Macs in Chemistry

Insanely Great Science

molSeeker: Find molecular structures.

 

At the start of 2020 I decided that I'd try learning to program in Swift using Xcode, I've never had any formal programming training and I've always regarded myself as a cut-and-paste programmer. I've dabbled with various languages from AppleScript and shell scripting through ApplescriptObjC to Python. After reading how Xcode was supposed to greatly simplify the process I thought I'd give it a try. After going through a couple of tutorials and reading this excellent introduction to Swift I set about writing my first app.

I thought I'd capture my efforts and share them in and perhaps encourage others to have a go.

The final product from my efforts "molSeeker" is available for free download. It is a simple app that uses a couple of web services to get molecular structures, SMILES and inChiKeys.

Full details here,

molSeeker


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xterm problems under Catalina

A few people have reported issues using xterm under Catalina

cd documents
ls
ls: Operation not permitted

However if you try the same commands in the Terminal all works fine.

The solution was described here:-

solution was to give "Full Disk Access" to /bin/bash. This is a bit counter-intuitive, since I actually use /bin/tcsh for my shell (yeah, I know, I'm a luddite). I'm not sure whether bash is involved because my tcsh is a descendant of a bash process, or because the ls command is using bash in some way. But it is certainly true that I can toggle whether "ls ~/Documents" works by checking/unchecking bash in the Full Disk Access panel.

fulldisc

Dr. Burkhard Schmidt from Max-Planck-Institut provided an insightful explanation

Indeed giving Full Disk Access to /bin/bash is the correct solution. Why? Well, assuming the standard location for XQuartz, look at /Applications/Utilities/XQuartz.app/Contents/Info.plist. Under the key CFBundleExecutable you will find the value X11 which is /Applications/Utilities/XQuartz.app/Contents/MacOS/X11. The command ?file /Applications/Utilities/XQuartz.app/Contents/MacOS/X11? returns ?/Applications/Utilities/XQuartz.app/Contents/MacOS/X11: Bourne-Again shell script text executable, ASCII text?, so X11 is actually not a binary but a shell script. Open it with your favourite text editor. The first line reads ?#!/bin/bash?, so eventually /bin/bash is executed upon opening (double-clicking) XQuartz. All further X11 processes are child processes to it and inherit the Full Disk Access right.

This applies not only to Xterm but to all applications using X11 (thinking of grace, xfig, gimp and friends).

More info on Scientific Applications under Catalina here.

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Adding scientific terms to dictionary

 

A while back I described how to add a custom chemistry dictionary. There have been a few changes so I thought I'd post an update. If you are creating scientific documents you probably find that many of the scientific terms, chemical names and drug names are underlined by a red squiggle. You can add these words individually to the dictionary or you can edit the dictionary to add a batch of appropriate words all in one go.

To uncover the file you want to edit first open a Finder window, then hold down the Option key and click on the "Go" in the Finder top menu bar, this will give access to the Library folder.

gomenu

Now navigate to the "Spelling" folder, the file that you need to edit is "LocalDictionary". Open this file in a text editor (not a word processor), I used BBEdit. This file should contain any words that you have added, you can now add any scientific terms you want directly.

Chemdictionary

Over the years I've accumulated nearly 200,000 items in this file, you can download it here http://macinchem.org/blog/files/LocalDictionary.zip. Feel free to add these items if you feel they would be useful.

Now if I could find a way to add them to my iOS devices……


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Alvascience software

 

Alvascience recently released three new software packages for QSAR and chemoinformatics:

  • alvaMolecule is a free software (for academic use) to visualise, analyse, curate and standardize molecular dataset.
  • alvaModel is a software tool to create Quantitative Structure Activity/Property Relationship (QSAR/QSPR) models. The models developed using alvaModel can be easily deployed as 'alvaRunner projects'. Once a model has been deployed, it can be used by anyone via alvaRunner.
  • alvaRunner is a free software (for academic use) to apply QSAR/QSPR regression models, developed with alvaModel, on a set of molecules. It calculates the descriptors and fingerprints needed to apply the given QSAR/QSPR regression models and it does not need any other software to be used. You can find some alvaRunner projects here

There are also some introductory videos, also available on the YouTube channel: https://www.youtube.com/channel/UCoiZMgz4L0XT9W_YIpLb2xg.


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ChemDoodle Web Components v9 is Available

 

Version 9 is a major update to the ChemDoodle Web Components library. There has been a complete refactor of the library to ES6 best standards. The sketcher and editor UIs have been improved with SVG button icons. New Cloud features include advanced CIP stereochemistry support, reaction equation balancing, and stereochemistry enforcement in mechanism matching. The ChemDoodle Web Components website has been recreated to be responsive, much easier to read, and support high-DPI displays for clarity.

The website has some great examples of what can be generated.

webchemdoodle

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