Surge - A Fast Open-Source Chemical Graph Generator

Chemical structure generators are used in cheminformatics to produce or enumerate virtual molecules based on a set of boundary conditions. The result can then be tested for properties of interest, such as adherence to measured data or for their suitability as drugs. The starting point can be a potentially fuzzy set of fragments or a molecular formula. In the latter case, the generator produces the set of constitutional isomers of the given input formula. Here we present the novel constitutional isomer generator surge based on the canonical generation path method. Surge uses the nauty package to compute automorphism groups of graphs. We outline the working principles of surge and present benchmarking results which show that surge is currently the fastest structure generator. Surge is available under a liberal open-source license.

MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle

The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering. Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked in single-threaded mode against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution PMG. Based on the benchmarking, MAYGEN is on average 47 times faster than PMG and on average three times slower than MOLGEN in performance.

MAYGEN - an Open-Source Chemical Structure Generator for Constitutional Isomers Based on the Orderly Generation Principle

<p>The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering.</p><p>Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution OMG. MAYGEN outperforms OMG by an order of magnitude and gets close to and occasionally outperforms MOLGEN in performance.</p>

MAYGEN - an Open-Source Chemical Structure Generator for Constitutional Isomers Based on the Orderly Generation Principle

<p>The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering.</p><p>Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution OMG. MAYGEN outperforms OMG by an order of magnitude and gets close to and occasionally outperforms MOLGEN in performance.</p>

MAYGEN - an Open-Source Chemical Structure Generator for Constitutional Isomers Based on the Orderly Generation Principle

<p>The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering.</p><p>Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution OMG. MAYGEN outperforms OMG by an order of magnitude and gets close to and occasionally outperforms MOLGEN in performance.</p>

Crystal Structure Prediction of Energetic Materials and a Twisted Arene with Genarris and GAtor

A crystal structure prediction (CSP) workflow, based on the random structure generator, Genarris, and the genetic algorithm (GA), GAtor, is applied to the energetic materials 2,4,6-trinitrobenzene-1,3,5-triamine (TATB) and 2,4,6-trinitrobenzene-1,3-diamine (DATB),...

Rekonstrukcja i rewitalizacja zagrożonych wymarciem języków z wykorzystaniem narzędzi lingwistyki komputerowej

RECONSTRUCTION AND REVITALISATION OF ENDANGERED LANGUAGES USING COMPUTATIONAL LINGUISTICS TOOLS The monograph presented here consists of an introduction, six chapters and a conclusion. The first chapter briefly discusses the current linguistic situation, paying particular attention to the languages with a small number of speakers, which are threatened with extinction, and provides a thorough analysis of reasons for the disappearance of such languages. In the following chapters, namely chapters two, three and four, the authors reviewed the current linguistic situation in the western part of Europe. They briefly discuss selected languages spoken in this area which are threatened with extinction and belong respectively to the Germanic (second chapter) and Romance (third chapter) language groups. The fourth chapter discusses the languages in danger of extinction in Europe which belong to other groups of the Indo-European language family, with particular emphasis on the Celtic language group. The fifth chapter contains a description of the syntactic structure generator of Norwegian, developed by the authors. This kind of software may serve as a model for building analogous systems for other languages in danger of extinction. At this point, it is worth mentioning that the Norwegian language chosen by the authors exists in two official variants. One of them – New Norwegian (Nynorsk) – is currently perceived as a language potentially threatened with extinction. On the other hand, the sixth chapter of the monograph presents further prospects for the development of the system elaborated by the authors. In particular, the possibilities of its evolution into Machine-Aided Human Translation software have been considered. The task of this software would be to support the process of translating texts into the endangered languages. It is important to mention here that, thanks to the use of machine learning techniques, especially deep learning artificial neural networks, the issue of computer translation has already been solved in a largely satisfactory manner in the general sense, which not so long ago seemed like a scenario from a science fiction novel.