Search Results for "output"
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Showing 26 open source projects for "output"
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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. A rich scripting language and a well-developed web API allow easy customization of the user interface. ... -
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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. HBAT 2 is migrated from PERL to Python. Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal... -
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ShelXle
ShelXle is a Qt GUI for SHELXL
ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps. See J. Appl. Cryst. (2011). 44, 1281–1284. for details. -
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Software and codes created in "Laboratorio de Química Computacional" of "Facultad de Ciencias y Tecnología" of "Universidad de Carabobo"
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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 using gaussian cube files (also color-mapped surfaces according to potential) - schematic representation of vibrations using arrows - user-defined arrows representing vectorial properties - measuring gauges - combinations of these features (more orbitals together, orbitals and arrows together etc.) ... -
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VASPMO
Visualization of wavefunctions calculated by VASP (New release: v0.41)
VASPMO aims at visualizing wavefunctions (or molecular orbitals) from VASP calculations. It reads VASP's output files PROCAR and CONTCAR, and exports an *.out file in Gaussian's output format, which can be visualized by many popular visualization tools, such as JMol, Molekel, Chemcraft, Gabedit and Molden, etc. These tools can further generate *.cube files, which can be visualized by an even wider range of softwares. 读入VASP计算得到的PROCAR和CONTCAR文件，输出Gaussian结果文件。 -
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qmol
A simple molecular weight calculator
qmol is a simple molecular weight calculator, available for Linux and Windows, derived from Tomislav Gountchev's KMol. You can enter a formula, (e.g. CH3(CH2)2OH) and get its molecular weight (60.0959 g/mol) and its elemental composition (C3H8O: C 59.96; H 13.42; O 26.62 %). See the features list below for more details or consult the wiki page: https://sourceforge.net/p/qmol/wiki/Home/. For Windows binary and source code see the files section:... -
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QMForge reads output from various quantum mechanical calculations and provides tools for analyzing these results. Specifically, population (Mulliken and C-squared), fragment, and charge decomposition analyses are available. See https://qmforge.net for more info.
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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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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. The program has been published in Computer Physics Communications 182 (2011) 1183–1186. ... -
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In silico fragmentation evaluation
Comparative analysis of open source in silico fragmentation tools
We compared the performance of four publicly available in silico fragmentation tools that help in structure elucidation of metabolites (MetFrag, CFM-ID, MAGMa+ and MS-FINDER). Using the output of these tools we developed a voting/consensus model which is combining, re-ordering and re-ranking the candidates file and increases the correct hit percentage. We used 520 compounds from the 2016 CASMI challenge with 312 compounds for training and 208 compounds for validation purposes. -
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E-Plater
The firmware for the PIC18F2XK22 to do pulsed electroplating
"E-plater" is a device that was specially developed by Engenharia Caseira (engenhariacaseira.com.br) to make pulsed and reversed pulsed electroplating (PED). Research shows that molecules on the surface of electrically deposited material using direct current are sometimes disorganized which can result in uneven surface and color. It is possible to control the composition and thickness of the deposited layer in an atomic order by configuring the amplitude and width of a pulse. The... -
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orbkit (Moved to Github)
A Modular Python Toolbox for Cross-Platform Post-Processing of Quantum
PLEASE NOTE ORBKIT HAS BEEN MOVED TO https://github.com/orbkit/orbkit orbkit is a parallel Python program package for post-processing wave function data extracted from output files of MOLPRO (Molden File Format), TURBOMOLE (AOMix file format), GAMESS-US, PROAIMS/AIMPAC (wfn/wfx file format), and Gaussian (Output File and Formatted Checkpoint File) output files. Futhermore, an interface to cclib, a parser for quantum chemical logfiles, is provided. If you use orbkit in your work, please cite it as follows: Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay, Beate Paulus, Hans-Christian Hege, and Axel Schild, "ORBKIT: A Modular Python Toolbox for Cross-Platform Postprocessing of Quantum Chemical Wavefunction Data", J. ... -
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ConvertMAS
ConvertMAS converts Chemical File Formats mol, mol2 and sdf.
...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. Various online tools are available for conversion of Chemical file formats; but ConvertMAS mainly works on mol, mol2 and sdf effectively. -
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binana
BINANA (BINding ANAlyzer) is a python-implemented algorithm for analyz
...As input, BINANA accepts receptor and ligand files in the PDBQT format. PDBQT files can be generated from the more common PDB file format using the free converter provided with AutoDockTools. As output, BINANA describes ligand binding. NOTE: The latest version of BINANA is now hosted at http://git.durrantlab.com/jdurrant/binana . Versions on SourceForge are not up to date. -
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ccwatcher
A computational chemistry monitoring, parsing and plotting application
ccwatcher monitors the progress of computational chemistry calculations during runtime. It has both a GUI and a "Command Line Interface" to which it parses important output and plots SCF energies. -
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...Please use the flowing pages for up-to-date information about cclib: Repository (source code, tracker) - https://github.com/cclib/cclib Online documentation - http://cclib.github.io/ cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, Firefly, GAMESS, GAMESS-UK, Gaussian, Jaguar and ORCA.
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WebChemViewer
A simple program for sharing molecular structures with associated data
Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed in any modern web browser, on any operating system (including mobile), without requiring the installation of additional software. The output can also be easily incorporated into existing web pages. WebChem Viewer is released under the FreeBSD license. It was created by Jacob Durrant, a post-doc in the lab of Rommie E. ... -
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NBO Analyzer
Analyze output of NBO computations
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pyisocalc
Isotopic pattern calculator in python 2.x
This is an isotopic pattern calculator written in python. It depends on re, sys, numpy, operator, itertools, and matplotlib. -
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This is a continuation of the OpenGamma project by Marcelo Maduar with his permission. It is for gamma ray (radiation) spectroscopy and isotope identification. It accepts output files from several types of MCA's. Real time input will be added.
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Datagam is a tool for extracting data from output or punch files produced by GAMESS(US) or FireFly (old name PC GAMESS) packages. Mac GUI wrapper also available. Upstream version of the project goes to the launchpad. Only final versions of the source code and compiled binars will be available from this domain.
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Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output.
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