Macs in Chemistry

Insanely Great Science

Comparing energy usage between M1 Mac and Intel

 

The pages comparing cheminformatics/compchem apps on the MacBook Pro M1max are proving very popular. Several readers have asked me to compare energy usage which is an excellent suggestion.

Based on a suggestion I purchased Nevsetpo Power Meter UK Plug Power Monitor Watts Meter Plug and I've used it to test a selection of tasks. Once plugged into a socket it monitors total energy consumption of anything device plugged in. Both machines were fully charged and the "Optimised battery charging" was switched off.

I tried a few computationally intensive tasks and details of energy consumption are here..

M1chip

Comments

OpenMM update

 

OpenMM version 7.7.0 has been released

A major focus of this release is on improved force field support. The following have been added.

  • GLYCAM is now available for use with Amber14. This is a force field for simulating carbohydrates and glycosylated proteins.
  • GBSA implicit solvent is now available for use with Amber14 and CHARMM36. We previously had it for earlier Amber force fields, but not for the more recent ones.
  • AMOEBA 2018 is now available, superseding the older 2013 version.

Full details here https://github.com/openmm/openmm/releases.

ARM based Macs are fully supported.

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

conda install -c conda-forge openmm
Comments

Pharmacophore searching MacBook Pro M1 max.

 

Pharmacophore searching is a critical part of virtual screening and is can be used to search very large datasets. Pharmacophore query generation in general requires user interaction and is not well-suited for batch mode. Pharmacophore search, on the other hand, can be done in MOE/batch using an SVL script or runnable file that invokes the SVL function ph4_Search. The search was run on a dataset of 274K structures using a predefined query. CCG also provided me with timings from other architectures and the results are shown below. As you can see the MacBook Pro M1 max out-performs all other platforms tested, this is particularly noticeable in the multicore performance, evaluating over 20,000 molecules per second.

moebatch

You can read the full evaluation of MOE on a MacBook Pro M1max here https://www.macinchem.org/reviews/MacBooks/moe.php

And the list of all applications evaluated here https://www.macinchem.org/reviews/MacBooks/m1macbookpromax.php.

Comments

AutoDock Vina 1.2.0

 

A new publication describes and update to AutoDock Vina "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings" DOI.

AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks support for modeling specific features such as macrocycles or explicit water molecules. Here, we describe the implementation of this functionality in AutoDock Vina 1.2.0. Additionally, AutoDock Vina 1.2.0 supports the AutoDock4.2 scoring function, simultaneous docking of multiple ligands, and a batch mode for docking a large number of ligands. Furthermore, we implemented Python bindings to facilitate scripting and the development of docking workflows. This work is an effort toward the unification of the features of the AutoDock4 and AutoDock Vina programs.

The source code is available at https://github.com/ccsb-scripps/AutoDock-Vina.

  • AutoDock4.2 and Vina scoring functions
  • Support of simultaneous docking of multiple ligands and batch mode for virtual screening
  • Support of macrocycle molecules
  • Hydrated docking protocol
  • Can write and load external AutoDock maps
  • Python bindings for Python 3 (Linux and Mac)
  • AutoDock Vina is distributed under the Apache License, Version 2.0.
Comments

PyMOL session file for visualising the COVID-19 spike protein

 

Manish Sud the creator of MayaChemTools has created a PyMOL session file for visualising the COVID-19 spike protein. On it he has mapped the mutations for alpha, beta, gamma, delta, and omicron spike variants on a full-length model of glycosylated spike protein in open state conformation.

COVIDspikeProteinPymolfile

Manish has made the PyMOL session freely available to download. (32MB) here

SARS-CoV-2-Spike-Protein-Open-Complex-Model-And-Variants.pse.zip.

Comments

Comparing a M1 MacBook with Intel MacBookPro for Cheminformatics/CompChem

 

As some of you may have seen I've started the comparison of my new MacBook Pro Apple M1 max with my old Intel MacBook.

M1macbookpromax

I'm slowly working through a variety of cheminformatics toolkits and computational chemistry applications, I'm trying to run some "real world" workflows so you can see what kind of performance improvement you might expect.

The index page is here https://www.macinchem.org/reviews/MacBooks/m1macbookpromax.php and I'll update it as a test more applications

When possible I've used the latest builds for the M1 arm architecture. Both machines were connected to power and had no other applications running. To date I've looked at the following.

More to come.

Comments

Additions to MayaChemTools

 

A couple of new scripts have been added to the excellent MayaChemTools growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.

RDKitFilterTorsionLibraryAlerts.py - Filter torsion library alerts Direct Link

And

Psi4CalculateInteractionEnergy.py - Calculate interaction energy Direct Link.

Comments

ChemDoodle 3D v6.5: 3D Printing

 

Whenever I post anything on 3Dprinting it always generates interest so this update of ChemDoodle 3D will probably be of wide interest.

Export your ChemDoodle 3D creations into many popular 3D model file types for import into other CAD applications and for 3D printing:

  • 3D Manufacturing Format {.3mf}
  • Additive Manufacturing File Format {.amf}
  • COLLADA Digital Asset Exchange {.dae}
  • Extensible 3D Graphics {.x3d}
  • Polygon File Format {.ply}
  • STereoLithography {.stl}
  • Virtual Reality Modeling Language {.wrl}
  • Wavefront Object File {.obj}
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RCSB and RSC CICAG workshop on the PDB

 

For any scientists working with biomolecules be it, medicinal chemist, structural biologist, biochemist etc. the most valuable source of primary structural information is the Protein Data Bank (PDB). This resource has now been running for 50 years so it very timely to hear about the history of the RCSB PDB and the different components that make up the repository both from a depositor and a user. The second workshop describes some of the recent changes in particular the development of Mol* a 3D viewer capable of rendering from macromolecular assemblies down to atomic details.

Workshop 1

  • History of the Protein Data Bank (PDB) and the Worldwide PDB Stephen K. Burley, RCSB Protein Data Bank
  • PDBx/mmCIF Data Standard and PDB Data Deposition with OneDep Ezra Peisach and Jasmine Young
  • Small Molecules in the PDB -talk + tutorial Chenghua Shao, RCSB Protein Data Bank
  • OneDep Tutorial - Jasmine Young and Ezra Peisach

Workshop 2

  • wwPDB Validation: Assessing the Quality of PDB structures John Berrisford, Protein Data Bank in Europe
  • How to Interpret the Quality of a PDB Structure using the wwPDB validation report - tutorial David Armstrong/John Berrisford/Jack Turner, Protein Data Bank in Europe
  • 3D Visualisation of PDB Data with the Mol* viewer -James Tolchard, Protein Data Bank in Europe
  • Impact of AI and Future of PDB Data: Next Generation PDB Archive - Sameer Velankar, Protein Data Bank in Europe
  • Round Table Discussion - Sameer Velankar, Protein Data Bank in Europe, Stephen K. Burley, RCSB Protein Data Bank

Workshop 1

Workshop 2

This is part of the RSC CICAG workshops on Open Chemical Sciences, all 17 workshops are on the RSC CICAG YouTube playlist https://www.youtube.com/playlist?list=PLBQwbn0mPhvWfOx6ce_vUjr54ftLBmSH0.

If you have any suggestions (or would like to volunteer) for future workshops feel free to get in touch.

Comments

Install Homebrew on M1, M1 Pro, M1 Max Macs

 

A useful tutorial showing how to install Home-brew on Apple Silicon Macs.

Comments

Scientific Applications under macOS 12 Monterey Update 1

 

General Issues with Monterey

After a period of open beta testing MacOS 12 Monterey is here.

monterey

If you want an overview of Monterey I'd recommend the excellent arstechnica review.

Monterey supports both Intel and Apple Silicon Macs, the list of supported Macs:

  • Early 2015 and later MacBook Air
  • Early 2015 and later MacBook Pro
  • Early 2016 and later MacBook
  • Late 2015 and later iMac
  • Late 2014 and later Mac mini
  • 2017 and later iMac Pro
  • Late 2013 and later Mac Pro

You can find out your Mac model by tapping on the Apple icon in the menu bar and going to About This Mac. Unsupported Macs will continue to get security updates for Big Sur (for 2 years) and Catalina (this is last year?).

Scientific Applications

I've contacted all developers I know and their responses to date are shown below, first impressions are this is a relatively benign update.

4-Peaks

Absoft Absoft Pro Fortran 2022 For macOS Fully compatible with macOS Monterey (12.0)

alvaDesc We have tested our tools on Monterey and they work fine.

Amsterdam Modeling Suite

Anaconda

APE New version uploaded for Monterey

Avogadro no issues reported

BBEdit version 14.0.2 is recommended with macOS Monterey.

Brainsight

ChemAxon Most of our software in general requires Java, so as long as the appropriate Java version is installed, there should be no problem.

ChemDraw no issues with initial tests

ChemDoodle ChemDoodle 2D and ChemDoodle 3D are both fully supported on macOS 12 Monterey with no known issues

Chirys View no issues with initial tests

Conquest and Mercury from CCDC The full CSD software portfolio, including Mercury, ConQuest, Mogul, GOLD, CSD-CrossMiner, the CSD Python API, and other components, is expected to be fully supported on macOS 12 Monterey from the next major release - the 2021.3 CSD Release which is due in December 2021. We don't anticipate any significant problems with Monterey based on our initial checks, but we are running more extensive platform tests now to confirm that."

Cresset testing underway

CrystalMaker supports all from macOS 10.12 "Sierra" to 12.x "Monterey"

We are also very-pleased to announce the immediate availability of CrystalMaker 10.6 for Mac, SingleCrystal 4.1 and CrystalDiffract 10.9 for Apple Silicon: these are Universal Binaries and provide 100% native performance on the new Apple Silicon Macs, as well as 100% native performance on Intel.

CYLView 1.0

DataWarrior Seems to be working fine.

Delta

DEVONagent fine under Big Sur on Intel, not tested on Apple Silicon.

DEVONthink fine under Big Sur on Intel, not tested on Apple Silicon.

Elemental Fine under Monterey and on Apple Silicon

EndNote

EnzymeX

EverNote

Findings

Fujitsu ScanSnap .

GAMESS

Gaussaian We do not currently have an official report for support under macOS Monterey 12. We will be working on this over this week and list it on our website as a supported release if our tests pass successfully. I should also mentioned that we have not received any reports from users about issues with macOS Monterey. We have also run GaussView 6.1.1 and the Gaussian 16 rev. C.01 utilities on beta releases of macOS Monterey prior to the official release. Thus, we do not anticipate any issues with GaussView 6.1.1 and Gaussian 16 rev. C.01 (64-bit) under macOS Monterey on Macs equipped with Intel CPUs.

gFortran Standalone installer of GCC 11.2, including gfortran 11.2, for macOS Monterey (macOS 12). This is for machines with Intel processor.

Highlights

Homebrew For most seems to work fine, remember to reinstall Xcode command line tools.

ICM products. We have not experienced or had any reported issues with Monterey.

Other products that are compatible include:

IDL Version 8.8.1 adds support for M1 Macs

Igor Pro

iNMR

JalView

KaleidaGraph

KNIME no issues with initial tests

Manuscripts no issues reported

Matlab MATLAB is compatible with macOS 12 (Monterey) Running MATLAB and Simulink on Apple silicon Macs is supported in MATLAB R2020b Update 3 and newer. On Apple silicon Macs, MATLAB runs using the Rosetta 2 environment.

Mathematica Mathematica running fine on MacOS Monterey

Mendeley

Microsoft Office any Office for Mac which works with ‘Big Sur’ macOS v11 is OK with ‘Monterey’.

Mnova

MOE Initial tests showed no issues with this version.

MOPAC

NAG Fortran compiler Robust and highly tested Fortran Compiler, valued for its checking capabilities and detailed error reporting. Available on Linux, Microsoft Windows and Mac OS X, including Apple Silicon Macs.

ODYSSEY

Orca Orca and openmpi working fine under Big Sur. I then updated again to Monterey - still working fine.

Papers

PGOPHER

pro Fit

PYMOL On Intel Macs with macOS 12, PyMOL works fine, no known issues.

Python Python 2.7 is no longer included - use Python 3 instead Python works fine on Apple Silicon and is "mad fast!".

QMForge 2.4

R Releases for either Intel or Apple Silicon

RDKit All seems fine (Note: -Python 2.7 is no longer supported - use Python 3 instead)

Samson

Schrodinger macOS 12 Monterey is incompatible with past Schrödinger Suite releases up to and including 2021-4.We are aiming to support macOS 12 in the Schrödinger Suite 2022-1.

SeeSAR

Simply Fortran Fortran development environment for macOS 11.6 or higher on Intel, experimental build for Apple Silicon.

Sketch the latest Sketch release is fully compatible with Apple’s new operating system. And of course, when Universal Control lands in a future macOS Monterey update, it’ll work perfectly with Sketch. Plus, if you’ve recently upgraded to a brand new MacBook Pro, Sketch already supports the new M1 Pro and M1 Max chips. So you can work faster than ever with all the power of your new machine

Spartan Intel or M1 chip, 4 GB RAM or higher, OS 10.12 (Sierra) through OS 12.X (Monterey), ​128 GB disk space or higher

SPSS

Stardrop a quick update regarding StarDrop 7.1's performance on the new Mac Monterey OS. Our test engineer has begun the process of running our standard testing procedures and noted that there are a couple of very minor cosmetic issues in the GUI but no show-stoppers in terms of performance or functionality. The couple of issues identified are flagged up to be sorted for StarDrop 7.2, which will release in Q1-2022.

Swiss-PdbViewer Swiss-PdbViewer is a 32 bits application and will * NOT * run.

TensorFlow and TensorFlow Addons This pre-release delivers hardware-accelerated TensorFlow and TensorFlow Addons for macOS 11.0+. Native hardware acceleration is supported on Macs with M1 and Intel-based Macs through Apple’s ML Compute framework.

UCSF ChimeraX Details on building M1 version https://www.rbvi.ucsf.edu/chimerax/data/czi-nov2021/apple_m1.html

VMD

Vortex Vortex works perfectly on Intel Macs under Monterey, and on Apple Silicon

WINE

Wizard

wxMacMolPlt

Xcode need to update to latest version. Remember to reinstall command line tools

XQuartz OpenGL and OpenCL are still here, even on Apple Silicon Macs

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

Last update 8 November 2021

Comments

Generating IUPAC names for molecules

 

I was recently asked if I could generate IUPAC names for a series of molecules for a patent filing. There are many chemical drawing packages that will generate the IUPAC for a single compound and whilst I could have spent several hours cutting and pasting I decided to write a simple Vortex script to do the task.

Read the details here ….

vortexChemicalnames


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RSC CICAG Open Source Tools workshop, PDB

 

Registration for the November RSC CICAG workshops is open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)

Given that it is the 50th anniversary of the PDB archive it is appropriate that the two final workshops for 2021 are describing this absolutely invaluable resource.

Protein Data Bank Workshop (16 November 2021 15.00 – 17.00 GMT)

The Protein Data Bank https://www.wwpdb.org archives information about the 3D shapes of proteins, nucleic acids, and complex assemblies that help students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. Open access PDB data are used by hundreds of data resources and millions of users exploring fundamental biology, energy, and biomedicine. The PDB is a vast resource and this workshop will be invaluable to anyone seeking to get full value from the PDB.

Mol* Workshop (18 November 2021 15.00 – 17.00 GMT)

Mol* is a modern web-based open-source toolkit for visualisation and analysis of large-scale molecular data. More information can be found here: https://molstar.org. High-performance graphics and data handling of the Mol* Viewer allow users to simultaneously visualise up to hundreds of (superimposed) protein structures, play molecular dynamics trajectories, render cell-level models at atomic detail with tens of millions of atoms, or display huge models obtained by I/HM such as the Nuclear Pore Complex.

David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; DOI.

If you want to learn more about the history of the PDB there is a video here.

These workshops are sponsored by Liverpool ChiroChem

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Stop Mail compressing embedded images

 

Several folks have asked me this question "How do you stop Mail from compressing embedded images".

If you include an image in mail it can get reduced in size, this can make any text unreadable. When you add an image a dropdown menu appears as highlighted below in red.

mailsmall

If you change this to "Actual Size" the embedded image will be sent as you intended.

mailactual

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KNIME workshop on clustering molecules

 

The latest RSC CICAG Open-Source Tools for Chemistry Workshop is now on YouTube. RSC CICAG Open Source Tools for Chemistry :- Clustering using KNIME.

Clustering is an invaluable cheminformatics technique for subdividing a typically large compound collection into small groups of similar compounds. One of the advantages is that once clustered you can store the cluster identifiers and then refer to them later, this is particularly valuable when dealing with very large datasets. Clustering is often used in the analysis of high-throughput screening results, or the analysis of virtual screening or docking studies.

knimeWorkshop

There is a comparison of clustering options here.

The previous 14 workshops are available on a CICAG YouTube playlist.

You can still register for next months workshops here https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617.

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Open Source Antibiotics Structures

 

The OpenSourceAntibiotics project is a consortium of researchers interested in open ways to discover and develop new, inexpensive medicines for bacterial infections. All data is in the open and anyone can contribute. Whilst all data is on the wiki it can be tricky to sometimes link structure to identifier, in an effort to make these more accessible and hopefully indexed by search engines a page containing structures, identifiers, SMILES and InChiKey has been created.

You can view the page here https://opensourceantibiotics.github.io/murligase/CompChemTools/ForIndexing/OSA_data.html.

This page is updated nightly via a cron job. This calls a shell script that runs a Python script that reads the data from the master spreadsheet, uses RDKit to generate the images of the structures and create the html page. The shell script then uploads the html file to GitHub.

Hopefully the html page will be indexed by search engines which will allow anyone to search for the structures. Please feel free to share.

Comments

AI3SD Autumn Seminar Series

 

AI3SD have just announced the Autumn Seminar Series! https://www.ai3sd.org/ai3sd-online-seminar-series/autumn-seminar-series-2021/.

The event on the 3rd November is now open for registration: AI & ML 4 Drugs & Materials - 13:00-15:45 https://ai3sd-autumn-series-031121.eventbrite.co.uk/.

This event consists of three talks: 


Combining robotics and Machine Learning for accelerated drug discovery – Dr Tom Fleming (Arctoris)

Abstract: Artificial intelligence has an increasing impact on drug discovery and development, offering opportunities to identify novel targets, hit, and lead-like compounds in accelerated timeframes. However, the success of any AI/ ML model depends on the quality of the input data, and the speed with which in silico predictions can be validated in vitro. The talk will cover laboratory automation and robotics and the benefits they offer in terms of quality and speed of data generation synergise with AI/ ML-powered drug discovery approaches. The talk will cover some of the general trends in the industry, and also highlight successfully implemented case studies that show the how the combination of robotics and AI/ ML lead to accelerated project timelines and superior research outputs.

Bio: Tom Fleming MChem is the COO of biotech platform company Arctoris, which he co-founded in Oxford in 2016. Tom’s background is in cancer research, having worked in academia as well as at leading CROs and pharmaceutical corporations. A chemical biologist by training, he has unique insights into preclinical drug discovery, including the critical steps from target identification and high-throughput screening up to lead optimization. Tom was a Fellow of the Royal Commission of 1851 at the University of Oxford, and is a SME Leader of the Royal Academy of Engineering.


Machine Learning and AI for Drug Design – Professor Ola Engkvist (AstraZeneca & Chalmers University)

Abstract: Artificial Intelligence has become impactful during the last few years in chemistry and the life sciences, pushing the scientific boundaries forward as exemplified by the recent success of AlphaFold2. In this presentation I will provide an overview of how AI have impacted drug design in the last few years, where we are now and what progress we can reasonably expect in the coming years. The presentation will have a focus on deep learning based molecular de novo design, however, also aspects of synthesis prediction, molecular property predictions and chemistry automation will be covered.

Bio: Dr Ola Engkvist is head of Molecular AI in Discovery Sciences, AstraZeneca R&D. He did his PhD in computational chemistry at Lund University followed by a postdoc at Cambridge University. After working for two biotech companies he joined AstraZeneca in 2004. He currently lead the Molecular AI department, where the focus is to develop novel methods for ML/AI in drug design , productionalize the methods and apply the methods to AstraZeneca’s small molecules drug discovery portfolio. His main research interests are deep learning based molecular de novo design, synthetic route prediction and large scale molecular property predictions. He has published over 100 peer-reviewed scientific publications. He is adjunct professor in machine learning and AI for drug design at Chalmers University of Technology and a trustee of Cambridge Crystallographic Data Center. 


Accelerating design of organic materials with machine learning and AI – Professor Olexandr Isayev (Carnegie Mellon University)

Abstract: Deep learning is revolutionizing many areas of science and technology, particularly in natural language processing, speech recognition, and computer vision. In this talk, we will provide an overview of the latest developments of machine learning and AI methods and application to the problem of drug discovery and development at Isayev’s Lab at CMU. We identify several areas where existing methods have the potential to accelerate materials research and disrupt more traditional approaches. First we will present a deep learning model that approximates the solution of Schrodinger equation. We introduce the AIMNet-NSE (Neural Spin Equilibration) architecture, which can predict molecular energies for an arbitrary combination of molecular charge and spin multiplicity. The AIMNet-NSE model allows to fully bypass QM calculations and derive the ionization potential, electron affinity, and conceptual Density Functional Theory quantities like electronegativity, hardness, and condensed Fukui functions. We show that these descriptors, along with learned atomic representations, could be used to model chemical reactivity through an example of regioselectivity in electrophilic aromatic substitution reactions. Second, we proposed a novel ML-guided materials discovery platform that combines synergistic innovations in automated flow synthesis and automated machine learning (AutoML) method development. A software-controlled, continuous polymer synthesis platform enables rapid iterative experimental–computational cycles that resulted in the synthesis of hundreds of unique copolymer compositions within a multi-variable compositional space. The non-intuitive design criteria identified by ML, which was accomplished by exploring less than 0.9% of overall compositional space, upended conventional wisdom in the design of 19F MRI agents and led to the identification of >10 copolymer compositions that outperformed state-of-the-art materials.

Bio: Olexandr Isayev is an Assistant Professor at the Department of Chemistry at Carnegie Mellon University. In 2008, Olexandr received his Ph.D. in computational chemistry. He was Postdoctoral Research Fellow at the Case Western Reserve University and a scientist at the government research lab. During 2016-2019 he was a faculty at UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill. Olexandr received the “Emerging Technology Award” from the American Chemical Society (ACS) and the GPU computing award from NVIDIA. The research in his lab focuses on connecting artificial intelligence (AI) with chemical sciences.


Comments

RSC CICAG KNIME workshop materials

 

Just got this message from Greg Landrum

The workshop tomorrow will have a hands-on component. This isn't mandatory, but I think you'll get more from the workshop if you follow along with what we're doing in your own local copy of the workflow.

In order to get you started and make sure that you have all the KNIME pieces that you need installed, I created a space in the public KNIME hub for the workshop and have uploaded some introductory material there:

https://hub.knime.com/greglandrum/spaces/Public/latest/Presentations/2021/20211020RSCWorkshop/ClusteringIntro.

If you are logged into the KNIME hub (registration is free), you can download the workflow and data by simply using the download button:

KNIMEimage

Once you've downloaded the workflow package, you should be able to import everything into the KNIME Analytics Platform by double clicking the "ClusteringIntro.knar" file which is downloaded.

If for some reason you don't want to register, then you'll need to navigate to the page for the workflow and the Data folder, download everything individually, and import them into KNIME Analytics Platform manually. You should be able to find information online for how to do this, but I won't be able to help you with this during the workshop due to time constraints.

When you open the 01_Clustering workflow, you may be asked if you want to install missing extensions. Please do this in order to ensure that you have everything necessary to follow along during the workshop. Everything we install as part of this process is free and open source.

Shortly before the workshop starts I will share an additional workflow which we'll use for the main part of the workshop. I'll give you this link during the workshop.

Note that the sample workflows we are using were created with KNIME 4.4 (the version released this summer). For workshops like this we like to use recent versions of KNIME so that we can show you the newest features and capabilities. If you have an older version of KNIME things may or may not work correctly and you may have to replace one or more of the nodes with older equivalents.

You can download KNIME here https://www.knime.com/downloads

Comments

New MacBook Pros

 

The new MacBook Pros are out and they look fantastic, powered by M1Pro or M1Max chips they offer outstanding performance and retain low power consumption. As expected, Apple has added a HDMI port, and an SD card slot, AND has brought back MagSafe.

m1Max

Details on the chip design

You can also watch the promotional video here

Comments

Machine Learning in Chemistry meeting

 

This looks a really impressive line up of speakers.

Machine Learning in Chemistry Friday, Oct 29 11:00 AM - 1:00 PM EDT Details and registration.

11:00 - 11:30 AM A Star Wars character beats Quantum Chemistry! A neural network accelerating molecular calculations. Adrian Roitberg, University of Florida

11:30 AM - 12:00 PM Machine learning energy gaps of molecules in the condensed phase for linear and nonlinear optical spectroscopy. Christine Isborn, UC Merced

12:00 - 12:30 PM Accelerated molecular design and synthesis for drug discovery. Connor Coley, MIT

12:30 - 1:00 PM More than mimicry? The challenges of teaching chemistry to deep models. Brett Savoie, Purdue University

Comments

mols2grid

 

mols2grid is an interactive chemical viewer for 2D structures of small molecules, based on RDKit.

It can be installed using conda

conda install -c conda-forge mols2grid

Or pip

pip install mols2grid

Code is available on GitHub https://github.com/cbouy/mols2grid/tree/v0.1.0.

demo

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JupyterLite runs entirely in a web browser

 

I've only just stumbled across this. JupyterLite is a JupyterLab distribution that runs entirely in the browser built from the ground-up using JupyterLab components and extensions, no need to start a Python Jupyter server on the host machine.

Python kernel backed by Pyodide running in a Web Worker Initial support for interactive visualization libraries such as altair, bqplot, ipywidgets, matplotlib, and plotly JavaScript and P5.js kernels running in an IFrame View hosted example Notebooks and other files, then edit, save, and download from the browser's IndexDB (or localStorage) Support for saving settings for JupyterLab/Lite core and federated extensions Basic session and kernel management to have multiple kernels running at the same time Support for Code Consoles

You can try it out here https://jupyterlite.readthedocs.io/en/latest/_static/lab/index.html, all you need is a static web page.

Could be very useful for teaching.

Comments

JupyterLab Desktop App now available

I started using iPython Notebooks many years ago, these became Jupyter notebooks and I'm now transitioning to JupyterLab

I noticed recently there is now a JupyterLab desktop app.

JupyterLab App is the cross-platform standalone application distribution of JupyterLab. It is a self-contained desktop application which bundles a Python environment with several popular Python libraries ready to use in scientific computing and data science workflows.

It is available from GitHub https://github.com/jupyterlab/jupyterlab_app#download.

JupyterLab App works on Debian and Fedora based Linux, macOS and Windows operating systems.

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ChemDoodle 3D update with a custom VSEPR force field

Version 6.4 includes the ability to add charges, radicals and electron pairs to atoms. This allows them to create a unique VSEPR force field which is perfect for students and instructors to use and demonstrate why certain atom centers, along with electron pairs, lead to certain shapes in molecular structures.

Full details are here https://ichemlabs.com/news/read?post=cd3d64released.

vsepr

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QuickLookProtein

QuickLookProtein is a macOS Quick Look extension to preview protein/3D structure files (PDB, SDF, CIF).

It works in all places where macOS uses Quick Look, e.g. in Finder and Spotlight. In Finder, just select the protein structure file and press Space to open Quick Look.

The rendering of the 3D structure is performed using 3Dmol.js.

The extension is packaged into a main app, whose purpose is to set a few settings used for the display of the 3D models. QuickLookProtein requires macOS Big Sur (version 11.0+).

Comments

Some new Chemistry Apps

 

I've updated the Mobile Science site the latest addition is Periodic Table Chemistry 4 that has been optimized for iOS 13, iPadOS and watchOS 6.

periodicTable4

There are also a companion app for the Mac Periodic Table Chemistry 4 and a study app ElementCard.

Comments

Web apps for fragment-based drug discovery,

The next RSC CICAG Open Source Tools for Chemists workshop will be held next week.

23 September 2021 14.00 – 16.00 GMT

Web apps for fragment-based drug discovery, fragalysis and more with Rachael Skyner, Diamond Light Source More information about fragalysis at Diamond can be found here: https://fragalysis.diamond.ac.uk/viewer/react/landing. fragalysis

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

These workshops are sponsored by Liverpool ChiroChem

Comments

Download Flare Viewer for free

 

Flare Viewer is a free version of Flare, a ligand-based and structure-based drug design solution enabling research chemists to discover novel small molecules more efficiently and effectively in a single platform.

flareViewer

There is a review of Flare here and a look at the Flare python api here.

Comments

Accessing Alphafold2 from ChimeraX

 

A new video showing how to access Alphafold2 from ChimeraX.

We run AlphaFold to predict the structure of the protein avidin (from chicken). We start the computation using ChimeraX which runs it on Google Colab servers.

Added to the RSC CICAG Open Source tools for Chemistry play list https://www.youtube.com/playlist?list=PLBQwbn0mPhvWfOx6ce_vUjr54ftLBmSH0.

Comments

Comparing M1 mac mini with AMD 5900HX Mini PC

 

Head to head comparison, both cost $899.

Comments

Following CICAG activities

 

RSC-Group-Logo-Chemical Information and Computer Applications

The RSC Chemical Information and Computer Applications Group (CICAG) workshop YouTube videos https://www.youtube.com/c/RSCCICAG have now been watched nearly 8000 times. A number of folks have asked about future workshops and CICAG activities.

YouTubeVideos

The details of the future workshops are here on Eventbrite all workshops are free to attend. We will be thinking about possible workshops for 2022 soon, so feel free to suggest ideas.

CICAG are also co-organisers of the 4th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Monday-Tuesday, 27th-28th September 2021 full details are here.

If you want to keep in touch with CICAG activities there are several options. If you are an RSC member then you can choose to join the interest group.

When you renew your Royal Society of Chemistry membership you can choose “Chemical Information and Computer Applications Group” (group 86) as one of your groups to be a member of. If you have already submitted your form you can make a request to join a group via email (membership@rsc.org) or telephone (01223 432141).

If you are not an RSC member you can follow CICAG activities on Twitter or on LinkedIn


Comments

Molecular Docking with Open Access Software

The last couple of years have disrupted classes for many students, I helped devise a course for MRes students at UCL undertake a computational drug discovery project using open source tools. A pleasure to work with a group of really bright and enthusiastic group of students

The workflow has now been written up as a Lab Manual which is available for anyone to use.

The publication describing the work is now available (Open Access) Molecular Docking with Open Access Software: Development of an Online Laboratory Handbook and Remote Workflow for Chemistry and Pharmacy Master’s Students to Undertake Computer-Aided Drug Design DOI.

In response to the closure of many university laboratories due to the Covid-19 pandemic in 2020, a handbook and remote webinar approach designed to support students in the use of software tools for computer-aided drug design has been developed. Specifically, the course has been designed for chemistry and pharmacy students who have little or no experience of computational techniques and can use open-source software on their own machines. In this way a flexible and relevant course, giving a rigorous academic experience, could be delivered even in the most challenging of circumstances. We believe that this laboratory protocol will help to “democratize” the scientific process in this field.

The lab Manual is available in a GitHub repository. https://github.com/UCL/OpenDockingLab_Handbook.

This repository is the place to store and edit the lab handbook for UCL teaching courses that involve the use of open source tools in molecular docking.

Files currently available are shown above, on this "code" tab. The most recent version of the lab manual is there, for download and the manual is also available in full on the wiki as a living document that can be updated by anyone, year on year. If you'd like to suggest edits it's easy to do that by opening an Issue (tab above).

We'd love to hear of new docking tools or scoring functions that we could include.

Feel free to contribute.

You might also be interested in the RSC CICAG YouTube channel https://www.youtube.com/c/RSCCICAG that contains many workshops highlighting Open Source tools for Chemistry.

Comments

An introduction to cheminformatics, data analysis and machine learning

The video of the latest RSC CICAG Open Source Tools for Chemistry is now online.

Part of the RSC CICAG Open Chemical Sciences workshop series. Workshop given by Pat Walters (http://practicalcheminformatics.blogspot.com) entitled "An introduction to cheminformatics, data analysis and machine learning".

A hands-on workshop on building and validating ML models, including:

  • Initial exploratory data analysis
  • ML model building
  • Model evaluation
  • Making predictions on a larger data set

The notebooks for the tutorial are here https://mybinder.org/v2/gh/PatWalters/chem_tutorial/HEAD. If there are any problems, you should be able to just reload the page. The code and notebooks are in a GitHub repo.

The video is here YouTube.

More workshop videos are available on the RSC CICAG playlist

Comments

Open Babel is now available for Apple Silicon!

Open Babel is now available for osx-arm64 on conda-forge to support Apple Silicon Twitter. Available here https://anaconda.org/conda-forge/openbabel.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

Comments

New additions to MayaChemTools

 

There have been a couple of new additions to the fabulous list of tools and scripts on MayaChemTools.

MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.

o Psi4GenerateConstrainedConformers.py http://www.mayachemtools.org/docs/scripts/html/Psi4GenerateConstrainedConformers.html>

o Psi4PerformConstrainedMinimization.py http://www.mayachemtools.org/docs/scripts/html/Psi4PerformConstrainedMinimization.html.

o Psi4PerformTorsionScan.py http://www.mayachemtools.org/docs/scripts/html/Psi4PerformTorsionScan.html.

These scripts rely on the presence of Psi4 https://psicode.org/ and RDKit in your environment. In addition, the script RDKitPerformTorsionScan.py http://www.mayachemtools.org/index.html for further details.

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

BBEdit 14 released

 

Everyone's favourite text editor has been updated. BBEdit 14 requires Mac OS X 10.14.2 or later, and is compatible with macOS 10.15 "Catalina" and macOS 11 "Big Sur". Native on Macs with the M1 processor

What's New

Anaconda Virtual Environments - Anaconda is particularly popular with data scientists, as well as with others who need to rapidly switch between different tooling and library configurations. BBEdit 14 will use conda or miniconda to detect your virtual environments, and provides a mechanism for switching the active environment for use when running Unix tools and scripts from within BBEdit.

New Built-In Languages - BBEdit 14 adds built-in syntax coloring and function navigation support for Go, R, Rust, Lisp-family languages (Common Lisp, Scheme, Clojure), and Pixar Universal Scene Description (USD) text files.

Enhanced Developer Features - BBEdit 14 enables several new features and significant improvements to its built-in coding aids for developers, including:

Enhanced language-specific text completions; Improved Find Definition; Assistance for specifying function parameters; New code-navigation features; In-window highlighting of syntax and semantic issues; Language-specific document reformatting. These feature improvements are the result of new built-in support for the Language Server Protocol ("LSP") by which user-installed local "language servers" implement key language-sensitive behaviors. Specific available features may vary by language and by server.

Full details are here.

Comments

Augmented Reality Science Apps

 

There have been an increasing number of augmented reality since apps recently. If you search for "augmented" on the Mobile Science database you can find a selection.

Molecule Viewers are particularly notable.

MolAR lets you visualize proteins and molecules through augmented reality.

MolAR

AR VR Molecules Editor allows one to build and manipulate 3D molecules models of organic and inorganic compounds.

ARmoleditor

If I've missed any please let me know about them.

Comments

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

 

An updated program for the 4th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Meeting is now available and there is the usual excellent range of speakers. Registration is now open https://www.maggichurchouseevents.co.uk/bmcs/AI-2021onlineregistration.htm. There are also opportunities for sponsorship.

Confirmed Speakers

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

Keynote: Challenges and opportunities for machine learning in drug discovery Patrick Walters, Relay Therapeutics, US

PyPEF – an integrated framework for data-driven protein design and engineering Mehdi Davari, Leibniz Institute of Plant Biochemistry (IPB), DE

Efficient ML strategies to explore chemical reactivity Fernanda Duarte, University of Oxford, UK

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

Machine learning models for predicting human in vivo PK parameters using chemical structure and dose Olga Obrezanova, AstraZeneca, UK

Molecular transformer-aided biocatalysed synthesis planning Daniel Probst, IBM Research Europe, CH

Best practice for chemical language model de novo design of GPCR ligands: datasets, scoring functions and optimization algorithms Morgan Thomas, University of Cambridge, UK

Presentation title to be confirmed (provisional) Andrea Volkamer, Charité Universitätsmedizin Berlin, DE

‘Attending’ to co-crystals in the Cambridge Structural Datacenter Aikaterini Vriza, University of Liverpool, UK

Driving lead optimisation with BRADSHAW Ian Wall, GlaxoSmithKline, UK

Comments

Schrödinger Software Release 2021-3

 

This quarterly release includes:

  • Intuitive enhancement of the protein preparation workflow and kinase conservation annotations for structure enablement
  • Addition of filters to improve drug-likeness for medical chemistry design using Ligand Designer
  • A new diversity approach to select compounds for Active Learning Glide workflows for hit discovery and lead optimization
  • Greater control of custom R-group enumerations for hit discovery and lead optimization for multiple simultaneous substitutions

A detailed account of this release is available https://www.schrodinger.com/releases/new-features?

Comments

RSC CICAG workshops

 

The next of the monthly RSC CICAG workshops is on 19 August 2021 is entitled "An introduction to cheminformatics, data analysis and machine learning" with Pat Walters, Relay Therapeutics and blogger, if you don't follow his blog have a look now http://practicalcheminformatics.blogspot.com.

This will be a hands-on workshop on building and validating ML models, including:

  • Initial exploratory data analysis
  • ML model building
  • Model evaluation
  • Making predictions on a larger data set

I'm sure this will be a really invaluable experience. Over 150 have already registered and you can 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)

These workshops are sponsored by Liverpool ChiroChem

Comments

iNMR update, runs on Apple silicon

 

The very popular NMR application iNMR has been updated to version 6.4 in addition iNMR reader has also been updated. It requires Mac OS 11 or higher and it runs on the Apple M1 chip machines.

inmr

There are more details here

It is labelled as "Universal" by the Mac Finder. It means that it actually contains two program (it's really fat). One program runs on Intel Macs. The other program runs natively on Macs with the M1 chip. I had also discovered that the previous Mac version worked perfectly with Ma OS 10 but not everything looked the same on Mac OS 11. I have fixed the known issues. Quite likely you'll have had a few minor issues as well. If you are so kind to report them I will happily fix everything during next week. You'll also see a new, corresponding version, of iNMR reader. Another plan was to "notarize" the Mac version. If you are a Mac user you probably know that the Mac, by default, refuses to run iNMR. You are required to right-click the iNMR icon, select "Open" and then authorise iNMR. With the notarization things get simpler. I would like to know: how much is this important for you? I hope you don't care, because for the moment being iNMR is not notarized yet. I have worked mainly on the QuickLook plugin. Please somebody test it. Beware: if you had activated the option "create Thumbnails", then iNMR have surely created many .tiff files that look nice but are not visible in the Finder.

Comments

RSC CICAG YouTube playlist

 

The playlist for the RSC CICAG Open Source tools for Chemists workshops has been updated. There are now 11 two hour videos covering a wide variety of tools from data analysis, docking, molecular visualisation, fragment screening etc. These videos have now been watched over 6000 times and have attracted significant praise.

Two hours of distilled pure science.

I am not sure why this software is not famous. This is presumably the best chemoinformatics software I have seen

screenshot-2021-07-27-at-09.46.12.png

Registration for future free workshops is open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21) Liverpool Chirochem sponsor the Open-Source Tools for Chemistry Workshop series.

Comments

OPIG (Oxford Protein Informatics Group) antibody modelling tools workshop

 

Part of the RSC Open Chemical Sciences workshop series. Workshop given by Charlotte Deane, Fergus Boyles and Matthew Raybould 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. Now available on YouTube

Download for workshop materials http://macinchem.org/Temp/OPIGworkshop.zip.

Registration for future free workshops is open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21) Liverpool Chirochem sponsor the Open-Source Tools for Chemistry Workshop series.

Comments

ChemDoodle 2D update

 

The very popular chemical drawing package ChemDoodle 2D has been updated to version 11.6 Release details.

Handling relative and absolute stereochemistry of molecules is a major challenge and this release of ChemDoodle provides an enhancement to the the ability to define, edit, input and output enhanced stereochemistry definitions to a handful of compatible file formats.

Enhanced Stereochemistry. You may now define enhanced stereochemistry for chemical structures, using or and & modifiers. All stereocenters are absolute (abs) by default. Groupings will be automatically determined via incrementation, but you may also manually define group numbers for more advanced stereochemistry queries. Enhanced stereochemistry definitions are read and written from ChemDoodle Documents, ChemDoodle JSON, ChemDraw files, ChemAxon Marvin Documents and MDL CT files (limited in v2000, full support in v3000).

chemdoodlestereochem

Comments

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

 

The confirmed speaker list for the 4th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry meeting has been updated. This very popular meeting will be held as a virtual event (Monday-Tuesday, 27th-28th September 2021),

AI2021

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

Keynote: Challenges and opportunities for machine learning in drug discovery Patrick Walters, Relay Therapeutics, US

PyPEF – an integrated framework for data-driven protein design and engineering Mehdi Davari, Leibniz Institute of Plant Biochemistry (IPB), DE

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

Machine learning models for predicting human in vivo PK parameters using chemical structure and dose Olga Obrezanova, AstraZeneca, UK

Molecular transformer-aided biocatalysed synthesis planning Daniel Probst, IBM Research Europe, CH

Best practice for chemical language model de novo design of GPCR ligands: datasets, scoring functions and optimization algorithms Morgan Thomas, University of Cambridge, UK

‘Attending’ to co-crystals in the Cambridge Structural Datacenter Aikaterini Vriza, University of Liverpool, UK

Further details and registration can be found on the conference website https://www.maggichurchouseevents.co.uk/bmcs/AI_2021.htm.

Comments

ORCA update

 

ORCA is an ab initio quantum chemistry program package that contains modern electronic structure methods including density functional theory, many-body perturbation, coupled cluster, multireference methods, and semi-empirical quantum chemistry methods. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties.

ORCA 5.0 is not just an update to the program. Even if much of the output will look very similar to previous versions, ORCA 5.0 is pretty much a completely new program. We have spent major efforts in redesigning and streamlining the core engine of the program. In fact, in designing the new engine, we have deeply re-thought the conceptual basis for quantum chemical program development for the next decades to come. The result is a program that is much leaner, much more efficient and much fitter for future extensions in an ever shifting hardware landscape. The full transition to our final vision of a modern quantum chemical program suite will likely be completed with ORCA 6, that we plan to release 2022. However, the improvements made in ORCA 5.0 are so numerous and so vast that we felt that now is the appropriate moment to share our work with the general public.

The link to the download is on the ORCA forum (requires registration) https://orcaforum.kofo.mpg.de/app.php/dlext/?cat=13.

Comments

Open Source Antibiotics Docking and Scoring

 

There is an interesting thread on the Open Source Antibiotics GitHub repository.

Jan Jensen is looking at docking and scoring molecules into Mur Ligase C (MurC). In preparation for looking at a genetic algorithm to score docked poses they have docked 260K ligands using Glide. All details are in a Google CoLab Notebook. https://github.com/opensourceantibiotics/murligase/issues/46

As with all the work on OSA everything is in the public domain.

If you want an opportunity to test out your docking algorithm, scoring function or binding affinity prediction tool this looks like a great opportunity.

Comments

More RSC CICAG workshops

 

The next of the monthly RSC CICAG workshops sponsored by Liverpool ChiroChem is on June 24 featuring DataWarrior, and over 250 have registered. These workshops are usually in 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)

The RSC CICAG Open Source tools workshop on DataWarrior is on 24 June

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.

Comments

Amsterdam Modeling Suite, AMS2021.1 released

 

The first 2021 release of the Amsterdam Modeling Suite, AMS2021.1, features many improvements and new functionality.

Automated reaction pathway searching
The new potential energy surface (PES) exploration tasks in the central AMS driver enable researchers to automatically discover transition states and local minima with any of our or external engines. Further improvements in the AMS driver Spherical wall potential (nanoreactors) D4 dispersion corrections also available for periodic systems (BAND, DFTB) force bias Monte Carlo available for all engines ForceField engine: performance optimization ForceField has been sped up by 2-3 orders of magnitude through a combination of improvements: MPI with force decomposition, particle mash Ewald, default non-bonded cutoff reduced to 15Å.

ParAMS: scripting toolbox for ReaxFF and DFTB parametrization
ParAMS was silently released last year. We are looking forward to your findings and suggestions when you test ParAMS to build your training data and optimize parameters.

ADF
Polarizable force field: QM/FQ Quantum Mechanics/Fluctuating Charges Unrelaxed dipole moment excited states Transition dipole moment between excited states POLTDDFT for fast excitation spectra: more fit sets for most elements r2SCAN-D4 XC functional (also for BAND) Eigenvalue-only self-consistent GW (evGW), New TZ3P and QZ6P basis sets for Many Body Perturbation Theory New Ligand-Field DFT(LFDFT) spectroscopy: ESR g-tensor doublets, XMCD

COSMO-RS
Improved handling of fluid thermodynamics with multiple species, e.g. different protonation and dissociation states, aggregation (with solvent), conformers (Graphical) User Interface improvements Package manager to (de)install additional components (COSMO-RS database, Quantum ESPRESSO, Machine Learning Potentials, Ligand-Field DFT) Option to output results into a spreadsheet Graceful interactive termination, also via GUI Improved UI to handle multiple molecules Sinkbox and Safebox for MD with molecule gun Support for PES exploration and other new features, and more…

Installation under MacOSX on YouTube https://youtu.be/BJe8iFoeUcg.

Comments

Using JDBC Driver to access Athena from Vortex

 

This tutorial is a step by step guide to access data in Athena from Vortex.

Amazon Athena is an interactive query service that makes it easy to analyze data in Amazon S3 using standard SQL. Athena is serverless, so there is no infrastructure to manage, and you pay only for the queries that you run. Athena is easy to use. Simply point to your data in Amazon S3, define the schema, and start querying using standard SQL. Most results are delivered within seconds. With Athena, there’s no need for complex ETL jobs to prepare your data for analysis. This makes it easy for anyone with SQL skills to quickly analyze large-scale datasets.

Comments

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)

Comments

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

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/

Comments

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

Comments

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

Comments

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.

Comments

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
Comments

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.
Comments

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

Comments

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.

Comments

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.

Comments

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.

Comments

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.

Comments

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

Comments

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/.

Comments

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.

Comments

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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