ChemAxon
By drc at Tue, Aug 14 2007 4:35am |
As many know I wrote a GUI for the opensource cheminformatic toolkit Openbabel called iBabel. One of the options is to use the java applet Marvin for structure display and editing. A couple of people have asked me about the availablity of Marvin from ChemAxon so I thought I'd mention they also have a suite of java-based cheminfomatics tools that all function on the Mac. A number of the tools are free for limited or academic use and they have a pretty comprehensive set of demos on their website full details of which are here.
Comments
Quartz
After reading the news about ChamAxon, I downloaded their suite of free programs (MarvinSketch, MarvinSpace and MarvinView). I fell in love with them. They are probably better than ChemDraw and I hope that they can remain available and updated forever. There are two things that dissapoint me, however. First: when I copy a picture to export into another application, I get a non-scalable picture. This happens with ChemDraw too and with who knows how many other application. Marvin has an excuse (it's a Java, cross-platform, application). From what understand ChemDraw is only apparently ported to Mac OS X: it's still based on QuickDraw, not on Quartz (correct me if I'm wrong). In practice, if you want to use ChemDraw (and other programs...), it's more convenient if you OS 9.
The second thing that bugs me is: why nobody complains? Have you find some work-around? Has anybody found an application that reads .mol files (and .cdx, etc...) and renders them in Quartz?
The problem is not limited to Chemistry, nor to Science, but quite general. Up to system 9, all applications exported their pictures into a common format ('PICT'). Today, to be good citizens of OS X, they should all export into the new standard format ("com.adobe.pdf"), but often they don't. It's possible, of course, to paste a PICT into an Quartz application, and even to scale it up, but you lose all the advantages of PDF.
What I mean with "advantages" is the possibility to copy a picture from application A into the application B; then copy a larger picture from B (with the picture from A embedded) and paste it into C, then into D, E... and eventually print the whole work without losing the quality (resolution).
copy/paste image format
Hi,
Thanks for the kind words. I am not the right person to comment on this but a quick scan of the ChemAxon forum yielded these topics
http://www.chemaxon.com/forum/viewpost7997.html#7997
http://www.chemaxon.com/forum/ftopic350.html&highlight=mac+copy
http://www.chemaxon.com/forum/ftopic1055.html&highlight=mac+copy
If you have questions - the forum is the best place to find/ask.
Alex
PS - if you love Marvin then the Instant JChem may be a second honeymoon ;)
is WMF better?
Great to see that you follow Macresearch. My problem, however, is ancient and general, not limited to Marvin. The problem is that there is no consistency on the Mac platform and, to make things worse, nobody cares. I feel that Windows users don't have this problem, because there is a single graphic standard there.
Those who must send a picture to an editor for publication can understand me. Copy & Pasting is not enough. It is necessary to choose the right file format, the right line tickness and the right resolution. I feel that the task of creating a picture for publication has not become easier in the years, but even more difficult. Probably my comment was Off Topic.
Copy/Paste images
I'm not an expert but I did talk to some people about this a while back. I think when you copy a chemical structure to the clipboard you actually copy across several layers of information in addition to the image. Perhaps an option would be to have a "Copy Image" only option, or perhaps save as pdf file format?
ChemDraw to Keynote or OmniGraffle: PICT => PDF
I can't comment on "all" Quartz programs, but I certainly know that if I copy/paste from ChemDraw into Keynote or OmniGraffle, I get a fully vector output. Similarly, this works for MS Word and PowerPoint.
Now, I don't know if CambridgeSoft has updated recent versions of ChemDraw to output PDF when possible. I haven't checked the clipboard types it exports.
I do know that there is code for rendering or converting PICT format into PDF inside your program. Indeed, a quick Google search turned up this Apple documentation:
http://developer.apple.com/documentation/Carbon/Conceptual/QuickDrawToQuartz2D/tq_moving_data/chapter_5_section_2.html
I knew that page
The work-around is not the solution and what is good for you may be not enough for somebody else. PDF is more accurate than QuickDraw, therefore it would be better if all applications could generate Quartz pictures directly. Is this too much to ask? Unfortunately even PDF sometimes is not enough. In the old days EPS proved to be more powerful. With OS 9 and Word 98 I could generate EPS files (with the Print dialog), import them into Word, rescale them end get perfect results. Today I need at minimum an additional step (convert from PDF into EPS using Graphic Converter, hoping it works). If you are curious, the problem arose when a colleague of mine wanted to export a Picture from ChemDraw into iNMR (no problem up to this point) and then export the iNMR picture (formula included) into Word. Eventually he found the solution reported above (through Graphic Converter). Otherwise the formula became very... unprofessional.
EPS format
We plan to implement EPS (Encapsulated PostScript) export in Marvin. Probably, OS X supports EPS copy. If yes, it can be the alternative to provide a pastable vector graphics format for OS X.
Editable Chemical Structures
Whilst I can see that being able to copy an image may be useful in many cases the problem is that is then only an image and you have lost all the chemical content. I can't for instance copy it back into a chemical drawing package and edit it. I don't have a good solution (is it possible to embed a SMILES in the image somehow?) but I'd be interested to hear about ant suggestions.
In theory...
In theory, the clipboard allows pasting in multiple formats, including arbitrary "rich" data formats like chemistry.
In practice, I haven't seen this. For example, do ChemAxon and ChemDraw support a clipboard interchange format like SMILES or SDF?
As for EPS, I'm not sure there's much you can do. But PDF formats certainly allow embedded data. Take a look at LaTeXiT for example. And several people (e.g., Henry Rzepa) have been pushing for embedded chemical data in PDF journal articles.
Clipboard and svg
With the launch of Marvin 5.0 (soon, we promise) the users (and developers) will be able to set preferences on how they want clipboard to function. If you visit this (still pretty buggy) 5.0 alpha and open a Marvin Applet and go to "Edit>Preferences>copy" you can set what goes to clipboard. See this page for more on the current release version (4.x) support for clipboard.
A quick hunt in our forum found this this Image generation example - any potential?
On the 'structure in image file' issue our lead developer reports "we support SVG ..., I can imagine to store the molecule source somehow in comment or as a meta data in the SVG source. Since Marvin 5.0, OLE copy are going to be enabled in Windows (to paste Marvin object into Office documents). OLE includes both the molecule source and the image. But it is a Windows technology, so there is no chance to work it in OS X. "
Since we support PDF export this could be relevant but we think this will problematic - if there are any guides/implementations let me know here or post a request to our forum (better since all relevant developers are tracking.
It might be worth looking at
It might be worth looking at Linkback (http://www.linkbackproject.org/) for OLE type technology.