Search Results for "linux command" - Page 2
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Showing 77 open source projects for "linux command"
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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,... -
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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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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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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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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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Larch: Data Analysis for X-ray Spectra
Data Processing and Analysis for X-ray Spectroscopy and More
Larch is a scientific data processing language that is designed to be easy to use for novices and complete enough for advanced data processing and analysis. Larch provides a wide range of functionality for dealing with arrays of scientific data, and basic tools to make it easy to use and organize complex data. Larch has been primarily developed for dealing with x-ray spectroscopic and scattering data, especially the kind of data collected at modern synchrotrons and x-ray sources. ... -
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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... -
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Computing with units
Calculator that takes care of measurement units.
Java program for computations with values expressed in terms of physical or other units. Supports complicated mathematical expressions and user-defined functions. Invoked from scripts, line command, or as GUI. Extensive units data base. -
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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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AutoMap
AutoMap is a tool for structural biology and drug design.
AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes. -
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SunlightDPD
Open source codes related to dissipative particle dynamics
SunlightDPD provides a home for open source codes related to the dissipative particle dynamics (DPD) simulation method. Currently the file release contains the HNC integral equation code. -
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MPQC
Massively Parallel Quantum Chemistry program
The Massively Parallel Quantum Chemistry program, MPQC, computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. -
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RASPnmr
Protein NMR backbone resonance assignment
RASP uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. This enables rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins. RASP takes as input spin systems assembled on the basis of an arbitrary set of conventional triple-resonance NMR experiments. Uniquely, RASP is capable of extensive assignments even in the abscence of... -
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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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nwbas2ecce
nwbas2ecce converts nwchem basis set files to the ECCE format
The basis sets included with ECCE have -- as far as I can tell -- not been updated for many years. In addition, many of the newer basis sets that come with nwchem aren't included, such as the def2- series. nwbas2ecce is a python script that aims to automate as much as possible of the conversion process of a nwchem basis set file into the files necessary for ECCE to included it in the basis set tool. The process isn't completely automatic, but I also believe that it shouldn't be to... -
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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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The pySpec project is a set of data analysis routines written in python for analysis of x-ray diffraction data produced by the SPEC X-Ray Diffraction and Data Acquisition software. This repo has moved to : https://github.com/stuwilkins/pyspec
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RMol : SD/Molfile information in R
RMol: Transforming SD/Molfile structure information into R Objects
RMol is an R script with a collection of functions to link information of SD/Molfile structure databases with powerful graph analysis packages in R. -
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A high-performance simulation package for sampling the chemical and reaction-diffusion master equations. Primarily intended for running stochastic simulations of microbial cells.
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We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.
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The aim of our project is to develop a simulation system to calculate the measurement uncertainty corresponding to the 'Guide To The Expression Of Uncertainty In Measurement' (GUM).
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Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.
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Methods and testing of methods for automatic analysis of in situ cyclic voltammetry data. This, at least initially, is the code from my masters thesis, which was done as a contribution to a larger project called Aevum. Aevum is being developed at t
