Search Results for "pdb files"
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Showing 64 open source projects for "pdb files"
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x64dbg
An open-source x64/x32 debugger for windows
An open-source binary debugger for Windows, aimed at malware analysis and reverse engineering of executables you do not have the source code for. There are many features available and a comprehensive plugin system to add your own. Fully customizable color scheme. Dynamically recognize modules and strings. Import reconstructor integrated (Scylla). Fast disassembler (Zydis). User database (JSON) for comments, labels, bookmarks, etc. Plugin support with growing API. Extendable, debuggable... -
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KOReader
An ebook reader application supporting PDF, DjVu, EPUB, FB2, etc.
KOReader is a document viewer for E Ink devices. Supported fileformats include EPUB, PDF, DjVu, XPS, CBT, CBZ, FB2, PDB, TXT, HTML, RTF, CHM, DOC, MOBI and ZIP files. It’s available for Kindle, Kobo, PocketBook, Android and desktop Linux. Runs on embedded devices (Cervantes, Kindle, Kobo, PocketBook, reMarkable), Android and Linux computers. Developers can run a KOReader emulator in Linux and MacOS. Multi-lingual user interface with a highly customizable reader view and many typesetting options. ... -
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DBConvert is a cross converter for HanDBase-, List-, JFile-, MobileDB-, PilotDB-, MariaDB-, MySQL-, PostgreSQL-, SQLite-, MS-Access-, SQL Server-, Firebird- , DBase- and Foxpro- databases, as well as MS-Excel and Calc spreadsheets, CSV- , JSON-, vCard-, hCard-, jCard-, xCard-, YAML- and XML files. Source files: https://github.com/TvBreukelen/fnpdbservices
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x64dbg
An open-source x64/x32 debugger for windows.
An open-source x64/x32 debugger for windows. Development is done on GitHub (https://github.com/x64dbg/x64dbg). Daily snapshots are uploaded here, snapshots for every commit can be found on http://releases.x64dbg.com -
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Genetic algorithm for EOM
A python GA code for EOM in SAXS/WAXS
Because GAjoe of ATSAS cannot deal with WAXS range, and no parameters can be modified. I made a code by myself to use GA for finding best EOM for SAXS/WAXS. The project need ATSAS crysol and a folder with multiple pdb files to use. -
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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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Cecil
Cecil is a library to inspect, modify and create .NET programs
...If you're using Cecil, or depend on a framework, project, or product using it, please consider sponsoring Cecil. Cecil 0.10 beta 5 addresses a long standing issue: previously, a rewrite of native pdb files would lose some debugging information, including the list of namespaces that were used in methods (and thus breaking the expression evaluation) or the scopes in generators (for iterators or async methods). -
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RedtDec
RetDec is a retargetable machine-code decompiler based on LLVM
The decompiler is not limited to any particular target architecture, operating system, or executable file format. ELF, PE, Mach-O, COFF, AR (archive), Intel HEX, and raw machine code supported. 32-bit: Intel x86, ARM, MIPS, PIC32, and PowerPC 64-bit: x86-64 supported. Demangling of symbols from C++ binaries (GCC, MSVC, Borland). Reconstruction of functions, types, and high-level constructs. Output in two high-level languages: C and a Python-like language. Generation of call graphs,... -
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AWS GameKit Plugin for Unreal
The AWS GameKit Plugin for Unreal
...Game projects created in Unreal versions later than 4.27 are not backward compatible. AWS GameKit supports Unreal Engine version 4.27. Create the Visual Studio Solution for your game. Build GameKit C++ and copy over the DLL/PDB files. Make sure to checkout the matching version from the .gkcpp_version file in this repository. -
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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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Vexed for Windows
Classic PalmPilot Vexed Puzzle newly coded for Windows
...Same level packs, new 'cleanroom' code for Windows implements all play features, plus more, of the original. Click sample images below to see the full window Install files are under the Files tab, and all additional Puzzle Packs are under Files-PuzzlePacks. All original Puzzle Packs are ready, be sure to download from here. Each Puzzle Pack typically has 60 puzzles and are in an ini format not the pdb format. There are more than 2900 puzzles available! There is a PortableApps version under the Files tab /PortablePgm as well. ... -
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CheUP
Gromacs Topology Builder - OPLS AA Based. Support many charge model
...Moreover, user can use own parameter as well as original OPLS parameter. Finally, user also can add and edit the topology within the software. Main Features: 1. Generate GROMACS OPLS AA topology and structure (PDB, GRO, MOL2, etc) 2. Support quantum calculation for determining charge (MOPAC7.1 is included) 3. Calculate CM1A – LBCC and CM5 Charge Model 4. Read many files formats structure using Open Babel library and Quantum Output (MOPAC7.1, ORCA, GAUSSIAN, FIREFLY) 5. Nice Ways Adding Hydrogen -
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silico
Libraries and scripts for molecular modelling written in Perl
A perl molecular toolkit designed to assist in general molecular modelling activities. Silico provides file format conversion, molecular manipulation and analysis and a simple way to write wrapper scripts around other preexisting software packages. -
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POWAINDv1.0
Protein Water Interactions Determination, version 1.0
Crystallographic shell-waters that originate from diffraction data are an essential component, but not bulk water, of protein structure and stability. It interacts with various polar and non-polar components of protein. Polar backbone is constituted by O-type and N-type atoms of all residues. Polar side-chains are O, N, S containing groups of amino acid residues. Notably, ordered shell-waters form bridge interactions. Disordered shell-water may occupy central hydrophobic-cavity of protein.... -
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JSiteDescriptor
Binding site descriptor generation for SVM based classification.
A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too). -
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chops
Convex Hull Of Protein Surface
This program will calculate all k-th convex hulls of protein surface when input a protein pdb file (pdb format), it is supplied in source code form along with the required data files and run under the windows/linux. -
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vcproj2cmake
Visual Studio .vc[x]proj to CMakeLists.txt (make, Ninja ...) enabler
Elaborate Visual Studio .vcxproj / .vcproj projects to CMakeLists.txt converter, enabling Makefile or Ninja or IDE builds, i.e. full multi-platform CMake functionality (Linux, Mac, Windows...). Live Update capability: supports side-by-side tracking of evolving original proj files, within build tree!! Script hooks for static CMake defs, powerful definition-to-variable mapping. Access to project data content is via git repository _only_ (it's a developer infrastructure project, thus... -
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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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chemfiles
Modern library for chemistry file reading and writing
Chemfiles is a modern and high-quality library for reading and writing trajectory files created by computational chemistry simulations program. These trajectories contains atomic positions, velocities, names, topology and sometimes more. Running simulations produce enormous amounts of data, which has to be post-processed to extract physical information about the simulated system. Chemfiles provides an interface to access this information which is - unified: the same code will work with... -
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cosurim
Computation of composition of core, rim and surface of PDB files
Authors: Parth Sarthi Sen Gupta, Rifat Nawaz Ul Islam and Amal K Bandyopadhyay Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India. A fully automated procedure that can analyze a large database of crystal structures with variable number of chains in them , for the results of absolute and normalized compositions of the core, surface and rim of any number of x-ray structures with any number of chains in them. -
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irayMol
Molecular visualization
Analyses and Interactive visualizations of the structures, functions and actions of biomolecules including molecular surface computation, and protein-ligand interface and protein-ligand docking where the ligand could a small compound, a nucleic acid, membrane and other proteins, written in C++/Qt/openGL/GLSL with more than 125,000 lines of codes. In addition to Qt, the only external library needed is GSL everything else is coded from the scratch. -
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...New project page: https://github.com/yesint/pteros New documentation page: https://yesint.github.io/pteros/ Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.
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PDBManip
PDBManip is a free program for editing PDB (Protein Data Bank) Files
PDBManip is a free program for editing and manipulating PDB (Protein Data Bank) files. It has a graphical user interface and it is provided as an executable file for running on Windows® operating systems. There is a bunch of free programs on the internet for the same purpose. What discriminate between PDBManip and those programs is that PDBManip uses AngelScript language which is very similar to C/C++ language, to write scripts to do our editing tasks. -
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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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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
...The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/
