SAMSON

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SAMSON

The main user interface.

Developer(s)| OneAngstrom
Stable release|

SAMSON 2021 / 2021

Written in| C++ (Qt)
Operating system| Windows, macOS, Linux
Platform| x86, x86-64
Available in| English
Type| Molecular design
License| Proprietary[1]
Website| www.samson-connect.net

SAMSON (Software for Adaptive Modeling and Simulation Of Nanosystems) is a computer software platform for molecular design being developed by OneAngstrom and previously by the NANO-D group at the French Institute for Research in Computer Science and Automation (INRIA).[2]

SAMSON has a modular architecture that makes it suitable for different domains of nanoscience, including material science,[3] life science,[4] and drug design[5].[6][7][8][9][10][11]

## SAMSON Elements[edit]

SAMSON Elements are modules for SAMSON, developed with the SAMSON software development kit (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.

SAMSON Elements may contain different class types, including for example:

* Apps – generic classes with a graphical user interface that extend the functions of SAMSON
* Editors – classes that receive user interaction events to provide editing functions (e.g., model generation, structure deformation, etc.)
* Models – classes that describe properties of nanosystems (see below)
* Parsers – classes that may parse files to add content to SAMSON's data graph (see below)

SAMSON Elements expose their functions to SAMSON and other Elements through an introspection mechanism, and may thus be integrated and pipelined.

## Modeling and simulation[edit]

SAMSON represents nanosystems using five categories of models:

* Structural models – describe geometry and topology
* Visual models – provide graphical representations
* Dynamical models – describe dynamical degrees of freedom
* Interaction models – describe energies and forces
* Property models – describe traits that do not enter in the first four model categories

Simulators (potentially interactive ones) are used to build physically-based models, and predict properties.

## Data graph[edit]

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.[12][13][14]

## Node specification language[edit]

SAMSON has a node specification language (NSL) that users may employ to select data graph nodes based on their properties. Example NSL expressions include:

* `Hydrogen` – select all hydrogens (short version: `H`)
* `atom.chainID > 2` – select all atoms with a chain ID strictly larger than 2 (short version: `a.ci > 2`)
* `Carbon in node.selected` – select all carbons in the current selection (short version: `C in n.s`)
* `bond.order > 1.5` – select all bonds with order strictly larger than 1.5 (short version: `b.o > 1.5`)
* `node.type backbone` – select all backbone nodes (short version: `n.t bb`)
* `O in node.type sidechain` – select all oxygens in sidechain nodes (short version: `O in n.t sc`)
* `"CA" within 5A of S` – select all nodes named CA that are within 5 angstrom of any sulfur atom (short version: `"CA" w 5A of S`)
* `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`)
* `residue.secondaryStructure helix` – select residue nodes in alpha helices (short version: `r.ss h`)
* `node.type sidechain having S` – select sidechain nodes that have at least one sulfur atom (short version: `n.t sc h S`)
* `H linking O` – select all hydrogens bonded to oxygen atoms (short version: `H l O`)
* `C or H` – select atoms that are carbons or hydrogens

## Features[edit]

SAMSON is developed in C++ and implements many features to ease developing SAMSON Elements, including:

* Managed memory
* Signals and slots
* Serialization
* Multilevel undo-redo
* Introspection
* Referencing
* Unit system
* Functors and predicate logic
* SAMSON Element source code generators

## SAMSON Connect[edit]

SAMSON, SAMSON Elements and the SAMSON Software Development Kit are distributed via the SAMSON Connect website.[6] 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.

## See also[edit]

* Comparison of software for molecular mechanics modeling
* Gabedit
* Jmol
* Molden
* Molecular design software
* Molekel
* PyMol
* RasMol
* UCSF Chimera
* Visual Molecular Dynamics (VMD)

## References[edit]

1. ^ "Terms of use". SAMSON Connect. Retrieved 2020-05-30.
2. ^ NANO-D - INRIA
3. ^ 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.
4. ^ 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.
5. ^ 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.
6. ^ a b SAMSON Connect
7. ^ SAMSON 0.7.0 is available - Macs in Chemistry
8. ^ RDKit in SAMSON - Macs in Chemistry
9. ^ 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.
10. ^ 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.
11. ^ 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.
12. ^ 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.
13. ^ 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.
14. ^ 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.

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