Search Results for "molecules"
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Showing 92 open source projects for "molecules"
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Xournal++
A handwriting notetaking software with PDF annotation support
... by using page previews. Add images and create various shapes, from circles to splines to axis. Snap objects to rectangular grid or degrees of rotation. Create anything from differential equations to electrical circuits or the structural formula of molecules using our built-in LaTeX editor. Customize your toolbar to create a new layout, tailor-made for you. -
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HomotopyContinuation.jl
A Julia package for solving systems of polynomials
.... An example of an non-algebraic objective function whose derivative is algebraic is the Kullback–Leibler divergence. Homotopy continuation methods allow us to study the conformation space of molecules as for example cyclooctane (CH₂)₈. This molecule consists of eight carbon atoms aligned in a ring, and eight hydrogen atoms, each of which is attached to one of the carbon atoms. -
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Molly.jl
Molecular simulation in Julia
Much of science can be explained by the movement and interaction of molecules. Molecular dynamics (MD) is a computational technique used to explore these phenomena, from noble gases to biological macromolecules. Molly.jl is a pure Julia package for MD, and for the simulation of physical systems more broadly. The package is described in a talk at Enzyme Conference 2023 and an earlier talk at the JuliaMolSim minisymposium at JuliaCon 2022. Slides are also available for a tutorial in September... -
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ChainSafe UI Monorepo
ChainSafe Files & Storage UI Monorepo
The repository is broken up into packages, managed using yarn workspaces. You can find these in the packages directory. Various components (atoms/molecules) are used in the development of UI's. This package forms the base of the UI providing composable components, form elements, icons, small-scope elements. Theme context and other utilities for generating and using the theming capabilities. -
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Diffusers
State-of-the-art diffusion models for image and audio generation
Diffusers is the go-to library for state-of-the-art pretrained diffusion models for generating images, audio, and even 3D structures of molecules. Whether you're looking for a simple inference solution or training your own diffusion models, Diffusers is a modular toolbox that supports both. Our library is designed with a focus on usability over performance, simple over easy, and customizability over abstractions. State-of-the-art diffusion pipelines that can be run in inference with just a few... -
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DIG
A library for graph deep learning research
The key difference with current graph deep learning libraries, such as PyTorch Geometric (PyG) and Deep Graph Library (DGL), is that, while PyG and DGL support basic graph deep learning operations, DIG provides a unified testbed for higher level, research-oriented graph deep learning tasks, such as graph generation, self-supervised learning, explainability, 3D graphs, and graph out-of-distribution. If you are working or plan to work on research in graph deep learning, DIG enables you to... -
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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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Weinberg-R2R
Faster creation of aesthetic RNA secondary structure diagrams
R2R is a program to assist in aesthetic drawings of RNA secondary structures. It is primarily aimed at drawing consensus diagrams, but can also draw single RNA molecules. R2R is freely available under the GNU Public License, and runs as a command-line program under UNIX-like systems such as Linux, MacOS Darwin or Cygwin on Windows. R2R was written by Zasha Weinberg. If you use it, please cite this paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-3 -
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Charmol
Program for molecular graphics
Charmol is a cross-platform GUI/command-line based program for making high-quality pictures of molecular structures, nowadays working on Linux, MacOS and Windows. As output, it produces POV-Ray rendered images or files in VRML format. Charmol is capable of making pictures containing: - from small- to large-size molecules - more molecules together (different settings possible) - orbitals using molden and fchk files (GTO functions up to 'h' angular momentum supported) - surfaces... -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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ADFRsuite
Automated docking software tools from the Sanner lab at Scripps
the ADFRsuite provides a self contain python-based software environment with various tools for automated docking. visit ccsb.scripps.edu/adfr for more info -
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HostDesigner
General purpose de novo molecular design software
Although many potential applications exist in chemistry and material science, software to allow the general application of de novo structure-based design methods in supramolecular chemistry was non-existent. To address this limitation we created HostDesigner, a code that builds and evaluates millions of molecules in minutes. This command line executable builds 3D molecular structures by covalently connecting user-defined input fragments with pre-computed hydrocarbon fragments from a library... -
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MOF-VR is a virtual reality program developed for Microsoft Windows and HTC Vive that allows for hypothetical metal-organic frameworks (MOFs) to be constructed and tested in molecular dynamics simulations of guest molecules.
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Gabedit is a Graphical User Interface for FireFly (PC-Gamess), Gamess-US, Gaussian, Molcas, Molpro, MPQC, NWChem, OpenMopac, Orca, PSI4 and Q-Chem computational chemistry packages.
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geostd is an open-source set of restraints for molecules involved in macromolecular structure refinement. The restraints reduce the number of variables making the solution of protein structures a more tractable process.
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Open Drug Discovery Toolkit (ODDT)
Modular and comprehensive toolkit for use in cheminformatics
... and additional handles. These extensions allow to use of toolkits at all its grace and some features may be backported from others to introduce missing functionalities. Most important and handy property of Molecule in ODDT are Numpy dictionaries containing most properties of supplied molecule. Some of them are straightforward, other require some calculation, ie. atom features. Dictionaries are provided for major entities 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... -
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ParamIT
a Toolset for Molecular Mechanical Force Field Parameterization
ParamIT is a toolkit aiding the development of molecular mechanical force field parameterization of small, drag like, molecules within CHARMM general force field (CGenFF) protocol. 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... -
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easy-dhpsf
GUI for fitting 3D single-molecule images using the double-helix PSF
This package of MATLAB routines with accompanying GUI allows scientific users to measure the 3D location of single molecules when using the double-helix point spread function (DH-PSF) widefield microscope. 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... -
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cdview
"cdview" is a visualization soft for molecular simulation
"cdview" can visualize coordinates of particles, such as atoms and molecules in molecular simulation. -
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ATLAS_mPBPK
Modeling and Simulation of mPBPK models
ATLAS mPBPK is a MATLAb-based tool for modeling and Simulation of minimal Physiology Based Pharmacokinetic (mPBPK) models of small and large molecules. The tool enables the users to perform: i) PK data visualization, ii) simulation, iii) parameter optimization, and iv) local sensitivity analysis (SA) of mPBPK models in a simple and efficient manner. -
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ForceGen
Derives force constants from Gaussian QM for Gromacs MD
... the second order tensor of the Hessian from molecular fragments. The output has been made compatible with the Gromacs topology format. Examples of use include the derivation of bond force constants and equilibrium values for: -bonded metals in protein active sites -modified amino acids -small molecules/drug molecules A zip of examples files can be found by following the "Browse All Files" link. Written by Dr Anthony Nash (Oxford) Supported by Dr Thomas Collier, Prof Helen Birch & -
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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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Distribution of Solution Conformations (DISCON) is a software package designed for determining the major solution conformations of organic molecules or small peptides based on NMR experiments. Copyright 2011 University of Pennsylvania
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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...