Search Results for "console command"
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Showing 17 open source projects for "console command"
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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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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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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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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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MolTPC
MolTPC provides a solution for fully automatic tautomer enumeration.
Besides all their conformational degrees of freedom, drug-like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection of... -
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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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psicode
An open-source quantum chemistry program package
PSI is an open-source program for computing molecular properties using high-accuracy, ab initio, quantum mechanical models. -
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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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Starch CLD fit
Least-squares fit of amylopectin chain-length distribution
This FORTRAN program package finds the parameters involved in amylopectin chain-length distribution (CLD) biosynthesis by fitting experimental CLD data to a model which incorporates the underlying starch biosynthesis. The amylopectin CLD biosynthesis model used by this program is explained in the article “A Parameterized Model of Amylopectin Synthesis provides key insights into the Synthesis of Granular Starch”, by Alex Chi Wu, Matthew K. Morell and Robert G. Gilbert. The downloadable... -
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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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Wio-gpc is a command line driven perl application designed for polymers molecular weight calculations based on chromatographic data. Results of GPC, SEC or GFC analysis can be converted to Mn, Mw and molecular weight distributions (MWD).
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A family of programs for building coarse-grained models (eg. of macromolecules), manipulating them (geometrical transformations and more) and calculating their X-ray scattering patterns (1D and 2D too). Uses PVM for parallelization.
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