Macs in Chemistry

Insanely Great Science

Mnova 14.1.2 has been released

 

A minor update to Mnova has been released.

Mnova is a multivendor software suite designed for combined NMR, LC/GC/MS and Electronic & Vibrational Spectroscopic techniques. The new version Mnova 14 is a major release incorporating many new features in most plugins. We have integrated three new products Mnova ElViS, BioHOS and StereoFitter

The full release notes are here

Comments

Getting the structures for drug names in publications

 

A number of times recently I've come across interesting publications regarding molecules that might be of interest for treating COVID-19.

An example being and this review by The Centre for Evidence-Based Medicine provides an excellent summary of the trials that are taking place. Unfortunately, it does not include the structures of the drugs named.

You can use molSeeker to get an individual molecule but what if you want to get a list of molecules?

Fortunately, you can use iBabel to get all the structures from PubChem.

Here is a 2 minute video showing how it is done.

You can download iBabel here.

Comments

iBabel version 4.0 released

 

At the start of 2020 I decided that I'd try learning to program in Swift using Xcode, my first project was molSeeker a tool for searching online resources using chemical identifiers. This was really just a vehicle for me to learn Swift and now I'm delighted to be able to release a more substantial effort, a complete rewrite of iBabel.

iBabel is a graphical user interface (GUI) to the open-source cheminformatics toolkit Open Babel described in an article in J Cheminformatics, Open Babel: An open chemical toolbox DOI. iBabel was originally written as an AppleScript Studio application which underwent several updates. However, recent changes have made this unsupportable so I decided on a complete Cocoa/Swift rewrite.

You can read all about the new version of iBabel here including the links to the download. I've attached a couple of screenshots to give you an idea of what functionality is available.

File Conversion Tools

convert

Viewing Molecule Files

viewerTab

Extension of molSeeker

seekerTab

iBabel 4.0 is freely available for download.

Many thanks to Peter Ertl and Bruno Bienfait for the JSME editor and David Koes for 3Dmol.js the 3D viewer and all the OpenBabel team.

Comments

The beta of the 2020.03 RDKit released

 

The beta of the 2020.03 RDKit is now available on GitHub https://github.com/rdkit/rdkit/releases/tag/Release202003_1b1.

Backwards incompatible changes:

  • Searches for equal molecules (i.e. mol1 @= mol2) in the PostgreSQL cartridge now use the dochiralsss option. So if dochiralsss is false (the default), the molecules CC(F)Cl and C[C@H](F)Cl will be considered to be equal. Previously these molecules were always considered to be different.
  • Attempting to create a MolSupplier from a filename pointing to an empty file, a file that does not exist or sometihing that is not a standard file (i.e. something like a directory) now generates an exception.
  • The cmake option RDKOPTIMIZENATIVE has been renamed to RDKOPTIMIZEPOPCNT

Highlights:

  • The drawings generated by the MolDraw2D objects are now significantly improved and can include simple atom and bond annotations
  • An initial implementation of a modified scaffold network algorithm is now available
  • A few new descriptor/fingerprint types are available - BCUTs, Morse atom fingerprints, Coulomb matrices, and MHFP and SECFP fingerprints

Plus lots of bug fixes.



Comments

Both dftd4 and xtb are now on conda-forge

 

xtb - An extended tight-binding semi-empirical program package can now be installed using conda

The extended tight binding program provides the geometry, frequency and non-covalent interaction (GFN) parametrisations of the tight binding Hamiltonians GFN1-xTB (JCTC 2017) and GFN2-xTB (JCTC 2019) and a preliminary version of the new GFN0-xTB https://doi.org/10.26434/chemrxiv.8326202.v1. All parametrisations consistently cover the entire periodic system up to Z=86 and include a continuum solvation model (GBSA) for common solvents.

conda install -c conda-forge xtb

Or

conda install -c conda-forge/label/cf202003 xtb

The user guide is available online https://xtb-docs.readthedocs.io/en/latest/contents.html and the source code is on GitHub https://github.com/grimme-lab/xtb/

dftd4 - A generally applicable London dispersion correction

This program implements the D4 London dispersion correction for molecular and 3D periodic systems. DOI and DOI.

conda install -c conda-forge dftd4

Or

conda install -c conda-forge/label/cf202003 dftd4

The source code is available on GitHub https://github.com/dftd4/dftd4 and includes build instructions and example usage.

To compile this version requires

  • gfortran (8.2.1) or ifort (17.0.7 or 18.0.3) compiler
  • meson (0.49.0) and ninja (1.8.2) as build system
  • asciidoc (8.6.10) to build the man-page


Comments

Apple unveils new iPad Pro

 

As expected Apple released a new iPad Pro together with a new keyboard including trackpad.

Apple today announced its most advanced iPad Pro. Now with the A12Z Bionic chip, iPad Pro is faster and more powerful than most Windows PC laptops. The new iPad Pro adds an Ultra Wide camera, studio-quality mics and a breakthrough LiDAR Scanner that delivers cutting-edge depth-sensing capabilities, opening up more pro workflows and supporting pro photo and video apps. The LiDAR Scanner, along with pro cameras, motion sensors, pro performance, pro audio, the stunning Liquid Retina display and powerful apps, extends the lead of iPad Pro as the world’s best device for augmented reality (AR). The new iPad Pro is available to order starting today on apple.com. With iPadOS 13.4, Apple brings trackpad support to iPad, giving customers an all-new way to interact with their iPad. Rather than copying the experience from macOS, trackpad support has been completely reimagined for iPad. As users move their finger across the trackpad, the pointer elegantly transforms to highlight user interface elements. Multi-Touch gestures on the trackpad make it fast and easy to navigate the entire system without users ever lifting their hand.

Apple_new-iPad-Pro_03182020

I do like the new keyboard/stand.



Comments

programming help

 

I'm looking at using spectrophores for comparing molecules https://openbabel.org/docs/dev/Fingerprints/spectrophore.html there is a commandline tool for creating the fingerprints and I've written the code below for calculating the euclidian distance between the finger prints.

The output from the obspectrophore tool is shown below for an individual record and the "ID_000002" is the identifier for each molecule record.

*******************************************
SPECTROPHORE(TM) CALCULATOR: OBSPECTROPHORE
*******************************************

Input file:       /Users/username/Desktop/SampleFiles/publishedfrags.sdf
Normalization:    No
Accuracy:         20 degrees
Stereo treatment: No
Resolution:       3 Angstrom

ID_000002   1.49549 2.12041 1.75615 3.2692  4.92872 3.76183 3.61444 3.72374 3.76777 6.28071 6.29508 3.72293 2.84116 2.85055 10.5207 10.5353 15.5128 13.9755 11.3767 20.0578 16.3018 16.4986 20.8431 15.5037 28.5218 31.3143 29.1957 24.1175 20.2475 20.7571 6.87729 23.1364 21.7477 26.0813 9.92146 25.4475 0.937131    0.87351 2.91767 2.9165  0.823157    0.845468    0.39668 3.15164 1.9814  0.923294    0.769458    3.01774

The file that I want to search will have many, many records.

My script is shown below, it works fine but I'm wondering if I can speed it up, in particular the calculation of the euclidian distance between the finger prints I've heard of the accelerate framework but can find much in terms of examples or tutorials of how to use it,

import AppKit
import PlaygroundSupport
import Foundation


var mainFilePath = "/Users/username/Desktop/SampleFiles/publishedfrags.spectrophore" // main file to search against
var theFullpathString = "/Users/username/Desktop/SampleFiles/publishedfrags.txt" // results output file

var iFilepath = "/Users/username/Desktop/SampleFiles/selectedfrag.sdf" //query molecule

var oFilePath = "/Users/username/Desktop/SampleFiles/selectedfrag.txt"

var obshellCommand = ""

var queryMoltitle = ""
var mol1array:[String] = []
var mol1Doubles: [Double] = []
var mainMoltitle = ""
var mainMolarray:[String] = []
var molRecord:[String] = []
var molDouble:[Double] = []

var obspectrophoreResults = ""

//MARK: function for submitting obabel shell scripts
func shell(_ command: String) -> String {
       let task = Process()
       task.launchPath = "/bin/bash"
       task.arguments = ["-c", command]

       let pipe = Pipe()
       task.standardOutput = pipe
       task.launch()

       let data = pipe.fileHandleForReading.readDataToEndOfFile()
       let output: String = NSString(data: data, encoding: String.Encoding.utf8.rawValue)! as String

       return output
    }
obshellCommand = "usr/local/bin/obspectrophore" + " -i " + iFilepath

let theText = shell(obshellCommand)

let index = theText.range(of: "Angstrom\n\n") // remove header
var thend = index?.upperBound

let forArray = theText[(thend!)..<theText.endIndex]
mol1array = forArray.components(separatedBy: "\t")  //might need to be \t or 4 spaces
queryMoltitle = mol1array.first!

mol1array.removeFirst(1)
mol1array.removeLast(1) // need to remove because command returns ended with linefeed

mol1Doubles = mol1array.map { (value) -> Double in return Double(value)! }


//

let themainText = try! String(contentsOfFile: mainFilePath, encoding: String.Encoding.utf8)

let mainIndex = themainText.range(of: "Angstrom\n\n")
var themainend = mainIndex?.upperBound

let textForarray = themainText[(themainend!)..<themainText.endIndex]

let forMainArray = textForarray.components(separatedBy: "\n") as [String]
//let forMainArray = textForarray.split(separator: "\n")
//print(forMainArray)

//let mainMolarray = forMainArray.components(separatedBy: "\t")  //might need to be \t or 4 spaces


let thelength = (forMainArray.count)
print(thelength) // file created by obspectrophore contains final carriage return
for n in 1...(thelength - 1) {
    var sum = 0.0
    var result = 0.0
    molRecord = forMainArray[n - 1].components(separatedBy: "\t") as [String]
    mainMoltitle = molRecord.first!
    molRecord.removeFirst(1) // remove moltitle
    molRecord.removeLast(1)  // remove trailing tab
    molDouble = molRecord.map { (value) -> Double in return Double(value)! }
    //mol1Doubles is query molecule
    for i in 0..<mol1Doubles.count
    //calc distance
    {
      let temp =  ((mol1Doubles[i] - molDouble[i])*(mol1Doubles[i] - molDouble[i]))
        sum = sum + temp
        result = Double(sqrt(sum))

    }
    let theResult = mainMoltitle + "\t" + String(format: "%0.2f", arguments:[result])
 //print(mainMoltitle, result)


    let myshellcommand = "echo " + theResult + " >> " + oFilePath
    shell(myshellcommand)

}


Comments

Coronavisrus stats online.

 

If you are a using a UNIX based operating system (such as Mac OS X) just type this command in a Terminal window

curl https://corona-stats.online/

coronavirus

Looks to be about 12 hours behind latest data.

From https://twitter.com/nixcraft.



Comments

Remote working and videoconferencing

 

As more people are considering working from home it is worth thinking about how to make this work more efficiently.

There have been a few threads on twitter

https://twitter.com/prsarahevans/status/1237914530606247936

https://twitter.com/shannyHTX/status/1238242730117074944

https://twitter.com/loganbartlett/status/1237821386640576512

One thing I would also add purchase a good quality headset because you are likely to be wearing it much of the day. I tried a few and settled on the Jabra Evolve 75, works with desktop, laptop, iPad etc.

And of course remember

https://twitter.com/TedGoas/status/1237484797288742915


Comments

BBEdit updated

 

BBEdit has been updated to version 13.0.5, this contains no new features but a number of important bug fixes.

BBEdit 13.0 requires Mac OS X 10.14.2 or later, and is compatible with macOS 10.15 "Catalina".

The full release notes are here.

I feel that BBEdit is the best text editor available for Mac OS X, and it is an essential tool for anyone needing to manipulate text file, be it, programming in most languages, automating text manipulations, find/replace, searching using grep, across multiple files across multiple folders, including very, very large text files.


Comments

Google Summer of Code Open Chemistry

 

The Open Chemistry Google Summer of Code will be open for proposals on March 16 2020.

Just enough time to have a look at the GSoC Ideas 2020 lots of opportunities to contribute and learn.

The Open Chemistry project is a collection of open source, cross platform libraries and applications for the exploration, analysis and generation of chemical data. The organization is an umbrella of projects developed by long-time collaborators and innovators in open chemistry such as the Avogadro, Open Babel, and cclib projects. These three alone have been downloaded over 1,000,000 times and cited in over 2,000 academic papers. Our goal is to improve the state of the art, and facilitate the open exchange of chemical data and ideas while utilizing the best technologies from quantum chemistry codes, molecular dynamics, informatics, analytics, and visualization.

If you are interested in contributing why not download the source code for one of the projects, have a play around and get familiar with the code.


Comments

ChemRPS a Chemical Registration and Publishing System

 

Whilst there are many commercial packages for creating structure searchable chemical databases there is little in the way of Open Source packages, in particular a solution that provides a web front end. There is the RDKit PostgreSQL cartridge however installing PostgreSQL and building the database is probably a step to far for those unfamiliar with the use of the command line.

chemrpsresultstable

I recently came across ChemRPS whilst this uses the same RDKit PostgreSQL cartridge a search engine (API) and a preconfigured webserver with register/search web pages including structure editor Ketcher from EPAM, the installation comes as a Docker image which should make things much easier.

The system had not been tested on a Mac so I've detailed the instructions in this review…


Comments

Freepascal install on macOS 10.15 Catalina

 

Whilst I've not tried it myself it looks like Freepascal is now running under Catalina, details are in this thread.


Comments

ChEMBL Compound Curation Pipeline

 

With the imminent release of ChEMBL 26 I was interested to hear about the new chemical curation pipeline that had been developed.

The pipeline includes three functions:

  1. Check Identifies and validates problem structures before they are added to the database

  2. Standardize Standardises chemical structures according to a set of predefined ChEMBL business rules

  3. GetParent Generates parent structures of multi-component compounds based on a set of rules and defined list of salts and solvents

The code is all on GitHub https://github.com/chembl/ChEMBLStructurePipeline and notebooks are available.


Comments

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


Comments

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.

Comments

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……


Comments

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.


Comments

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

Comments

Scientific Applications under Catalina: 2500 views

 

I just checked the analytics data and the Scientific Applications under Catalina has now been accessed around 2500 times.

It is a fair bit of work putting the data together so I'm delighted to see it is viewed by so many people. Many thanks to all who contributed.

Comments

SAMSON 2020 is out!

 

The latest update to SAMSON 2020, the open molecular modelling platform is now available.

InterfaceRaw

This update brings one feature that I'm many having been asking for.

  • Molecular builder, you can build molecules by adding individual atoms or by adding Assets, an assets can be anything: rings, fragments, radicals, whole molecules, proteins, nanoparticles, 2D materials, etc.
  • Tooltips, Hovering nodes now displays information about them and their ascendants.
  • Tutorials, SAMSON now contains step-by-step Interactive tutorials that guide you through SAMSON’s features at your own pace.
  • The SAMSON API has been upgraded to expose the new functionalities of this release and let developers create fantastic molecular modelling experiences that they can distribute on SAMSON Connect.

SAMSON itself is free, and so are many SAMSON Elements (extensions). For non-free extensions, it essentially works like Netflix. Monthly and yearly subscriptions are available, with lower prices for academia (typically 60% off). Users subscribe directly online at https://www.samson-connect.net. When they need group or site licenses, they contact us at sales@oneangstrom.com for quotes.

There are Elements for conformational analysis, docking, molecular dynamics, crystal creator, molecular optimisation, protein alignment and much more.

Create your own elements

It’s C++ and Qt for the interface there’s a tutorial to develop an app for example, and they actually put up slides about C++ as a refresher :-) here.

It's also possible to use python: https://documentation.samson-connect.net/scripting-guide/.

The core of SAMSON is not open source, but developers can do what they want with their modules (give their source or not), and the source of some of the modules are available on Github at https://github.com/SAMSON-Connect.

There is much more on Github https://github.com/1A-OneAngstrom/SAMSON-Developer-Tutorials.

Comments

Flang : The Fortran frontend of LLVM

 

The Fortran on a Mac page is always one of the most read pages so I thought I'd post this bit of Fortran news.

Flang : The Fortran frontend of LLVM was described in a technical talk recently given by Kiran Chandramohan.

This talk introduces Flang (F18), the new Fortran frontend of LLVM being written in modern C++. The talk will provide a brief introduction to Flang, motivation for writing this new compiler, design principles, architecture, status, and an invitation to contribute. F18 project started at PGI/Nvidia as a new Fortran frontend designed to work with LLVM. The aim of the project is to create a modern Fortran frontend (Fortran 2018 standard) in modern C++. In April of this year, it was accepted as an LLVM project (https://lists.llvm.org/pipermail/llvm-dev/2019-April/131703.html).

The slide deck is available here

Comments

Skype for business app problems

 

I sometimes have to use the Skype for business app and I find that if I click on the link in an email or on my calendar it usually fails to open correctly. I then end up trying to use the web app which rarely works.

By accident I've found a way to get the Skype for business app to work regularly.

Firstly don't click on a link in a an email of calendar, instead copy the meeting URL.

Then open the Skype for business app, you should see the window below. Don't add your email instead click the "Join Meeting as Guest link highlighted in red below.

SkypeBusiness1

This should take you to the following window, don't try to sign in using the Office 365 account. Paste the meeting URL into the box, then enter your name and then click Join as Guest. This has worked every time for me.

SkypeBusiness2

Comments

Cambridge Cheminformatics Meeting

 

A brief reminder about the next Cambridge Cheminformatics Network Meeting on Wednesday, 12 February 2020, at the Cambridge Crystallographic Data Centre (CCDC, https://www.ccdc.cam.ac.uk/), starting at 3.30pm with coffee and talks from 4pm onwards - this time it will be a 'startup event', with the program being as follows:

"Quantum Software for Quantum Chemistry"
Joan Camps, Riverlane
https://riverlane.io/

"Improving virtual screening by combining molecular docking and hydrophobic profile similarity"
Javier Vazquez, Pharmacelera
https://new.pharmacelera.com/

"Imputation of heterogeneous assay data using deep learning"
Tom Whitehead, Intellegens
https://www.intellegens.co.uk/

We will as usual retreat to the Alma afterwards (around 5.30pm) - no registration is necessary, and everyone is welcome to attend. (If you plan to attend please aim to turn up somewhat before the event starts, given that participants need to sign in upon arrival at the CCDC which may take a few minutes.)

Comments

CICAG Winter 2019 Newsletter

 

The latest issue of the RSC CICAG newsletter is now available online, the winter 2019 issue has continued the trend to include more original content and news on chemical information.

CICAGNewsletter

This issue includes

  • Chemical Information & Computer Applications Group Chair's Report
  • CICAG Planned and Proposed Future Meetings
  • Periodic Table brought to life at Catalyst!
  • From Nantwich to Oxygen: Joseph Priestley’s Journey of Discovery
  • Dr Andy Vinter 1943 - 2019
  • Open Force Field Initiative on Energetics for Molecular Modelling
  • Obituary Dr William Geoffrey Town
  • Extending InChI to Include Inorganic & Organometallic Compounds
  • Wendy Warr named 2020 Herman Skolnik Award Winner
  • A Practical Case for WebAssembly
  • Tony Kent Strix Award and Annual Lecture 2019
  • Meeting Report: 20 Years of the Rule of Five
  • Meeting Report: 2nd RSC BMCS & CICAG AI in Chemistry Meeting
  • Chemical Information / Cheminformatics and Related Books
  • News from CAS
  • News from the RSC
  • News from AI3SD

This newsletter also includes articles from Prof David Mobley, Dr Wendy Warr, Dr Alex M Clark, Jane List, Dr Rajarshi Guha and Dr Dan Ormsby, and CICAG is very appreciative of these external contributions to this widely-read publication. If readers have any suggestions for contributions that would be of interest to the CICAG community, please get in touch.

Past issues of the newsletter are available on the website.

Comments

VESTA updated

 

Just got a message that VESTA has been updated to version 3.4.8 with several bug fixes, support for dark mode, and Improved support for pdb file format.

mac-main01

VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. Some of the novel features of VESTA are listed below.

  • Deal with multiple structural models, volumetric data, and crystal morphologies in the same window.
  • Support multiple tabs corresponding to files.
  • Support multiple windows with more than two tabs in the same process.
  • Deal with virtually unlimited number of objects such as atoms, bonds polyhedra, and polygons on isosurfaces (theoretical limit on 32bit operating system is 1,073,741,823)
  • Support lattice transformation from conventional to non-conventional lattice by using matrix. The transformation matrix is also used to create superlattice and sublattice.
  • Visualize interatomic distances and bond angles that are restrained in Rietveld analysis with RIETAN-FP.
  • Transparent isosurfaces can be overlap with structural models.
  • Isosurface can be colored on the basis of another physical quantity.
  • Arithmetic operations among multiple volumetric data files.
  • High quality smooth rendering of isosurfaces and sections.
  • Export high-resolution graphic images exceeding Video card limitation.
Comments

ChemDoodle v10.2 Released

 

The latest update of the popular chemical ChemDoodle 2D drawing package has been released.

This is a significant feature update to ChemDoodle 2D v10. This update is recommended for all ChemDoodle 2D users. Major changes include an updated shape system allowing you to edit shapes while you draw them, greatly speeding up figure drawing. A significant amount of work has culminated in a brand new and powerful table tool for creating rich data graphics. ChemDoodle 2D can also now balance any drawn reactions or typed chemical equations.

10_2_release_social_post

Full release notes are available here

In particular note

Quicklook plugin works again and has been rebuilt with the latest version of Xcode on Catalina.


Comments

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

Comments

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

Comments

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

Comments

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


Comments

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.

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.

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).

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

Comments

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

Comments

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



Comments

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.”


Comments

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.


Comments

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


Comments

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? .


Comments

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.


Comments

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.


Comments