Search Results for "console windows"
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Showing 41 open source projects for "console windows"
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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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) -... -
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JSmol
JavaScript-Based Molecular Viewer From Jmol
JSmol is the extension of the Java-based molecular visualization applet Jmol (jmol.sourceforge.net) as an HTML5 JavaScript-only web app. It can be used in conjunction with the Java applet to provide an alternative to Java when the platform does not support that (iPhone/iPad) or does not support applets (Android). Used in conjunction with the Jmol JavaScript Object (http://wiki.jmol.org/index.php/Jmol_Javascript_Object), JSmol seamlessly offers alternatives to Java on these non-Applet... -
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GenForm
Generation of molecular formulas by high-resolution MS and MS/MS data
This is an open source implementation of molecular formula calculation by high resolution MS and MS/MS data as described in M. Meringer, S. Reinker, J. Zhang, A. Muller: MS/MS Data Improves Automated Determination of Molecular Formulas by Mass Spectrometry. MATCH Commun. Math. Comput. Chem. 65, 259-290, 2011. The software user manual is available here: https://www.researchgate.net/publication/307964728_MOLGEN-MSMS_Software_User_Manual Example MS and MS/MS data files for GenForm can... -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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CoolingPower
Print Steam Tables; Plot diagrams and cycles from equations of state
CoolingPower is NOT in a condition for use at this time. A couple of bugs have been discovered that severely affect the calculation accuracy. While I troubleshoot, use at your own risk. Once completed, CoolingPower will have the capability to plot diagrams of thermodynamic properties, construct Steam Tables, and plot thermodynamic cycles. Initial fluid will be water/steam, but functionality will extend to include a variety of working fluids. CoolingPower operates in GUI format and, for... -
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Pysces
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis. -
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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... -
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orthos
Simulation of EPR spectra of nitroxide biradicals
The program Orthos is developed to performed simulation (including nonlinear least-squares fitting) of EPR spectra of nitroxide biradicals. The program capabilities include simulation of rigid-limit and slow-motional spectra, of both isotropic and aligned samples. The spectra of multiple paramagnetic species, both bi- and monoradicals can be modeled. NB: Please note that now (as of Nov 2016) the distribution is being updated so that to improve reliability, OS-universality, and the quality... -
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Mathpad
A Python based command line math utility.
Mathpad is a command line utility. It will later have a GUI, but not at this time. -
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LipidWrapper
Create lipid-bilayer models of arbitrary geometry.
LATEST VERSION NOW LOCATED AT http://git.durrantlab.com/jdurrant/lipidwrapper As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro,... -
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WISP
Weighted Implementation of Suboptimal Paths (WISP)
UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path... -
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Hy3S uses advanced MPI parallelized hybrid stochastic simulation methods to quickly compute the dynamics of biochemical networks with thousands of species/reactions. Many features included (see Home Page). An easy-to-use GUI (Matlab req) is included.
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nwhess2freq
Calculates frequencies/modes from an nwchem generated hessian
This is a simple Octave script which calculates the frequencies/normal modes from an nwchem generated hessian matrix. The advantage of having a separate script for this is that you can use the same hessian to calculate frequencies for different isotopic substitutions i.e. you only have to run one nwchem calculation. The script is finished in its current form in the sense that it is feature complete. Feel free to amend, translate, copy, steal etc. See the README in the code repository... -
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mobcalPARSER
A cross-platform interface for the *.mfj file format.
mobcalPARSER is a command line based PERL frontend/interface for MOBCAL with limited wrapper functionality. "MOBCAL - A Program to Calculate Mobilities" is available from Professor Martin F. Jarrold's webpage http://www.indiana.edu/~nano/software.html. -
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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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UPDATE: The latest version of NNScore1 can be found here: http://git.durrantlab.com/jdurrant/nnscore1 The latest version of NNScore2 can be found here: http://git.durrantlab.com/jdurrant/nnscore2 ================ NNScore is a scoring function for characterizing the potency of receptor-ligand complexes. It is based on neural networks, computational models that simulate the microscopic organization of the brain.
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A Library for Chemical Formula Parsing. Syntax only, no semantics. No external library dependencies, namespace std:: only. Uses UnitTest++ during development to ensure consistent behaviour.
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aufbau
"aufbau" is a program that creates electron configuration of an atom.
This is version 1.2 of "aufbau". Its purpose is to create electron configuration of an atom, molecule or ion, following, of course, the "Aufbau" Principle. You can subscribe to the project's mailing lit here: https://lists.sourceforge.net/lists/listinfo/atomic-aufbau-news -
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The repository has been moved to: https://github.com/wojdyr/fityk. Fityk is nonlinear curve-fitting and data analysis software. It is specialized in fitting peaks (bell-shaped functions like Gaussian, Loretzian, Pearson7, Voigt) to experimental data.
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OpenThermo
Statistical thermodynamics package
OpenThermo is a program package for statistical thermodynamics computations beyond rigid rotor - harmonic oscillator approximation -
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A reactor solver which uses stochastic particle methods to model particle population balances. This code is developed by the CoMo group in the chemical engineering department at the university of Cambridge (como.cheng.cam.ac.uk).
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Java Data Processing Project aims to manipulate text file containing scientific data such as time/intensity scan or spectrum. Jdpp provide large flexibility to read all possible time duration and date format. It is originally design to treat MS data.
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A matlab/octave based reaction transport model describing microbially mediated isotope fractionation processes in porous media.
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A univariate and multivariate analysis UI. This project is no longer under development. Please use as you wish.
