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SAMSON
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<h2 id="samson-elements">SAMSON Elements</h2> <p>SAMSON Elements are modules for SAMSON, developed with the SAMSON <a href="/facts/Software_development_kit/2Hkk6Hbs">software development kit</a> (SDK). SAMSON Elements help users perform tasks in SAMSON, including building new models, performing calculations, running interactive or offline simulations, and visualizing and interpreting results. </p><p>SAMSON Elements may contain different class types, including for example: </p> <ul><li><i>Apps</i> – generic classes with a <a href="/facts/Graphical_user_interface/wBlQFWDP">graphical user interface</a> that extend the functions of SAMSON</li> <li><i>Editors</i> – classes that receive user interaction events to provide editing functions (e.g., model generation, structure deformation, etc.)</li> <li><i>Models</i> – classes that describe properties of nanosystems (see below)</li> <li><i>Parsers</i> – classes that may parse files to add content to SAMSON's data graph (see below)</li></ul> <p>SAMSON Elements expose their functions to SAMSON and other Elements through an introspection mechanism, and may thus be integrated and pipelined. </p> <h2 id="modeling-and-simulation">Modeling and simulation</h2> <p>SAMSON represents nanosystems using five categories of models: </p> <ul><li><i>Structural models</i> – describe geometry and topology</li> <li><i>Visual models</i> – provide graphical representations</li> <li><i>Dynamical models</i> – describe dynamical degrees of freedom</li> <li><i>Interaction models</i> – describe energies and forces</li> <li><i>Property models</i> – describe traits that do not enter in the first four model categories</li></ul> <p>Simulators (potentially interactive ones) are used to build physically-based models, and predict properties. </p> <h2 id="data-graph">Data graph</h2> <p>All models and simulators are integrated into a hierarchical, layered structure that form the SAMSON data graph. SAMSON Elements interact with each other and with the data graph to perform modeling and simulation tasks. A signals and slots mechanism makes it possible for data graph nodes to send events when they are updated, which makes it possible to develop e.g., adaptive simulation algorithms.<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a><a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a><a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> </p> <h2 id="node-specification-language">Node specification language</h2> <p>SAMSON has a <i>node specification language</i> (NSL) that users may employ to select data graph nodes based on their properties. Example NSL expressions include: </p> <ul><li>Hydrogen – select all hydrogens (short version: H)</li> <li>atom.chainID > 2 – select all atoms with a chain ID strictly larger than 2 (short version: a.ci > 2)</li> <li>Carbon in node.selected – select all carbons in the current selection (short version: C in n.s)</li> <li>bond.order > 1.5 – select all bonds with order strictly larger than 1.5 (short version: b.o > 1.5)</li> <li>node.type backbone – select all backbone nodes (short version: n.t bb)</li> <li>O in node.type sidechain – select all oxygens in sidechain nodes (short version: O in n.t sc)</li> <li>"CA" within 5A of S – select all nodes named <i>CA</i> that are within 5 angstrom of any sulfur atom (short version: "CA" w 5A of S)</li> <li>node.type residue beyond 5A of node.selected – select all residue nodes beyond 5 angstrom of the current selection (short version: n.t r b 5A of n.s)</li> <li>residue.secondaryStructure helix – select residue nodes in alpha helices (short version: r.ss h)</li> <li>node.type sidechain having S – select sidechain nodes that have at least one sulfur atom (short version: n.t sc h S)</li> <li>H linking O – select all hydrogens bonded to oxygen atoms (short version: H l O)</li> <li>C or H – select atoms that are carbons or hydrogens</li></ul> <h2 id="features">Features</h2> <p>SAMSON is developed in <a href="/facts/C%2B%2B/Et0F2qn9">C++</a> and implements many features to ease developing SAMSON Elements, including: </p> <ul><li>Managed memory</li> <li>Signals and slots</li> <li>Serialization</li> <li>Multilevel undo-redo</li> <li>Introspection</li> <li>Referencing</li> <li>Unit system</li> <li>Functors and predicate logic</li> <li>SAMSON Element source code generators</li></ul> <h2 id="samson-connect">SAMSON Connect</h2> <p>SAMSON, SAMSON Elements and the SAMSON Software Development Kit are distributed via the SAMSON Connect website.<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> The site acts as a repository for the SAMSON Elements being uploaded by developers, and users of SAMSON choose and add Elements from SAMSON Connect. </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Comparison_of_software_for_molecular_mechanics_modeling/RabeF7vR">Comparison of software for molecular mechanics modeling</a></li> <li><a href="/facts/Gabedit/rmtGg14k">Gabedit</a></li> <li><a href="/facts/Jmol/Ek2m784k">Jmol</a></li> <li><a href="/facts/Molden/D3bAa686">Molden</a></li> <li><a href="/facts/Molecular_design_software/BsLuzcbr">Molecular design software</a></li> <li><a href="/facts/Molekel/hjaIL2by">Molekel</a></li> <li><a href="/facts/PyMol/SbMJ9lPl">PyMol</a></li> <li><a href="/facts/RasMol/jA273JCz">RasMol</a></li> <li><a href="/facts/UCSF_Chimera/x4JpEHlH">UCSF Chimera</a></li> <li><a href="/facts/Visual_Molecular_Dynamics/J53Mox6h">Visual Molecular Dynamics</a> (VMD)</li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>NANO-D - INRIA <a href="http://team.inria.fr/nano-d/" target="_blank">http://team.inria.fr/nano-d/</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Contreras, M. Leonor; Villarroel, Ignacio; Rozas, Roberto (2021). "Automated Generation of Zigzag Carbon Nanotube Models Containing Haeckelite Defects". Intelligent Computing. Lecture Notes in Networks and Systems. Vol. 284. pp. 371–377. doi:10.1007/978-3-030-80126-7_28. ISBN 978-3-030-80125-0. S2CID 238030853. <a href="978-3-030-80125-0" target="_blank">978-3-030-80125-0</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Mostafa, Amr A.; El-Rahman, Soheir N. Abd; Shehata, Said; Abdallah, Naglaa A.; Omar, Hanaa S. (2021). "Assessing the effects of a novel biostimulant to enhance leafminer resistance and plant growth on common bean". Scientific Reports. 11 (1): 20020. doi:10.1038/s41598-021-98902-z. PMC 8501134. PMID 34625596. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8501134" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8501134</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Barazorda-Ccahuana, Haruna Lux; Nedyalkova, Miroslava; Mas, Francesc; Madurga, Sergio (2021). "Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations". Polymers. 284 (21): 3823. doi:10.3390/polym13213823. hdl:2445/182421. PMID 34771379. <a href="https://doi.org/10.3390%2Fpolym13213823" target="_blank">https://doi.org/10.3390%2Fpolym13213823</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>SAMSON Connect <a href="https://www.samson-connect.net/" target="_blank">https://www.samson-connect.net/</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>SAMSON 0.7.0 is available - Macs in Chemistry <a href="https://www.macinchem.org/blog/files/23588784239a539a2bbb56cd38671f38-2267.php" target="_blank">https://www.macinchem.org/blog/files/23588784239a539a2bbb56cd38671f38-2267.php</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>RDKit in SAMSON - Macs in Chemistry <a href="https://www.macinchem.org/blog/files/03dfaf3d94e9a910cad0069ed17539e0-2281.php" target="_blank">https://www.macinchem.org/blog/files/03dfaf3d94e9a910cad0069ed17539e0-2281.php</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Vaucher, Alain C.; Reiher, Markus (2016). "Molecular Propensity as a Driver for Explorative Reactivity Studies". Journal of Chemical Information and Modeling. 56 (8): 1470–1478. arXiv:1604.06748. doi:10.1021/acs.jcim.6b00264. PMID 27447367. S2CID 3549945. <a href="/wiki/ArXiv_(identifier)" target="_blank">/wiki/ArXiv_(identifier)</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Vaucher, Alain C.; Reiher, Markus (2017). "Steering Orbital Optimization out of Local Minima and Saddle Points Toward Lower Energy". Journal of Chemical Theory and Computation. 13 (3): 1219–1228. arXiv:1701.00128. doi:10.1021/acs.jctc.7b00011. PMID 28207264. S2CID 4406796. <a href="/wiki/ArXiv_(identifier)" target="_blank">/wiki/ArXiv_(identifier)</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Miao, Haichao; De Llano, Elisa; Sorger, Johannes; Ahmadi, Yasaman; Kekic, Tadija; Isenberg, Tobias; Gröller, M. Eduard; Barišić, Ivan; Viola, Ivan (2017). "Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures" (PDF). IEEE Transactions on Visualization and Computer Graphics. 24 (1): 1014–1024. doi:10.1109/TVCG.2017.2743981. PMID 28866510. S2CID 9479885. <a href="https://hal.inria.fr/hal-01581203/file/Miao_2018_MVS.pdf" target="_blank">https://hal.inria.fr/hal-01581203/file/Miao_2018_MVS.pdf</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Artemova, Svetlana; Redon, Stephane (2012). "Adaptively Restrained Particle Simulations". Physical Review Letters. 109 (19): 190201:1–5. Bibcode:2012PhRvL.109s0201A. doi:10.1103/PhysRevLett.109.190201. PMID 23215362. <a href="https://hal.inria.fr/hal-00756121/document" target="_blank">https://hal.inria.fr/hal-00756121/document</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Bosson, Mael; Grudinin, Sergei; Bouju, Xavier; Redon, Stephane (2012). "Interactive physically-based structural modeling of hydrocarbon systems". Journal of Computational Physics. 231 (6): 2581–2598. Bibcode:2012JCoPh.231.2581B. CiteSeerX 10.1.1.592.5537. doi:10.1016/j.jcp.2011.12.006. S2CID 15942141. <a href="/wiki/Bibcode_(identifier)" target="_blank">/wiki/Bibcode_(identifier)</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Bosson, Mael; Grudinin, Sergei; Redon, Stephane (2013). "Block-Adaptive Quantum Mechanics: An Adaptive Divide-and-Conquer Approach to Interactive Quantum Chemistry". Journal of Computational Chemistry. 34 (6): 492–504. doi:10.1002/jcc.23157. PMID 23108532. S2CID 2298570. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>SAMSON Connect <a href="https://www.samson-connect.net/" target="_blank">https://www.samson-connect.net/</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> </ol>