Macs in Chemistry

Insanely Great Science

Vega Hub

 

Vega Hub a variety of models for predicting properties.

Compared with many existing QSAR models, we have put greater emphasis on ensuring that the models generate transparent, understandable, reproducible and verifiable results. To achieve this, a series of tools has been optimised, which can relate the results obtained for the target chemical to the results obtained for similar (structurally related) compounds.

Models can be downloaded here

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PLUMED PLUgin for MolEcular Dynamics

 

PLUMED is a community-developed PLUgin for MolEcular Dynamics. PLUMED works together with some of the most popular MD engines, such as ACEMD, Amber, DL_POLY, GROMACS, LAMMPS, NAMD, OpenMM, ABIN, CP2K, i-PI, PINY-MD, and Quantum Espresso. In addition, PLUMED can be used to augment the capabilities of analysis tools such as VMD, HTMD, OpenPathSampling, and as a standalone utility to analyze pre-calculated MD trajectories.

Installation

  • MacPorts, ports plumed and py-plumed, both as a pre-compiled binary (with basic capabilities) and source code (with more MPI and compiler options and including optional modules). Port plumed-devel provides a snapshot of the current development version.
  • Conda-forge, recipes plumed and py-plumed, as pre-compiled binaries with basic capabilities. Other conda binaries containing development versions or nightly builds are available on the plumed channel.

The API is accessible from multiple languages (C, C++, FORTRAN, and Python).

The PLUMED consortium. Promoting transparency and reproducibility in enhanced molecular simulations, Nat. Methods 16, 670 (2019) DOI

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Interactive plots in Jupyter Notebooks updated

 

I've been using Jupyter notebooks for a while for a wide variety of projects.

I've been looking at ways to produce interactive plots within a Jupyter notebook and after trying a couple of options to produce interactive data frames, in addition to 2D and 3D scatterplots including structures on tooltips.

Full review and the Jupyter notebook are here.

plotjupyter

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Interactive plots in Jupyter notebooks

 

I've been looking at ways to produce interactive plots within a Jupyter notebook and after trying a couple of options I used Plotly. This seems fairly straight-forward to use and I can produce interactive data frames, in addition to 2D and 3D scatterplots.

More details are shown here together with the jupyter notebook. It is very much a work in progress and suggestions are welcome. In particular, whilst I can get text to appear when hovering over a data point I'd be interested in ideas of how to get the structure displayed when you mouse over a point.

3DplotinJupyter


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Scientific Applications under Catalina: Update 13

 

General Issues with Catalina

If you want an overview of Catalina I'd recommend the excellent ars-technical's review.

According to Wikipedia Santa Catalina is a rocky island off the coast of the U.S. state of California in the Gulf of Santa Catalina.

1280px-Santa_Catalina_Island_California_Panorama

By Thomas Pekin - Thomas Pekin, CC BY-SA 2.5

Apple has officially confirmed that the following Macs are compatible with Catalina:

  • MacBook (Early 2015 or newer)
  • MacBook Air (Mid 2012 or newer)
  • MacBook Pro 13"/15" (Mid 2012 or newer)
  • Mac mini (Late 2012 or newer)
  • iMac (Late 2012 or newer)
  • iMac Pro (2017 or newer)
  • Mac Pro (Late 2013 or newer)

There are a number of changes to the security, in particular installation into the root folder is not allowed. After upgrade you may find it moves items into a folder on your desktop called “Relocated Items,” in the Security folder.

zsh is the new default shell for new users (bash is the default shell in macOS Mojave and earlier), so if you are upgrading you may want to change your default shell to zsh. There is an Apple Support page giving details

zsh is highly compatible with the Bourne shell (sh) and mostly compatible with bash, with some differences. For more about zsh and its comprehensive command-line completion system, enter man zsh in Terminal.

You might also like to look at oh-my-zsh

A delightful community-driven (with 1,300+ contributors) framework for managing your zsh configuration. Includes 200+ optional plugins (rails, git, OSX, hub, capistrano, brew, ant, php, python, etc), over 140 themes to spice up your morning, and an auto-update tool so that makes it easy to keep up with the latest updates from the community.

This book might also be useful Moving to zsh.

Notarization

I suspect many users will now see more Notarization warnings.

notarisation

Notarization gives users more confidence that the Developer ID-signed software you distribute has been checked by Apple for malicious components. Notarization is not App Review. The Apple notary service is an automated system that scans your software for malicious content, checks for code-signing issues, and returns the results to you quickly. If there are no issues, the notary service generates a ticket for you to staple to your software; the notary service also publishes that ticket online where Gatekeeper can find it.

You can notarize several different types of software deliverables, including:

  • macOS apps
  • Non-app bundles, such as kernel extensions
  • Disk images (UDIF format)
  • Flat installer packages

Beginning in macOS 10.14.5, all new or updated kernel extensions and all software from developers new to distributing with Developer ID must be notarized in order to run. Beginning in macOS 10.15, notarization is required by default for all software.

You can still use the software but you need to go to the Systems and Privacy pane in the System Preferences, form there you get the option to open the application anyway, it should be remembered so you only have to do this once.

SysPrefSecurity

Apple have been warning for several years now that all support for 32-bit apps would end, Apple has a page describing the reasons for moving to 64-bit. In addition support for the legacy Java 6 has finished. Catalina does include Python 3 by default, where older versions of the operating system only included Python 2.7

Anyone tried running 32-bit apps using emulation (Parallels or VMWARE?).

Scientific Applications

I've contacted all developers I know and their responses to date are shown below.

4-Peaks no issues reported

alvaDesc software is completely 64 bit and it is ready for Catalina.

Amsterdam Modeling Suite the latest update works under Catalina. However there are still some minor issues (e.g. vtk bug on windows maximizing, should be sorted soon).

Anaconda Anaconda’s default install location in the root folder is not allowed, suggestion is Start fresh with a new Anaconda installation. Pay attention during installation to make sure that your install path is a subfolder of your home folder, such as /Users/me/anaconda3. You may be able to move the Anaconda folder from "Relocated Items" to a new location but be aware it may include hard coded paths. More discussion here.

APE A plasmid Editor If you are having trouble with crashing in Mojave or Catalina, re-download to get the latest update.

Avogadro no issues reported

BBEdit version 13 is compatible with macOS Catalina

BioSolveIT report SeeSAR and infiniSee have been tested successfully on Catalina

Brainsight Brainsight 2.4b6 and later have been tested against Catalina and there are no known problems.

ChemAxon Most of our software in general requires Java, so as long as the appropriate Java version is installed, there should be no problem. However maybe notarisation issues first time using. More info.
Update

We are pleased to inform you that the MarvinSketch installers are notarized from version 19.26. When you download our latest Marvin installer for mac OS, GateKeeper will know that the software is safe and allow you to install it without any problem

ChemDraw I've posted question on forum but no response yet. A reader reported "ChemDraw 18.2 appears to run with no new issues".

ChemDoodle ChemDoodle v9 and ChemDoodle 3D v4 are fully supported, signed for Gatekeeper, and notarized by Apple on macOS Catalina. There is only a single reported issue from some users, where either program will fail to fully startup on Catalina if they were installed prior to upgrading the OS to Catalina. In these cases, removing the “ChemDoodleSettings” folder or the “ChemDoodle3DSettings” folder in the user’s Documents folder and restarting the application will resolve the issue. We have no other known issues on Catalina at this time.

Conquest and Mercury from CCDC CSD software from the CCDC. The full CSD software suite, including Mercury, ConQuest, Mogul, GOLD, CSD-CrossMiner and other components, have been tested and are working on Catalina. Whilst our applications are all signed, due to the new "notarisation" feature on Catalina, users may need to authorise the software via the Security option in System Preferences at the point of installation. Our next major software release, the 2020.0 CSD Release which will be available before the end of 2019, will be formally supported on macOS 10.15 Catalina, as well as 10.14 Mojave and 10.13 High Sierra.

Cresset all works fine but there are notarisation issues.

CrystalMaker

  1. CrystalDiffract 6.8.3 is a 64-bit “Cocoa” app and works fine.

  2. CrystalMaker X 10.4.6 - another 64-bit app “Cocoa” app - also runs seamlessly with “Catalina”

  3. SingleCrystal 3 is a 32-bit app and so won’t run. However…

  4. SingleCrystal 4 PUBLIC BETA works beautifully on Catalina. More information - including a sign-up form - can be found at:

    http://crystalmaker.com/singlecrystal4/

SingleCrystal 4 PUBLIC BETA will run until the end of December and is free to eligible users. All applications are code-signed and officially “notarized” by Apple.”

CYLView 1.0 does not work under Catalina.

DataWarrior

Delta Delta V5.3.1 is not supported by Apple macOS 10.15 Catalina. Delta will not install or operate under macOS 10.15 Catalina. We are working on an update for Delta to run on macOS 10.15 Catalina and will post it as soon as it is available.

DEVONagent here's a minor incompatibility that keeps the application's splash screen from being closed. You can expect a free maintenance update for DEVONagent that addresses this issue later this month.

DEVONthink version 3 is 64-bit compliant

Elemental We have a new one. Think it got stuck in “notarization”. Will appear on the support site in a few days hopefully.

EndNote EndNote X9 for macOS will be extensively updated for compatibility prior to the launch of Catalina.

EnzymeX no issues reported

EverNote No issues with Evernote but Safari extensions dropped so no Evernote Web Clipper

Findings seems to be working fine, no issues reported.

Fujitsu ScanSnap If you own one of the older Fujitsu ScanSnap scanners like the S300M, S500M, S510M or S1500(M). Fujitsu has announced that they will not update the ScanSnap Manager software that drives these scanners to make them compatible to macOS Catalina; only the newer ScanSnap Home will be available for current and future versions of the Mac operating system.

GAMESS

Gaussaian All 64-bit versions of Gaussian 16 for macOS will work fine with macOS Catalina.

Homebrew some issues reported, brew update / brew upgrade seems to resolve many. Probably need to have updated Xcode to version 11.x

All the ICM products are compatible with Catalina:

Other products that are compatible include:

IDL Through beta testing, we have identified an issue that requires a patch to IDL 8.7 in order to run on this new OS X release. The issue is caused by the existing 32-bit applications used in IDL (Applescripts and IDLSnapFileOpen), and they will be replaced with 64-bit versions. Other related concerns on this OS X release will also be addressed. This patch to IDL will be available very soon after the release of Catalina.

Igor Pro With Catalina, Apple dropped support for 32-bit applications, dropped the QuickTime framework that Igor uses to support most movie features, and added strict security features that prevent XOPs from running without special security certification ("notarization"). We recommend that you avoid Catalina if you need to use Igor Pro. However, we expect Igor Pro 8.04 (currently in beta) to work with the caveats explained below. We do not consider any version of Igor Pro 8 to be supported on Catalina, though we will do our best to fix Catalina specific bugs. Igor Pro 6 will not run because Catalina supports 64-bit applications only. The 64-bit Igor Pro 7 application (Igor64.app) may run, but WaveMetrics and/or third-party XOPs may not load. Igor Pro 7 is no longer maintained and will not receive any changes to improve Catalina support. Workarounds for Catalina XOP Problem has been described, both workarounds require that you "bless" a particular XOP (.xop file), meaning that you tell the OS that it is OK to run the XOP.

iNMR iNMR has been recently recompiled with Xcode 10.3. iNMR is a 64-bit app since 2012. No issues reported.

KaleidaGraph is currently still a 32-bit application and will not run under Mac OS 10.15. A 64-bit version is under development, although it will not be released before Catalina and we do not have a release date at this time. We will notify registered users as soon as a beta version is ready for testing.

KNIME most recent version of KNIME Analytics Platform is notarized and, hence, works with macOS Catalina.

Manuscripts

Matlab R2019b supports Catalina

Mathematica Wolfram products based on Wolfram Language 12.0 or later are fully 64 bit on macOS, and are therefore compatible with macOS 10.15, as well as earlier versions.

Mendeley Mendeley Desktop does not support OSX Catalina. If you choose to upgrade to OSX Catalina you may be unable to install or access Mendeley Desktop. You should alternatively use https://mendeley.com/library

Microsoft Office To provide you with the best experience, Office for Mac supports Apple’s three most recent versions of macOS. With the release of macOS 10.15 Catalina, Office 365 for Mac and Office 2019 for Mac support macOS 10.15, 10.14, and 10.13.

Mnova Mnova 14.1 is compatible with Catalina OS.

MOE MOE is now fully compatible with Catalina. Remember if you change to using zsh instead of BASH you will need to copy things from your BASH profile over.

MOPAC no issues reported.

Papers We have gotten a few reports of crashes happening on the new Mac OS 10.15(codename Catalina) for Papers 3. We have developed a fix and you should be able to update your Papers 3 to the new version. If you updated to Catalina before updating Papers 3 you can download the new version here

Parallels Parallels Desktop 15 for Mac is the fastest, easiest, and most powerful application for running Windows applications on a Mac without rebooting. Parallels Desktop 15 now supports Catalina, Sidecar, and DirectX 11.

PGOPHER not yet supported by PGOPHER. (Apple no longer supports 32 bit programs, and the required uderlying 64 bit library required has only recently become available in a useable state, and some development work is required for this to work with PGOPHER.)

pro Fit the latest version of pro Fit, version 7.0.15, runs on Catalina.

PYMOL The +python37 variant of pymol runs fine under its Qt interface on Catalina

QMForge 2.4 apparently doesn't work on Catalina, hoping to get a fix in the coming weeks.

R In general works fine but with >20,000 packages available there may be issues with some.

RDKit no reported issues

Schrodinger Unfortunately, MacOS Catalina is not yet supported by Schrödinger products and is being tested. We are planning to start supporting it from our 19-4 release.

SeeSAR

Spartan

  • Spartan’18 Parallel Suite
  • Spartan’18 (single core)
  • Spartan Student Edition v.7
  • Odyssey Instructor Edition v.6
  • Odyssey Student Edition v.6

Are all compatible with Catalina.

SPSS We’ve spent weeks testing against the beta and now the generally available operating system. Overall, SPSS Statistics and Catalina are compatible.

Stardrop is compatible.

Swiss-PdbViewer is a 32 bits application and will * NOT * run on OSX Catalina. If you absolutely need it, refrain from updating, boot from an older OSX version, or use the PC version within a virutal machine. I currently have no plan to update it to run on OSX 10.15

UCSF Chimera

VMD is a 32-bit app and will not run under Catalina. While VMD has supported 64-bit platforms for 20 years, the "catch" in support for 64-bit MacOS X is that 64-bit MacOS X requires different graphical user interface APIs in 64-bit mode than it does in 32-bit mode, resulting in some ongoing stability problems for the FLTK and Tk libraries that VMD depends on. The issue is that we have to create a specially modified version of FLTK (which is not written by us) to be compatible with both Catalina and Tcl/Tk. As yet we don't have any ETA to provide users at this time. We are working on building a version of VMD for MacOS X Catalina, using patched versions of FLTK/Tk that resolve their MacOS X-specific 64-bit incompatibilities, but as yet this work is still ongoing. From VMD mailing list https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/31208.html.

I have put together a binary for VMD 1.9.4a38 (from the source dated 2019-10-17) which I would like to invite you to test. - You can download the app at https://www.dropbox.com/s/700vi9kkpglf6m6/VMD%201.9.4a38.zip?dl=0. - Install it into your Applications folder before running it. Please let me know if it works for you, or if some things are broken.

Vortex Should just work. Isn’t notorized yet though so right click Open if it complains. You only have to right click Open once.

WINEIn downloading WINE devel portable from https://dl.winehq.org/wine-builds/macosx/ , you can run the wine64 binary through the terminal, with ‘$ wine64 wine cfg’ to configure it and ‘$wine64 ’ to run a .exe. The only issue here is that Apple’s new notorisation system means that every file executed by wine64 will need to be manually allowed in the macOS security settings, which the first few times can take a lot of clicking, but after all is said and done, things are surprisingly stable, so long as the windows .exe is also 64 bit. It’s also possible to create an Automator application to launch the application, by using the “bash script” module, so that the windows application can be launched like any other.

Wizard has been tested to work with Catalina.

wxMacMolPlt The currently available (64 bit) binary does run on Catalina. However, while it is “signed” it is not “notarized” so you do have to jump through a couple hoops to convince the OS to launch it the first time.

Xcode need to update to version 11.x

XQuartz some users reporting issues, seems to be a mixture of enhanced security and/or folders moved to relocated items. Best solution seems to be to reinstall XQuartz.

I’ll add more updates later, feel free to contact me and thanks for the comments to date.

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A review of infiniSee

 

infiniSee from BioSoveIT enables similarity searching, based on a query molecule, through billions of compounds in chemical spaces. Currently two chemical spaces from commercial compound vendors can be explored: the well-known Enamine REAL Space with 13 billion compounds and WuXi’s GalaXi with 1,7 billion compounds.

infiniSee_5

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pyjanitor

 

Data clean up is often one the most time-consuming parts any form of data analysis and I thought I'd mention pyjanitor.

pyjanitor is a project that extends Pandas with a verb-based API, providing convenient data cleaning routines for repetitive tasks.

It can be installed using conda

conda install pyjanitor -c conda-forge

Or PIP

pip install pyjanitor

There is extensive Documentation, including a section on cleaning chemistry data.

I've added it to the Open Source Python Data Science Libraries



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ChemDoodle tools to search in SciFinder

 

Starting with ChemDoodle 10, new tools are included for directly querying substances, reactions, references and suppliers in SciFinder

“We are proud to extend our collaboration with CAS to introduce a direct integration of our desktop ChemDoodle software with SciFindern” said Kevin Theisen, President, iChemLabs, LLC. “Our focus is to provide the best experience for chemistry researchers. By streamlining the communication between ChemDoodle and SciFindern, this integration increases researchers’ efficiency and optimizes the workflow between these popular applications.”


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Small molecules approved by FDA in 2019

 

After I posted Small molecules approved by FDA in 2019 a number of people contacted me asking for the dataset, they then asked how it was created. So I thought I'd put together a brief description of the process.


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Mobile Science Updated

 

Finding scientific applications for your iPhone to iPad has always been a little hit and miss since there is no “science” category on the iTunes store. To help out I created a database that can be searched via a web interface, https://www.macinchem.org/mobsci/index.php. I've tried to tag all apps with appropriate comments so hopefully searching should identify the relevant applications.

I've recently added a few more apps.

Biological Buffer Calculator
QIAGEN App
Molarity Abacus
BioLegend Lab Tools
TLC Chemistry Tools
SHIMADZU IR
SHIMADZU UV

Feel free to send me details of any I've missed


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Annual Website Review

 

At the end of each year I have a look at the website analytics to see which items were the most popular.

Over the year there were 71,100 visitors spending an average of 2.5 minutes per session, looking at the regular visitors there are around 4000 who visited 20-200 times per year. The US provided 29% of the visitors and the UK 7% with Germany, India, Canada and Japan around 5%. As might be expected 54% of the visitors were using a Mac, but 23% of the visitors were Windows users, 12% iOS and 5% Android. There has been a gradual increase in the number of visitors using mobile devices.

Looking at the last month 48% of visitors are using Catalina (Mac OSX 10.15), 32% Mojave (Mac OSX 10.14), all other versions are down in single figures, so as ever Mac users are moving to the latest version of the operating system. For iOS the transition to version 13 is almost complete with over 80% of visitors to the site using the latest update. This seems to be a general case with mixpanel data supporting the observation.

iOS13use

Another interesting datapoint is that over 70% of the audience no longer support Java, a figure that is increasing year on year.

Again the most popular page was Fortran on a Mac which has been updated a couple of times this year with reader suggestions. Other popular pages include the Reviews and the Hints and Tutorials, page describing the use of LaTeX in Pages being particular popular.

The post about Scientific Applications under Catalina only made it to number 15 in the years listing but elicited a significant amount of reader feedback.

The Mobile Science site has seen increased visitor numbers, as might be expected during the International year of the Periodic Table, the periodic table apps proved very popular.

Merck PTE
The Periodic Table Project
Periodic Table

Also popular were

PocketCAS: Mathematics Toolkit
IBM Micromedex Drug Info
Human Anatomy Atlas 2019
ChemTube3D.

The Twitter feed @macinchem has steadily attracted new followers and currently has 675 followers.

The most popular tweets were the polls

In which area is Artificial Intelligence likely to most impact Chemistry

and

We have had a significant unallocated student bursaries for both @RSCBMCS and @RSCCICAG meetings over the last few years and we would like to find out why? .


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Fortran framework for neural networks

 

I've just had a suggestion I include this on the Fortran on a Mac page.

A parallel Fortran framework for neural networks and deep learning.


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Dealing with large data files

 

Spotted this on twitter https://twitter.com/baoilleach/status/1212322491101634560

I've added xsv to the page of tips for handling very large data files.

xsv is a command line program for indexing, slicing, analyzing, splitting and joining CSV files.


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