I bookmarked this paper a while back but have only just had time to read it through, STK: A Python Toolkit for Supramolecular Assembly. STK is a tool for the automated assembly, molecular optimization and property calculation of supramolecular materials. It has a simple Python API and integration with third party computational codes.
Additional linking functional groups can be defined as SMARTS and STK can be extended by adding additional optimisation force-fields.
I just stumbled across a fascinating series of lectures. These are recordings of the live discussions behind the ongoing software development led by Stephen Wolfram.
Of particular interest might be the discussion on incorporating chemistry into the Wolfram language.
A little while back I mentioned BioConda. You can read more details in this publication "Bioconda: A sustainable and comprehensive software distribution for the life sciences", DOI. Conda is a platform- and language-independent package manager that sports easy distribution, installation and version management of software.
The conda package manager has recently made installing software a vastly more streamlined process. Conda is a combination of other package managers you may have encountered, such as pip, CPAN, CRAN, Bioconductor, apt-get, and homebrew. Conda is both language- and OS-agnostic, and can be used to install C/C++, Fortran, Go, R, Python, Java etc
The bioconda channel is a Conda channel providing bioinformatics related packages for Linux and Mac OS. Looking through the packages it is clear there it already contains a number of chemistry packages. These include: Updated 24 November 2017
- Autodock Vina
Bioconda offers a collection of over 3100 software tools, which are continuously maintained, updated, and extended by a growing global community of more than 330 contributors. Rather than try to duplicate this effort for a "Chemconda" it seems more efficient to encourage chemists to contribute to Bioconda. If you do package a chemistry application for Bioconda please let me know and I'll publicise it on my blog and add it to the list above. To start things rolling I've added PubChem.py to Bioconda and I've written a page describing how to create a bioconda recipe.
Virtual reality apps for the iPhone are becoming more common and the latest is Learning Carbons VR. This is an educational virtual reality (VR) app where students can learn about the various forms of carbon.
For many of these types of apps you will need a VR Google Cardboard headset with head straps and a Bluetooth gamepad (MFi certified - made for iPhone).
iScienceSearch is an internet search portal for scientists that allows you to perform a search across multiple data sources with a single query. I wrote a review a while back but it has undergone several updates since then and has been significantly expanded.
iScienceSearch allows both text and structure based searches, but the really interesting thing is that when you do a search using a single query item it automatically searchs in the background for other synonyms, structure, CAS Registry Number, InChI etc.
The screenshot below (click to enlarge) was generated using a structure-based query, as you can see the search results also include the results from text-based queries using synonyms. The filters on the left-hand side allow you to sort and filter the results to allow you to focus on the most relevant information.
The searching is free and requires no registration.
The GPView program is a C++ package for wave function analysis and visualization.
It is developed and maintained by Tian Shi and Ping Wang Ref](http://arxiv.org/abs/1602.07302)
In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular orbitals and electron density related with electronic excited states, such as natural orbitals, natural transition orbitals, natural difference orbitals, hole-particle density, detachment-attachment density and transition density. The visualization module of GPView can display molecular and electronic (iso-surfaces) structures. It is also able to animate single trajectories of molecular dynamics and non-adiabatic excited state molecular dynamics using the data stored in existing files. There are also other utilities help to extract and process the output of quantum chemistry calculations. The GPView provides full graphic user interface (GUI) which makes it very easy to use.
LaTeX is used for the markup and publication of scientific documents, it is particularly popular in mathematics, physics, computer science. I know some chemists use it so I thought I'd mention this resource of Chemistry LaTeX packages. It includes packages for most of the major Chemistry journals.
The ChemSpider Website has been updated.
ChemSpider is a free chemical structure database providing fast text and structure search access to over 34 million structures from hundreds of data sources.
The secret of a good iOS app is often finding a niche that is both useful but does not require lots of functionality or screen real estate. Chemical Names Spell Checker ticks both boxes nicely.
The Chemical Names Spell Checker provides chemical name spell checking and chemical name synonym look-up. Data are provided by the ChemSpell service that contains more than 1.3 million chemical names related to organic, inorganic, pharmaceutical, toxicological, and environmental health topics.
Once checked the name can be copied to the clipboard for use in another application.
The ChemSpell Web Service API is free of charge. Neither registration or licensing is required. This app nicely underlines the power of chemistry web services.
Well worth all chemists having on their iPhone or iPad.
I thought I would highlight a recent publication I read in Journal of Cheminformatics “Molecule database framework: a framework for creating database applications with chemical structure search capability” Journal of Cheminformatics 2013, 5:48 DOI.
From the abstract
Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:Chemical structure searches combined with property searches. Support for multi-component compounds (mixtures) mport and export of SD-files. Optional security (authorization). For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files.
While not a drag and drop solution it provides a means to create your own personal chemically searchable database.
Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.
I was recently sent a link to an educational chemistry app Chemistry By Design: Learning by Using the Graphical Language of Organic Chemistry by University of Arizona. I had a quick look at it and it seems quite an interesting way to learn organic synthesis. There around a thousand synthetic routes to explore and it seems to cover a wide range of synthetic organic chemistry, the synthetic targets include natural products and pharmaceuticals. I was particularly delighted to see that Woodward’s 1954 synthesis of strychnine is included.
Whilst looking it up I noticed several other educational chemistry apps, Organic Chemistry Essentials, Organic Chemistry FlashCards. What is clear is it would be very useful to have a science category to help find these sort of applications.
There is a list of mobile science apps here.
There was an interesting entry on the ChemSpider blog this week, apparently they are starting to capture spectral information
The RSC now encourages authors for several of our journals to supply extra information, structures and spectra in their original file formats – which are attached to the article as supplementary information. Already we’ve seen several submissions of data that we have incorporated into ChemSpider records, both enriching the ChemSpider database and also showcasing the research of these authors through their publications. In this way, the RSC hopes to encourage the addition of reusable data files to the research paper as the start of its efforts to promote increased data sharing within chemical science research. In a few short weeks we’ve received a number of submissions from authors that include key chemical structures as mol files and in some cases extra data including 1H and 13C NMR spectra as well as UV and IR spectra.
Once you have done that you can see the spectra displayed using a Java applet.
The Open Chemistry Group have just announced the availability of the first beta release of a suite of software packages for chemists.
It consists of Avogadro 2 an update to the well established molecular editing package, see a recent paper describing it for more details “Avogadro: an advanced semantic chemical editor, visualization, and analysis platform” DOI.
Some notable new features of Avogadro 2 include:
- Scalable data structures capable of addressing the needs of large molecular systems.
- A flexible file I/O API supporting seamless addition of formats at runtime.
- A Python-based input generator API, creating an input for a range of quantum codes.
- A specialized scene graph for supporting scalable molecular rendering.
- OpenGL 2.1/GLSL based rendering, employing point sprites, VBOs, etc.
- Unit tests for core classes, with ongoing work to improve coverage.
- Binary installers generated nightly.
- Use of MoleQueue to run computational codes such as NWChem, MOPAC, GAMESS, etc.
The final element of this first beta release is a chemically aware database MongoChem built on MongoDB intended to address the need for researchers and groups to be able to effectively store, index, search and retrieve relevant chemical data. It uses Open Babel to provide the cheminformatics input
There is a slide presentation describing the project in more detail here/
I’ve previously highlighted the use of ChemDoodle web components to display molecular structures within a web page, and a recent publication DOI by Henry Rzepa lead me to explore some of the newer additions to the means to render molecules within a web page without the use of applets or plugins.
In addition to searching a wide range of databases it provides access to Chemicalize.org which gives access to chemical properties, and PASS (Prediction of Activity Spectra for Substances) to evaluate chemical structures.
There is a growing collection of software reviews here.
ChemEquate automatically formats and balances chemical equations. Copy with one click for use in word processing applications. Molecular weights are also conveniently provided.
- Create clear and professional looking chemical equations
- Powerful tool for balancing chemical equations instantly
- Export beautifully formatted equations to other applications
- Quickly calculate the molecular weight of any compound
- Save equations to Favorites list for future use
SPRESImobile provides direct access to ChemReact, a subset of the SPRESI structure and reaction database, which contains more than 400,000 unique reaction types and the related references. SPRESImobile allows searching by name and structure queries, exact, substructure and All-in-one (Flex) search. There is a list of iOS applications on the mobile science page.
- Instant JChem Personal (an new OS independent desktop application for working with chemical and non chemical data) and Marvin, a chemical editor and viewer suite are free for all users
- All products are free for academic teachers and researchers - including the enterprise edition of Instant JChem
- Most products are free for freely accessible, non commercial websites