Search Results for "small linux"

BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis...

mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.

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.) ...

We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and...

hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.

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.

This project aims to provide a set of routines to easily read in and manipulate the output of the Heidelberg MCTDH code. The goal is to enable a new user to quickly get started with writing custom analysis programs. Also, it should enable more experienced users (== us) to write small, clean, and testable analysis programs, something that seems incompatible with the Fortran-77 code of the Heidelberg MCTDH package.

OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments. The details can be found in the original publication "OpenGrowth: an automated and rational algorithm for finding new protein ligands" (J. Med. Chem., http://dx.doi.org/10.1021/acs.jmedchem.5b00886). To use OpenGrowth, you will need OpenGrowth_1.0.zip and Resources_1.0.2.zip that can be found by clicking on the Files menu in the horizontal bar at the top...

Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS...

This software searches the potential energy surface of small to medium size atomic systems for global minima using quantum ab initio techniques. It performs bond rotations and molecule translations and rotations on a Linux cluster with MPI.

The Fortran program MOLLY generates atomic positions in a molecule from those of a small number of prototype atoms and the molecule's point symmetry. It is intended as a time-saving aid in preparing input data for computational physics software.

A small java API library for running the MM3 molecular mechanics package from within a java environment. It does not include MM3, nor implement MM3. The MM3 binaries have to be available on the user system.

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

MCDL is a small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation. Features include accurate structure diagram generation, and Kekule chemical structure creation from aromatic bond list.

This project is intended to perform Monte-Carlo-Simulations to calculate small clusters (2 to 13 atoms) of the rare gas "argon".

md-utils is a set of command line tools written in C designed to perform certain operations and analysis on the molecular dynamics data. The supported operations involve trajectory coordinate transformation to the COM system, Cartesian coordinate transformation to selected internal coordinates and to projected normal mode coordinates, trajectory merging, selecting subsets of trajectory frames, selecting subsets of atoms, permuting atoms, etc. Analysis tools involve 1D, 2D and 3D data...