Search Results for "java open source" - Page 7
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Showing 530 open source projects for "java open source"
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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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orbkit (Moved to Github)
A Modular Python Toolbox for Cross-Platform Post-Processing of Quantum
PLEASE NOTE ORBKIT HAS BEEN MOVED TO https://github.com/orbkit/orbkit orbkit is a parallel Python program package for post-processing wave function data extracted from output files of MOLPRO (Molden File Format), TURBOMOLE (AOMix file format), GAMESS-US, PROAIMS/AIMPAC (wfn/wfx file format), and Gaussian (Output File and Formatted Checkpoint File) output files. Futhermore, an interface to cclib, a parser for quantum chemical logfiles, is provided. If you use orbkit in your work,... -
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Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
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Periodic Table of Elements
Periodic Table of Elements a quick reference tool
Periodic Table of Elements is a quick reference tool that allows you a quick glance to get general information about an element. The program is for educational purposes. -
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pyMDMix
Molecular dynamics with aqueous-organic solvent mixtures
This python package aims to help people set up and analyze molecular dynamics simulations in aqueous-organic solvent mixtures. See D. Alvarez-Garcia et al. Journal of Medicinal Chemistry, 2014. -
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This software searches the potential energy surface of small to medium size atomic systems for global minima using quantum ab initio techniques. It performs bond rotations and molecule translations and rotations on a Linux cluster with MPI.
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Morpheus search algorithm
a mass spectrometry–based proteomics database search algorithm
...We have discovered that for high-resolution MS/MS, simple spectrum preprocessing and scoring performs superior to more complex algorithms originally developed for low-resolution MS/MS, such as Sequest, Mascot, and OMSSA. Morpheus is also very fast—up to nearly 5 times faster than OMSSA for large human datasets. It is written in C# and is available open source under the permissive MIT License. -
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Grafana: The open and composable observability platformGrafana is the open source analytics & monitoring solution for every database.
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Mathpad
A Python based command line math utility.
Mathpad is a command line utility. It will later have a GUI, but not at this time. -
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ConvertMAS
ConvertMAS converts Chemical File Formats mol, mol2 and sdf.
ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. Various online tools are available... -
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ChemClipse 3rd Party Libraries
ChemClipse Third Party Libraries
The ChemClipse 3rd Party Libraries are plug-ins which encapsulate the functionality of other open-source projects to be usable through Eclipse/OSGi bundles within the ChemClipse Rich Client Platform (RCP). -
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An open-source software to convert SDF files into TINKER XYZ files (and viceversa) with automatic assignment of MMFF94 atom types, bond types and charges
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A periodic table written in qt4. Inspired by the great kde app Kalzium. 64 bit windows users: There are 64 bit windows binarys in the file section.
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binana
BINANA (BINding ANAlyzer) is a python-implemented algorithm for analyz
BINANA (BINding ANAlyzer) is a python-implemented algorithm for analyzing ligand binding. The program identifies key binding characteristics like hydrogen bonds, salt bridges, and pi interactions. As input, BINANA accepts receptor and ligand files in the PDBQT format. PDBQT files can be generated from the more common PDB file format using the free converter provided with AutoDockTools. As output, BINANA describes ligand binding. NOTE: The latest version of BINANA is now hosted at... -
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Chemical structure sketching tool, for use with various cheminformatics applications. Convenient to use and moderately sophisticated. Suitable for viewing, creating and editing MDL MOL files.
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ccwatcher
A computational chemistry monitoring, parsing and plotting application
ccwatcher monitors the progress of computational chemistry calculations during runtime. It has both a GUI and a "Command Line Interface" to which it parses important output and plots SCF energies. -
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xylib is a portable library for reading x-y data from powder diffraction, spectroscopy and other experimental methods. Supported formats: VAMAS, pdCIF, Bruker, Philips, Rigaku DAT, Sietronics CPI, DBWS/DMPLOT, Koalariet XDD and others.
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Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.
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gMol
gMol molecular graphics
We've moved to https://github.com/tjod/gMol/wiki gMol is an interactive visualization system used to display and manipulate 3-dimensional models of scientific data, such as molecular structures and surfaces. It contains both OpenGL and web browser widgets that enable flexible user interfaces. -
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LipidWrapper
Create lipid-bilayer models of arbitrary geometry.
LATEST VERSION NOW LOCATED AT http://git.durrantlab.com/jdurrant/lipidwrapper As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro,... -
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Gecko Hamaker
Calculates Hamaker coefficient,interaction free energy,force,torque.
The Gecko Hamaker open-source software project is a full implementation of the fully retarded Lifshitz formulations for isotropic and anisotropic plane-plane and cylinder-cylinder interactions with intervening interlayer materials, planar systems of up to 99 layers, and graded interfaces for the modeling of grain boundaries or other continuously changing systems, accompanied by a database of material optical properties spectra. -
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FingerID
Metabolite identification via machine learning.
[NOTICE!] FingerID since version 1.4 will be hosted on github: https://github.com/icdishb/fingerid A metabolite identification software using tandem mass spectrometry and kernel methods. The related paper can be found at http://bioinformatics.oxfordjournals.org/content/early/2012/07/18/bioinformatics.bts437.abstract. Now it supports unix/linux like system. -
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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.
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MolTPC
MolTPC provides a solution for fully automatic tautomer enumeration.
Besides all their conformational degrees of freedom, drug-like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection of...
