Search Results for "molecule"
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Showing 31 open source projects for "molecule"
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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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Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling.
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Aestel
Applications for data management
...The reporting application provides a query builder and spreadsheet template designer. Both applications work with any relational data model. (Postgres and Oracle have been tested). The two applications have been initially developed for small molecule drug discovery research. However, they can be extended for use in other data domains. -
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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.
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ParamIT
a Toolset for Molecular Mechanical Force Field Parameterization
...The developed toolkit helps the researchers in following ways: 1) automating the creation of multiple input files for quantum and molecular mechanics programs, 2) automating the output analysis and 3) substitute the use of full MM programs with a faster specialized one. The developed tools include: 1) generator of molecule-water complexes with graphical user interface (GUI), 2) semi-automatic frequency analysis using symbolic potential energy distribution matrix and comparison of optimized internal coordinates, 3) GUI for charge fitting with three modes: manual, Monte-Carlo sampling or brute force, and 4) GUI for dihedral terms fitting. The usage of these tools decreases the labor effort, lowers manual input errors and reduces the time needed for accurate MM parameterization efforts. -
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easy-dhpsf
GUI for fitting 3D single-molecule images using the double-helix PSF
...Version 2 also includes code that facilitates combining localization data from two spectral channels using a locally-weighted quadratic 3D registration function Features - Double-Gaussian estimator is calibrated via an axial scan of bright immobile fluorescent emitters (e.g. beads) - DH localization is performed through template matching and subsequent double Gaussian fitting - Tiff stacks of SM images are analyzed using template matching followed by double-Gaussian fitting to extract estimates of the molecule positions - Two spectral channels are registered by generating a locally-weighted quadratic mapping function from control point pairs -
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CRP - Chemical Reaction Prediction
Predicting Organic Reactions using Neural Networks.
The intend is to solve the forward-reaction prediction problem, where the reactants are known and the interest is in generating the reaction products using Deep learning. This Graphical User Interface takes simplified molecular-input line-entry system (SMILES) as an input and generates the product SMILE & molecule. Beam search is used in Version 2, to generate top 5 predictions. Maximum input length for the model is 15 (excluding spaces). -
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SMSD
SMSD is a Java based software library for calculating MCS.
SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will help us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure). -
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BioPPSy
A biochemical property prediction system
Computationally predicts the pharmacokinetic properties of drug candidates using Quantitative Structure Property Relationships (QSPR) modelling. Assembles a set of tools and databases for predicting the physical properties of small molecules. The program models a given property's dependence on a collection of molecular and structural descriptors using a training set of molecules. Neural networks and support vector regression are available, as well as linear models. The models generated by... -
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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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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. -
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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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Chemical Reaction
Balance chemical reaction and compute material balance
This Python program is used to balance a chemical reaction and to compute the material balance. Furthermore, it's able to check molecules and to write the condensed strutural formula from the name of an organic molecule. (Those both functionalities are still limited.) -
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ParaSim
Parallelized calculation of molecular similarities
Diversity assessments and comparisons of large compound databases require calculating similarities of millions of compounds in an affordable time. ParaSim addresses this challenge by parallelizing the calculations according to the number of computing cores available on a single machine. It is optimized for the throughput of very large numbers of query structures against very large numbers of reference structures. As as special feature, ParaSim allows to store and and to access frequently... -
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javadbchem
A universal chemistry database system, using Java and any rdbms
...The system holds atoms and bonds as entities in the rdbms, this makes it possible to have properties recorded using foreign keys and referential integrity. Apache Torque is used for database access. The build system of the project makes it possible to add properties directly to the molecule/atom/bond tables. This makes it more flexible than systems where structures are saved as monolithic blobs in a single table. -
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aufbau
"aufbau" is a program that creates electron configuration of an atom.
This is version 1.2 of "aufbau". Its purpose is to create electron configuration of an atom, molecule or ion, following, of course, the "Aufbau" Principle. You can subscribe to the project's mailing lit here: https://lists.sourceforge.net/lists/listinfo/atomic-aufbau-news -
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The Xtal System is a comprehensive suite of small molecule structural solution, refinement and analysis software, supporting both X-ray, neutron and electron diffraction data. It runs on both Unix and MS Win32 platforms and uses tcl/tk graphics.
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ChemAzTech is a Web chemistry software (for Linux server) connected to a MySQL database (L.A.M.P. software) which is storing molecules. Manage your chemical database, with product's properties. Draw, edit molecules and record it !
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MIPGen
Simple Molecular Interaction Potential Generator in Python
Molecular Interaction Potential Generator MIPGEN is a python program that will calculate Molecular Interaction Potential grids over a given molecule, that could be either a protein or a small organic compound (drug). The output will be a series of grids with DX format (*.dx) that the user will be able to visualize using any Molecular visualization program like VMD, PyMol, Chimera... For more information on dependencies and usage, please read the Documentation. Users are welcome to post any bug or request under BUGS & REQUESTS menu. ... -
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Graphical editor using HTML5 canvas for input of chemical structures, molecule interactions, as well as protein sequence and 3D structural motifs. Facilitates searches in chemo-informatics, bioinformatics and structural biology .
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OpenThermo
Statistical thermodynamics package
OpenThermo is a program package for statistical thermodynamics computations beyond rigid rotor - harmonic oscillator approximation -
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An editor for small organic molecules, written in C using gtk+. It can read and write SMILES and cml and can save to dia's file format. It is suitable for creating chemical molecule diagrams for lower level chemistry/ochem lab reports.
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