To be honest I can't remember when I last used Perl but this publication brought back a few memories DOI.
HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods.
There is also a very interesting extension HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program
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 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.
I use markdown extensively on my websites, and whilst I mainly use BBEdit I do keep an eye out for new Markdown editors to add to this listing. I was recently alerted to Texts is a cross platform editor that uses plain text Markdown as file storage format. Documents can be published to PDF, HTML, DOCX, EPUB, and other formats from single source.
I just thought I'd like to thank all those who contributed to the Scientific Applications under Yosemite web page, many users and developers contacted me either via email or in the comments section and they certainly added information about applications that I don't have access to.
To date the page has been viewed well over 10,000 times with readers from 188 different countries. Viewers spent an average of just under two minutes on the page and it still attracts 800 pages views a month.
Given that 75% of the visitors to the site are now using Yosemite I suspect most scientists have now made the transition and I won't be updating the page any more. Once again thanks for the contributions.
This will probably be the last update, the page has been viewed by over 10,000 people so it looks like it was a very worthwhile effort. Many thanks to all those who contributed.
Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Given that this seems to be such a major upgrade I thought I’d set up a spare machine to test applications before I update my main machine. I’ll update the list regularly and feel free to send in information.
I have a number of applications/libraries/toolkits installed using Homebrew and installed in usr/local, this is known to cause extended installation times for Yosemite. So don’t worry if it appears the instal is stuck at 1 min remaining.
If you do use Homebrew then it is worth updating
brew update brew upgrade
Aabel 3 appears to be working fine
BBEdit version 10.5.13 and newer are compatible with Yosemite
Beaker all seems OK
Brainsight 2.2.12 is best used under 10.10.2
Ch Professional offers numerical computing and plotting which works for Yosemite.
ChemBioDraw versions 12, 13 and 14 all function as before. In particular round-trip editing still works! There are a couple of issues emerging * Sometimes it becomes "almost" unresponsive. Quiting and reopening the application usually fix the problem. * There is a frequent crash on quit. * Sometimes the popup window for "save as" is too large and the "save" and "cancel" buttons get outside the screen.
ChemDoodle all seems to work fine
Chenomx NMR Suite latest version developed under Yosemite but website not yet updated.
Chimera aka UCSF Chimera versions 1.10 and higher are working on Yosemite.
Conquest and Mercury from CCDC works fine but you may need to reinstall Quartz (see below)
COMSOL 5.0 works out of the box on Mac OS X 10.10 Yosemite. We now have instructions and a patch for installing and running COMSOL 4.4 Update 2 on Mac OS X 10.10 Yosemite. You can find the instructions at www.comsol.com/support/updates/comsol44p3 COMSOL 5.0 works out of the box on Mac OS X 10.10 Yosemite.
Cytoscape 3.1.1 seems to be working fine
DataWarrior no issues
EndNote X7.2 works well with Yosemite.
Findings Electronic Notebook no issues, only small issue is that the ‘+’ button of the window does not trigger full-screen, though it can still be done via the Window menu.
Graph Builder has been updated to support Yosemite, the movies at http://www.vvidget.org show Graph Builder on Yosemite and also show how to build a custom data visualization application using Xcode, the Swift programming language and Graph Builder and a link to the Xcode project files to build the app.
Gravity Lab updated to allow printing under Yosemite.
IDL 8.2 and earlier gags on a missing reference in libPng.dyld, but IDL 8.3 and later is OK
Igor Pro version 22.214.171.124 works fine
iNMR A minor problem has been reported just once, only with the latest version of Mac OS Yosemite. When the the user opens the dialog that adds experiments to a Cross Peaks Manager, the list therein contained does not show the first item. It reappears after manual scrolling. The solution has been found and the problem will disappear completely with the next version of iNMR for Mac. If you have seen the same kind of problem in another dialog, please report it.
KaleidaGraph all OK.
LabQuest Viewer has preliminary support for Yosemite.
MacVector 13.0.6 No significant issues reported
Maestro 10.10 and the rest of Schrödinger Release 2014-4 are all Yosemite-compatible
Mathematica no issues reported
MOE works fine but you may need to reinstall Quartz (see below), no problems reported with running the license server under Yosemite, MOE 2014.0901 update runs fine.
Molden I just got this message from the developers, “I just got round to compiling molden on yosemite and everything worked as expected”
OpenBabel no issues so far
Opsin all works fine
OSRA no issues
Papers Current version is compatible but not optimised, they hope to have a beta out of a substantially redesigned version next week.
Pro Fit 6.2 appears to work fine.
PhySyCalc - The only scientific and engineering calculator on the app store with units just updated.
Pybel no issues reported
PyCharm works fine
Pymol All these are confirmed to work:
- MacPyMOL 126.96.36.199
- MacPyMOLX11Hybrid 188.8.131.52 after XQuartz reinstall (see below)
- Open-Source PyMOL with homebrew
Known issues with MacPyMOL:
- Movie export broken.
Edu-only-PyMOL (free Student version)
Does not work.(Now updated to work with Yosemite)
No reports so far about about - Other legacy versions (0.99 etc.) Apparently progam will not open - Open-Source PyMOL with fink or macports
PyRx 0.8 for docking works fine
RDkit no issues reported
RMN - multi-dimensional signal processing for Bruker NMR, Varian/Agilent NMR, JEOL NMR, Tecmag NMR, Chemagnetics Spinsight, and one-dimensional JCAMP datasets.
SeeSAR all seems to be working fine
Sente 6.7.8 seems to run fine, except that it cannot open a reference library from the File > Open... dialog box. Workaround is to open from Finder.
SMARTCyp downloaded app runs fine.
Spartan 14 does not work because the Sentinel drivers are broken in Yosemite. The problem is NOT with Spartan, it is with the SafeNet developed Sentinel Run-Time Environment driver (the license manager). SafeNet has not given a definitive date when they will release an updated driver with Yosemite compatibility, but they are working on this. Best advice is to not upgrade but if you have to then contact email@example.com for a temporary alternative license procedure. UPDATE Spartan’14 version 1.1.9 includes the new Yosemite supported driver from SafeNet. (http://www.wavefun.com/support/spmac/supportmacLV.html)
Torch no issues
VarSeq no issues
Vortex Upgraded when the developer preview came out. All works fine
The VVI products work well enough on Yosemite, but I'd like to achieve a higher level of quality for Yosemite (and iOS/iPad). There is an ongoing beta program for this product: https://itunes.apple.com/us/app/graph-ide/id904733611?mt=8 which is Graph Builder reincarnated on the iPad. There is also a beta program ramping for Graph Builder on Yosemite: https://itunes.apple.com/us/app/graph-builder/id470597599?mt=12 but a last minute interaction bug with Yosemite has delayed that for perhaps a few days. Please feel free to broadcast this information as you see fit. Beta program participation should be directed to firstname.lastname@example.org
VMD no issues reported
WHICHCyp downloaded app runs fine
Wizard Pro is fully Yosemite compatible
XQuartz it seems the Yosemite installer deleted the symlink between /opt/X11 and /usr/X11; you can either reinstall Quartz or try "ln -s /opt/X11 /usr/X11"
Updated 10 February 2015