Obstacle for chemists to use Ubuntu = ChemDraw

[tak1150]

I'm a contributor to gchemutils (which has now incorporated gchempaint) and an Ubuntu developer so I'm especially interested in getting gchempaint in better shape in Ubuntu.

Wow, thank you so much for what you do. You guys are very much appreciated.

Thanks for the review, I'm often amazed at how many apps we have for essentially the same task, and yet many just seem to fall short of the "standard".

Yes. And it seems to a simpleton like me that each app has slightly different strengths and if they pool the resources together they could make something that would challenge ChemDraw?

I'm curious, what version of gchempaint did you try?

currently ver 0.7.91

Since I'm so happy to have a real developer in the audience, allow me to continue my selfish review

As somebody who has draw chemical structures everyday for living, I would really love to see compatibility with ChemDraw files (i've said this before, but b/c everybody else sends me ChemDraw files and I need to send C-D files to them). The moment that feature appears in either Gchmpaint or BKChem, I will erase my Windows partition forever!

OpenOffice.org copy-n-paste support

That'd be awesome!

BTW, what I meant by "resolution" in the last post is how it looks when it's pasted (or inserted) into PowerPoint or Impress and shown on a big screen.

Also what I meant by

bad when it comes to heteroatoms

is that the way you draw in heteroatoms is too much of a hassle for me. In ChemDraw (and I think in XDrawchem) you just place the mouse cursor on the atom and type the atom. Without this feature I cannot draw structures as fast as I need to.

Thanks for reading!
Tak

[Enverex]

Just out of interest, have all bugs for ChemDraw been logged in Wine's Bugsite with all relevant data?

[Iridos]

Hi,

after my attempt to get some info on the bug, I looked some further - this problem here looks similar:
http://bugs.winehq.org/show_bug.cgi?id=4529

An bad mask for characters could also rather well explain the phenomenon...

Also - they are not necessarily "black boxes", but also yellow, blue or green boxes - according to the current text color.

Debugging suggests that it's not one of the 1bpp drawings, that is erasing the letter.
I.

[Iridos]

And about your question if the bug has been entered at wineHQ - I cannot find any bugreports regarding this issue... might even not be so hard to fix. Volunteers?
Problem is, that Chemdraw is proprietary... so someone might have to donate a version to them before they fix it. I.

[modestmelody]

This thread is worth bumping. It's just so much hassel to use Chemsketch in Wine which runs horribly slow and does have some issues (templates appear with strange boxes).

GChem is so close, but totally misses the mark with heteroatoms as stated. There is no way I should have to open up a seperate window to access heteroatoms. It should be easy to add things like R groups etc. It should be easy to draw reaction mechanism arrows, etc.

I need to be able to read/write in Chemdraw format as well as export into a high quality, transparent (preferably), vector format which can be scaled easily and beautifully (for presentations or for varying size within papers), etc. There just isn't a great chemical structure drawing program on Linux, yet.

Oh yeah, and perhaps most important-- structure correction. Sometimes it's a pain in the ***, but it's a great thing to be able to quickly draw something without attention to angle and length and then letting the program standardize it.

[tak1150]

GChem is so close, but totally misses the mark with heteroatoms as stated. There is no way I should have to open up a seperate window to access heteroatoms. It should be easy to add things like R groups etc. It should be easy to draw reaction mechanism arrows, etc.

I need to be able to read/write in Chemdraw format as well as export into a high quality, transparent (preferably), vector format which can be scaled easily and beautifully (for presentations or for varying size within papers), etc. There just isn't a great chemical structure drawing program on Linux, yet.

Hi modestmelody,

Since I started this thread, I have made quite a few contacts with the developer of Gchempaint. He/she (I don't know) has been extremely helpful and responsive (often s/he replies back in a couple of minutes by email!!). Gchempaint 0.8.2 now does the hassle-free heteroatom drawing by keyboard keys! Thanks to Jean (the developer from France).

And yes, s/he has been working on the ChemDraw compatibility issues as well. I think now that it's possible that gchempaint will get to a real production level product within 6 mo to 1 year.

Jean also mentioned that 0.8.3 will come out any day now. I suggest that you give this latest version a try. It's much different than say, 0.8.0.

Blessings,
Tak

[glotz]

A chemist-to-be here. Interesting thread. I use Ubuntu all the way.

[chemicalscum]

I don't think that Chemdraw is the standard for organic chemists, some use MDL ISIS others use Chemwindows/Knowitall as well as those that use Chemsketch.

In my personal view the best 2D chemical drawing program is Chemaxon's Msketch. It is proprietary but is free as in beer. Chemaxon is to Hungary what ACD is to Canada. Chemaxon's bioinformatics and chemoinformatcs software is widely used in the EU by the pharmaceutical industry and they use Msketch as a free loss leader. Similarily ACD's physical porperties, spectroscopy and chromatography products are widely used in North America with Chemsketch as their free loss leader.

Msketch is a Java program that will run on any platform with a recent Sun Java. It is available from:

http://www.chemaxon.com/products.html

You can register for free downloads or you can try it out using Java webstart (if you have Sun Java installed on Feisty then Firefox is Webstart enabled):

http://www.chemaxon.com/marvin/jnlp/msketch.jnlp

At work over the past 10 years we have been through the Chemwindows/Knowitall stream with some use of Chemsketch but we have now dropped Knowitall (Chemwindows went downhill when it became Knowitall) and I have got pretty much everyone on board with Msketch.

It is nice because I can use it at home on Ubuntu and at work on XP. It doesn't cut and paste to OOo but it does cut and paste to Abiword and it is quite convenient to create a page or so of structures in Abiword then export them to OOo as an .odt or.doc. You can then cut and paste them internally in OOo. Now the bad news for tak1150, it doesn't support Chemdraw file formats. So you would have to rely on Openbabel (what Xdrawchem uses) to convert the files, the latest Openbabel claims it will export to .cdxml how good it is I don't know. You can also use Chemsketch in Wine to do file conversion.

Of the FOSS 2D drawing applications gchempaint seems to be coming along really well (though Bkchem is a nice tool too). What I like is that I can download a SDF file from Pubchem and Firefox offers to open it in gchempaint. Hey presto you have the full structures even from a multi part SDF displayed in gchempaint. You then right click on a molecule and it offers to transfer it to ghemical, It transfers the structure to the excellent ghemical quantum chemistry OpenGL based graphical front end, and you can start doing quantum chemistry 3D visualizations using the MOPAC semi-empirical and the MPQC ab initio packages. This makes an Ubuntu desktop a powerful quantum chemistry workstation.

A last word, from way back when I was a grad student 18 years ago the MDL molfile format was the standard for exchanging molecular structures (both 2D and 3D) and it still is. Now you also have the SDF multipart format to extend its capabilities. If you want to exchange structures the MDL formats are the best supported between a large number of different chemistry applications. On this basis the Chemdraw formats should be deprecated. We now have the CML fully open standard for molecular structures but unfortunately I find the structures created in one applicatiion in CML will often not open in another application. I don't know if this is a weakness in the standard or the implementations.

[qwen71n]

In my personal view the best 2D chemical drawing program is Chemaxon's Msketch.

After trying many programs, all of them already discussed above, I also stick to Marvin Sketch, at least for now. It has a number of nice features, but also lacks many things I need, such as drawing simple orbital shapes. I don't have control how the lone pairs and charges look like and I can not move them the way I like. So, I have to draw a reaction scheme then save as an SVG image, and edit it in Inkscape, which is not too easy since Marvin's SVGs are not too edit-friendly.

The result looks very good, but it takes lots of time! There are many, many things I didn't like about ChemDraw, and sometimes I had to use post-editing in CorelDraw, but still it took less time to get exactly what I want.

I'll try to install the latest GChemPaint now, its early versions seemed promising. By the way, does anybody know if there is a BkChem deb package available? I generally don't like to have too many programs hand-compiled.

[tak1150]

I'll try to install the latest GChemPaint now, its early versions seemed promising. By the way, does anybody know if there is a BkChem deb package available? I generally don't like to have too many programs hand-compiled.

Last time I tried BKChem, it is a binary python package that you download and you don't compile it. You just run "python bkchem.py" or something like that.

As for GChempaint, it is somewhat tricky to get all the dependencies; you have to compile most of them yourself since you need the latest of everything to get the latest gchempaint. If you have trouble, post here. I did take notes of what I did to install it that I could post.