties with chemical structures.

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Being able to visualize the contents of arbitrary CDX files this way is an important aid to debugging and a prerequisite to developing full-featured graphical display capability.

Why Read ChemDraw Files in JavaScript?

It's a pretty safe bet that any organic chemist who has written a report, submitted a journal manuscript, or filed a patent has used ChemDraw. As a result, ChemDraw files are everywhere in chemistry.

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If you've spent any time watching how chemists work, the need to manipulate CDX files may be obvious. Even so, I'd like to offer a specific example taken from a recent project that illustrates that the need to work with CDX files can come from some unlikely places.

Reagents is iOS Organic Chemistry reference app that I co-developed with James Ashenhurst. It makes heavy use of ChemDraw CDX files to display structures and reaction schemes.

These structures and reactions schemes are automatically pre-rendered through AppleScript automation of the ChemDraw application. Although this works, it's far from optimal. For example, Reagents runs on iPad 3 (retina) displays. To prevent pixellation, our horizontal resolution measures in the thousands of pixels. The large size of the resulting images means more storage space and longer download times. But the biggest problem lies in the fact that every time we make changes to these ChemDraw files, we must regenerate the corresponding raster image.

It would be so much better to dynamically render these ChemDraw files inside an iOS UI element such as UIWebView.

We'd also like to do interesting things with the ChemDraw files themselves. I won't spill the beans here, but suffice it to say that if we're successful you'll be seeing one or more new iOS apps that repurpose the Reagents content in some interesting ways.

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Yet another use case for a pure JavaScript CDX reader and display component would be in interfacing the system clipboard with a paste target in a Web page. ChemWriter currently supports this capability on Windows, but there's much more we could do.

Larger Vision

JavaScript has established a strong foothold in every area of modern computing: tablets; mobile; web browser; and server. But at the same time, there is no full-featured cheminformatics platform, commercial or otherwise, for building chemistry software in JavaScript.

We have many of the components for such a platform, but they're spread over different products and applications. Having been developed over the course of a couple of years, the code itself show signs of needing a refresher. A unified, well-designed JavaScript platform centralizing core cheminformatics functionality would be a valuable asset in the continued development of useful tools and applications.

Given the centrality of the CDX file format in chemistry, we're starting there first.

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Go to http://www.cambridgesoft.com/login/; to login to you Account. If you don't have a CambridgeSoft Account yet, register first at http://www.cambridgesoft.com/register/Default.aspx using your MIT email address.

NOTE: if you are a PC user with Windows XP, you might have to install Microsoft .NET Framework Version 2.0before you are able to install BioChemDraw.

New Users

Once you have logged in:

  • Go to My Site Subscription (right hand side under Services)
  • See Accessing Your Software in the middle of the screen and click 'Download Site License Software'. This will take you to a page of links to download the software.
  • Scroll down to ChemBioDraw Ultra 12.0 Download edition
  • Choose the appropriate download link (PC or MAC version) and go ahead with the download.
  • The Serial Number and Registration Code (MACs only) will be emailed to you immediately. Look for an email from customer_service@cambridgesoft.com. You will need this to complete the installation.
  • In case you do not receive an email with your codes, please check your spam filters or visit http://www.cambridgesoft.com/login log in with your email ID & Password, click on 'My Downloads'. You will be able to see the details and the serial number.
  • Complete the installation using the serial number (and registration code)

Version 12.0 Reactivation

MIT Libraries has renewed ChemDraw annual site license, and in order to maintain your working copy of ChemDraw Ultra 12.0, please follow the steps below. If you experience any trouble, contact Chemistry Librarian.

  • PC users: choose option I, II or III
  • MAC users: option choose IV or V

I. If you are using ChemBioDraw Ultra 12.0 version 12 on a PC:

You need to reactivate with your existing serial number. Reactivating will extend your current software's license until 10/6/2011.

  1. To reactivate, launch the ChemDraw application and click 'Activate' on the 'Help' menu then put in your serial number (it shows up automatically if you originally activated on the same machine).
  2. Click on 'Activate over the Internet' to complete the activation.
  3. The software will display a warning message one month before the previous expiration date, and you can close that window then click 'Activate' on the 'Help' menu.
  4. If your software has already expired, you will be immediately prompted to activate when you launch ChemDraw.
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II. If you are using ChemBioDraw Ultra 12.0 version 10 or version 11 on a PC:

You may either upgrade to version 12, or may keep version 10 or 11 by reactivating with your existing serial number. Reactivating will extend your current software's license until 10/6/2011.

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  1. To reactivate, launch the ChemDraw application and click 'Activate' on the 'Help' menu then put in your serial number (it shows up automatically if you originally activated on the same machine).
  2. Click on 'Activate over the Internet' to complete the activation. If that fails (because you don't have an Internet connection) then you can activate by phone, fax, or email to receive an activation code.
  3. The software will display a warning message one month before the previous expiration date, and you can close that window then click 'Activate' on the 'Help' menu.
  4. If your software has already expired, you may upgrade to version 12 now or anytime, by re-downloading (and getting a new serial number) via http://sitelicense.cambridgesoft.com/sitelicense.cfm?sid=488%20%3Chttp://sitelicense.cambridgesoft.com/sitelicense.cfm?sid=488http://sitelicense.cambridgesoft.com/sitelicense.cfm?sid=488

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III. If you are using ChemBioDraw Ultra 12.0 version 9 on a PC:

You need to download the 12 version. Your 9.0 version will stop working on 10/6/2010 and there is no way to extend that older version.

  1. To download the version 12 software, go to: http://sitelicense.cambridgesoft.com/sitelicense.cfm?sid=488%20%3Chttp://sitelicense.cambridgesoft.com/sitelicense.cfm?sid=488http://sitelicense.cambridgesoft.com/sitelicense.cfm?sid=488
  2. You will be emailed a new serial number which will be valid until 10/6/2011. In other words, you will simultaneously be extending your license AND upgrading your version.

IV. If you are using ChemBioDraw on a Mac

You need to get a new serial number and registration code.

  1. 1. To get your new codes, look for the link about renewed serial numbers on the following page: http://sitelicense.cambridgesoft.com/sitelicense.cfm?sid=488; login with your MIT email address.
  2. 2. Click on the 'download software' link under MAC version of 'ChemBioDraw Ultra 12.0 Download Edition: One Year Subscription'. This will set new serial number and registration code for. You do not actually have install the software if you already have version 12.0.
  3. 3. You will be emailed a new serial number and registration code which will be valid until 10/6/2011. The Mac software and serial number are included on the same download page and same email message as PC users, but are marked as Mac.

V. If you wish to continue using an older version of ChemDraw on a Mac

  1. If you want to upgrade to the latest version, see instructions in item IV above. The following instructions are only if you prefer to continue using an older version on the Mac.
  2. If you want to keep the older version, send an email from your institutional email address to customer_service@cambridgesoft.com with the following information included:
    1. The exact product name and version that you are using
    2. Your current serial number
    3. The institution name for your site license
  3. You'll receive an email back with a new registration code (you re-use the same serial number).
  4. Enter that registration code on the popup message that indicates your site license is expiring.

If you have questions about obtaining this software, email vsls@mit.edu.

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