3/15/2023 0 Comments Crystalmaker add atoms![]() ![]() Whilst offering many interesting and useful features, these projects suffer from the same issues centering around effective reuse of existing code, well commented and documented code, and easy extension to add new features and adapt for specialized areas. which focus on particular computational packages (i.e., GAMESS-US for MacMolPlt). and some highly specific editors such as MacMolPlt Several new applications are available today that focus on both building and visualizing molecular structure. would be used, to secure semantic and chemical data and allow easy interoperability with other chemistry software.Īt the time of writing, it is apparent that other researchers have perceived similar needs. Further, the open, standardized Chemical Markup Language (CML) file format The creation of an open and extensible framework that implements many of the necessary foundations for a molecular builder and visualizer would facilitate more effective research in this area. One of the main issues with both commercial and open-source applications is a lack of extensibility many of the applications also only work on one or two operating systems. However, it suffers from a restrictive license and it uses an antiquated graphical toolkit, which is not native on most modern operating systems.īroad goals for the design of a molecular editor were identified following a case study of the available applications. application was also available, able to build up small molecules and analyze output from several quantum codes. This led them to found a new project to address the issues they had observed in Ghemical and other packages. Two of the authors (Hutchison and Curtis) contributed to Ghemical previously, but had found that it was not easily extensible. was one of the only projects satisfying these needs at the time. The selection of free, open-source, cross-platform, three-dimensional, molecular builders was quite limited when the Avogadro project was founded in late 2006. ![]() Furthermore, in most cases, these programs use custom, proprietary file formats, and semantic and chemical data can be lost in conversion to other data formats. If the company were to change its direction or focus, this can lead to a loss of a significant research investment in a commercial product. They are, however, not available for all operating systems (most of them only run on Microsoft Windows), and are not easily extensible, customized, or integrated into automated workflows. , which are polished and capable of constructing many different types of molecular structures. There are existing commercial packages, such as CAChe/Scigress The choice of software capable of building chemical structures in three dimensions is far smaller. The aforementioned viewers are all freely available, and most of them are available under open-source licenses and work on the most common operating systems (Linux, Apple Mac OS X, Microsoft Windows, and BSD). The field of molecular graphics is dominated by viewers with little or no editing capabilities, such as RasMol Many fields such as chemistry, materials science, physics, and biology, need efficient computer programs to both build and visualize molecular structures. ![]()
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