Macs in Chemistry

Insanely Great Science

3rd AI in Chemistry Posters

 

The heavily oversubscribed 3rd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry will taking place next week 28th-29th September 2020 Twitter hashtag - #AIChem20. There is an accompanying poster session and there is a chance to talk to the poster presenters in the breakout rooms at the end of each day (You will need the latest version of Zoom 5.3.0).

Most of the posters are now available for viewing on Twitter so you can always have a browse and ask questions on Twitter even if you won't be at the meeting #AIChem20poster,

Below is a table containing all posters.

Poster Number Name Title Twitter link
P01 Antreas Afantitis Enalos cheminformatics tools: development of a de novo drug design module View on twitter
P02 Nurlybek Amangeldiuly Transfer learning with graph neural networks for protein_ligand binding kinetics prediction View on twitter
P03 Andy Sode Anker Characterising the atomic structure of mono_metallic nanoparticles from x_ray scattering data using conditional generative models View on twitter
P04 Jenna Bilbrey A look inside the black box: using graph_theoretical descriptors for the post_hoc interpretation of neural networks View on twitter
P05 Nicolas Bosc MAIP: a prediction platform for predicting blood_stage malaria inhibitors View on twitter
P06 Xiaojing Cong Receptor_ligand prediction by proteochemometric modeling: an application to G protein_coupled olfactory receptors View on twitter
P07 Simon Durr EVOLVE: a genetic algorithm to predict thermostability View on twitter
P08 Umberto Esposito Building a connected data pipeline to target drug development challenges
P09 Benedek Fabian MolBERT: molecular representation learning with advanced language models and useful auxiliary tasks View on twitter
P10 Miguel Garcia_Ortegon Improving VAE molecular representations by tailoring them to predict docking poses and scores View on twitter
P11 Wenhao Gao Can we synthesize molecules proposed by generative models View on twitter
P12 Helena Gaspar Proteochemometric models using multiple sequence alignments and a SentencePiece_based masked language model: application to CYP and kinome selectivity modelling View on twitter
P13 Ed Griffen An explainable AI system for medicinal chemists View on twitter
P14 Ed Griffen "Chemists: AI is here, unite to get the benefits" View on twitter
P15 Thomas Hadfield Explicit incorporation of structural information into a fragment elaboration model via deep reinforcement learning View on twitter
P16 Hans Hanley "GENerateZ: designing anticancer drugs using transcriptomic data, genetic algorithms, and variational autoencoder" View on twitter
P17 Fergus Imrie Generating property_matched decoy molecules using deep learning View on twitter
P18 Kjell Jorner Uniform quantitative predictive modelling for route design View on twitter
P19 Itai Levin Computationally assisted synthesis planning for hybrid chemoenzymatic pathways View on twitter
P20 Timur Madzhidov Deep conditional variational autoencoder for reaction conditions prediction View on twitter
P21 Gergely Makara AI_assisted lead optimization with derivatization design View on twitter
P22 Neann Mathai Performance and scope of a similarity_based and a random forest_based machine learning approach for small_molecule target prediction View on twitter
P23 Janosh Menke Enhancing molecular fingerprints using neural networks View on twitter
P24 Juan Carlos Mobarec Evolutionary chemistry for the design of desired pharmacological profiles View on twitter
P25 Rohit Modee Neural network potentials for representing potential energy surface and their applicability for geometry optimization View on twitter
P26 Joseph Morrone Challenges and progress in combining docking programs with deep neural networks View on twitter
P27 Eva Nittinger Non_additivity in public and inhouse data and its influence on ML performance View on twitter
P28 Ferruccio Palazzesi Integrating multi task graph convolutional neural network with a deep generative model View on twitter
P29 Yashaswi Pathak Deep learning enabled inorganic material generator View on twitter
P30 Quentin Perron Integrating data_driven computer_aided synthetic planning with generative AI
P31 Daniel Probst Classification of chemical reactions through NLP_inspired fingerprinting View on twitter
P32 Mikolaj Sacha Molecule edit graph attention network: modeling chemical reactions as sequences of graph edits View on twitter
P33 withdrawn
P34 Jenke Scheen Data_driven estimation of optimally_designed perturbation networks in relative alchemical free energy calculations View on twitter
P35 Philippe Schwaller RXNMapper: unsupervised attention_guided atom_mapping View on twitter
P36 Matthew Segall Imputation versus prediction and applications in drug discovery View on twitter
P37 Vishnu Sresht Can generative models learn privileged substructures and identify new bioisosteres? View on twitter
P38 Gergely Takács Analysis of commercial and public compound databases by self_organizing maps View on twitter
P39 Morgan Thomas Towards integrating deep generative models with structure_based design View on twitter
P40 Hao Tian What is hidden behind allostery? An integrated framework to decipher key components in AuLOV dimerization View on twitter
P41 Alain Vaucher Learning how to do chemical reactions from data View on twitter
P42 Alexander van Teijlingen Beyond tripeptides _ two_step active machine learning for very large datasets View on twitter
P43 James Wallace eApps – enabling a predict first culture for computational medicinal chemistry View on twitter
P44 withdrawn
P45 Yuanqing Wang Bayesian active drug discovery via deep graph kernel learning View on twitter
P46 Robbie Warringham DigitalGlassware: structuring and contextualising chemical outcomes for faster discovery View on twitter
P47 withdrawn
P48 Jerome Wicker AIScape: a machine learning platform for activity and ADME predictions View on twitter

Some of the presenters have also recorded 2 min lightning presentation describing their work, these are available on the RSC CICAG YouTube channel.

Day 1 (odd numbered posters) https://youtu.be/ikbrrnjOvdc

Day 2 (even numbered posters) https://youtu.be/tf8cGodlWfU

Enjoy!!



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3rd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry

 

The heavily oversubscribed 3rd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry will taking place next week 28th-29th September 2020 Twitter hashtag - #AIChem20.

This is now an online virtual event, this has required an immense amount of reorganisation behind the scenes and significant expenditure. This would not have been possible without the generous support of the event sponsors. AstraZeneca and MSD and the exhibitors CCDC, Concept Life Sciences, IKTOS, Liverpool ChiroChem, Mcule, o2h discovery.

Some of the exhibitors have kindly provided videos describing their work, why not have a browse.

IKTOS

Liverpool ChiroChem

Mcule

o2h discovery

If you are at the meeting they will also be able to talk to you directly at the breakout session at the end of each day.

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ChemDoodle 2D updated

 

The very popular chemical drawing package ChemDoodle has been updated.

ChemDoodle 2D v11.1 is a feature and stability update and is recommended for all users. The major new feature is advanced repeat unit support, both in graphical drawing and cheminformatics interpretation and expansion. Other notable features include improved reaction building interfaces and feedback, arc-length controls, and smaller EPS file output. This update also corrects an issue introduced by macOS 10.15.6, leading to corrupted and missing windows. So if you are experiencing these issues, make sure to install this update.

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COVID-19 diagnosis using ocular image

 

This could be a very interesting result.

Preprint on medrxiv A New Screening Method for COVID-19 based on Ocular Feature Recognition by Machine Learning Tools DOI.

… we found that the confirmed cases of COVID-19 present the consistent ocular pathological symbols; and we propose a new screening method of analyzing the eye-region images, captured by common CCD and CMOS cameras...

As ever, treat preprints with caution, but certainly well worth following.

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MolController for VMD

 

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. However, it still lacks a graphical user interface (GUI) for molecular manipulations when doing some modeling tasks.

A recent publication DOI describes work using the Tcl/Tk toolkit to develop a user-friendly GUI for VMD, named Molcontroller.

All the scripts and installation instructions are available https://github.com/ChenchenWu-hub/Molcontroller.

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AI in Chemistry Conference

 

The heavily oversubscribed 3rd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry will taking place 28th-29th September 2020 Twitter hashtag - #AIChem20. This has been converted to a virtual event and those registered will be getting more details soon.

There is an accompanying poster session, the posters are being hosted on twitter and you can see them all using the hashtag AIChem20posters. A number of the poster presenters have also created 2 min lightning presentations which will be uploaded to YouTube once the last few presentations have been included.

If you are registered and find you can no longer attend, please send an e-mail to the BMCS Secretariat promptly, so that your place can be allocated to one of those on the waiting list.

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Online Events

 

The current global pandemic means that more events are moving online, here are details of a few that have been sent to me

Dotmatics User Symposium | Cambridge 2020 14th & 15th October Details and Registration.

KNIME Introduction to Working with Chemical Data October 12 - 16, 2020 details and registration.

Virtual RDKit UGM 6-8 October 2020 details and registration.

16th German Conference on Cheminformatics and EuroSAMPL Satellite Workshop 2-3 November 2020 details

Open Chemical Science 9 - 13 November 2020 details.

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UCSF ChimeraX latest release

 

UCSF ChimeraX is the next-generation visualization program from the Resource for Biocomputing, Visualization, and Informatics at UC San Francisco.

The image below shows the COVID-19 MPro with a fragment bound taken from Project Moonshot.

ChimeraX

The release candidate is available here https://www.rbvi.ucsf.edu/chimerax/download.html.

chimerax-rc.dmg built: 2020-09-07 04:36:35 PDT committed: 2020-09-06 22:34:34 PDT size: 337.3 MiB

Download is a disk image containing the application. Tested on macOS 10.13. This application does not run on 10.12 or older due to operating system changes.

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An open source chemical structure curation pipeline using RDKit

 

I just thought I'd flag a recent paper in Journal of Cheminformatics described "An open source chemical structure curation pipeline using RDKit" DOI. As anyone who has had to curate a molecular dataset knows standardising the chemical structures is one of the absolutely key elements of the process.

A chemical curation pipeline has been developed using the open source toolkit RDKit. It comprises three components: a Checker to test the validity of chemical structures and flag any serious errors; a Standardizer which formats compounds according to defined rules and conventions and a GetParent component that removes any salts and solvents from the compound to create its parent. This pipeline has been applied to the latest version of the ChEMBL database as well as uncurated datasets from other sources to test the robustness of the process and to identify common issues in database molecular structures.

The ChEMBLStructurePipeline is freely available on GitHub https://github.com/chembl/ChEMBLStructurePipeline/releases/tag/1.0.0.

Or using Anaconda

conda install -c conda-forge chembl_sructure_pipeline
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NMR shift prediction using machine learning competition results

 

A while back a Kaggle competition called Champs for developing ML models that predict NMR coupling constants with DFT accuracy was initiated https://www.kaggle.com/c/champs-scalar-coupling.

"Champs received 47,800 ML model predictions from 2,700 teams in 84 countries. Within 3 weeks, the Kaggle community produced models with comparable accuracy to our best previously published ‘in-house’ efforts. A meta-ensemble model constructed as a linear combination of the top predictions has a prediction accuracy which exceeds that of any individual model, 7-19x better than our previous state-of-the-art."

More details on Computational Chemistry Highlights.

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ChemDoodle 3D updated

 

iChemLabs have just released version 6.1 of ChemDoodle 3D.

ChemDoodle 3D v6.1 is a significant update to ChemDoodle 3D with a focus on the molecular modeling engine. Notable additions include parallel processing support, an implementation of the General Amber Force Field, improved Minimizer widget performance, and a new tool for easily twisting bonds to change torsion angles. This update is recommended for all users.

There is a very nice introductory video available from last year that gives a great overview.

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iBabel downloaded over 500 times

 

I just noticed that the latest update to iBabel has now been downloaded over 500 times.

iBabel is a graphical user interface (GUI) to the open-source cheminformatics toolkit Open Babel described in an article in J Cheminformatics, Open Babel: An open chemical toolbox DOI. iBabel was originally written as an AppleScript Studio application which underwent several updates, but gradually became unsupportable. So rather than try to patch the AppleScript Studio/ApplescriptObjC application I decided on a starting afresh with a complete rewrite using Cocoa/Swift to take advantage of new technologies, this has meant some features have been lost, some new ones added but hopefully the core features are still there.

pubchemsearch

Instructions for download and installing are on the main iBabel page, remember you need to install OpenBabel first.

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Schrödinger Software Release 2020-3

 

Just heard an update is available.

We are pleased to announce Schrödinger software release 2020-3, which is available for download now. This update includes usability improvements and performance enhancements across our entire suite of tools and features the first full release of Ligand Designer - an automated tool for medicinal chemists to quickly design and evaluate ideas - as well as a revamped Multiple Sequence Viewer that makes working with sequences easier than ever.

Full details here https://www.schrodinger.com/releases/new-features?.

Supports macOS 10.13 - 10.15.

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AI3 Science Discovery Network+ YouTube Channel

 

The AI3SD Network+ (Artificial Intelligence and Augmented Intelligence for Automated Investigations for Scientific Discovery) YouTube channel is now up and running.

The network+ is funded by EPSRC and hosted by the University of Southampton and aims to bring together researchers looking to show how cutting edge artificial and augmented intelligence technologies can be used to push the boundaries of scientific discovery.

  1. Drug Repositioning for COVID-19 - Professor John Overington (Medicines Discovery Catapult) - https://youtu.be/gcgeTVfiVl4
  2. InChI: Measuring the Molecules - Professor Jonathan Goodman (University of Cambridge) - https://youtu.be/B881b5BasnU
  3. Design Fiction as a Method and why we might use it to consider AI - Dr Naomi Jacobs (Lancaster University) - https://youtu.be/AxXZRk6CLws.
  4. Neural Networks and Explanatory Opacity - Dr Will McNeill (University of Southampton) - https://youtu.be/3rSnjnUjpo0
  5. Dimensionality in Chemistry: Using multidimensional data for machine learning - Dr Ella Gale (University of Bristol) - https://youtu.be/NhR7xWlAO4g
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BBEdit update

 

Everyone's favourite text editor BBEdit has been updated to version 13.1.3

This update is simply a bug fix there are no new features.

The release notes are here.

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Vortex running on ARM-based Mac

 

Sounds like performance is not an issue.

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WebPlotDigitizer has been updated

 

I just noticed that WebPlotDigitizer has recently been updated.

It is often necessary to reverse engineer images of data visualizations to extract the underlying numerical data. WebPlotDigitizer is a semi-automated tool that makes this process extremely easy.

More details on the Data Analysis Tools Page.

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Mobile Science Apps updated

 

A couple of the Apps on the Mobile Science site have been updated.

Most notably the Human Anatomy Atlas, which is currently the fifth most viewed app on the site.

What’s New Jul 27, 2020 Version 2021.1.64 Introducing Visible Body User Accounts! With your VB User Account, you can:

  • Save and share all your newly created custom interactive content!
  • Make 3D Views and Tours that include tags, 3D drawings, and notes, and edit them whenever you want.
  • Share your 3D views with other Atlas 2021.1 users.

Note: Visible Body accounts have replaced iCloud in Human Anatomy Atlas 2021.1 or later.

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3rd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry

 

Registration is open!!

Synopsis.
Artificial Intelligence is presently experiencing a renaissance in development of new methods and practical applications to ongoing challenges in Chemistry. Following the successes of two “Artificial Intelligence in Chemistry” meetings in 2018 and 2019, we are pleased to announce that the Biological & Medicinal Chemistry Sector (BMCS) and Chemical Information & Computer Applications Group (CICAG) of the Royal Society of Chemistry are once again organising a conference to present the current efforts in applying these new methods. The meeting will be held over two days and combine aspects of artificial intelligence and deep machine learning methods to applications in chemistry

The Call for Abstracts is Open.
Applications for both oral and poster presentations are invited. Posters will be displayed during a dedicated poster session and, at the time of submission, applicants are asked if they wish to provide a two-minute lightning oral presentation. The closing date for all submissions is Friday, 31st July.

There will be a mix of plenary and keynote talks as well as poster sessions with some lightning poster talks. There will also be exhibitor sessions, and we are currently exploring options for providing breakout rooms for discussions.

Confirmed Speakers
Teaching neural network to attach and detach electrons from molecules
Keynote: Olexandr Isayev, Carnegie Mellon, US

DNA-encoded small molecules libraries meet machine learning
Keynote: Patrick Riley, Google, US

Artificial neural network enhanced synthesis and retrosynthesis prediction
Esben Jannik Bjerrum, AstraZeneca, SE

Machine learning for free energy calculations
Hannah Bruce McDonald, Memorial Sloan Kettering Cancer Center, US

Data driven representations for predicting molecular properties: benchmarking and applications in generative chemistry
Jessica Lanini, Novartis, CH

Using machine learning for molecular dynamics simulations
Sereina Riniker, ETH Zürich, CH

Registration Participation is free of charge, although registration is required so we can ensure the numbers are covered by the virtual meeting software license:
- online via this link (no payment required) I

AI - second announcement

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MOPAC updated

 

A new version of MOPAC has been released full details are in this publication "A New Release of MOPAC Incorporating the INDO/S Semiempirical Model with CI Excited States" DOI.

We have incorporated the semiempirical INDO/S Hamiltonian into a new release of MOPAC2016, which has long been at the forefront of semiempirical quantum chemical methods (SEQMs). Our new code enables the calculation of excited states using the INDO/S Hamiltonian combined with a configuration interaction approach using single excitations (CIS), single and double excitations (CISD), or multiple reference determinants (MRCI) where reference determinants are generated using a complete active space (CAS) approach. The capacity to perform excited-state calculations beyond the CIS level makes INDO/CI one of the few low-cost computational methods capable of accurately modeling states with substantial double-excitation character. Solvent corrections to the ground-state and excited-state energies can be computed using the COSMO implicit solvent model, incorporating state-specific corrections to the excited states based on the solvent refractive index. We demonstrate that this code produces physically reasonable electronic structures, absorption spectra, and solvatochromic shifts at low computational costs for systems up to hundreds of atoms, and for both organic molecules and metal clusters.

The release notes are here.

And downloads here.

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Keyboard for Macs

 

A while back the external keyboard I was using for my MacBook Pro broke and I've been looking around for a replacement. I know the choice of keyboard can be very personal, particularly if you are in a job where you are using it for much of the day.

After reading many reviews and trying a few out at various places I eventually settled on the Logitech MX Keys Advanced Wireless Illuminated Keyboard for Mac, at the time it was only available for preorder from Amazon. It arrived yesterday and I have to say I'm delighted with it.

The MX Keys for Mac is a full-sized keyboard with a proper numeric keypad and it’s backlit, the keys have a nice level of travel when typing and don't make the horrible clacking sound you get with some keyboards. This look and feels like a Mac keyboard, it has the command key in the correct place and usual brightness and volume controls. The keyboard feels very solidly built and does not slide when typing "vigorously".

IMG_2848

It can be connected using wireless or bluetooth and both seem to work flawlessly. Apparently the keyboard can be used for 10 days with backlight on between charges, and 5 months without the backlight.

Can apparently be connected to up to 3 Macs/iPads with buttons on the keyboard to switch between them, but I have not tried that yet.

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Camelot site change

 

I've just been told the link to Camelot has changed, I've updated the link on the Data Analysis Tools Page.

Camelot: PDF Table Extraction for Humans. Camelot is a Python library that makes it easy for anyone to extract tables from PDF files!

To install using Anaconda

conda install -c conda-forge camelot-py

Or

After installing the dependencies, tk and ghostscript, you can simply use pip to install Camelot:

pip install camelot-py[cv]

Camelot only works with text-based PDFs and not scanned documents.

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Latest CICAG newsletter is out

 

The latest RSC Chemical Information and Computer Applications Group newsletter is out.

https://www.rsc.org/images/CICAGNewsletterSummer2020tcm18-252147.pdf

  • Chemical Information & Computer Applications Group Chair's Report
  • CICAG Planned and Proposed Future Meetings
  • Open Chemical Science Online Webinars & Workshops in 2020
  • Time to add "Cheminformatics" to Keywords Indexing Science
  • COVID-19 and the Identification of "Drug Candidates"
  • DP4-AI: High-Throughput Automatic Assignment of NMR Spectra
  • The Collaborative Computational Project Number 4 Release 7.1
  • Meeting Report: AI & ML in Drug Discovery Meeting
  • Predicting the Activity of Drug Candidates when there is no Target
  • News from CAS
  • News from AI3SD
  • Other Chemical Information Related News

Huge thanks to all who contributed.

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alvaBuilder

 

alvaBuilder is a software tool for de novo molecular design. With its simple interface, it can be used to generate novel molecules having a desirable set of properties (e.g., similarity to a given molecule, MW, logP, SAscore, QED, etc.) starting from a training set of your choice.

alvaBuilder

There is a video introduction here.

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IGMPlot release version 2.6.7 - June 2020

 

Independent Gradient Model Plot ( IGMPlot )

By using IGMPlot you can identify and quantify molecular interactions over a broad range: from non-covalent to covalent bonding, through metal coordination. This tool can be helpful for interpretation accessible to a wide community of chemists (organic, inorganic chemistry, including transition metal complexes and reaction mechanisms).

New Features:

  • IBSI index: an Intrinsic Bond Strength Index (does not belong to the conventional class of bond orders like Mulliken or Mayer, or the Delocalization Index)
  • BAF index: a Bond Asymmetry Factor
  • WFX file format is now supported
  • Development of a scoring function from promolecular electron density (possibility to probe noncovalent interfragment interactions or weak intramolecular interactions)
  • Quantifying intramolecular pipi stacking at the QM level of theory
  • Accelerated performances

The program is written in C++. IGMPlot has been installed and tested on several platforms: Linux, (computational center, laptop), MacOS, Windows10. It is a standalone program. Multi-core execution can be leveraged. In that case, the OpenMP programming interface must be installed prior to IGMPlot compilation for higher performances (optional).

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Mid year Macinchem site stats

 

I just thought I'd have a quick look at the stats relating to visits to the website.

The site has been visited by over 44,000 users in the first 6 months of 2020 and there have been over 81,000 page views, with visitors spending on average two and half minutes per page.

The most popular pages are shown below, and again Fortran on a Mac tops the list.

iBabel the GUI for Openbabel has now been downloaded over 350 times since April when it was released.

viewerSSS

Looking at the operating systems used by visitors as you might expect most use Mac OS but there are a significant number of Windows users.

Macintosh 60%
Windows 22%
iOS 10%

With the remainder made up of Linux, Android, Chrome OS and various flavours of UNIX. Looking at the versions of Mac OS it seems the majority have upgraded to Catalina, and older version of the operating system tail off pretty rapidly.

10.15 58%
10.14 24%
10.13 11%
10.12 4%

The Mobile Science Site now has 260 entries and I add new entries when I find out about them.

The most popular apps are:

ChemTube3D

If you know of any Mobile Apps I've missed please let me know.

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Open Chemical Science Meeting

 

There is currently much discussion about how access to data, information, knowledge and the software tools essential for 21st century chemical science research can be increased and simplified while ensuring that quality is maintained. Significant progress is being made, but the myriad of policies, repositories, standards, sources, tools and subscription models is at the same time complicating the landscape.

Postcard

To address the many questions concerning the rapidly evolving open research landscape, towards the end of last year (before Covid-19), the CICAG Committee started to plan a series of three one-day events in November 2020, covering open access publishing, open data and open source software. The aim was to examine the benefits, risks and likely future developments and their impact on research. The aim hasn’t changed but, due to Covid-19, the events will now be run as a series of online webinars to take place over five days, from 9-13 November 2020. CICAG have decided to make them free of charge - this has been possible because the cost of running online events is much less than for face-to-face meetings.

For further information and to register see:

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Installing AmberTools20 using conda

 

Someone just pointed out to me that you can now install AmberTools20 using conda.

conda install -c conda-forge ambertools=20

This should work for Linux and MacOS systems, but it does not provide access to parallel or gpu-optimized codes. It provides a simple way to get started with AmberTools, and to install it into many workflows, but is not a substitute for the full source-code distributions

Full details are here http://ambermd.org/GetAmber.php.

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Computational Tools for Drug Discovery Workshops

 

The RSC Chemical Information and Computer Applications Group in collaboration with the SCI Fine Chemicals Group have just finished a series of virtual workshops on Computational Tools for Drug Discovery. This series of events was put together to replace a physical one-day workshop due to be held in Leeds. The one day event would have been able to accommodate 50-60 attendees and I'm delighted to report that the online Wednesday workshops were attended by a total of 538 people, so we were able to support an order of magnitude larger audience.

I'd like to thank all the companies that participated in the workshops,

  • MedChemica - MedChemica’s MCPairs Online - An idea generation tool based on Matched Molecular Pair Analysis and Machine Learning.
  • OpenEye - Practical drug discovery in the cloud using ORION.
  • Cresset - Combining ligand and structure-based approaches to improve molecule design using Cresset desktop solutions.
  • CCDC - Structure-based drug design with CSD-Discovery.
  • Optibrium - Guided Multi-Parameter Optimisation of 2D and 3D SAR.
  • KNIME - An interactive workflow for hit list triaging.
  • CDD Vault – Managing, Archiving, Mining, Reporting, and Analyzing Collaborative Drug Discovery Data

The feedback from attendees has been very positive and there will now be a short break whilst we organise the next series of workshops for later in the year.

RSC-Group-Logo-Chemical-Information-and-Computer-Applications

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ChemDoodle 2D v11 is Released

 

The latest update to the very popular chemical drawing package ChemDoodle has been released. This update brings fully chemically aware and self-calculating stoichiometry tables, automatic electron pushing arrows, and with the ability to recover chemical data embedded in Microsoft Office files.

Chemical data recovery from Microsoft Office files: (experimental feature) Round-trip editing is the process of embedding data from one application into another, that can then be recovered later. Chemists use this all the time when creating chemistry documents in Microsoft Word. ChemDoodle 2D has provided round-trip editing functionality on Windows, macOS and Linux since its inception and starting with version 10.4, users can paste chemical data from embedded ChemDraw images on macOS in ChemDoodle 2D.

However, there are several issues when relying on round-trip editing, as the user may not have continued access to the originating chemistry program or Microsoft Office, or may be working with an individual on a different operating system. Several times, Microsoft has removed the round-trip editing functionality in Office products. In all of these cases, the chemistry data in these files cannot be used. ChemDoodle 2D now provides a very unique solution for this problem, and can search and extract chemical data embedded in Microsoft Office files, regardless of the program they were created in, including ChemDoodle, ChemDraw, ChemSketch and Biovia Draw, and regardless of the operating system. You can now recover your chemical data from Word documents you created on Windows if you switch to Linux, and you can now edit chemical figures from a Word document on macOS with ChemDoodle from a colleague who uses ChemDraw on Windows.

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fpocket a very fast open source protein pocket detection algorithm

The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.

What's new compared to fpocket 2.0 (old sourceforge repo)

fpocket:

  • is now able to consider explicit pockets when you want to calculate properties for a known binding site
  • cli changed a bit
  • pocket flexibility using temperature factors is better considered (less very flexible pockets on very solvent exposed areas)
  • druggability score has been reoptimized vs original paper. Yields now slightly better results than the original implementation.
  • compiler bug on newer compilers fixed

mdpocket:

  • can now read Gromacs XTC, netcdf and dcd trajectories
  • can also read prmtop topologies
  • if topology provided, interaction energy grids can be calculated for transient pockets and channels (experimental)

The GitHub page https://github.com/Discngine/fpocket contains detailed instructions for installation. This project is licensed under the MIT License

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New addition to MayaChemTools

 

I've just heard about a new addition to the superb 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.

The latest addition RDKitPerformTorsionScan.py

Perform torsion scan for molecules around torsion angles specified using SMILES/SMARTS patterns. A molecule is optionally minimized before performing a torsion scan. A set of initial 3D structures are generated for a molecule by scanning the torsion angle across the specified range and updating the 3D coordinates of the molecule. A conformation ensemble is optionally generated for each 3D structure representing a specific torsion angle. The conformation with the lowest energy is selected to represent the torsion angle. An option is available to skip the generation of the conformation ensemble and simply calculate the energy for the initial 3D structure for a specific torsion angle

The torsions are specified using SMILES or SMARTS patterns. A substructure match is performed to select torsion atoms in a molecule. The SMILES pattern match must correspond to four torsion atoms. The SMARTS patterns containing atom indices may match more than four atoms.

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Swift or Objective-C?

 

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WWDC 2020 details

 

Apple have released more details of the lineup for the 2020 WWDC, for the first time ever this will be an online only event.

I suspect many will be interested in the Special Event Keynote and Platforms State of the Union.

Special Event Keynote June 22, 10 a.m. PDT
Platforms State of the Union June 22, 2 p.m. PDT

I'm also looking forward to hearing about the entries to the Swift Student Challenge

Showcase your love of coding by creating an incredible Swift playground on the topic of your choice. Winners will receive an exclusive WWDC20 jacket and pin set. This challenge is open to students around the world.

Now would be a good time to download the Apple Developer App to find out what is planned.

I see that MacRumours has a good roundup of all the gossip around what might be announced.

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BBEdit Update

 

Everyone's favourite text editor has been updated to version BBEdit 13.1.

The release notes describe all the changes in detail.

Updated Markdown support

BBEdit has built-in support for cmark as well as "classic" Markdown (Gruber's original Markdown.pl script). In addition, if you have Discount, MultiMarkdown, cmark-gfm, or Pandoc installed, BBEdit can use those as well. If a particular tool is not installed, its corresponding option on the menu is disabled.

There's a new command on the Text menu: "Run Unix Command". This opens a sheet into which you can enter a Unix command line, and choose where the output goes, this can be extremely useful for quick (or simple) "one shot" Unix commands that aren't worth the effort of writing a filter.

Added language-specific settings for Python, to provide explicit control over, which Python to use (python or python3, or a custom one of your choosing), whether to allow the document's "#!" line to override the choice of interpreter and whether to use flake8 for syntax checking.

And a number of other new features for tidying text and HTML.

I also liked reading amount the bug fixes

Fixed weirdness in the Pattern Playground window when making certain edits in the search pattern field. (I'm sure that the people who wrote NSTextView can explain why it does that, but probably nobody else can.)

Comments

ConstruQt

 

Just came across this site ConstruQt a molecular design tool that allows automated library-scale deployment of quantum chemical calculations.

  • Transforms molecular drawings into accurate 3D structures and energies of conformational, tautomeric and stereoisomeric space
  • Interactive visual navigation of the energies and structures
  • Contribute to the worlds largest repository of relevant molecules for chemical research. Fully open to all.

They are also looking for feedback https://www.surveymonkey.com/r/5L9TMNX

Comments

Flare™ V4 release

 

About a year ago I wrote a review of Flare a tool for structure-based drug design.

EditedLigand

The key new features of Flare V4 includes significant improvements to Free Energy Perturbation (FEP), new and improved force fields, new Dynamics analysis tools, plus new and improved GUI functionality.

The implementation of the Open Forcefield now allows users to update themselves.

FEP has been implemented in Flare DOI and this release improves performance.

In terms of speed, all FEP calculation in Flare V4 are significantly faster thanks to an improved algorithm with a 20% increase in performance, and they are fully parallelizable. This means that each bit of the transformation of one compound into another (the lambda windows) can be run on separate GPUs: the results will be merged at the end of the calculation. This can bring the calculation time for a single transformation on a medium-sized protein to less than 2 hours on a small cluster of 10 GPUs (for example AWS g4dn.xlarge, Tesla T4 spot instances).


Comments

250 downloads of iBabel4

 

I just noticed there have been 250 downloads of iBabel4, I can count these like citations right ? 😁 x You can download iBabel here.

iBabel is a graphical user interface (GUI) to the open-source cheminformatics toolkit Open Babel

3DView

I'm starting to compile a list of updates/additions, if you have any suggestions let me know.

Comments

VMD for Catalina

 

There is a new test build of VMD for Catalina.

Latest version (May 8) Updated modeling plugins updated for Tk 8.6 (grid vs. pack corrections)

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

There are details of many other scientific applications under Catalina here

Scientific Applications under Catalina: Update 13

Comments

PyMOL 2.4 released

 

PyMOL 2.4 has been released. Download ready-to-use bundles from https://pymol.org/ or update your installation with

conda install -c schrodinger pymol

Highlights:

  • Incentive PyMOL only:

    • Support for https://lookingglassfactory.com/schrodinger
    • Pi-Pi and Pi-Cation interactions (A > find > pi-interactions)
    • WaterMap result presets (A > preset > WaterMap ...)
    • APBS Plugin improvements (multi-state assemblies, propka pH calculation)
  • Open-Source and Incentive PyMOL:

    • Distinguish .mrc and .ccp4 formats (origin interpretation)
    • Trajectory handling improvements
    • Improved error handling in Python API with exceptions
    • ... many bug fixes

This will be the last release with support for Python 2.7.

Full release notes https://pymol.org/dokuwiki/?id=media:new24

Comments

Schrödinger Software Release 2020-2

 

This quarterly release includes usability improvements and performance enhancements across all of the software. Full release notes are here https://www.schrodinger.com/releases/new-features?.

Comments

WWDC 2020 June 22nd

 

The 31st Apple WWDC will take place just over a month from now. This normally a hugely over-subscribed event with a lottery deciding who gets to attend. This year things will be different, it will be an online event that can be accessible to millions around the globe.

wwdc2020

Now would be a good time to download the Apple Developer App to find out what is planned.

Comments

RSC President Election 2020

 

The election of the new president of the RSC is upon us, there are a number of excellent candidates but I'd like to draw attention to one.

I've known David Rees for many years and I can't think of a better person to lead the RSC at the present time. A really top class scientist with an excellent career in Drug Discovery, whilst maintaining contacts with academic research and holding important roles within the RSC.

If one thing COVID-19 has taught is we need to increase support for collaboration between Academia and Industry in healthcare, but also we should not lose sight of the oncoming challenges set by climate change. These are major challenges and we need build further collaborations.

Diversity is correctly high on many peoples radar, but David is someone who realises diversity goes beyond gender and is a great supporter of providing opportunities to all.

For a while I think chemistry has been thought of as simply a service, recent events have underlined chemistry as a key component of research and the economy, we need to take the opportunity for the RSC to take a leading role in ensuring that the recent momentum is maintained, and David would be a passionate advocate.

All RSC members should have received a unique voter code, and I hope you all take the opportunity to vote.

This year, the RSC are holding elections for the following positions:

  • RSC President (one vacancy)
  • Elected member of Member Communities Board (two vacancies - one representative of Interest Groups; one representative of Local Sections)
  • Elected member of Professional Standards Board (one vacancy)
  • Elected member of Analytical Division Council (two vacancies)
  • Elected member of Chemistry Biology Interface Division Council (two vacancies)
  • Elected member of Dalton Division Council (two vacancies)
  • Elected member of Education Division Council (two vacancies)
  • Elected member of Environment, Sustainability and Energy Division Council (two vacancies)
  • Elected member of Materials Chemistry Division Council (two vacancies)
Comments

Backblaze Hard Drive Stats Q1 2020

 

A while back I wrote an article on Backing up data which seemed to attract a fair amount of interest. One of the things that was highlighted was the reliability of hard drives.

Of course the reliability of the internal disc drives can vary, fortunately Backblaze who obviously use a vast number of drives keep a regular report on hard drive reliability for both manufacturers and disk models/sizes.

The stats for Q1 2020 are now out on the Backblaze site, it does seem that the drives continue to improve in reliability.

The Annualized Failure Rate (AFR) for Q1 2020 was 1.07%. That is the lowest AFR for any quarter since we started keeping track in 2013.

The actual failure rate varies from 0% to 1.4% depending on the model so well worth having read before you purchase.

Comments

ChemDoodle 2D v10.4 Update Available

 

I just heard about a new update to ChemDoodle today, and this looks like a really significant update.

This update includes a number of features, and improves several aspects of the application. We continue to improve our 2D structure cleaning algorithm, this time with a focus on structures with unavoidable overlaps when standard angles and lengths are used. ChemDoodle can now accept pastes of ChemDraw® PDF on macOS, recovering the original ChemDraw data; this essentially allows you to recover chemical data from ChemDraw images pasted into programs like Microsoft Office on macOS. A number of other smaller features is included based on customer feedback. This update is recommended for all users.

This will be a really popular addition, greatly helping interoperability.

The full release notes are here https://www.ichemlabs.com/news/read?post=cd104released.

Comments

AmberTools20 is now available!

 

New and updated forcefields:

  • FF19SB for proteins
  • Amber-Dyes parameters for fluorescent dyes and linkers
  • SIRAH model for coarse-grained simulations
  • Amoeba and GEM polarizable force fields, via gem.pmemd

Also

Now builds with cmake; conversion to python3

AmberTools consists of several independently developed packages that work well by themselves, and with Amber20 itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL)

Comments

SingleCrystal 4 Launched

 

CrystalMaker Software Ltd have just announced the release of SingleCrystal 4, this is a complete rewrite of thr Apple Design Award winning software in Objective-C, resulting in a state-of-the-art multi-core, multi-touch, multi-structure program. It’s 100% native Mac code - no emulation; no translators - and hence delivers a seamless Mac 64-bit experience with Retina graphics, multi-touch control, haptic feedback, Finder thumbnails, Quick Look previews, Full Screen Mode, Dark Mode and a dedicated Touch Bar interface for MacBook Pro.

The new Live Intensity Mode lets users edit a crystalline material at the atomic level in real time (moving atoms, changing site occupancies, rotating structural groups) - and immediately see the simulated single-crystal diffraction pattern update.

autoindexing

The software is sold directly by CrystalMaker Software Ltd (http://crystalmaker.com/crystalmaker). Multi-user, education and student licensing options are available.

Comments

f90wrap: an automated tool for constructing deep Python interfaces to modern Fortran codes

 

f90wrap is a tool to automatically generate Python extension modules which interface to Fortran libraries that makes use of derived types. It builds on the capabilities of the popular f2py utility by generating a simpler Fortran 90 interface to the original Fortran code which is then suitable for wrapping with f2py, together with a higher-level Pythonic wrapper that makes the existance of an additional layer transparent to the final user. f90wrap has been used to wrap a number of large software packages of relevance to the condensed matter physics community, including the QUIP molecular dynamics code and the CASTEP density functional theory code.

The full paper is here https://iopscience.iop.org/article/10.1088/1361-648X/ab82d2

Install using PIP

pip install f90wrap

Source code is on GitHub https://github.com/jameskermode/f90wrap.

Now added to the Fortran on a Mac page

Comments

Apple updates 13-inch MacBook Pro

 

Apple updates 13-inch MacBook Pro with Magic Keyboard, double the storage, and faster performance.

Apple_macbook_pro-13-inch-magic-keyboard_screen_05042020


I wonder if we will get a Touch Bar on an external keyboard soon?

#MacBookPro

Comments

Mailinglist for the Fortran language

 

Just got a message about a mailing list for the Fortran programming language.

https://groups.io/g/fortran-lang

More info on GitHub.

The Fortran on a Mac page is always very popular.

Comments

infiniSee 2.0 released

 

The amount of chemical space that is now accessible has increased rapidly over the last couple of years with vendors now offering billions of molecules either available from stock or via rapid synthesis, this has made searching increasingly difficult. infiniSee is a tool for searching these vast chemical spaces rapidly using a feature tree search.

Under the hood lies the FTrees similarity engine. FTrees employs a fuzzy pharmacophore descriptor that is able to pick out structurally distinct (therefore distant) molecules that are actually close neighbours in pharmacophore space.

This major update introduces a new user interface making infiniSee more intuitive and easy-to-use. In addition to the new interface, the update brings a new mode called Web Service. It allows power-users to shift the heavy-duty computing to a different machine.

2020-04-29_infiniSee

There is a review of an older version of infiniSee here.

Comments

Open Chemical Science – three-day series of events

 

The Royal Society of Chemistry’s Chemical Information and Computer Applications Group (CICAG) is organising a series of three one-day events with the theme “Open Chemical Science” on 11-13 November 2020. Venue: RSC, Burlington House, London, United Kingdom To find out more and to register, visit the web pages for the events:

Submissions of abstracts for oral or poster presentations are invited for the "Open Access Publishing for Chemistry" and "Open Data for Chemistry" days. The submission forms, information about deadlines and the submission process are on the web pages above. Please contact Gillian Bell, cicageventsmanager@gmail.com, with any enquiries.

A number of bursaries are available to support registration and travel costs for postgraduate students, the retired and those on career breaks. An application form is available on this page and further information regarding travel grants available for RSC members can be found at: www.rsc.org/awards-funding/funding/#funding-options.

* If it is not possible to run the meetings at Burlington House due to Covid-19, they will be held as webinars or online events.

Comments

Swift for Tensorflow (and other things).

 

After creating MolSeeker and iBabel4 I've been investigating the use of Swift and in particular the open-source use.

Swift.org provides a nice introduction and overview, it also highlights the Google Summer of Code Swift projects which are a fabulous way for students to get involved.

The Google Swift for TensorFlow group have been very active, and Tyrolabs have recently posted a detailed summary, including a comparison with other languages.

Two years ago, a small team at Google started working on making Swift the first mainstream language with first-class language-integrated differentiable programming capabilities. The scope and initial results of the project have been remarkable, and general public usability is not very far off.

They have now provided support for Jupyter notebooks https://github.com/google/swift-jupyter

There is also an interesting blog post here fast.ai.

IBM also seem to be using swift https://developer.ibm.com/technologies/swift/ and are highlighting leveraging Watson.

Developers can take advantage of the Watson Developer Cloud’s Swift SDK to easily build Watson-powered applications for iOS or Linux platforms. Leverage the power of Watson’s advanced artificial intelligence, machine learning, and deep learning techniques to understand unstructured data and engage with users in new ways.

Since Swift is a relatively new language it is worth looking at the ongoing evolution.

Comments

CCP4 7.1 Released

 

Just got this message

The CCP4 Core Group is very pleased to announce the release of the latest version of the CCP4 Software Suite. Version 7.1 (Skipton) is now available from the CCP4 download website. The release is available for all Windows, Linux and Mac OSX platforms.

This update includes

COOT 0.9. The latest version of Interactive Model Building Software from Dr. Paul Emsley, MRC/LMB, Cambridge, with many improvements and new features. Currently available only for Mac OSX and Linux users.

CCP4 7.1 represents the final state of 7.0 update series, complemented with newest versions of many important components.

Including new packages such as CCP4 Cloud. A framework for distributed CCP4 Computation

The release notes are here.

Comments

150 downloads of iBabel4

 

I just noticed there have been 150 downloads of iBabel4, I can count these like citations right ? 😁

You can download iBabel here.

iBabel is a graphical user interface (GUI) to the open-source cheminformatics toolkit Open Babel

3DView

Comments

Display 3D structures in iBabel

 

A minor update to iBabel Currently when you use the Viewer tab to display molecules only a 2D display is available as shown below.

2Dview

However, now there are a couple of radio buttons below the image that can be used to choose either a 2D viewer or 3D viewer, this should be particularly useful when looking at the conformation of docked ligands. It should be noted that this does not actually generate a 3D structure it merely displays the input file using a 3D viewer 3Dmol.js if the file only contains 2D coordinates a 2D structure will be displayed.

3DView

You can read more and download iBabel here.

Comments

Online workshop on Computational Tools for Drug Discovery

 

More details here https://www.soci.org/events/scirsc-workshop-on-computational-tools-for-drug-discovery

workshop

Comments

Adding titles to molecules in an sdf file using iBabel

 

The current COVID-19 pandemic has resulted in many groups sharing chemical structure files, however it is useful to understand the file format definition to do so accurately. There are many chemistry file formats, iBabel using the OpenBabel toolkit supports around 100 different file formats. One of the most popular is the sdf file format.

When handling, searching, combining sdf files it is often very useful to have a unique identifier to act as a key for each molecule, many software packages expect this to be the first line or title, unfortunately this line is often left blank and the unique identifier is held in a data field that might be called "ID", "IDNUMBER", "MOL", "molNAME"……..

iBabel can be used to generate the title in these cases, there is a detailed description of how to do this here.

You can download iBabel here.

Comments

FortranCon 2020

 

Whilst I'm not a big user of Fortran I know that the Fortran on a Mac page is one of the most frequently accessed pages so I thought I'd mention this.

I was just sent details of an upcoming meeting on Fortran.

FortranCon 2020, the first international conference targeting the Fortran programming language, will take place on July 2-4, 2020, in Zürich, Switzerland.

The FortranCon 2020 is organized in two full days with speaker presentations (2. and 3. July) and a half-day workshop (4. July)

In recent years Fortran has seen a series of new standards, improving the language in regards to object-oriented, parallel and general-purpose programming. This has spurred the development of several new projects written in and for Fortran, helping the Fortran programmers - in particular, the scientific community - to modernize their code and make it more maintainable.

The call for abstracts is open https://tcevents.chem.uzh.ch/event/12/abstracts/.

Comments on the Covid-19 situation:

Even before the current pandemic we've planned to enable virtual participation (for both speakers and participants). In case the current situation persists, the conference will be held completely virtually.

Comments

Jupyter notebook to access IBM RXN AI-assisted retrosynthesis

 

A python wrapper for the IBM RXN api has been released, available on GitHub https://github.com/rxn4chemistry/rxn4chemistry

To install

pip install rxn4chemistry

You will need to register and get an api key from here https://rxn.res.ibm.com/rxn/user/profile.

This demo shows how to use for retrosynthesis ideas.

ibmrxn_notebook

The page also includes links to download the notebook.

Comments

Jupyter notebook to access IBM RXN API

 

A python wrapper for the IBM RXN api has been released, available on GitHub https://github.com/rxn4chemistry/rxn4chemistry

To install

pip install rxn4chemistry

You will need to register and get an api key from here https://rxn.res.ibm.com/rxn/user/profile.

Simple demo using Jupyter Notebook

IBMRXNdemo

This is going to be very useful.

Comments

The updated APIs of IBM RXN for Chemistry are now available.

 

IBM RXN is a free web service for predicting chemical reactions.

Whether it’s daily research activity or experiments for fun, IBM RXN can help you predicting chemical reaction outcomes or designing retrosynthesis in just seconds

  • We provide a state-of-the-art trained artificial intelligence (AI) model that can be used in your daily research activities irrespective of the purpose
  • Use the prediction mode to open a project and invite collaborators to collectively plan complex synthesis.
  • Use the challenge mode to test your Organic Chemistry knowledge and prepare for class exams Design your retrosynthesis either using the automatic or the interactive mode. In the interactive mode, IBM RXN for Chemistry – just like an assistant – recommends disconnections and you choose.

For testing the synthesizability of a molecule or for digitizing recipes, use the RXN APIs whenever you need an AI-driven organic chemistry assistant in your code.

The full documentation is here.

Comments

Mnova 14.1.2 has been released

 

A minor update to Mnova has been released.

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

The full release notes are here

Comments

Getting the structures for drug names in publications

 

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

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

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

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

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

You can download iBabel here.

Comments

iBabel version 4.0 released

 

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

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

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

File Conversion Tools

convert

Viewing Molecule Files

viewerTab

Extension of molSeeker

seekerTab

iBabel 4.0 is freely available for download.

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

Comments

The beta of the 2020.03 RDKit released

 

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

Backwards incompatible changes:

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

Highlights:

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

Plus lots of bug fixes.



Comments

Both dftd4 and xtb are now on conda-forge

 

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

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

conda install -c conda-forge xtb

Or

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

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

dftd4 - A generally applicable London dispersion correction

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

conda install -c conda-forge dftd4

Or

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

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

To compile this version requires

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


Comments

Apple unveils new iPad Pro

 

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

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

Apple_new-iPad-Pro_03182020

I do like the new keyboard/stand.



Comments

programming help

 

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

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

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

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

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

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

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

import AppKit
import PlaygroundSupport
import Foundation


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

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

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

var obshellCommand = ""

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

var obspectrophoreResults = ""

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

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

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

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

let theText = shell(obshellCommand)

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

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

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

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


//

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

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

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

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

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


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

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


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

}


Comments

Coronavisrus stats online.

 

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

curl https://corona-stats.online/

coronavirus

Looks to be about 12 hours behind latest data.

From https://twitter.com/nixcraft.



Comments

Remote working and videoconferencing

 

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

There have been a few threads on twitter

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

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

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

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

And of course remember

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


Comments

BBEdit updated

 

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

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

The full release notes are here.

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


Comments

Google Summer of Code Open Chemistry

 

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

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

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

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


Comments

ChemRPS a Chemical Registration and Publishing System

 

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

chemrpsresultstable

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

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


Comments

Freepascal install on macOS 10.15 Catalina

 

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


Comments

ChEMBL Compound Curation Pipeline

 

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

The pipeline includes three functions:

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

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

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

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


Comments

molSeeker: Find molecular structures.

 

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

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

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

Full details here,

molSeeker


Comments

xterm problems under Catalina

A few people have reported issues using xterm under Catalina

cd documents
ls
ls: Operation not permitted

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

The solution was described here:-

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

fulldisc

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

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

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

More info on Scientific Applications under Catalina here.

Comments

Adding scientific terms to dictionary

 

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

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

gomenu

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

Chemdictionary

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

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


Comments

Alvascience software

 

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

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

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


Comments

ChemDoodle Web Components v9 is Available

 

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

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

webchemdoodle

Comments

Scientific Applications under Catalina: 2500 views

 

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

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

Comments

SAMSON 2020 is out!

 

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

InterfaceRaw

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

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

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

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

Create your own elements

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

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

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

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

Comments

Flang : The Fortran frontend of LLVM

 

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

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

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

The slide deck is available here

Comments

Skype for business app problems

 

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

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

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

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

SkypeBusiness1

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

SkypeBusiness2

Comments

Cambridge Cheminformatics Meeting

 

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

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

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

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

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

Comments

CICAG Winter 2019 Newsletter

 

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

CICAGNewsletter

This issue includes

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

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

Past issues of the newsletter are available on the website.

Comments

VESTA updated

 

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

mac-main01

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

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

ChemDoodle v10.2 Released

 

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

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

10_2_release_social_post

Full release notes are available here

In particular note

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


Comments

Vega Hub

 

Vega Hub a variety of models for predicting properties.

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

Models can be downloaded here

Comments

PLUMED PLUgin for MolEcular Dynamics

 

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

Installation

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

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

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

Comments

Interactive plots in Jupyter Notebooks updated

 

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

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

Full review and the Jupyter notebook are here.

plotjupyter

Comments

Interactive plots in Jupyter notebooks

 

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

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

3DplotinJupyter


Comments

Scientific Applications under Catalina: Update 13

 

General Issues with Catalina

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

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

1280px-Santa_Catalina_Island_California_Panorama

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

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

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

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

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

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

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

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

This book might also be useful Moving to zsh.

Notarization

I suspect many users will now see more Notarization warnings.

notarisation

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

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

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

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

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

SysPrefSecurity

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

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

Scientific Applications

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

4-Peaks no issues reported

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

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

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

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

Avogadro no issues reported

BBEdit version 13 is compatible with macOS Catalina

BioSolveIT report SeeSAR and infiniSee have been tested successfully on Catalina

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

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

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

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

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

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

Cresset all works fine but there are notarisation issues.

CrystalMaker

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

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

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

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

    http://crystalmaker.com/singlecrystal4/

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

CYLView 1.0 does not work under Catalina.

DataWarrior

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

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

DEVONthink version 3 is 64-bit compliant

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

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

EnzymeX no issues reported

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

Findings seems to be working fine, no issues reported.

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

GAMESS

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

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

All the ICM products are compatible with Catalina:

Other products that are compatible include:

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

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

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

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

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

Manuscripts

Matlab R2019b supports Catalina

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

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

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

Mnova Mnova 14.1 is compatible with Catalina OS.

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

MOPAC no issues reported.

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

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

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

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

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

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

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

RDKit no reported issues

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

SeeSAR

Spartan

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

Are all compatible with Catalina.

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

Stardrop is compatible.

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

UCSF Chimera

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

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

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

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

Wizard has been tested to work with Catalina.

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

Xcode need to update to version 11.x

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

A few people have reported issues using xterm under Catalina

cd documents
ls
ls: Operation not permitted

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

The solution was described here:-

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

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

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

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

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

Comments

A review of infiniSee

 

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

infiniSee_5

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pyjanitor

 

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

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

It can be installed using conda

conda install pyjanitor -c conda-forge

Or PIP

pip install pyjanitor

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

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



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ChemDoodle tools to search in SciFinder

 

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

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


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Small molecules approved by FDA in 2019

 

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


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Mobile Science Updated

 

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

I've recently added a few more apps.

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

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


Comments

Annual Website Review

 

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

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

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

iOS13use

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

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

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

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

Merck PTE
The Periodic Table Project
Periodic Table

Also popular were

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

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

The most popular tweets were the polls

In which area is Artificial Intelligence likely to most impact Chemistry

and

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


Comments

Fortran framework for neural networks

 

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

A parallel Fortran framework for neural networks and deep learning.


Comments

Dealing with large data files

 

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

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

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


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