Search Results for "cif"
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Showing 31 open source projects for "cif"
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Protenix
A trainable PyTorch reproduction of AlphaFold 3
Protenix is an open-source, trainable PyTorch reimplementation of AlphaFold 3, developed by ByteDance with the goal of democratizing high-accuracy protein structure prediction for computational biology and drug-discovery research. Protenix provides a complete pipeline for turning protein sequences (with optional MSA / sequence alignment) or structural inputs (e.g. PDB/CIF) into full 3D atomic-level structure predictions. It supports both “full” models and lightweight variants such as “Protenix-Mini,” offering a trade-off between speed/compute cost and predictive accuracy — making structure prediction accessible even in resource-constrained environments. The project also includes support for constraints (e.g., specifying residue- or atom-level contact constraints, or pocket constraints) to guide predictions toward biologically or experimentally relevant conformations, which enhances its utility for tasks like modeling complexes, ligands, or antibody–antigen interactions. -
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CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.
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Jmol
An interactive viewer for three-dimensional chemical structures.
...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 quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. ... -
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xrayutilities
a package with useful scripts for X-ray diffraction physicists
xrayutilities is a python package used to analyze x-ray diffraction data. It can support with performing diffraction experiments and used for common steps in the data analysis. It can read experimental data from several data formats (spec, edf, xrdml, ...); convert them to reciprocal space for arbitrary goniometer geometries and different detector systems (point, linear as well as area detectors); for further processing the data can be gridded (transformed to a regular grid). More... -
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ePnR
ePnR is an IC block standard cell placement & routing tool
...However, un-routed connections will be left with rubberband connections and marked start and end points for subsequent manual routing using a third party layout editor. ePnR outputs in CIF 2.0 and GDS stream format readable by e.g. the free KLayout editor. -
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Covid19 Lab Info System
A free and open-source Covid-19 Information System
...Besides, we need to help each other out. Features: - Web application so it can be accessible by any devices in the network - Follows Philippines' Department of Health guidelines in case investigation (CIF v8) Functionalities: - Patient Management and Monitoring - Employee Management - Lab Inventory Management - Contact Tracing - Lab Test Management - Files and reports export For more details, view the README.md here. https://sourceforge.net/p/nih-covid19lis/svn/ -
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Crystalsim - XRD hkl simulation
X-ray diffraction (XRD) analysis for hkl simulation of any crystal.
Crystalsim is a simple freeware program with a neat graphical user interface for X-ray diffraction (XRD) data analysis . It can simulates all possible {hkl} planes data for the selected crystal. Crystallographic Information File (.cif) can also be used. Analyze both powder diffraction and single crystal data . Indexed at International Union of Crystallography (IUCR). Crystalline lattice parameters such as ‘a’, ‘b’, ‘c’ as well as interfacial angles such as alpha, beta, gamma can also be entered manually. Processed data can be saved as .csv file format. ... -
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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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Scidb
Chess Database Application
Scidb is an open-source chess database application for Windows, Unix/Linux. It is a new development inspired by Scid. -
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CIF2Cell
Generating cells for electronic structure calculations from CIF files
CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The program currently supports output for a number of popular electronic structure programs, including ABINIT, ASE, CASTEP, CP2K, CPMD, CRYSTAL09, Elk, EMTO, Exciting, Fleur, FHI-aims, Hutsepot, MOPAC, Quantum Espresso, RSPt, Siesta, SPR-KKR, VASP. Also exports some related formats like .coo, .cfg and .xyz-files. -
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LinXTL is a text editor and a crystallographic toolbox for structural solution and refinement. It includes support for commonly used X-ray programs, makes it easer to generate publication materials and appendices for PhD thesis.
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propCIF
CIFs of the Material Properties Open Database
This repository hosts CIFs and CIF dictionaries of the Material Properties Open Database. -
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TESTIMAGES
Testing images for scientific purposes
The TESTIMAGES archive is a huge and free collection of sample images designed for analysis and quality assessment of different kinds of displays and image processing techniques. The archive includes more than 2 million images originally acquired and divided in three different categories: SAMPLING and SAMPLING_PATTERNS (aimed at testing resampling algorithms), COLOR (aimed at testing color rendering on different displays) and PATTERNS (aimed at testing the rendering of standard geometrical... -
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LibOpenCIF
A library to load CIF (Caltech Intermediate Form) files.
LibOpenCIF is an open source library for GNU/Linux that bring to the user basic loading of CIF (Caltech Intermediate Form) files. The library is writed and intented to be used in C++. -
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Cartes
For all kinds of geometry transformations of molecules and crystals
功能： A. 晶体坐标变换 -分数坐标和直角坐标互转 -向ａ,ｂ,ｃ三个方向堆积i,j,k个晶胞 -按给定对称关系得出所有相关原子 -按空间群对称性由不等价原子推出晶胞内所有原子 -查看空间群信息及对称等价位置 -自动转换*.cif文件 B. 分子坐标变换 -按指定对称操作任意平移、旋转、反映或反演当前的坐标 - 将一组坐标的中心平移到原点 -自动点群识别 -自动调整分子取向，包括 1)自动将分子的主轴调整到x,y,z轴上 2)自动将分子的自定义的某个轴调整到自定义的另外一个轴上 C. 各种文件格式的转换 注：Windows Vista使用注意：将cartes.exe的兼容模式改成Windows XP，并从用“管理员运行模式” -
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C/CIF
Compact/ Chess Interchange Format
C/CIF is an interchange format for chess applications. This format is supporting all features of a chess application - PGN does not provide this - and can be used to transfer chess archives without any loss via an application independent format. C/CIF is supporting two formats: the binary format CCIF, and the human readable format CIF (in XML). -
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Project CIF(Core Information Foundation)
c++ and c library to help build win32 software and others platforms
...JCM (Joint Core Module) used as base in project. Properly support for a class available TPT (Template Properly Type) and VTM (Value Type Macro). BTS,EVS,JCM,TOM,TPT,VTM are parts of project CIF. CIF5SDK used in project Bytes Counter. Project Core Information Foundation (CIF) is created by Muhammad Arshad Latti. -
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...Features: all angle, font generator, macros, boolean operations, design rule checker, supported formats:Calma GDSII, OASIS (Open Artwork System Interchange Standard), OpenAccess, DXF, CIF (Caltech Intermediate Form), ...
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ci-framework
the cif project
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EpiMiner
epiminer
Detecting and visualizing nonlinear interactive effects of Single Nucleotide Polymorphisms (SNPs) or epistasis are important topics of signal processing and are both mathematical and computational challenges. To address these problems, a multi-stage method, epiMiner, is proposed based on co-information theory. In screening stage, Co-Information Filter (CIF) is employed to visualize and rank contributions of individual SNPs to the phenotype. The number of top ranking SNPs retained to next stage is specified by users directly or a support vector machine classifier automatically. In testing stage, co-information and co-information based permutation test are conducted sequentially to exhaustively search epistasis within the retained SNPs and the final results are then ranked by their p-values. ... -
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A Collection of STAR/CIF processing libraries and related tools, including sub-projects: AStar, TEStar and others...
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vcif is an open source software for validation of Crystallographic Information Files. It supports lexical, parser and dictionary validation (DDL 1 and 2 are fully supported, DDLm draft partially supported)
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cifget is a DDLm dictionary import expansion utility, which generates expanded dictionaries that could be used when reading, writing, or validating CIF files
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