Macs in Chemistry

Insanely Great Science

ChemDoodle Web Components

 

There is a very nice review of ChemDoodle Web Components in the latest issue of Journal of Cheminformatics 2015, 7:35 DOI

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses canvas and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.

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Protein-Ligand Interaction Profiler

 

Whilst this is not a Mac application I thought I'd mention it since it seems a very nice implementation.

The Protein-Ligand Interaction Profiler (PLIP) is a web service and command line tool for fully automated characterization of non-covalent interactions between proteins and ligands in 3D structures.

You can either upload a PDB format file or use the search facility to use a PDB by protein, ligand or enzyme-commission number. You can combine multiple search terms to be more specific (AND search).

I used the PDB code 3EQB, the software correctly identified two ligands, ATP and the more interesting ligand CHEMBL485945.

You can view the results using the embedded 3D molecule viewer JSmol shown in the image below.

plip

PLIP is based on a python command-line application. In case you plan local mass/batch processing, you may want to use this one directly. The source code can be found on PLIP on Git Hub.

I first tried this out on my desktop machine and it worked beautifully, I then tried it out on my iPad and iPhone and the website functioned exactly as expected.

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Macs in chemistry Annual site review

 

It is interesting to look at the Google Analytics data for the website at the end of each year to see what was popular.

Overall there were nearly 200,000 page views with around 70% of the visitors being new to the site. The visitors come from 186 different countries and spent an average of 2 mins on the site.

Around 86% are using a desktop or laptop and 14% using a mobile device (Phone or tablet). 60% of the visitors are using Mac OS, 23% Windows and 10% iOS, with remainder split between Linux, Android and a variety of alternative mobile OS. Safari, Chrome and Firefox are the most popular browsers.

As might have been expected the most popular blog entry was the Scientific Applications under Yosemite, followed by the instructions for installing Molden and 3D stereo viewing on a Mac.

Looking at the blog categories the top 3 were Chemical Drawing, Molecular Modelling and Computational Chemistry.

The most popular review articles were Comparison of clipboard managers, Fortran on a Mac and the review of the metabolism prediction software FAME.

In the Hints and Tutorials section the most popular was the tutorial describing How to create Safari Extensions, Setting up a Mac for Cheminformatics and the ChemDoodle Reviews.

In the AppleScript Section the Curl script was the most popular, followed by the Print clipboard script.

Other popular pages include Data Analysis tools, Spectroscopy and Reference Management.

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Chemplore

 

I was recently sent details of a new website Chemplore the aim is to provide an modern, interactive and easy way to visualize small molecules and macromolecules in the browser. It's built using many modern web technologies and tools including WebGL, SVG and Go.

It pulls data from a variety of sources including PubChem and PDB, and provides interactive 2D and 3D viewers plus a variety of chemical information.

chemplore

It is currently beta and the developers are looking for feedback.


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Status of WebGL

Here is an interesting article highlighting the current status of WebGL. WebGL is finally available by default in all browsers on all platforms and on both desktop and mobile devices.

Scientific applications now have the ability to creatively communicate information in both 2D and 3D through HTML5 across all platforms and can be distributed freely over the internet. We have been making sure that WebGL support in the ChemDoodle Web Components remain compliant and thorough throughout its development. So no worries if you have not yet learned WebGL, as you can take advantage of this powerful 3D graphics technology for free under the GPL license through the ChemDoodle Web Components, joining hundreds of other projects that currently use our library to create the most stunning scientific web and mobile apps.

There is a demo of what can be done with ChemDoodle Web components in the hints and tutorials.

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The MacInChem website annual report

 

Over 55,000 unique visitors, 40% of which are returning visitors

175,000 page views with visitors reading 2 pages per visit on average.

63% of the visitors use MacOS, 22% Windows and about 8% iOS, interestingly if we look at just the week after Christmas iOS usage increases to 15-20%.

The five most popular pages are

MacInChem Home
Mobile Science
MacInChem Blog
iBabel
Applications A-C

Other sections that deserve an honourable mention are

Data Analysis Tools
Reviews
Hints and Tutorial

The two most popular blog entries were

Installing Molden
Science Applications under Mavericks

The two most popular blog categories were chemical drawing and Markdown editors

Chemical Drawing
Markdown Editors

The two most popular applescripts were

Applescript and curl
Applescript and Geektool

The two most popular reviews were

Knime
Markdown Editors

The two most popular hints and tutorials were

Safari Extensions
Remote Printing using Dropbox

The top search queries were
chemdoodle,
markdown pro,
knime tutorial,
jsmol,
ispartan

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MultiMarkdown Composer Updated

I’ve just added MultiMarkdown Composer to the list of Markdown editors, it has just had a major rewrite and includes a host of user requested new features. Full details are in the knowlegebase



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Displaying structures using JSmol and GLMol

I’ve previously highlighted the use of ChemDoodle web components to display molecular structures within a web page, and a recent publication DOI by Henry Rzepa lead me to explore some of the newer additions to the means to render molecules within a web page without the use of applets or plugins.



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Markdown Live

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I mainly use BBEdit and regard it as the “gold standard” but I keep an eye out for other markdown editors.

I added a recent addition Markdown Live to the list of available editors.



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Website Stats

As we come to the end of the year I thought I’d have a look at the website stats.

The site is currently averaging over 20,000 hits per month and around 35% are returning visitors, this compares with around 15,000 hits last year and just under 30% returning visitors. The majority of readers are Mac users (61%) but there are also a number of Windows users (26%), the big change has been with mobile usage which has doubled to around 10% nearly all iOS.

The geographic coverage has expended with the US and UK now accounting for 40% (last year it was 55%), in total 118 different countries are represented in the web logs.

The top search terms were emolecules, Spotlight, Chemdoodle and Vortex.

The top pages were (ignoring the home page)

Mobile Science
Comparison of Chemical Drawing packages
Chemdoodle 5 Review
Applescript
Clipboard Managers
iBabel
Data Analysis Tools

The most popular blog posts this year were

Review of ChemDoodle 5
Elemental for iPad
Chemical Drawing Packages

The most popular blog post of all time remains Siri knows chemistry

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Markdown Editors

Just added Mou to the list of Markdown Editors, Mou offers syntax highlighting, live preview, sync scroll, fullscreen mode, auto save, powerful actions to allow rapid code inclusion, auto pair, custom themes (for those who like to write with green letters on a back background) and CSS, HTML and PDF export, enhanced CJK support. It also supports a variety of Asian languages, and auto-completion but I think only for English.

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Markdown Editors

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I tend to regard BBEdit as the “gold standard” but I keep an eye out for other markdown editors.

I’ve previously mentioned Markdown Pro which has been recently updated, this two pane editor allows you to write your document in one pane whilst giving you an instant preview of how the document will look. Markdown Pro now lets you add custom templates to the in built selection of templates. The application was built for Mac OS X so takes advantage of many Mac OS features.

I’ve also heard good things about Marked it also has two panes and it will update a preview as you work (with several high-quality themes to choose from, or design your own), refreshing every time you save. It can even automatically scroll the preview to where you’re currently editing in your document. With one click you can copy HTML for posting online or including in web pages, copy rich text, save a PDF or print your work. Marked includes tools for handling page breaks, titles, table of contents and much more.

I’ve just come across another editor LoremIpsum, this also has a realtime markdown preview and has been enhanced for Mountain Lion. It includes,, Bookmarks, Markdown smart editing, Cool light and dark themes, Comprehensive keyboard shortcuts, Word and character counters with live update, Autosave and document recovery, In-app themed HTML previews for Markdown documents with in-page anchors, Export your Markdown document to HTML, Well-designed Rich Text editor for .RTF documents.

As they say choice is good.

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Markdown Pro

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I tend to use BBEdit a lot but I keep an eye out for markdown editors.

Markdown Pro has been recently updated, this two pane editor allows you to write your document in one pane whilst giving you an instant preview of how the document will look. Markdown Pro now lets you add custom templates to the in built selection of templates. The application was built for Mac OS X so takes advantage of many Mac OS features.

markdownPro

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Website Update

The migration of the site is now complete, and I think all the missing images, incorrect formatting, broken links etc. are now fixed, many thanks to all those who reported problems.

I’ve been adding Google Analytics to pages so I have a better idea of what is popular and to get a better view of the readership. It is early days yet but it looks like the site is getting 15 - 20, 000 hits a month, with around 70% being new visitors to the site. The average time spent on the site is 4 mins which would suggest most find content that they want to read. As you might expect 70% of the visitors are using Mac OS X, 20% Windows but interestingly 5.5% are now using an iPad. In fact >95% of the visitors using a mobile device are using iOS. Nearly 40% of the visitors from the US and 15% from the UK, the remaining european countries contribute a couple of percent each as do Japan, India, China and Australia there was even one visitor from Trinidad and Tobago who spent 4 minutes browsing the site.

The top search terms are iBabel, emolecules, chemical drawing, atom modelling knime and tutorial.

The most popular pages are the blog, mobile science, the reviews, data analysis tools and applescript.

The RSS feed and Twitter feed seem to be picking up new readers each week.

I’ll look again in six months and see how things have progressed





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RapidWeaver Update

RapidWeaver has been updated to version 4.4, this version requires Mac OS X 10.5 or greater and uses a new document format. This is a free upgrade for users of version 3.6 and higher. Read More...
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Top Queries

Top queries made using site search box Read More...
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Rapidweaver

Rapidweaver update Read More...
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