5 May 2013 mbanck   » (Journeyer)

Debian 7.0 "wheezy" has been released this weekend!

Quite a few new Debichem packages are now available in a stable Debian release for the first time:

  • Ab-Initio Quantum Chemistry Packages:

    • ACES III
      ACESIII is an electronic structure calculation program with a focus on correlated methods. It is the parallel successor to ACESII, employing the Super Instruction Assembly Language (SIAL) as parallelization framework.
    • CP2K
      CP2K is a program to perform simulations of solid state, liquid, molecular and biological systems. It is especially aimed at massively parallel and linear scaling electronic structure methods and state-of-the-art ab-inito molecular dynamics (AIMD) simulations.
    • NWChem
      NWCHem is a computational chemistry program package. It provides methods which are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
    • Quantum ESPRESSO
      Quantum ESPRESSO (formerly known as PWscf) is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving, ultrasoft, and PAW).

  • Cheminformatics Toolkits:

    • Cinfony
      Cinfoy provides a common Python interface to various cheminformatics toolkits. This makes it possible to use the complementary features of cheminformatics toolktis using a common interface. If functionality is provided by more than one toolkit, the Cinfony user can choose the implementation they prefer.
    • Indigo
      Indigo is a C++ based organic chemistry and cheminformatics software environment.
    • RDKit
      RDKit is a Python/C++ based cheminformatics and machine-learning software environment.

  • Other Cheminformatics packages:

    • chemfp
      Chem-fingerprints is a set of formats and related tools for the storage, exchange, and search of cheminformatics fingerprint data sets.
    • fmcs
      Fcms finds the maximum common substructure (MCS) of a group (or cluster) of chemical structures and report the result as a SMARTS string.
    • Opsin
      OPSIN (Open Parser for Systematic IUPAC Nomenclature) converts IUPAC compound names to semantic chemical information and outputs a structure either as as CML (Chemical Markup Language), SMILES, or InChI.

  • Visualization Packages:

    • Jmol
      Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. It includes with features for chemicals, crystals, materials and biomolecules. Jmol might be useful for students, educators, and researchers in chemistry and biochemistry.
    • Qutemol
      QuteMol is an interactive, high quality molecular visualization system. It exploits the current GPU capabilities through OpenGL shaders to offer an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.
    • ShelXle
      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.
    • XCrySDen
      XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It can run on most UNIX platforms, without any special hardware requirements.

  • Data Parsing Packages:

    • cclib
      cclib is a Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner.
    • JGromacs
      JGromacs is a Java library designed to facilitate the development of cross-platform analysis applications for Molecular Dynamics (MD) simulations. The package contains parsers for file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages.

  • Development Libraries:

    • libint
      The libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. The idea of the library is to let computer write optimized code for computing such integrals. There are two primary advantages to this: much less human effort is required to write code for computing new integrals, and code can be optimized specifically for a particular computer architecture (e.g., vector processor).

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