Chemistry Add-In for Microsoft Word

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Chem4Word 2020 is here!

2nd September 2020 by Andy

You can now upgrade to the latest version of Chem4Word! Download it from here and see the new features.

Library

The Chemistry Add-In for Microsoft Word now comes with a pre-loaded structure library from CEVOpen – This data represents about 2100 unique chemical names of volatile plant chemicals (essential oils) from the EssoilDB 1.0 database (compiled from the scientific literature over about 10 years in Dr Yadav’s laboratory). They are made available for re-use by anyone for any purpose (CC0). We would appreciate acknowledgement of EssoilDB and the following people who extracted and cleaned the data during 2019. (Gitanjali Yadav, Ambarish Kumar, Peter Murray-Rust).

The new library is default for brand new installations, but if you already have a library of your own, installing the latest release will leave your library in place.

ACME

You’ve already read that we have a new editor. The editor allows us to create new features in future versions. We’re looking at a number of opportunities to improve Chem4Word. As an example, we’re looking to include the drawing of chemical reactions.

The future

We’re in the process of making some video tutorials of the new features, and we’ll post these as soon as we can.

Meanwhile, keep in touch via our Facebook group where you will hear first about the new features and video tutorials.

And as always, Chem4Word is free and will remain so.  What are you waiting for?  Download it now!

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Chem4Word has a new Library!

1st September 2020 by Andy

The Chemistry Add-In for Microsoft Word now comes with a pre-loaded structure library from CEVOpen https://github.com/petermr/CEVOpen – This data represents about 2100 unique chemical names of volatile plant chemicals (essential oils) from the EssoilDB 1.0 database (compiled from the scientific literature over about 10 years in Dr Gita Yadav’s laboratory). They are made available for re-use by anyone for any purpose (CC0). We would appreciate acknowledgement of EssoilDB and the following people who extracted and cleaned the data during 2019. (Gitanjali Yadav, Ambarish Kumar, Peter Murray-Rust).

The new library is default for brand new installations, but if you already have a library of your own, installing the latest release will leave your library in place.

If you want the new library and to keep the structures from your existing library, we’ll provide instructions on how to do that shortly after release.

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Functional groups now included in Chem4Word 2020

31st August 2020 by Andy

Fed up with having to draw out common functional groups in your molecules?  ACME, our new structure editor now provides easy shortcuts that can save you time and effort.

In the background, we capture the correct chemical formula, so that the correct formula can be calculated. This feature is in its early stages of development. Right now, we are unable to calculate InChI keys and find names from structures with embedded functional groups, but this feature is on the roadmap, so you can expect improvements in future releases.

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A new molecule editor in Chem4Word 2020 – Introducing ACME!

30th August 2020 by Andy

The biggest change in Chem4Word 2020 is the way in which you can draw and edit chemical structures.

ACME is the Advanced CML-based Molecule Editor.  ACME uses Windows’ hardware-accelerated graphics for seamless, scalable drawing and editing.

ACME supports all common molecule editing operations complete with full undo and redo.
 

Whether you’re editing a molecule that is already in your document, or drawing a new one, ACME is the new tool to do the job.

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What’s coming up in Version 3 – Under the hood

12th April 2017 by Andy

A completely new version of Chem4Word

In the last post, we showed you some of the improvements we’re making in the new version of the Chem4Word addin, and how they improve the experience of our users.  In this post, we’d like to share with you some of the changes that we’ve made, but from a developer’s perspective

Changes to the chemistry storage model!

Chem4Word currently stores everything in Chemical Markup Language (CML).  We aren’t going to stop doing this.  CML makes all the information readily available to both software and humans. This is a key advantage that Chem4Word has over other tools.

We looked at how the CML was being stored in the document.  Currently, Chem4Word wraps the CML in a rather complex way before presenting it to you, the user.

The current storage model is directly coupled to word objects by their internal ID. This is what made it impossible to copy and paste chemistry between sections or documents.

We have developed a new loosely coupled storage model, the major benefit is you can now cut and paste structures directly within a document, or even between documents without going through the Navigator.  The Navigator will still be there, and we think you’ll like the changes we’ve made (it now as its name suggests allows you to navigate round the linked chemistry objects).

Better Performance!

Not only does the current version store the chemistry as CML (a dialect of XML), it also manipulates that CML directly.  Every time we draw an atom or bond we have got to go back to the CML document.  This clobbers rendering performance, but it gets even worse when you try to change anything.  Every little change means that we have to traverse the XML document directly, locate the information and transcribe it.  XML is a rather verbose text format.  The overhead of reading and changing this text incurs a big performance penalty.

So, in the new version, we built in an intermediate layer of chemical objects  that sit between the CML stored in the document, and the visual chemistry itself.  So, instead of working directly on the CML, we load it up into the object model,  make our changes there, and either save it back or draw it.  No longer do we have to work directly with text describing the chemistry.  The object model works as a chemist would imagine it would, with bonds connecting atoms.

Initial results are…well, we were about to say ‘encouraging’, but ‘astounding’ would be more accurate.  Small structures show a five-fold quicker rendering.  Large structures, such as insulin, render up to one hundred and twenty times quicker!  What used to be a matter of several minutes to render a large structure now takes a few seconds!

Don’t blink, or you’ll miss it.

FlexDisplay

Because it’s now much easier and quicker to work with the chemistry directly, this opens up all sorts of exciting new possibilities.  On-screen rendering is now much easier than it was, so we don’t have to rely on storing the bitmaps with the structure.

Using the magic of Windows Presentation Foundation (WPF), we’ve been able to replace the old grainy-style bitmaps used for previewing the chemistry with an up-to-date vector graphic. We call this new component the FlexDisplay.

You’ll be seeing a lot more of the FlexDisplay in the new version of the addin.  It’s used  in the new Navigator (viz), the Library (which replaces the gallery), and in the enhanced Search function.  The FlexDisplay also shows atom and bond labels on hovering, helping you to identify them in the underlying CML.

The FlexDisplay is a reusable software component in its own right. So are the object model and rendering components.  A Windows programmer can make their software chemically capable using these three tools, freely available under the permissive Apache license.

New Navigator and Library

We have completely overhauled the Navigator in this new version.  Adding the FlexDisplay to the Navigator tool, along with clearer, office-style  buttons makes the Navigator a little more user-friendly.  All of this is done with data-binding to the document’s chemistry models, meaning lightning-fast response, along with the better graphics.

 

Old Navigator New Navigator

Goodbye Gallery – Hello Library!

The old Gallery stored structures in a Word document template.  This inefficient storage model also causes problems for users of the add-in, wiping out customization that they may have made to document styles.  It was one of the drivers for us to make significant changes to the add-in.

The Library no longer uses document  templates to store its structures. We now use a simple SQLite database to store the chemistry.  This approach allows  users to edit structure names easily and search them, so the Library can potentially store thousands of structures and you can find them easily.  It also opens up storing future metadata with the structures, like text tags, and searching on them.

Plug-in Architecture

This is the least visible improvement to Chem4Word.  It is also the most important.  We’ve restructured the program from the bottom up.  Plug-in components now provide configurable searching, editing and rendering. If a new online data source comes along, or you want to incorporate a new editor, then it’s simply a case of writing a wrapper to predefined standards and installing it.

We will publish these standards as part of the new version release.  If you want a preview of this version, then please get involved in the beta testing.  We want to make this the best version of Chem4Word yet!

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Filed Under: News, Under the Hood Tagged With: Chem4Word, Developer, FlexDisplay, Gallery, Library, Navigator

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