Open Source C++ Molecular Science Software
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C++ Molecular Science Software
View 201 business solutionsBrowse free open source C++ Molecular Science Software and projects below. Use the toggles on the left to filter open source C++ Molecular Science Software by OS, license, language, programming language, and project status.
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.
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OpenCFU
An application to count bacterial colonies and other circular objects
OpenCFU is a completely open source lightweight application designed to enumerate clustered circular objects such as bacterial colonies. It can handle digital pictures as well as live stream from a video device/webcam. OpenCFU is cross-platform, fast, reliable and allows the user to implement intuitive filters. Additional information is provided on the website: http://opencfu.sourceforge.net/ OpenCFU is published on PLoS ONE: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054072 -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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Molsketch
2D molecule editor
Molsketch is a 2D molecular editing tool. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats. -
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RasTop is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules based on the popular Rasmol software. The program is aimed at the rapid visualization and analysis of molecules.
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/ -
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GSim - free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.
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CAMPARI
Software for molecular simulations and trajectory analysis
We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion. CAMPARI offers the user a very high level of control over all implemented features. For more information and features, please refer to the project's homepage at http://campari.sourceforge.net/V5 -
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SeaBreeze
Open-source cross-platform spectrometer device driver
SeaBreeze is a device driver library that provides an interface to select Ocean Optics spectrometers. It is written in C/C++ and builds and runs on Windows (XP/7/8), MacOSX, and Linux (x86/x64/ARM). -
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Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
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ShelXle
ShelXle is a Qt GUI for SHELXL
ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps. See J. Appl. Cryst. (2011). 44, 1281–1284. for details. -
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Ocean Optics Sample Pack
Sample code for Ocean Optics OmniDriver spectrometer device driver
Sample code demonstrating how to use OmniDriver to drive Ocean Optics full range of spectrometers from C, C++, C#, Java, LabVIEW, Delphi, MATLAB and more. -
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MPQC
Massively Parallel Quantum Chemistry program
The Massively Parallel Quantum Chemistry program, MPQC, computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. -
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RDML-Ninja is an editor for qPCR data. It is the reference implementation for the RDML data standard allowing to visualize, edit and reanalyze qPCR data.
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RDKit
Open-Source Cheminformatics and Machine Learning
A collection of cheminformatics and machine-learning software written in C++ and Python. NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches. -
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qmol
A simple molecular weight calculator
qmol is a simple molecular weight calculator, available for Linux and Windows, derived from Tomislav Gountchev's KMol. You can enter a formula, (e.g. CH3(CH2)2OH) and get its molecular weight (60.0959 g/mol) and its elemental composition (C3H8O: C 59.96; H 13.42; O 26.62 %). See the features list below for more details or consult the wiki page: https://sourceforge.net/p/qmol/wiki/Home/. For Windows binary and source code see the files section: https://sourceforge.net/projects/qmol/files/ Binary packages (rpm/deb) for openSUSE Leap 15.2-42.2, xUbuntu 20.10-19.10, 17.04, Fedora 33, CentOS 8, Scientific Linux 7, and Debian 10.0-8.0 can be found at: http://download.opensuse.org/repositories/home:/lineinthesand/ -
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TUBE
Generating structures of nanotubes and some fullerenes
A Windows software for generating structures of nanotubes and some fullerenes. You can generate any kind of nanotubes (n,m) with chirality indices n and m ranging from 0 to 60, and the number of repetitive unit cells up to 50. You can also generate some typical fullerene cages from C20 up to C320. -
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psicode
An open-source quantum chemistry program package
PSI is an open-source program for computing molecular properties using high-accuracy, ab initio, quantum mechanical models. -
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WavePacket (C++/Python)
Time-dependent simulation of open and closed quantum systems
Note: This package has been superseded by a Python-only package. See https://github.com/ulflor/wavepacket for the follow-up project. WavePacket is a program package for numerical simulation of quantum-mechanical wavepacket dynamics of distinguishable particles. It can be used to solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate modern experiments involving ultrashort light pulses in photo-induced physics or chemistry. WavePacket is suitable for teaching quantum mechanics as well as for research projects in physics and chemistry. The present C++ version is an object-oriented rewrite of the existing Matlab version aiming to be more flexible. In particular, the goals are easy handling of open and closed systems and support for unusual setups. -
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ED Software project contains several programs used (mostly) for processing gas-phase electron diffraction (GED) experimental data.
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ESBTL (Easy Structural Biology Template Library) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric analysis and advanced constructions.
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Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.
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4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
