Search Results for "sdf"
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Showing 44 open source projects for "sdf"
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SDF Merger
Desktop application for merging multiple SDF files into a single SDF
SDF Merger: A Desktop and Web Tool for Merging Chemical Structure Data Files (v1.1). Zenodo. https://doi.org/10.5281/zenodo.18291398 -
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MolecularGraph.jl
Graph-based molecule modeling toolkit for cheminformatics
MolecularGraph.jl is a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia. -
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Scribble Deluxe
Efficient, internationalized, text renderer for GameMaker
A modern text renderer for GameMaker 2023.8 by Juju Adams. Efficient, internationalized, multi-effects text renderer for GameMaker. Scribble Deluxe is a comprehensive text rendering library designed to replace GameMaker’s native draw_text() functions without adding unnecessary complexity. Scribble’s design should feel familiar and intuitive for GameMaker users. Scribble Deluxe supports all GameMaker export platforms, with the exception of HTML5. -
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LÖVR
Lua Virtual Reality engine
...Writen in C99 and scripted with LuaJIT, includes optimized single-pass stereo rendering. Out of the box you get fast stereo rendering, VR controllers, hand tracking, haptics, spatial audio, 3D physics, PBR materials, SDF fonts, multiplayer, and more. The entire engine is 1MB and runs on LuaJIT, the fastest JIT compiler round these parts. Projects are just folders with scripts and assets in them, organized however you want. -
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PyTorch3D
PyTorch3D is FAIR's library of reusable components for deep learning
...PyTorch3D also includes utilities for loading, transforming, and sampling 3D assets, so models can be trained end-to-end from 2D supervision or partial data. Its modular design allows easy extension—components like differentiable rasterizers, mesh blending, or signed distance field (SDF) modules can be swapped or combined to test new architectures quickly. -
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Chem-Parser
Molecule Sketcher and Immediate Parser to Excel, .SMI and 3D SDF
Chem-Parser is an intuitive and efficient utility designed to streamline the data curation process for QSAR (Quantitative Structure–Activity Relationship) modeling and cheminformatics workflows. This versatile tool allows users to draw chemical structures, parse multiple SMILES strings, and automatically populate a structured table with associated compound names and custom-defined value tags such as biological activity or physicochemical properties. By enabling rapid structure-to-data... -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us -... -
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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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TopoIndices
Calculator of topological indices of molecular graphs (from SDF file)
The first step was taken - the 118 topological indices (2D indices) of molecular graphs can be calculated. The description of topoindices is in the file topoindices.pdf (docs folder). For each index there is at least one literature reference. Several indices were not taken into account for this project: some of them are depending on parameters, some are generally not calculable in the real numbers (square roots of negative numbers). The BASIC code was written for JustBASIC (the free... -
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sdsorter
Easy manipulation of sdf molecular data files.
sdsorter provides convenient routines for manipulating the contents of sdf molecular data files based on the embedded sd tags. -
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dualword-chem
chemical viewer
chemical viewer written in C++ (Qt, RDKit) Source code: http://github.com/dualword/dualword-chem -
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SDF or Structures Data File is a file format developed by MDL to handle a list of molecular structures with associated properties. The SDF toolkit provides small tools to read and parse SDFs, filter, and add/remove properties.
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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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DeepSDF
Learning Continuous Signed Distance Functions for Shape Representation
DeepSDF is a deep learning framework for continuous 3D shape representation using Signed Distance Functions (SDFs), as presented in the CVPR 2019 paper DeepSDF: Learning Continuous Signed Distance Functions for Shape Representation by Park et al. The framework learns a continuous implicit function that maps 3D coordinates to their corresponding signed distances from object surfaces, allowing compact, high-fidelity shape modeling. Unlike traditional discrete voxel grids or meshes, DeepSDF... -
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CompactView
Viewer for Microsoft® SQL Server® CE database files (sdf).
CompactView is a viewer for Microsoft® SQL Server® Compact Edition (SQLCE) database files (sdf). This software requires Microsoft® .NET Framework 4.0 to operate. -
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Braile Sound
Program for Blind youth to learn their braille alphabet.
I have written the program in QB64 using keys sdf and jkl on a computer as done with a braille writter. it displays the dot pattern and letter useful for a sighted person. Now I am attempting to add sound for the blind person using eSpeak. However I get no sound when using FUNCTION WinExec (lpCmdLine AS STRING, BYVAL nCmdShow AS LONG) . -
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SDF Toolkit #1
Tools to manipulate SDF files
Toolkit #1 1. Duplicate removal & 2. Convert to Rows 1. Duplicate removal a. Drag in an SDF file. b. Choose one of the tags. c. Remove all the entries that have the same value in that tag (just leaving one). 2. Convert to Rows a. Drag in an SDF file. b. Choose as many of the tags as you want to convert to rows. c. Make a tab delimited file where each of the entries is transposed into a column. The output does not contain the structure information. -
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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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...These tools provide a Java and C API for actions called when parser rules are completed. It also provides Fortran interfaces to the OpenCL runtime (new). IMPORTANT NOTICE: The Open Fortran Project has switched to using a parser based on SDF (Syntax Definition Formalism). Please consider using our new work at https://github.com/OpenFortranProject/ofp-sdf. While the SDF parser is not as advanced as the ANTLR-based parser, it provides much more capabilities, including a term rewriting system for creating a Fortran AST (Abstract Syntax Tree) using Stratego/XT (see http://strategoxt.org) and other custom program transformations. ...
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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. It will generate output files in less time. ... -
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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 structure sketching tool, for use with various cheminformatics applications. Convenient to use and moderately sophisticated. Suitable for viewing, creating and editing MDL MOL files.
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Calculates Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. NP-likeness is a useful criterion to screen compound libraries and to design new lead compounds. Maven dependancy: <dependency> <groupId>uk.ac.ebi.cheminformatics</groupId> <artifactId>NP-Likeness</artifactId> <version>2.1</version> </dependency> Required repository: <repositories> ...
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