Chemistry Add-In for Microsoft Word
CML is Cool
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.
The new version will allow you to use our brand new, intuitive Chemistry editor (ACME).
Have a guess to see what ACME stands for.
The first Chem4Word course is now available on Udemy! And it’s free, just like 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
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).
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!
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.
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.
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| Old Navigator | New Navigator |
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.
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!
We have been working on a new version of the Chemistry addin for Microsoft Word and we’d like to show our progress so far. The new Ribbon and Library are shown in the picture below. We also have a new version of the Chemistry Navigator and a replacement for the old Gallery, now called the Library.
We decided it was time to take stock. It’s about ten years since Chem4Word was first released. A lot has happened since then, and we wanted to make sure we could meet both present and future challenges.
We had a long discussion among the team about what direction we should take after we released the last version. We came up with two possibilities:
We could have followed both of these approaches But it made more sense to put the product on a firmer footing before we built anything new onto it.
So, what have we done to improve the product? Well the first thing we did was to listen to your feedback and address some longstanding gripes.
You complained about the idiosyncratic ways that Chem4Word stored its stuff in a Word document template. So we dealt with those issues first. Then we went on to address performance problems. We also had some issues with the way that the Gallery and Navigator displayed structures as low-quality pictures.
You should find the new version of Chem4Word familiar. Most of the old features are still there. We’ve just made them work much better! And we’ve got rid of those you didn’t like or didn’t use.
Our first step was to change the way that the chemistry information is stored inside the Word document, before it is presented to you in the form of a structure/label or formula in the document. A radical change to the storage model means that you can now copy and paste structures inside a document and even between documents.
We also addressed the performance of the code that generates the structures that you see in your documents. By changing the way the add-in works with the chemistry information in the document, we have made it very much quicker to render more complex structures with larger numbers of atoms and bonds. To give you an idea of the speed improvement, have a look at this video that compares the performance of the current add-in with the version currently in development.
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 low quality bitmaps of the structure for the Gallery and Navigator tools.
We have used this new tool, the FlexDisplay in the new Navigator and the new Library to get high quality display of chemical structures in these two tools.
We completely overhauled the Navigator. This lists all the chemistry in the current document, and allowing you to paste copies and links to embedded chemistry. The new version does much the same as the old one. It also includes new Browse buttons. These allow you to locate and show all the instances of a given chemical within the document.
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| Old Navigator | New Navigator |
As you can see, it follows the new-look Office style. It also uses the FlexDisplay to display chemistry, making the display much clearer (and quicker). See how much clearer and more colourful the structures are compared to the old-style Navigator.
One of the biggest gripes you had about the way Chemistry for Word worked was that it replaced the document’s template with it’s own version, thus eliminating any styles and other customizations you had done.
You hated this, so we have completely removed the Gallery and replaced it with a new component: the Library. The Library superficially resembles the Gallery, but as you can see above it lives in its own task pane, flanking the document along with the Navigator. You can save structures to the Library, change their names, and insert them wherever you want to in your document. This is handy when you are constantly referring back to a core set of structures, say, when preparing teaching materials.
Best of all, the Library doesn’t use any templates to store its structures, so you won’t lose any document customizations that you have already made.
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