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Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical T...

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Autores principales: Mills, Matthew J. L., Sale, Kenneth L., Simmons, Blake A., Popelier, Paul L. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5656898/
https://www.ncbi.nlm.nih.gov/pubmed/28857244
http://dx.doi.org/10.1002/jcc.25054
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author Mills, Matthew J. L.
Sale, Kenneth L.
Simmons, Blake A.
Popelier, Paul L. A.
author_facet Mills, Matthew J. L.
Sale, Kenneth L.
Simmons, Blake A.
Popelier, Paul L. A.
author_sort Mills, Matthew J. L.
collection PubMed
description Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter‐free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add‐On” named Rhorix for the state‐of‐the‐art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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spelling pubmed-56568982017-11-01 Rhorix: An interface between quantum chemical topology and the 3D graphics program blender Mills, Matthew J. L. Sale, Kenneth L. Simmons, Blake A. Popelier, Paul L. A. J Comput Chem Software News and Updates Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter‐free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add‐On” named Rhorix for the state‐of‐the‐art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. John Wiley and Sons Inc. 2017-08-31 2017-11-05 /pmc/articles/PMC5656898/ /pubmed/28857244 http://dx.doi.org/10.1002/jcc.25054 Text en © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software News and Updates
Mills, Matthew J. L.
Sale, Kenneth L.
Simmons, Blake A.
Popelier, Paul L. A.
Rhorix: An interface between quantum chemical topology and the 3D graphics program blender
title Rhorix: An interface between quantum chemical topology and the 3D graphics program blender
title_full Rhorix: An interface between quantum chemical topology and the 3D graphics program blender
title_fullStr Rhorix: An interface between quantum chemical topology and the 3D graphics program blender
title_full_unstemmed Rhorix: An interface between quantum chemical topology and the 3D graphics program blender
title_short Rhorix: An interface between quantum chemical topology and the 3D graphics program blender
title_sort rhorix: an interface between quantum chemical topology and the 3d graphics program blender
topic Software News and Updates
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5656898/
https://www.ncbi.nlm.nih.gov/pubmed/28857244
http://dx.doi.org/10.1002/jcc.25054
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