Search Results for "3d structure"
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Showing 40 open source projects for "3d structure"
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Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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iCn3D
Web-based protein structure viewer and analysis tool
"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. -
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COLMAP
Structure-from-Motion and Multi-View Stereo
COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a graphical and command-line interface. It offers a wide range of features for the reconstruction of ordered and unordered image collections. The software is licensed under the new BSD license. -
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AlohaMini
Open-Source Dual-Arm Mobile Robot with Motorized Lift
AlohaMini is a lightweight self-hostable productivity and note-taking platform designed to help individuals organize thoughts, tasks, and knowledge in a fast, minimal interface that avoids unnecessary complexity. It combines hierarchical notebooks, rich text editing, and tagging, allowing users to structure information the way they think and refine that structure over time. The platform focuses on speed and responsiveness, with a UI that loads instantly and feels smooth even on modest... -
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CADAM
CADAM is the open source text-to-CAD web application
CADAM is an open-source “text-to-CAD” web application that turns natural-language prompts into parametric 3D models, targeting a workflow where you describe what you want and the system produces editable geometry. It is designed around a browser-first experience, so users can iterate quickly without installing a heavyweight desktop CAD suite for every experiment. A key idea is that the generated output is parametric and scriptable, enabling repeatable edits and variations rather than a... -
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Jmol
An interactive viewer for three-dimensional chemical structures.
Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other... -
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CloudCompare
CloudCompare main repository
CloudCompare is a 3D point cloud (and triangular mesh) processing software. It was originally designed to perform comparison between two 3D points clouds (such as the ones obtained with a laser scanner) or between a point cloud and a triangular mesh. It relies on an octree structure that is highly optimized for this particular use-case. It was also meant to deal with huge point clouds (typically more than 10 million points, and up to 120 million with 2 GB of memory). -
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StormSewer
Free, open-source storm sewer design: Rational, Manning, HGL, HEC-22
StormSewer is a free, open-source desktop program for gravity storm-drain design and analysis. Draw the network on a scaled aerial or import it from a Hydraflow / Civil 3D Storm Sewers .stm file, LandXML or DXF, then run the Rational method, Manning capacity for circular, box, elliptical and arch conduits, and a standard-step HGL/EGL backwater pass with junction losses and tailwater. HEC-22 inlet interception carries bypass from one inlet to the next. Reports come out as a submittal PDF with a title block on every page, ruled pipe, structure and inlet schedules, a scaled plan, and a profile with real elevation and station axes. ... -
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Fosite - advection problem solver
numerical simulation code for solving transport equations in 1D/2D/3D
Fosite is a generic framework for the numerical solution of hyperbolic conservation laws in generalized orthogonal coordinates. Its main purpose is the simulation of compressible flows in accretion disks. The underlying numerical solution method belongs to the family of unsplit conservative finite volume TVD schemes. The method is 2nd order accurate in space and uses high order Runge-Kutta and multistep schemes for time evolution. In addition to the pure advection code several source terms... -
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grafx - Extensible Java Graphics Package
Extensible Line-drawing & Polygon-filling Rasterization Libs for Java
Line-drawing and polygon-filling rasterization algorithms in Java. Simple 2D package and more complex 3D package with Z-buffering. Texture mapping not supported at the moment. Color interpolation for lines, Gouraud shading for polygons fully supported. Floating point vertex coordinates, not integer. Pixel-level aliasing, not endpoint aliasing. Doesn't use Bresenham line style! Works with all Java versions. No external dependencies. Suitable for study in academic institutions,... -
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...Generate KPOINTS, POTCAR and INCAR for a given POSCAR file; 2. Elastic-constants using stress-strain or energy-strain methods; 3. Equation-of-state fitting; 4. Suggested k-paths for a given crystal structure; 5. Optical adsorption coefficient; 6. Band structure unfolding; 7. Fermi surface; 8. Density-of-states and band-structure; 9. Charge/spin density, Charge density difference; 10. Vacuum level and work function; 11. Wave-function analysis; 12. Molecular-dynamics analysis; 13. Effective mass of carrier; 14. Symmetry finding and operations; 15. 3D band structures; More details can be found in its official website https://vaspkit.com.
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awVoronoi
Computes dual structure of 3D additively weighted Voronoi diagrams
A console application that reads 3D points with weights and computes the dual structure (a set of tetrahedral cells) of the additively weighted Voronoi diagram. The diagrams can be visualized in the Viewer application (Windows only), which can be downloaded separately (Files/Viewer.zip). Viewer is no longer developed. The latest release is 1.0.6. -
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TPLS
High Resolution Direct Numerical Simulation (DNS) of Two-Phase Flows
...Evaporation and condensation can now be modelled. Domains with up to 300,000,000 cells have been simulated. We also provide a simplified version of the code 'S-TPLS' to help new users understand the code structure and algorithms. The next step will be to include a model of boiling. -
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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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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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Mayo 3D Cad Viewer
Free cad viewer for 3d drawings in different formats
A very nice 3d Cad viewer program. This software depends on the Opencascade library. To install opencascade V7.5.0 Beta on linux : sudo dpgk -i opencascade.deb To install mayo : sudo dpkg -i mayo-cad-viewer.deb -
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3d Linear Transformation Visualization
Visualize 3d linear transformations.
A linear transformation is a function from one vector space to another that respects the linear structure of each vector space. For visualizing this we can transform a vector, but it has an obvious problem, because the linear transformation transform the whole space, not just the vector, in other words it transforms the basis vectors thus every vector in the space gets transformed too. That's why i created this app so everyone can see how a transformation matrix change the whole space. -
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GMOL
A tool for 3D genome structure visualization
...If you use GMOL in your research, please cite: Nowotny, Jackson, Avery Wells, Oluwatosin Oluwadare, Lingfei Xu, Renzhi Cao, Tuan Trieu, Chenfeng He, and Jianlin Cheng. "GMOL: an interactive tool for 3D genome structure visualization." Scientific reports 6 (2016): 20802. -
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Lightweight Model Database
An easy to use and lightweight CAD model data management tool.
This little Tool was developed in order to tidy up the CAD models and other documents in my 3D printing project folder. Full description and Manual, see: http://encorecad.de/index.php/3d-druck/lightweight-model-database-en -
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Py3DN
Morphometric analysis and visualization of the 3D structure of neurons
...The application was developed in Python and uses Blender (an open source program) to produce detailed 3D representations of raw and processed data. Py3DN is described in the paper: Aguiar P et al, "Versatile morphometric analysis and visualization of the three-dimensional structure of neurons", Neuroinformatics, 2013, 11(4):393-403 doi: 10.1007/s12021-013-9188-z -
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Phanto_maJ
build three dimensional structure
PhantomaJ is a software which aims to help users designing complexe three dimensional structures and building phantom banks. This software, implemented as an ImageJ plug-in, has been designed to be intuitive. PhantomaJ is thus "ready to use" for most users, but advanced users can choose to modify specific parameters such as intersection mode, intensity decrease function or virtual real three dimension. In addition, adding a new "basic form" consiste for advanced users to write two short... -
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Q*Bot 3D Printer
Q*Bot 3D Printer Repository
After a couple of years that I follow 3D printer growth, I picked up all the best solutions, as magnetic joints and prismatic linear guides, and gather together in this project. A complete 3D Delta Printer that can be built with about 200 euro (with electronics and graphical display, hotend and motors excluded). Printable area: 200mm dia and 200mm height Q*Bot is based on commercial Aluminum "L" profile, 25x25x4, which work as structure and linear guides as well. ... -
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Protein Contact Matrix Generator
Command line application to generate contact matrix from proteins (3D)
A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). -
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FRETtranslator
Translate smFRET trajectories into RNA secondary strucutures
FRETtranslator is a frame work that allows you to predict a sequence of RNA seondary structure transitions for a given smFRET trajectory. At its core it uses Viterbi-decoding. FRETtranslator combines smFRET data with RNA secondary structure predictions and RNA 3D structure sampling. As such it relies on input from additional software for RNA secondary structure and 3D structure predictions. -
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VSViewer3D
3D Virtual Screening Viewer
This project is an interactive viewer for 3D virtual screening data. -
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NanoCap
Carbon Fullerene and Capped Nanotube Generator
...It provides an ideal tool to accompany the study of finite carbon molecules using computer simulation. The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the structure generation routines into pre-existing code.
