Search Results for "molecular"

CGAL or the Computational Geometry Algorithms Library is a C++ library that gives you easy access to a myriad of efficient and reliable geometric algorithms. These algorithms are useful in a wide range of applications, including computer aided design, robotics, molecular biology, medical imaging, geographic information systems and more. CGAL features a great range of data structures and algorithms, including Voronoi diagrams, cell complexes and polyhedra, triangulations, arrangements of curves, surface and volume mesh generation, spatial searching, alpha shapes, geometry processing, and many more. ...

CrystalCMP is a code for comparing crystal structures. It is using two basic approaches for this purpose - the fingerprint and the RMSD approach. Result of the comparison is a similarity matrix and dendrogram. Read more here: J. Appl. Cryst. (2016). 49, 2172-2183 (https://doi.org/10.1107/S1600576716016058) and also here: J. Appl. Cryst. (2020). 53, 841-847 https://doi.org/10.1107/S1600576720003787

Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.

Olex2 is visualisation software for small-molecule crystallography developed at Durham University/EPSRC. It provides comprehensive tools for crystallographic model manipulation for the end user and an extensible development framework for programmers. The project has been supported by Olexsys Ltd since 2010.

Chemfiles is a modern and high-quality library for reading and writing trajectory files created by computational chemistry simulations program. These trajectories contains atomic positions, velocities, names, topology and sometimes more. Running simulations produce enormous amounts of data, which has to be post-processed to extract physical information about the simulated system. Chemfiles provides an interface to access this information which is - unified: the same code will work with...

Molecular-Dreams was developed on Linux, but it could be easily ported to other platforms, as MacOSX, Windows, Android and others. Finally and simplifying my thoughts, I could say, Variables and Procedures are Energy-Quantum, Objects are Atoms, Applications are Molecules, and so System is the Matter.

Molecular-Dreams-GUI permits to develop applications with graphic interfaces based on Qt, simply using ".ui" Qt-Designer files. Its target consists of a wrapping structure around all QtObjects and QWidgets associated to GUI; MdWrappers will permit easily to use the Qt interface from Javascript applications. It also will make an using-abstraction of LibQwt.

...A key question in ping-pong cycle research is identification of piRNAs which are amplified through the cycle. PingPongPro is a command-line tool for detecting ping-pong cycle activity in piRNA-Seq data. PingPongPro was developed at the Institute of Molecular Biology gGmbH in Mainz.

This is a general open source Quantum Mechanics/Molecular Mechanics project with academic origin. Its intention is to produce free software tools to study molecular systems through QM/MM, in open collaboration.

Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.

bc2ld is a command line tool to translate molecular database files from BASECOL (obs. of Paris) to LAMDA format (Leiden University). This command line tool has academic use purposes.

Contains various algorithms that maps short reads produced from Illumina (Solexa) Genome Analyzer, or Applied Biosystems' SOLiD System, to a reference sequence or a set of reference sequences.

ChIPOTle 2.0 is a user friendly tool for performing peak detection in ChIP-chip signal. The tool also has functions for probe sorting, signal normalization, replication merging, and multiple correction testing in a windows interface or *nix command line.

The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.

GLARE is a library and a software for product based optimization of reagent lists in the context of a chemical combinatorial library design. Large virtual combinatorial libraries containing 10^12 products have been optimized within a second.

The Molecular Modeling Templates, MMT is a C++ class library for molecular simulation applications. MMT serves as a code basis that can be easily extended and modified to perform Monte Carlo and molecular dynamics simulations.