DebiChem Project
Summary
Input preparation and output processing
DebiChem input preparation and output processing

This metapackage will install graphical frontends and input generators/output processors for computational chemistry packages which might be useful for chemists.

Description

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DebiChem Input preparation and output processing packages

Official Debian packages with high relevance

Ase
Atomic Simulation Environment
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ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, stearing, and analyzing atomic simulations. ASE is part of CAMPOS, the CAMP Open Source project.

ASE contains Python interfaces to several different electronic structure codes including Abinit, Asap, Dacapo, Elk, GPAW and SIESTA.

This package provides the executable scripts.

Avogadro
Molecular Graphics and Modelling System
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Avogadro is a molecular graphics and modelling system targeted at molecules and biomolecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder.

Features include:

  • Molecular modeller with automatic force-field based geometry optimization
  • Molecular Mechanics including constraints and conformer searches
  • Visualization of molecular orbitals and general isosurfaces
  • Visualization of vibrations and plotting of vibrational spectra
  • Support for crystallographic unit cells
  • Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry packages
  • Flexible plugin architecture and Python scripting

File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as Gaussian, GAMESS and MOLPRO output.

Please cite: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison: Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. (eprint) J. Cheminf. 4:17 (2012)
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Ballview
free molecular modeling and molecular graphics tool
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BALLView provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features.

BALLView can be considered a graphical user interface on the basis of BALL (Biochemical Algorithms Library) with a focus on the most common demands of protein chemists and biophysicists in particular. It is developed in the groups of Hans-Peter Lenhof (Saarland University, Saarbruecken, Germany) and Oliver Kohlbacher (University of Tuebingen, Germany). BALL is an application framework in C++ that has been specifically designed for rapid software development in Molecular Modeling and Computational Molecular Biology. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

Please cite: Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof and Oliver Kohlbacher: BALLView: a tool for research and education in molecular modeling. (PubMed,eprint) Bioinformatics 22(3):365-366 (2006)
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Cclib
Parsers and algorithms for computational chemistry
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A Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner.

This package contains helper scripts for end users.

If you are looking for the unit tests and data files managed by cclib, they are distributed separately as in non-free package cclib-data.

Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. (eprint) J. Comp. Chem. 29(5):839-845 (2008)
Gabedit
graphical user interface to Ab Initio packages
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Gabedit is a graphical user interface to computational chemistry packages like:

  • MPQC
  • GAMESS-US
  • Gaussian
  • Molcas
  • Molpro
  • Q-Chem

These Ab Initio software packages might run locally or on a remote server (supporting FTP, RSH and SSH). Gabedit can display a variety of calculation results including most major molecular file formats. The advanced "Molecule Builder" allows one to rapidly sketch in molecules and examine them in 3D. Graphics can further be exported to various formats, including animations.

Please cite: Abdul-Rahman Allouche: Gabedit - A graphical user interface for computational chemistry softwares. (eprint) J. Comp. Chem. 32:174-182 (2011)
Gausssum
parse and display Gaussian, GAMESS, and etc's output
Maintainer: Debichem Team
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GaussSum parses the output files of ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar and PC GAMESS calculations to extract useful information.

GaussSum uses GNUPlot to display the progress of geometry optimisations, density of states spectrum, UV-VIS spectra, IR spectra, Raman spectra, and electron density difference maps. It can also display all lines containing an arbitrary phrase and more.

Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. J. Comp. Chem. 29(5):839-845 (2008)
Jmol
Molecular Viewer
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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.

File formats read by Jmol include PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton and VASP.

Please cite: A. Herráez: Biomolecules in the computer: Jmol to the rescue. (PubMed,eprint) Biochem Mol Biol Educ. 34(4):255-261 (2006)
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P4vasp
visualization suite for the Vienna Ab-initio Simulation Package (VASP)
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p4VASP is a visualization suite for the Vienna Ab-initio Simulation Package (VASP). It contains an extensible GUI framework, that can be used to view material structure, density of states, band-structure and more.

It provides a Python library, that greatly simplifies the process of manipulation of the VASP input and output data in Python scripts. P4vasp utilizes also many handy routines and objects e.g. for creating 2D graphs, data storage (xml,DOM) or simple matrix library.

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Travis
trajectory analyzer and visualizer
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TRAVIS (Trajectory Analyzer and Visualizer) is a free tool for analyzing and visualizing trajectories from all kinds of Molecular Dynamics or Monte Carlo simulations. The aim of TRAVIS is to collect as many analyses as possible in one program, creating a powerful tool and making it unnecessary to use many different programs for evaluating simulations. This should greatly rationalize and simplify the workflow of analyzing trajectories. The following analysis functions are available:

Static (time independent) Functions:

  • Radial, Angular, Dihedreal or Combined Distribution Function
  • Point-Plane or Point-Line Distance Distribution
  • Plane Projection Distribution
  • Fixed Plane Density Profile
  • Density, Spatial or Dipole Distribution Function

Dynamic (time dependent) Functions:

  • Velocity Distribution Function
  • Mean Square Displacement / Diffusion Coefficients
  • Velocity Autocorrelation Functions
  • Vector Reorientation Dynamics
  • Van Hove Correlation Function
  • Aggregation Functions (DACF, DLDF, DDisp)

Spectroscopic Functions:

  • Calculate Power Spectrum
  • Calculate IR Spectrum
  • Calculate Raman Spectrum

TRAVIS can read trajectory files in XYZ, PDB, LAMMPS or DLPOLY format.

Please cite: Martin Brehm and Barbara Kirchner: TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories. (eprint) J. Chem. Inf. Model. 51(8):2007-2023 (2011)
Viewmol
graphical front end for computational chemistry programs
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Viewmol is able to graphically aid in the generation of molecular structures for computations and to visualize their results.

At present Viewmol includes input filters for Discover, DMol3, Gamess, Gaussian 9x/03, Gulp, Mopac, PQS, Turbomole, and Vamp outputs as well as for PDB files. Structures can be saved as Accelrys' car-files, MDL files, and Turbomole coordinate files. Viewmol can generate input files for Gaussian 9x/03. Viewmol's file format has been added to OpenBabel so that OpenBabel can serve as an input as well as an output filter for coordinates.

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Xcrysden
Crystalline and Molecular Structure Visualizer
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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.

XCrySDen allows for real-time capture of display. Several movie encoders are supported, in particular for Animated-GIF convert (imagemagick), gifsicle, or whirlgif are necessary. For AVI/MPEG mencoder or ppmtompeg (netpbm) is required. For window dumps either imagemagick or xwd (x11-apps) needs to be present.

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