Macs in Chemistry

Insanely Great Science

Learning Molecular Simulations with Sophia

 

Sophia is an educational molecular simulation package. It runs as a plugin to Chimera, a molecular modeling application developed at UCSF. To run molecular simulations, Sophia uses the Molecular Modeling Toolkit (MMTK), which is embedded as a library in Chimera. ChimeraX, the next generation of Chimera, is not currently supported.

Sophia was developed on and optimized for MacOS. It’s still possible to run Sophia on Windows or Linux, but some features will not be available, like Monte Carlo and Langevin Dynamics.

Comments

XCode 13

 

Xcode 13 looks to have some interesting new features, Xcode Cloud and Source code Management should be worth exploring.

Xcode

Xcode 13 includes Swift 5.5 and SDKs for iOS 15, iPadOS 15, macOS Monterey, tvOS 15, and watchOS 8.
The Xcode UI has been refined with new navigator icons and a new always-on bottom bar.
The new Cloud tab in the Report navigator shows Xcode Cloud workflows and build results.

Xcode Cloud

Build, test, and deliver your apps using cloud-based tools built right into Xcode.
Run tests in parallel in the cloud, with results displayed in the report navigator.
View and edit workflows, and view build results in App Store Connect.
Distribute builds automatically to testers using TestFlight.

Source Code Management Integration

The all-new Pull Request experience deeply integrates the process of reviewing source code changes into Xcode.
Code review mode includes a new inline diff mode that lets you view diffs without leaving your current editing context.

Testing

Repeated testing lets you run tests until they fail, until they pass, or for a specified number of times to collect data on the failure rate.
XCTest adds support for memory tracking and iPadOS cursor interaction tests.

Editor

Swift code completion is faster and more robust.
Swift syntax highlighting is faster and more reliable.

Debugging

Column breakpoints give you subline breakpoint resolution.
The selective shader debugger lets you choose which functions to debug within a larger shader, reducing the time required to iterate and debug large shaders.

Other improvements

Crash reports from apps in TestFlight appear in the Xcode organizer within minutes, and can include user feedback.
The Xcode editor supports many of the common key combinations and editing modes familiar to Vim users.
The new Metal-accelerated GPU timeline view in Instruments provides smooth interactions for even the largest traces.
The CPU profiler template in Instruments offers cycle-based profiling.
The new HTTP network tracing tool helps developers and privacy researchers debug and analyze HTTP-based network traffic.

Comments

Upcoming DataWarrior workshop

 

The next RSC CICAG Open Source tools workshop is on 24 June and highlights DataWarrior, it will be given by Isabelle Giraud.

Registration is free and you will be sent login details at a later date. Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns. Chemical descriptors encode various aspects of chemical structures, e.g. the chemical graph, chemical functionality from a synthetic chemist’s point of view or 3-dimensional pharmacophore features.

If you have any questions about how to do things in DataWarrior please feel free to send them in.

DataWarrior2

All scientists working Chemistry need software tools for accessing, handling and storing chemical information, or performing molecular modelling and computational chemistry. There is now a wealth of open-source tools to help in these activities, however many are not as well-known as commercial offerings.

These workshops offer a unique opportunity for attendees to try out a range of open-source software packages for themselves with expert tuition in different aspects of chemistry.

Our aim is to have a once a month workshop, usually the third week of each month on Thursday (or within a day or two) you can find out more about the future workshops in the series and register using the link below.

Registration for these free workshops is now open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)

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4th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry

 

The 4th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry is now open for abstracts. Full details are here https://www.maggichurchouseevents.co.uk/bmcs/AI_2021.htm. This is always a highly popular event.

AI2021

This will be a virtual event and held Monday-Tuesday, 27th-28th September 2021. The first few confirmed speakers have been announced and there is already an interesting spread of topics.

AI for molecular design, past, present and future, Ola Engkvist, AstraZeneca, SE

Exploring molecular space and accelerating drug discovery with MegaMolBART, a transformer-based generative model, Michelle Gill, NVIDIA, US

Presentation title to be confirmed, Pat Walters, Relay Therapeutics, US

You can register online here https://www.maggichurchouseevents.co.uk/bmcs/AI-2021onlineregistration.htm.

Comments

WebMolKit Sketcher

 

This is part of the web_molkit hosted on GitHib.

webmolkit_sketcher

The sketcher is part of the WebMolKit project, which has been open source for quite some time: it has a lot of molecular manipulation functionality as well as the ability to draw molecules, and is one of the most advanced cheminformatics projects that is 100% web based, being written in TypeScript and cross-compiled to work on any JavaScript-based runtime.

The WebMolKit library may be used by anyone under the terms set by the general Gnu Public License (v3.0).

Comments

ChemDoodle 2D v11.5 has been released

 

ChemDoodle 2D v11.5 is a feature update. This update is all about databases. Google Patents is integrated to allow you to search the Google Patents and non-patent literature databases using structures drawn in ChemDoodle. The SciFinder-n interface has been improved and updated. A new PubChem protocol, PUG, replaces the old Entrez protocol for better results from the MolGrabber widget. RCSB PDB database connections have been switched to HTTPS. Additions

  • Google Patents searching is integrated. You may perform structure, substructure and similarity searching into the Google Patents and non-patent literature databases at Google using structures drawn in ChemDoodle.
  • The SciFinder-n interface has been updated and improved for better usability and with a UI matching the current SciFinder-n product.
  • PubChem access now uses the PUG REST protocol, which results in more stable communication with the PubChem database and higher quality results when using the MolGrabber widget.
  • Updated import of MMTF/PDB data from the RCSB.
  • There is now an option to disable the native file choosers used by ChemDoodle in the Preferences window, under the Files tab. Disable the native file choosers if you are having issues with them, for instance if you have a problem with iCloud on macOS and cannot get the file choosers to load.

More details here.

Comments

Open Source Tools for Chemistry Workshops:- GNINA

 

The latest in the Open Source tools for Chemistry, fantastic workshop using GNINA for docking.

GNINA 1.0 by David Koes. The use of docking to predict ligand binding to a receptor is now well established, this workshop will cover docking and structure-based virtual screening, with an introduction to the theory followed by practical examples. The slides for the Molecular Docking with GNINA 1.0 workshop are here and the Jupyter Notebooks are here.

Comments

InChI version 1.06: now more than 99.99% reliable

 

A nice review of the latest version https://doi.org/10.1186/s13321-021-00517-z.

In this paper, we report on the current state of the InChI Software, the details of the improvements in the v1.06 release, and the results of a test of the InChI run on PubChem, a database of more than a hundred million molecules. The upgrade introduces significant new features, including support for pseudo-element atoms and an improved description of polymers. We expect that few, if any, applications using the standard InChI will need to change as a result of the changes in version 1.06.

It can be downloaded here https://www.inchi-trust.org/downloads/

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Resources for underrepresented groups and allies in Computational Chemistry

 

The Binding Site is a resource for underrepresented groups and allies in CompChem. Sounds a great initiative.

There is a meeting on June 4th to find out more.

You can register here https://www.bindingsites.co.uk/meetings/currentmeeting

diversityCompchem

Comments

Open Chemical Sciences Workshops

 

All scientists working Chemistry need software tools for accessing, handling and storing chemical information, or performing molecular modelling and computational chemistry. There is now a wealth of open-source tools to help in these activities, however many are not as well-known as commercial offerings.

These workshops offer a unique opportunity for attendees to try out a range of open-source software packages for themselves with expert tuition in different aspects of chemistry.

Our aim is to have a once a month workshop, usually the third week of each month on Thursday (or within a day or two).

Registration for these free workshops is now open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)

22nd July 2-4 pm (UK time) Charlotte Deane workshop on the OPIG (Oxford Protein Informatics Group) antibody modelling tools. https://www.blopig.com/blog/2020/09/what-can-you-do-with-the-opig-antibody-suite-v2-0/ The OPIG Antibody Suite? V2.0 is a collection of informatics tools and databases, including CoV-AbDab: the coronavirus antibody database https://academic.oup.com/bioinformatics/article/37/5/734/5893556.

19th August 2-4 m (UK time) Pat Walters Relay Pharm and http://practicalcheminformatics.blogspot.com an introduction to Cheminformatics, data analysis and machine learning. A hands-on workshop on building and validating ML models.
- Initial exploratory data analysis - ML model building - Model evaluation - Making predictions on a larger dataset

23rd September 2-4 pm (UK time) Rachel Skyner https://fragalysis.diamond.ac.uk/viewer/react/landing and https://twitter.com/rachaelskyner Web apps for fragment based drug discovery, fragalysis and more.

21st October 2-4 pm (UK time) Daria Goldmann https://www.knime.com KNIME workshop. KNIME Analytics Platform is the open source software for creating data science. Intuitive, open, and continuously integrating new developments, KNIME makes understanding data and designing data science workflows and reusable components accessible to everyone. Knime can be downloaded here https://www.knime.com/downloads .

16th November 3-5 pm (UK time) PDB https://www.wwpdb.org workshop to coincide with PDB 50th anniversary. The Protein Data Bank archives information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

18th November 3-5 pm (UK time) Mol* https://molstar.org workshop, Mol* is a modern web-based open-source toolkit for visualisation and analysis of large-scale molecular data.

Comments

MNOVA has been updated

 

Mnova 14.2.1 has just been launched as a minor release version and includes a number of new features for many of the products, along with the usual bunch of bug fixes. There are also bringing some plugin updates together with six new Mnova Gears bricks.

Peak Report 1.0.0 Reads input data and automatically generates peak reports for each NMR spectrum in your preferred format

Multiplet Report 1.0.0 Automatically generates multiplet reports for each NMR spectrum in your preferred format

IUPAC Name 1.0.0 Innovative algorithm for the naming of molecular structures in batch mode and the generation of automatic reports

MPublish - A seamless automated preparation of supplementary research data for publication.

MS Scan processes total ion current (TIC) data and extracts mass spectra for the time ranges of your choice

DB Search - An excellent solution to identifying chemical structures that have already been analyzed and saved to a database

Comments

Modeller available for Apple Silicon

 

Modeller written in Fortran90 has been ported to Apple Silicon

They used the gfortran that's part of the gcc homebrew package (https://brew.sh/). They see about a 20% performance improvement with gfortran-10 on a 2020 Mac Mini (M1) compared to Intel Fortran on a 2018 Mac Mini (Intel).

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

If you are using the Homebrew package manager, you can install Modeller on recent Macs (either Intel or Apple Silicon, M1) by simply running

brew tap salilab/salilab
brew install modeller
Comments

Discovering quantum-mechanical simulations with CRYSTAL

 

Save the dates. More details coming soon on this virtual workshop.

MSSC2021 - Ab initio Modelling in Solid State Chemistry
Virtual Edition (New Users)
Discovering quantum-mechanical simulations with CRYSTAL
London (UK time), September 20-24,2021
Directors: S. Casassa - A. Erba - N.M. Harrison - G. Mallia

The week long school is designed for new users of CRYSTAL, PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis, magnetism and nano-science. It will provide an introduction to the capabilities of quantum mechanical simulations and to the practical use of CRYSTAL.

CRYSTAL is a general-purpose program for the study of periodic systems. The code may be used to perform consistent studies of the physical and chemical properties of crystalline solids, surfaces, polymers, nanotubes and molecules. The CRYSTAL program computes the electronic structure, structural features, vibrational, magnetic, dielectric (linear and non-linear electric susceptibilities up to forth-order), elastic, piezoelectric, photoelastic, thermodynamic (Quasi-Harmonic Approximation) and transport properties of periodic systems, within Hartree Fock, density functional or various hybrid approximations (global and range-separated hybrids).

CRYSTAL17 for Unix/Linux/MacOSX is supplied as binary executables or object files for a number of supported architectures. Precompiled executables include sequential (crystal, properties) and replicated data parallel version (Pcrystal). The massive parallel version (distributed memory, MPPcrystal) is only supplied as object files

Comments

ISOLDE updated

 

ISOLDE 1.2.0 is available, and ready to install for @UCSFChimeraX 1.2! As usual, just get the ChimeraX 1.2 release from https://www.rbvi.ucsf.edu/chimerax/download.html then install ISOLDE via "Tools/More Tools. Code is on GitHub https://github.com/tristanic/isolde.

ISOLDE is a plugin to UCSF ChimeraX, designed to ease the task of macromolecular model building into low-to-medium resolution maps derived from crystallographic or electron cryo-microscopy (cryoEM) experiments.

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use.

You can view snapshot here https://twitter.com/CrollTristan/status/1390709520876331009

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AI3SD & RSC-CICAG Protein Structure Prediction Conference

 

Registration is now open for the AI3SD & RSC-CICAG Protein Structure Prediction Conference. This online event looks like it will a brilliant meeting with a fantastic lineup of speakers. June 16 @ 9:45 am - June 17 @ 5:00 pm Free

Registration here Eventbrite Link: https://ai3sd-cicag-protein-structure-prediction.eventbrite.co.uk.

The challenge of protein structure prediction has advanced significantly in recent years, yet translation into impact, particularly in drug discovery, remains open. Furthermore, while we as a community have advanced in predicting protein structures, they offer only static snapshots, and do not yet consider effectively the protein dynamics and conformational change. Bringing together scientists working in this area, and those who work with the resulting data, this conference is intended as a pulse check on the status of the field and where we will start seeing impact and improvements for human benefit. The two days will contain a number of talks from speakers who are key opinion leaders in the field, together with an opportunity to present short talks and posters to a wider audience. Day 1 will finish with an online social event (separate links will be sent out to register for this closer to the time) and Day 2 and will close with a panel discussion by the speakers, which is intended to be provocative.

Current invited speakers include: Professor John Moult (University of Maryland), Dr Chris De Graaf (Sosei Heptares), Professor Debora Marks (Harvard University), Professor Cecilia Clementi (Freie Universität Berlin), Professor Aleksej Zelezniak (Chalmers University of Technology), Dr Oscar Méndez-Lucio (Janssen Pharmaceuticals), Professor Charlotte Deane (University of Oxford), Professor Tudor Oprea (University of New Mexico), Dr Derek Lowe (Novartis), Professor Stephen Burley (RCSB PDB, Rutgers University, USCD).

Conference web page is here.

Comments

RDKit UGM 2021 save the date: 14-15 October

 

A message from Greg Landrum

This year's RDKit UGM is going to take place October 14 and 15. It will, unfortunately, once again be a purely virtual event. Hopefully next year we will be able to travel again and all get together in one physical location, but this year it's not possible to really plan an in-person meeting.

Since it seemed to work well last time, we'll do a combination of zoom and either discord or some other text-based chat functionality and will have two sessions per meeting day: one earlier in the day which is easier for people in Asia to attend and one later in the day which is easier for people in the Americas.

Watch out for registration link in the next week or so.

Comments

OpenMM 7.5.1 released

 

OpenMM is a toolkit for molecular simulation using high performance GPU code.

This is a patch release. It contains a small number of bug fixes, as well as changes to enable two significant additions to the supported platforms.

First, this release provides preliminary support for ARM based Macs. The support has not been extensively tested and should be treated as beta quality. Please try it out and let us know if you encounter any bugs while using it.

Second, we are now providing conda packages for use with Pypy. This is an alternate Python interpreter that uses just-in-time compilation to provide much faster execution than CPython. You can create a conda environment that uses Pypy with the command

conda create -c conda-forge --name pypy pypy
Comments

Fortran package manager

 

I suspect this will be of interest.

Fortran Package Manager (fpm) is a package manager and build system for Fortran. Its key goal is to improve the user experience of Fortran programmers. It does so by making it easier to build your Fortran program or library, run the executables, tests, and examples, and distribute it as a dependency to other Fortran projects. Fpm's user interface is modeled after Rust's Cargo, so if you're familiar with that tool, you will feel at home with fpm. Fpm's long term vision is to nurture and grow the ecosystem of modern Fortran applications and libraries.

Available on GitHub https://github.com/fortran-lang/fpm

Comments

Open Chemical Sciences Workshops

 

The videos for the first two workshops sponsored by LiverpoolChiroChem are now on the CICAG YouTube channel.

21 April Chemical Structure validation/standardisation (Greg Landrum) Possibly the most important step in model or database building is data curation, this workshop will deal with chemical structure validation and standardisation. https://youtu.be/eWTApNX8dJQ.

25th March ChimeraX (https://www.rbvi.ucsf.edu/chimerax/) (Tom Goddard) Intro to ChimeraX for visualizing proteins, ligands and X-ray and electron microscopy maps. https://youtu.be/M2K72Kgk718.

The next workshops are

  • 27 May GNINA 1.0 (https://chemrxiv.org/articles/preprint/GNINA10MolecularDockingwithDeep_Learning/13578140) (David Koes) The use of docking to predict ligand binding to a receptor is now well established, this workshop will cover docking and structure-based virtual screening, with an introduction to the theory followed by practical examples.

  • 24 June Advanced DataWarrior (http://www.openmolecules.org/datawarrior/) Isabelle Giraud. The previous very popular introductory workshop brought DataWarrior to a new, wider audience, this workshop will highlight advanced features, macros and other topics that were brought up by users. So feel free to submit requests.

Registration is free and you will be sent login details at a later date.

Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

Comments

Updates to mobile science apps

 

A number of the mobile science apps have been updated with new signing certificates.

ChemTube3D is an Open Educational Resource containing interactive 3D animations and structures, with supporting information for some of the most important topics covered during an undergraduate chemistry degree. It was developed by the ChemTube3D team including students at the University of Liverpool.

Orange NMR App to predict 13C and 1H NMR spectra: draw a structure to see its spectrum. The accuracy of the algorithm is about 1.9 ppm for 13C and 0.21 ppm for 1H (RMSD=3.4 and 0.31 ppm correspondingly).

Elemental Elemental is the Dotmatics chemistry sketch utility provided at no charge within many Dotmatics products. We are happy to provide this as a FREE app on the iTunes store.

Chemistry By Design is an interactive virtual flashcard that allows students to test their skills using known synthetic sequences. The goal is to display the reagents, starting materials and products for every single step used in constructing a natural product or pharmaceutical. Students are provided with different browsing options to test themselves.

There are many more more science apps for iPhone or iPad listed in the Mobile science database.

mobilescience

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AI 4 Proteins Seminar Series 2021

 

The AI 4 Proteins Seminar Series 2021 is now in full swing, the first two presentations by Lucy Colwell and Melanie Vollmar were really brilliant and are now on the CICAG YouTube channel https://www.youtube.com/c/RSCCICAG.

You can find out more about the forthcoming events in the series here https://www.ai3sd.org/ai3sd-online-seminar-series/ai4proteins-seminar-series-2021/.

The final event is 2 day meeting on Protein Structure Prediction. This looks like it will be a great meeting with a fantastic lineup. Current invited speakers include: Professor Debora Marks (Harvard University), Professor Cecilia Clementi (Freie Universität Berlin), Professor Charlotte Deane (University of Oxford), Professor Tudor Oprea (University of New Mexico), Dr Derek Lowe (Novartis) and Professor Stephen Burley (RCSB PDB, Rutgers University, USCD).

There is still time to submit abstracts for short talks and posters.

Short Talk Abstract Submission Form. Deadline: 29/04/2021. Notification of Acceptance: 06/05/2021.
Poster Abstract Submission Form. Deadline: 29/04/2021. Notification of Acceptance: 06/05/2021.
Poster & Video Guidelines for Accepted Posters

Full details are here https://www.ai3sd.org/ai3sd-event/17-06-2021-ai3sd-rsc-cicag-protein-structure-prediction/.

Comments

Update to MayaChemTools

 

MayaChemTools is an ever increasing collection of python and perl scripts that support cheminformatics and computational chemistry.

The latest addition are based on PSI4 an open-source quantum chemistry package.

PSI4 provides a wide variety of quantum chemical methods using state-of-the-art numerical methods and algorithms. Several parts of the code feature shared-memory parallelization to run efficiently on multi-core machines. An advanced parser written in Python allows the user input to have a very simple style for routine computations, but it can also automate very complex tasks with ease.

The command line Python scripts based on Psi4 provide functionality for the following tasks:

  • Calculation of single point energies
  • Calculation of molecular properties and partial charges
  • Performing structure minimization
  • Generating molecular conformations
  • Visualizing frontier molecular orbitals and dual descriptors
  • Visualizing electrostatic potential on densities and molecular surfaces

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU LGPL as published by the Free Software Foundation.

Comments

Amsterdam Modeling Suite Update

 

The AMS2020.103 subrelease contains an important bug fix for analytic frequencies with PBE, see below for more details. Other improvements and bug fixes in COSMO-RS, AMSjobs, and other components are included in this subrelease as well, so we suggest updating to this subrelease.

The Amsterdam Modeling Suite provides a comprehensive set of modules for computational chemistry and materials science, from quantum mechanics to fluid thermodynamics.

Easy installation with downloadable binaries for Windows, Mac, and Linux. Graphical user interface to set up, run, monitor, visualize and analyze jobs. Run jobs on your laptop, desktop PC or a high-performance computing cluster. Python interface for advanced workflows, job management, and analysis

Comments

Chemical Structure validation/standardisation (Greg Landrum) by Greg Landrum

 

The next CICAG Open Source tools workshop is coming up.

21 April Chemical Structure validation/standardisation (Greg Landrum) Possibly the most important step in model or database building is data curation, this workshop will deal with chemical structure validation and standardisation.

Registration is free and you will be sent login details at a later date.

Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

These workshops are sponsored by LiverpoolChiroChem.

Some pre-event details for the upcoming workshop

The workshop will be hands-on, so you'll get the most out of it if you have the most recent versions of the RDKit and the ChEMBL Structure Pipeline installed. You can download a conda environment specification here that will create a minimal environment which should have everything you need for the workshop. The conda environment uses python 3.7 since that's what's available on google colab, but you should also be able to use python 3.8 or 3.9 without problems; just change the python version spec in the environment file.

I'll be using a sample dataset from PubChem Substance: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/Substance000000001000500000.sdf.gz

If you have problems creating (or don't want to create) a local environment, I also created a notebook  in google colab which you can use. The cells at the beginning of this notebook install all required software and download the sample dataset: https://colab.research.google.com/drive/1p33LA610-8SS4p5-F1DrAlmB31T8F-KB?usp=sharing
Best, -greg

Comments

XQuartz

 

Xlogo

XQuartz 2.8.0 was released for macOS 10.9 or later a couple of weeks ago.

I've now upgraded two machines (one Big Sur the other Catalina) and so far I've not had any issues.

This release also supports Apple Silicon.

Comments

Docker Desktop for Mac Apple Silicon machines

 

Docker is now available for M1 machines

docker-desktop-m1

The release note can be found here https://docs.docker.com/docker-for-mac/release-notes/

and you download it here.

https://docs.docker.com/docker-for-mac/install/

Comments

Happy Birthday BBEdit

 

29 years ago BBEdit was first released.

Since then in my eyes it is firmly established as the text editor that I compare all others with. I've been using it since the very start and I've lost count of the times that BBEdit has saved me when I've needed to edit vast text or data files. I still have a bunch of applescripts that I wrote that helped me automate the updating of my first website.

BBEdit It (still) doesn't suck.

Comments

Automated reaction mapping

 

A recent publication caught my eye.

Extraction of organic chemistry grammar from unsupervised learning of chemical reactions DOI.

Anyone who has been involved in building a reaction database will know that atom mapping reagents/starting materials onto products is a very time-consuming and tedious process, that is often fraught with errors. So any method that automates this process is a significant step forward.

Here, we demonstrate that Transformer Neural Networks learn atom-mapping information between products and reactants without supervision or human labeling. Using the Transformer attention weights, we build a chemically agnostic, attention-guided reaction mapper and extract coherent chemical grammar from unannotated sets of reactions. Our method shows remarkable performance in terms of accuracy and speed, even for strongly imbalanced and chemically complex reactions with nontrivial atom-mapping. It provides the missing link between data-driven and rule-based approaches for numerous chemical reaction tasks.

F3.large

They also supply a file containing Common patent reaction templates. This file contains the most common patent reaction templates (USPTO grants), including the year of the first appearance, the patent numbers, frequently used reagents, and the template count. The templates were extracted after applying RXNMapper to generate the atom-mapping.

Comments

DataWarrior update

 

A new version of DataWarrior has been released

v05.05.00: April 2021

  • 3D-Structure alignment considering shape and pharmacophoric features (PheSA)
  • Google Patent search and results in DataWarrior (keyword, structure, date, ...)
  • Link to Spaya synthesis planning server
  • Searchable and navigatable user manual
  • Macro to retrieve and visualize world-wide Corona virus spreading
  • Lots of new features, range filter animations, smarter labels, ...

DataWarrior2

Comments

MacVector on Apple Silicon

 

The very popular bioinformatics tool MacVector 18.1 is now available to download. MacVector 18.1 is a Universal Binary application, which means it runs natively on both Apple Silicon M1 Macs and Intel Macs. MacVector 18.1 matches the “Big Sur” look and feel. …and for the first time in many, many years the MacVector icon has changed to match the square look of macOS Big Sur icons.

macvector

We ran some benchmarks to see how much faster MacVector now runs on an Apple Silicon MacBook Pro. We compared this against MacVector 18.0, which runs using Rosetta2 emulation. In some cases you can see that the native Apple Silcon MacVector 18.1 runs 200% faster than the emulated MacVector 18.0.

More on benchmarks here.

Comments

XQuartz updated

 

Xlogo

XQuartz 2.8.0 has been released for macOS 10.9 or later. I've been in touch with a couple of users and they report no issues so far. This is the first version with Apple Silicon support.

The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple shipped with OS X versions 10.5 through 10.7.

Changes in 2.8.0

  • Adds native support for Apple Silicon Macs.
  • Removes support for versions of macOS older than 10.9
  • Uses system libXplugin
  • Removes build-time support for deprecated X11 libraries:
    • ibXaw8
    • libXevie
    • libXfontcache
    • libxkbui
    • libXp
    • libXTrap
    • libXxf86misc
  • Removes deprecated commands:
    • gccmakedep
    • makedepend
    • xdmshell
    • xfindproxy
    • Xfake
  • Removes xpyb
  • Removes older libpng

Full release notes are here https://www.xquartz.org/releases/XQuartz-2.8.0.html

Comments

ChemDoodle 2D v11.4 Update Available

 

A new version of ChemDoodle is available, this is a free update for all subscribers.

Whilst there are a few bug fixes and stability improvements the big news is the new feature enabling generation of a chemical structure from an image.

ChemDoodle now has the ability to recreate a chemical drawing from an image of a molecule, recovering the original chemical data. This function is performed using the File>Recover from Image... menu item. This function is different from inserting the image as inserting an image provides you with just a graphic, while recovering the chemical drawing allows you to regain access to the chemical information to use or edit further. We call this function Chemical Image Recovery (CIR). Some may also refer to this function as Optical Structure Recognition (OSR).

I can see this being a very popular feature.

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RSC Emerging Technologies Competition

 

The Emerging Technologies Competition is the Royal Society of Chemistry’s annual initiative for early stage companies and academic entrepreneurs who want to commercialise their technologies to make a societal impact.

The competition is a European programme seeking to identify start-ups and spin outs who are developing the most novel, innovative and promising chemistry tech.

More details here https://www.rsc.org/competitions/emerging-technologies/

Closing date for applications April 18th.

Winners will.....

  • Receive a cash prize of £20,000 (per competition category)
  • Be assigned a Royal Society of Chemistry mentor who will provide ongoing support for one year
  • Through discussion with their mentor, winners, who are an incorporated company, can be provided a business acceleration grant up to the value of £20,000
  • Gain wider support and advice from our competition partners and judges, during the final
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WWDC21

 

I just got an email about the Apple Worldwide Developers Conference (WWDC21), June 7 - 11.

The Apple Worldwide Developers Conference is coming to a screen near you, June 7 to 11. Join the worldwide developer community for an all-online program with exciting announcements, sessions, and labs at no cost. You’ll get a first look at the latest Apple platforms, tools, and technologies — so you can create your most innovative apps and games yet.

What caught my eye was the Swift Student Challenge https://developer.apple.com/wwdc21/swift-student-challenge/.

We continue our long-standing tradition of supporting students who love to code with this year’s exciting Swift Student Challenge. Showcase your passion for coding by creating an incredible Swift playground on the topic of your choice. Winners will receive exclusive WWDC21 outerwear, a customized pin set, and one year of membership in the Apple Developer Program. This challenge is open to students around the world.

  • Submissions open on Tuesday, March 30, 2021, at 6:00 a.m. PDT.
  • Deadline for submissions is Sunday, April 18, 2021, at 11:59 p.m. PDT.
  • Applicants can view their status by end of business day on Tuesday, June 1, 2021.
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RSC CICAG YouTube channel

 

The video of the ChimeraX workshop is now online https://youtu.be/M2K72Kgk718.

The RSC CICAG YouTube channel is building up a very useful collection of videos https://www.youtube.com/c/RSCCICAG.

CICAGYoutube

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Importing Open Source Antibiotics Data into DataWarrior

 

A couple of DataWarrior macros to import data directly from an online spreadsheet. Full details are here

Screenshot

The Open Source Antibiotics Consortium is a group of researchers working together to discover new antibiotics in an open source manner. All data is freely available and in the open. There is also an effort to develop open source solutions to the computational needs of the project. The CompChem Tools page provides links to a variety of Open-Source tools, scripts, Jupyter notebooks.

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MarvinSketch freezes on macOS Big Sur

 

Apparent MarvinSketch is freezing under Big Sur, This problem is caused by a change in tab behavior in Big Sur. Newly opened dialogs are handled as tabs by default now.  The issue can be solved by changing the tab preferences of the system.

Details are here https://chemaxon.freshdesk.com/support/solutions/articles/43000613604-marvinsketch-freezes-on-macos-big-sur.

There are more details of Scientific Applications Under Big Sur here.

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Open-Source Tools for Chemistry Workshops

 

Over the years RSC CICAG have held workshops providing tuition for various software packages, because of the physical limitations these workshops had to be limited to around 50 attendees leaving us with a waiting list of folks who missed out. Because of the COVID-19 pandemic the meetings have been moved online allowing much greater access. The recent Open Chemical Science workshops had attendees from 45 different countries. There was considerable interest in including further workshops and so CICAG have started a monthly workshop series, each month a workshop will be held highlighting a particular package/resource.

The first four workshops are now organised, you can register here. These look to be very popular with registrations already up to 150 for the first workshop, which is three-fold higher than we could have accommodated in a physical workshop.

There are four two-hour sessions in this series which will be run on Zoom.

Registration is free and you will be sent login details at a later date.

Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

These workshops are sponsored by LiverpoolChiroChem.

The previous workshops are now available on the RSC CICAG YouTube channel.

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Open Chemistry and Google Summer of Code

 

OpenChem is once again participating in the Google Summer of Code.

Avogadro 2 Project Ideas

  • Project: Python-based Compute and Data Server
  • Project: Biological Data Visualization
  • Project: Scripting Bindings
  • Project: Integrate with RDKit
  • Project: Tools for Interactive Molecular Dynamics

Open Babel Project Ideas

  • Project: Integrate CoordGen library
  • Project: Implement MMTF format
  • Project: Test Framework Overhaul
  • Project: Develop a JavaScript version of Open Babel
  • Project: Develop a validation and standardization filter

cclib Project Ideas

  • Project: Support for QCSchema JSON output
  • Project: Implement new parsers
  • Project: Discovering computational chemistry content online

QC-Devs Project Ideas

  • Project: Visualization of Molecular Structure and Reactivity
  • Project: Extended Interoperability of ChemTools and Quantum Chemistry Software
  • Project: Visualize Chemical Reactions
  • Project: Extended interoperability of GOpt and Quantum Chemistry Software
  • Project: Implement Workflows for Calculation and Usage of Databases of Isolated Atom Densities
  • Project: Orthogonal Procrustes for Rectangular Matrices
  • Project: Faster Molecular Integrals with Density-Fitting

3Dmol.js Project Ideas

  • Project: Improve 3Dmol.js

gnina Project Ideas

  • Project: Improve gnina

NWChem Project Ideas

  • Project NWChem-JSON
  • Project NWChem-Python-Jupyter Interface
  • JSON-LD for Chemical Data

DeepChem Project Ideas

  • Project: PyTorch Lightning Implementation
  • Project: Semiconductor Modeling Support
  • Project: Protein Language Models

Miscellaneous Project Ideas

  • Project: OneMol: Google Docs & YouTube for Molecules

There are more details of the potential ideas here https://wiki.openchemistry.org/GSoCIdeas2021 or contribute your own idea.

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CSD Software Portfolio from the CCDC upgraded for Big Sur

 

The full CSD software portfolio, including Mercury, ConQuest, Mogul, GOLD, CSD-CrossMiner, the CSD Python API and other components, has now been upgraded and tested for compatibility with Big Sur. We are pleased to report that the newly available 2020.3.1 CSD Release (only available on macOS) is fully supported on macOS Big Sur at point of release, both for Intel-based macs, as well as the newer M1 Apple silicon based macs. At this point we are aware of just two specific known issues for the newer silicon hardware machines:

  • The POV-Ray integration in Mercury for high-resolution graphics generation does not work on M1 Apple silicon based macs
  • The Aromatics Analyser component in the CSD-Materials menu of Mercury does not work on M1 Apple silicon based macs We expect that these final remaining issues will be addressed in the next CSD software release.

Full details are here https://www.ccdc.cam.ac.uk/solutions/whats-new/.

More details on scientific applications under Big Sur are here https://www.macinchem.org/blog/files/1fd84c61d3f91608c1b9c413c8064cd4-2692.php

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Open-Source Tools for Chemistry Workshops

 

Last year RSC CICAG held a five day conference entitled Open Chemical Science this online event proved to be enormously popular with attendees from 45 different countries. One feature of the meeting was a series of workshops highlighting a number of open-source software tools, these workshops are now available on the RSC CICAG YouTube channel.

There was considerable interest in including further workshops and so CICAG have started a monthly workshop series, each month a workshop will be held highlighting a particular package/resource.

The first four workshops are now organised, you can register here.

There are four two-hour sessions in this series which will be run on Zoom.

Registration is free and you will be sent login details at a later date.

Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

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Schrödinger Software Release 2021-1

 

Schrödinger have just announced the release of the latest update.

This release fully supports macOS 11, Big Sur, (with previous releases of the suite remaining unsupported on Big Sur).

Computers running ARM64-based processors such as the Apple M1 chip are unsupported.

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AI4Proteins webinar series

 

Save the dates!!

AI3SD are collaborating with RSC-CICAG (The Royal Society of Chemistry – Chemical Information and Computer Applications Group) and have teamed up to run an #AI4Proteins Seminar Series in 2021. This series starts on Wednesday 14th April 2021, and is made up of a set of sessions of 1-2 talks, ending with an all day virtual conference on Thursday 17th June 2021.

Full details are on the website here.

ProteinSaveTheDateFlyerV3

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Fortran on a Mac page updated

 

I've just updated the Fortran on a Mac page.

In particular

gfortran for ARM Big Sur (macOS 11.0) and Apple Silicon.

NAG Fortran compiler Fortran compiler for Apple Silicon Macs now available to download. Available on Linux, Windows and macOS, including Apple Silicon Macs.

Absoft Pro Fortran 2021 For macOS and OS X. Fully compatible with macOS Big Sur (11.0).

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Scientific computing on Apple M1

 

We are just starting to see a few benchmarks on the new Apple M1 chip using scientific applications.

This blog post looks like it will be really interesting to follow.

Scientific computing on Apple M1, vol 1: ASE and GPAW.

In this post, which I expect will be the first in a series, I’ll share the code that got me running with a basic Python 3.9, scipy, and matplotlib environment. However, I immediately took it further, getting a working – and quite well-performing – installations of the Atomic Simulation Environment (ASE), used for building, manipulating and visualizing atomistic structure files, as well as a parallel installation of the density functional theory code GPAW.

Bottom line

not even having 10 high-performance Xeon cores in the iMac Pro instead of only 4 high-performance M1 cores in the MacBook Pro brought the two systems to parity: the M1 MacBook Pro handily wins this comparison.

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Homebrew on Apple Silicon

 

Homebrew has been updated

Apple Silicon is now officially supported for installations in /opt/homebrew. formulae.brew.sh formula pages indicate for which platforms bottles (binary packages) are provided and therefore whether they are supported by Homebrew. Homebrew doesn’t (yet) provide bottles for all packages on Apple Silicon that we do on Intel x8664 but we welcome your help in doing so. Rosetta 2 on Apple Silicon still provides support for Intel x8664 in /usr/local.

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Ammolite

 

This looks really interesting, Ammolite enables the transfer of structure related objects from Biotite to PyMOL for visualization, via PyMOL’s Python API:

  • mport AtomArray and AtomArrayStack objects into PyMOL - without intermediate structure files
  • Convert PyMOL objects into AtomArray and AtomArrayStack instances.
  • Use Biotite’s boolean masks for atom selection in PyMOL.
  • Display images rendered with PyMOL in Jupyter notebooks.

To install

conda install -c conda-forge ammolite

Biotite package bundles popular tasks in computational molecular biology into a uniform Python library.

ammolite

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MOE and the XQuartz 2.8.0 Beta

 

I just heard that it seems that there is a problem with the XQuartz 2.8.0 beta version which will stop MOE from starting with the OpenGL graphics. They recommend that you keep using XQuartz 2.7.11 until there is a version of the 2.8 release that works properly.

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Python on Apple Silicon

 

A lot of people have been asking me about running data analysis on the new laptops with M1 chips. It looks like we are starting to see a few benchmarks appearing.

A recent blog post Are The New M1 Macbooks Any Good for Data Science? Let’s Find Out would suggest that the performance of the M1chip continues to impress.

Whilst all benchmarks come with caveats, some use "native" installations others require Rosetta

Python is approximately three times faster when run natively on a new M1 chip, Numpy looks to be slightly slower, Pandas is twice as fast, SciKit-Learn is twice as fast.

Instructions for installing TensorFlow 2.4 on Apple Silicon M1: installation under Conda environment have also been reported.

PyCharm, JetBrains’ IDE for Python development, now supports Apple Silicon M1 processors.

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Pro Fit supports Big Sur

 

pro Fit pro Fit 7 is now at version 7.0.18, supporting dark mode, Catalina, and Big Sur.

pro Fit is a macOS application for data/function analysis, plotting, and curve fitting. It is used by scientists, engineers and students to analyze their measurements and the mathematical models they use to describe them.

Highlights:

  • Data windows for storing and analyzing data
  • Drawing windows for plots and other graphics
  • Function windows for user defined functions
  • Write your own functions and scripts using Python or Pascal
  • Numerous Curve Fitting Algorithms:
  • Levenberg-Marquardt, Robust, Multi-dimensional
  • High resolution, high quality drawings and graphs
  • Full PDF support for exporting figures
  • Big Sur and Retina Support

There is a comprehensive list of scientific applications under Big Sur here

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Mapping chemical reaction space

 

Really nice paper looking at reaction classification based on text description, and visualisation using reaction fingerprints. Mapping the space of chemical reactions using attention-based neural networks. DOI

Can be installed using conda

All code is on GitHub https://github.com/rxn4chemistry/rxnfp/tree/master/.

annotated_atlas

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The official release of GROMACS 2021 is now available

 

You can find the code, manual, release notes, installation instructions and test suite at the links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2021.tar.gz.

Documentation: http://manual.gromacs.org/2021/index.html. (includes install guide, user guide, reference manual, and release notes)

Test Suite: ftp://ftp.gromacs.org/regressiontests/regressiontests-2021.tar.gz.

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Unix tips for dealing with very large files

 

I've updated the page describing a variety of unix commands that can be helpful when dealing with very large files. In particular I've added details of how to split very large files into more manageable chunks.

Dividing sdf files can be problematic since we need each division to be at the end of a record defined by "$$$$". I've spent a fair amount of time searching for a high-performance tool that will work for very, very large files. Many people suggest using awk

AWK (awk) is a domain-specific language designed for text processing and typically used as a data extraction and reporting tool. Like sed and grep, it's a filter, and is a standard feature of most Unix-like operating systems.

I've never used awk but with much cut and pasting from the invaluable Stack Overflow this script seems to work.

awk -v RS='\\$\\$\\$\\$\n' -v nb=1000 -v c=1 '
{
  file=sprintf("%s%s%06d.sdf",FILENAME,".chunk",c)
  printf "%s%s",$0,RT > file 
}
NR%nb==0 {c++}
' /Users/username/Desktop/SampleFiles/HitFinder_V11.sdf

The result is shown in the image below. There are a couple of caveats, this script only works with the version of awk shipped with Big Sur (you should be able to install gawk using Home Brew and use that on older systems), and it requires the file has unix line endings. The resulting file names is not ideal and if there are any awk experts out there who could tidy it up I'd be delighted to hear from you.

awkresults

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OpenMM on Apple silicon

 

The ARM OSX Migration seems to be quite active :-)

Update

And here it is

OpenMM is now available on condaforge for osx-64 to support new Apple hardware based on the Mac M1 chip!

To install

conda install -c conda-forge openmm

I'd be really interested in hearing about any benchmarking activities.

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AI in Chemistry literature

 

Some of the more popular pages on the site are the compilation of resources, a listing of Open-Source Cheminformatics toolkits and a list of useful python libraries for data science so I thought I'd flag a recent post by Pat Walters listing some interesting machine learning publications in 2020 on his practical cheminformatics blog.

His post AI in Drug Discovery 2020 is certainly an invaluable starting point.

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ChemDoodle 2D v11.3 Update

 

I just heard version 11.3 of ChemDoodle 2D software has been released.

ChemDoodle 2D v11.3 is a feature update. The main new feature is expert IUPAC naming support for free radicals. Other major features include new image output sizing options with previews, and stoichiometry table options.

ChemDoodle 2D is a popular and extensively featured Chemical Drawing and cheminformatics software tool.

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Mathematica System requirements

 

A couple of folks have asked me about running Mathematica on Apple Silicon. I don't use Mathematica but the system compatibility is on their website.

Mathematica 12.2 is optimized for the latest operating systems and hardware. mathematicaSystemRequirements

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Analyzing the runtime, energy usage, and performance of Tensorflow training on a M1 Mac Mini and Nvidia V100

 

An interesting comparison of Apple Intel and M1 chips machines with Nvidia 100 when using Tensorflow.

https://wandb.ai/vanpelt/m1-benchmark/reports/Can-Apple-s-M1-help-you-train-models-faster-cheaper-than-NVIDIA-s-V100---VmlldzozNTkyMzg

We ran a sweep of 8 different configurations of our training script and show that the Apple M1 offers impressive performance within reach of much more expensive and less energy efficient accelerators such as the Nvidia V100 for smaller architectures and datasets.

Code is available on Colab https://colab.research.google.com/drive/1RvZBpzJRW9MNPWQ2rZG8HIyHJbaCwnTI.

They also include tips on setting up a Mac mini to run Tensorflow.

Only initial results on modest data sets, will be interesting to see the performance when Apple releases more Pro hardware.

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Latest RSC CICAG newsletter

 

The latest RSC CICAG newsletter (Winter 2020) is now available http://rsccicag.org/newsletters.htm. It includes:-

Chemical Information & Computer Applications Group Chair's Report
CICAG Planned and Proposed Future Meetings
Memories of Dr Angus McDougall, 1934-2020
CASP14: DeepMind’s AlphaFold 2 – an Assessment
Meeting Report: 3rd RSC BMCS & CICAG AI in Chemistry Meeting
ReadMe and HowTo for Lightning Poster Presentations
As Conferences went Online: What do we miss the most?
Alan F Neville, 1943-2020, BSc, PhD
Parallel Processing for Molecular Modeling in ChemDoodle 3D
Catalyst Science Discovery Centre & Museum Trust: A Year in Review
The 6th Tony Kent Strix Annual Memorial Lecture 2020
Open Chemical Science Meetings and Workshops - Introduction
Open Access Publishing for Chemistry – Meeting Reports
Open Data for Chemistry – Meeting Reports
Open Source Tools for Chemistry – Workshop Reports
RSC Open Access Journals and Future Plans
RSC’s Journal Archives Available for Text and Data Mining
Chemical Information / Cheminformatics and Related Books
News from AI3SD 64 Other Chemical Information Related News

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Why Apple's M1 Chip is So Fast

 

A technical but still very accessible (15 min) analysis of the latest Apple M1 chip. Well worth spending a coffee break viewing.

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JupyterLab 3.0 released

 

JupyterLab is the next-generation web-based user interface for Project Jupyter.

JupyterLab 3.0 includes a number of new features and enhancements that are described on the Jupyter blog. Full details are described in the ChangeLog

To install using conda

conda install -c conda-forge jupyterlab=3

However note that some extensions may not yet have been updated.

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OpenChem

 

OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend. The goal of OpenChem is to make Deep Learning models an easy-to-use tool for Computational Chemistry and Drug Design Researchers.

You can read about in this publication DOI.

All code is available on GitHub https://github.com/Mariewelt/OpenChem.

Requires

  • Modern NVIDIA GPU, compute capability 3.5 or newer.
  • Python 3.5 or newer (we recommend Anaconda distribution)
  • CUDA 9.0 or newer

numpy, pyyaml, scipy, ipython, mkl, scikit-learn, six, pytest, pytest-cov

The software is licensed under the MIT license

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RDKit blog

 

If you are a RDKit user then you should bookmark Greg Landrum's RDKit blog https://greglandrum.github.io/rdkit-blog/about/. This is a new site and all the old content will be migrated in due course.

RDKitBlog

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Annual Site 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 90,006 visitors, an increase of 28% over 2019, 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 28% of the visitors and the UK 8% with Germany, India, China and Japan around 5%. As might be expected 57% of the visitors were using a Mac, but 23% of the visitors were Windows users, 9% iOS and 6% Android, also 4% Linux. There has been a gradual increase in the number of visitors using mobile devices.

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. The page describing the update to iBabel was particularly popular.

viewerTab

The post about Scientific Applications under Catalina made it to number 4 in the years listing and elicited a significant amount of reader feedback.

The Mobile Science site has seen increased visitor numbers.

The most popular apps viewed were.

Merck PTE
IBM Micromedex Drug Info
PocketCAS: Mathematics Toolkit
The Periodic Table Project
Periodic Table

Also popular were

Python3IDE Human Anatomy Atlas 2019
ChemTube3D.
Molecular Constructor

The Twitter feed @macinchem has steadily attracted new followers and currently has 993 followers.

The most popular tweets were

IOData: A python library for reading, writing, and converting computational chemistry file formats

and

Google Colab is very cool. .


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