In 2012, 2014 and 2017 Daniel Lowe (while at NextMove Software) released a large collection of reactions extract from USPTO patent applications as CC-Zero. We have made updates (currently quarterly) for customers of our Pistachio query tool and extended the reaction data to include USPTO Sketches and European patents. The next version of Pistachio will include data from WIPO PCT documents and include several enhancements to content and representation. Highlight these in a blog post made more sense than the usual release notes.  Number of Reactions The next release will contain >13,118 ..read more

Whilst working on an upcoming feature for our Arthor search system (the topic of another future blogpost!), I ran the feature through some performance profiling tools, partly out of curiosity and partly to check I hadn’t done anything too horrendous :). Looking through the flame chart for this new feature showed mostly what I was expecting, as well as an unexpected visitor, the equality operator (operator==) for our AtomType struct. For the sake of argument, it looks roughly like this: // in AtomType.h struct AtomType { unsigned char element; unsigned char isotope; char charge; unsign ..read more

This post is a follow up on the previous introduction – Part 1. Here I examine how we can capture fragment grouping in CXSMILES and other extensions. Fragment Grouping Fragment grouping (or component grouping) allows you group together separate fragments/components of a molecule. It is critical for reaction representation and therefore several independent SMILES extensions that have emerged. Common cases include keeping counter-ions, hydrates, and salts together as a single “molecule”. EP2305640A2 Example 11, Step v (SMILES) EP2305640A2 Example 11, Step v (CXSMILES with fragment grouping) Synt ..read more

ChemAxon Extended SMILES and SMARTS (CXSMILES) has become more popular in recent years for its ability to capture additional information on top of the core structural connectivity. At NextMove Software we think it’s great and have increasingly used CXSMILES over the years to capture information more precisely. US20150376312A1 (2)US20060205715A1 [0343]US20200002345A1 Ex 136 Such structures can be captured as CXSMILES: c12cccc1C=CC=C2.*[Zr](*)(Cl)Cl.c12cccc1C=CC=C2 |m:9:0.1.2.3.4,11:14.15.16.17.18| US20150376312A1 (2) [c-]12cccc1C=CC=C2.*[Zr++](*)(Cl)Cl.[c-]12cccc1C=CC=C2 |m:9:0.1.2.3 ..read more

SmallWorld allows the searching of chemical space by graph edit distance. It works by enumerating and connecting the common subgraphs of chemical structures into a large network. Similar molecules are found by traversing the network using a breath-first-search (BFS) to find the shortest path (minimum number of changes) between the molecules.  The latest database release (2021) contains 675 billion graphs and 9.16 trillion directed connections. To search the database we need efficient techniques to store, access and handle the data. We’ve just released version 5.0 of the SmallWorld search ..read more

Untitled The 3.0 release of Arthor brings many new features with it including an overhauled Python interface. This new interface has been written using Cython bindings to the C++ core of Arthor, with the goals of native speed for performing chemical searches as well as effortless interoperability with the existing Python data science ecosystem, i.e. numpy and pandas. Loading and searching databases¶ Databases can be opened using either the arthor.SubDb or arthor.SimDb classes for substructure and similarity searches respectively. Once opened, these classes have a .search() method which tak ..read more

Roger, Richard and I will all be attending the upcoming 258th ACS National Meeting in San Diego, so come say hi (and get your bandit sticker!). Our presentations are shown below, along with talks by Jian Zhang and John Irwin where we are listed as co-authors. As an addition to the official ACS agenda app, I’ve put together a spreadsheet showing all the talks in CINF, COMP, MEDI and ORGN ordered by session and time which you may find useful. Sunday 10:40 Grand Ballroom A, Omni CINF 5: Current challenges in text-mining for chemical information (Roger) 18:30 Exhibit Hall A, Conv Center CINF 44: M ..read more