Debian Science Project
Summary
Chemistry
Debian Science Chemistry packages

This metapackage will install Debian Science packages related to Chemistry. You might also be interested in the field::chemistry debtag and, depending on your focus, in the education-chemistry metapackage.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Chemistry packages

Official Debian packages with high relevance

Adun.app
Molecular Simulator for GNUstep (GUI)
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Adun is a biomolecular simulator that also includes data management and analysis capabilities. It was developed at the Computational Biophysics and Biochemistry Laboratory, a part of the Research Unit on Biomedical Informatics of the UPF.

This package contains UL, the Adun GUI frontend.

Please cite: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa: Framework-based design of a new all-purpose molecular simulation application: The Adun simulator. (PubMed) J. Comp. Chem. 26(15):1647-1659 (2005)
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Apbs
Adaptive Poisson Boltzmann Solver
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APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:

  • simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics,
  • implicit solvent molecular dynamics of biomolecules ,
  • solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design,
  • and biomolecular titration studies.

APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms.

Please cite: Nathan A. Baker, David Sept, Simpson Joseph, Michael J. Holst and J. Andrew McCammon: Electrostatics of nanosystems: application to microtubules and the ribosome. (eprint) Proc. Natl. Acad. Sci. 98(18):10037-10041 (2001)
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. J. Cheminf. 4:17 (2012)
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Bkchem
Chemical structures editor
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BKchem is a free chemical drawing program, which is written in Python.

Some of the features, you can expect:

  • Drawing (bond-by-bond drawing; templates for common rings; expanding of common-groups; draws radicals, charges, arrows; color support ...)
  • Editing (unlimited undo and redo capabilities; aligning; scaling; rotation (2D, 3D) ...)
  • Export/Import (fully supported SVG-, OpenOffice.org-Draw-, EPS-export; basic support for CML1 and CML2 import and export)
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Bodr
Blue Obelisk Data Repository
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Common repository of chemical and physical facts that aim to increase interoperability between chemistry programs.

See DOI 10.1021/ci050400b.

Please cite: Peter Murray-Rust: The Blue Obelisk (eprint) CDK News 2(2):43-46 (2005)
Chemeq
Parser for chemical formula and equilibria
Maintainer: Georges Khaznadar
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chemeq is a basic standalone filter written in C language, flex and bison. It inputs strings like:

 2H2 + O2 ---> 2 H2O
then it outputs LaTeX code and messages about the equilibrium of a

chemical reaction.

 example:~/src$ echo "2H2 + O2 ---> 2 H2O" | chemeq -lc
 2\,H_{2}\,+\,O_{2}\,\rightarrow\,2\,H_{2}O
 OK
Chemical-mime-data
chemical MIME and file type support for desktops
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Chemical MIME type integration for KDE, GNOME and possibly ROX desktops, based on Henry Rzepa's list at http://www.ch.ic.ac.uk/chemime/. Support is granted for KDE 3.x, GNOME 2.x and freedesktop.org systems.

Chemical-structures
set of molecular structures in open formats
Maintainer: Georges Khaznadar ()
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hundreds of molecular structures, in the following classes: alcohols, aldehydes, alkanes, alkenes, amides, amines, amino_acids, aromatics, carboxylic_acids, esters, ethers, fatty_acids, haloalkanes, ketones, nitriles,nucleobases, water.

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Chemtool
chemical structures drawing program
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Chemtool is a GTK+ based 2D chemical structure editor for X11. It supports many bond styles, most forms of text needed for chemical typesetting and splines/arcs/curved arrows.

Drawings can be exported to MOL and PDB format, SVG or XFig format for further annotation, as a PiCTeX drawing, as a bitmap or as Postscript files (several of these through XFig's companion program transfig).

The package also contains a helper program, cht, to calculate sum formula and (exact) molecular weight from a chemtool drawing file. Cht can either be called directly by Chemtool or on the console.

Please cite: Matthias Brüstle: Chemtool - Moleküle zeichnen mit dem Pinguin. (eprint) Nachr. Chem. 49(11):1310-1313 (2001)
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Cp2k
Ab Initio Molecular Dynamics
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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-initio molecular dynamics (AIMD) simulations.

CP2K is optimized for the mixed Gaussian and Plane-Waves (GPW) method based on pseudopotentials, but is able to run all-electron or pure plane-wave/Gaussian calculations as well. Features include:

Ab-initio Electronic Structure Theory Methods using the QUICKSTEP module:

  • Density-Functional Theory (DFT) energies and forces
  • Hartree-Fock (HF) energies and forces
  • Moeller-Plesset 2nd order perturbation theory (MP2) energies and forces
  • Random Phase Approximation (RPA) energies
  • Gas phase or Periodic boundary conditions (PBC)
  • Basis sets include various standard Gaussian-Type Orbitals (GTOs), Pseudo- potential plane-waves (PW), and a mixed Gaussian and (augmented) plane wave approach (GPW/GAPW)
  • Norm-conserving, seperable Goedecker-Teter-Hutter (GTH) and non-linear core corrected (NLCC) pseudopotentials, or all-electron calculations
  • Local Density Approximation (LDA) XC functionals including SVWN3, SVWN5, PW92 and PADE
  • Gradient-corrected (GGA) XC functionals including BLYP, BP86, PW91, PBE and HCTH120 as well as the meta-GGA XC functional TPSS
  • Hybrid XC functionals with exact Hartree-Fock Exchange (HFX) including B3LYP, PBE0 and MCY3
  • Double-hybrid XC functionals including B2PLYP and B2GPPLYP
  • Additional XC functionals via LibXC
  • Dispersion corrections via DFT-D2 and DFT-D3 pair-potential models
  • Non-local van der Waals corrections for XC functionals including B88-vdW, PBE-vdW and B97X-D
  • DFT+U (Hubbard) correction
  • Density-Fitting for DFT via Bloechl or Density Derived Atomic Point Charges (DDAPC) charges, for HFX via Auxiliary Density Matrix Methods (ADMM) and for MP2/RPA via Resolution-of-identity (RI)
  • Sparse matrix and prescreening techniques for linear-scaling Kohn-Sham (KS) matrix computation
  • Orbital Transformation (OT) or Direct Inversion of the iterative subspace (DIIS) self-consistent field (SCF) minimizer
  • Local Resolution-of-Identity Projector Augmented Wave method (LRIGPW)
  • Absolutely Localized Molecular Orbitals SCF (ALMO-SCF) energies for linear scaling of molecular systems
  • Excited states via time-dependent density-functional perturbation theory (TDDFPT)

Ab-initio Molecular Dynamics:

  • Born-Oppenheimer Molecular Dynamics (BOMD)
  • Ehrenfest Molecular Dynamics (EMD)
  • PS extrapolation of initial wavefunction
  • Time-reversible Always Stable Predictor-Corrector (ASPC) integrator
  • Approximate Car-Parrinello like Langevin Born-Oppenheimer Molecular Dynamics (Second-Generation Car-Parrinello Molecular Dynamics)

Mixed quantum-classical (QM/MM) simulations:

  • Real-space multigrid approach for the evaluation of the Coulomb interactions between the QM and the MM part
  • Linear-scaling electrostatic coupling treating of periodic boundary conditions
  • Adaptive QM/MM

Further Features include:

  • Single-point energies, geometry optimizations and frequency calculations
  • Several nudged-elastic band (NEB) algorithms (B-NEB, IT-NEB, CI-NEB, D-NEB) for minimum energy path (MEP) calculations
  • Global optimization of geometries
  • Solvation via the Self-Consistent Continuum Solvation (SCCS) model
  • Semi-Empirical calculations including the AM1, RM1, PM3, MNDO, MNDO-d, PNNL and PM6 parametrizations, density-functional tight-binding (DFTB) and self-consistent-polarization tight-binding (SCP-TB), with or without periodic boundary conditions
  • Classical Molecular Dynamics (MD) simulations in microcanonical ensemble (NVE) or canonical ensmble (NVT) with Nose-Hover and canonical sampling through velocity rescaling (CSVR) thermostats
  • Metadynamics including well-tempered Metadynamics for Free Energy calculations
  • Classical Force-Field (MM) simulations
  • Monte-Carlo (MC) KS-DFT simulations
  • Static (e.g. spectra) and dynamical (e.g. diffusion) properties
  • ATOM code for pseudopotential generation
  • Integrated molecular basis set optimization

CP2K does not implement conventional Car-Parrinello Molecular Dynamics (CPMD).

Drawxtl
crystal structure viewer
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DRAWxtl reads a basic description of the crystal structure, which includes unit-cell parameters, space group, atomic coordinates, thermal parameters or a Fourier map, and outputs a geometry object that contains polyhedra, planes, lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fourier contours and the unit-cell boundary.

Four forms of graphics are produced:

  • an OpenGL window for immediate viewing
  • the Persistence of Vision Ray Tracer (POV-RAY) scene language for publication-quality drawings
  • the Virtual Reality Modeling Language (VRML) for dissemination across the Internet
  • a Postscript rendering of the OpenGL window for those who want high-quality output but do not have POV-RAY installed.

File formats DRAWxtl can read include CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS and WIEN2k.

Please cite: Larry W. Finger, Martin Kroeker and Brian H. Toby: DRAWxtl, an open-source computer program to produce crystal-structure drawings. (eprint) J. Appl. Cryst. 40:188-192 (2007)
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Easychem
Draw high-quality molecules and 2D chemical formulas
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EasyChem is a program that helps you creating high quality diagrams of molecules and 2D chemical formulas that can be exported to PDF, PS, LaTeX and fig.

EasyChem was originally developed to create diagrams for chemistry books and is now frequently used for this purpose in commercial and non-commercial chemistry-related books.

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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)
Galculator
scientific calculator
Maintainer: Dmitry Smirnov
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galculator is a scientific calculator. It supports different number bases (DEC/HEX/OCT/BIN) and angles bases (DEG/RAD/GRAD) and features a wide range of mathematical (basic arithmetic operations, trigonometric functions, etc) and other useful functions (memory, etc) at the moment. galculator can be used in algebraic mode as well as in Reverse Polish Notation (RPN).

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Gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
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The General Atomistic Modelling Graphic Interface (GAMGI) provides a graphical interface to build, view and analyze atomic structures. The program is aimed at the scientific community and provides a graphical interface to study atomic structures and to prepare images for presentations, and for teaching the atomic structure of matter.

The package is enhanced by the following packages: gamgi-data gamgi-doc
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Garlic
A visualization program for biomolecules
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Garlic is written for the investigation of membrane proteins. It may be used to visualize other proteins, as well as some geometric objects. This version of garlic recognizes PDB format version 2.1. Garlic may also be used to analyze protein sequences.

It only depends on the X libraries, no other libraries are needed.

Features include:

  • The slab position and thickness are visible in a small window.
  • Atomic bonds as well as atoms are treated as independent drawable objects.
  • The atomic and bond colors depend on position. Five mapping modes are available (as for slab).
  • Capable to display stereo image.
  • Capable to display other geometric objects, like membrane.
  • Atomic information is available for atom covered by the mouse pointer. No click required, just move the mouse pointer over the structure!
  • Capable to load more than one structure.
  • Capable to draw Ramachandran plot, helical wheel, Venn diagram, averaged hydrophobicity and hydrophobic moment plot.
  • The command prompt is available at the bottom of the main window. It is able to display one error message and one command string.
Please cite: Damir Zucic and Davor Juretic: Precise Annotation of Transmembrane Segments with Garlic - a Free Molecular Visualization Program (eprint) Croatica Chemica Acta 77(1-2):397-401 (2004)
Gausssum
parse and display Gaussian, GAMESS, and etc's output
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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)
Gchempaint
2D chemical structures editor for the GNOME2 desktop
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GChemPaint is an editor for 2D chemical structures with a multiple document interface. Drawn molecules can be searched at NIST Webbook and PubChem.

Gcrystal
lightweight crystal structures visualizer
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GNOME Crystal is a light model visualizer for crystal-structures. It is based on the GNOME Chemistry Utils and should display models of all sorts of crystal microscopic structures using OpenGL.

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Gcu-bin
GNOME chemistry utils (helper applications)
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The GNOME Chemistry Utils provide C++ classes and Gtk+-2 widgets related to chemistry. They will be used in future versions of both gcrystal and gchempaint.

This package provides 4 applications:

  • a molecular structures viewer (GChem3D)
  • a molar mass calculator (GChemCalc)
  • a periodic table of the elements (GChemTable)
  • a spectra viewer (GSpectrum)
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Gcu-plugin
GNOME chemistry utils (browser plugin)
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The GNOME Chemistry Utils provide C++ classes and Gtk+-2 widgets related to chemistry. They will be used in future versions of both gcrystal and gchempaint.

This package provides a browser plugin for Gecko-based browsers. It does not (yet) work with WebKit-based browsers.

Gdis
molecular and crystal model viewer
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A GTK+ based program for the display and manipulation of isolated molecules, periodic systems and crystalline habits. It is in development, but is nonetheless fairly functional. It has the following features:

  • Support for several file types (CIF, BIOSYM, XYZ, XTL, MARVIN, and GULP)
  • A simple molecular creation and manipulation tool
  • A dialogue for creating starting configurations for molecular dynamics simulations
  • Assorted tools for visualization (geometry information, region highlighting, etc.)
  • Animation of BIOSYM files (also rendered animations, see below)

GDIS also allows you to perform the following functions through other packages:

  • Model rendering (courtesy of POVRay)
  • Energy minimization (courtesy of GULP)
  • Morphology calculation (courtesy of cdd)
  • Space group processing (courtesy of SgInfo)
  • View the Periodic Table (courtesy of GPeriodic)
  • Load additional filetypes, such as PDB (courtesy of Babel)
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Gdpc
visualiser of molecular dynamic simulations
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gpdc is a graphical program for visualising output data from molecular dynamics simulations. It reads input in the standard xyz format, as well as other custom formats, and can output pictures of each frame in JPG or PNG format.

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Gelemental
Periodic Table viewer
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gElemental is a GTK+ periodic table viewer that provides detailed information about chemical elements.

It features a table view which allows the elements to be coloured thematically by several properties, a sortable list view and an element properties dialog, displaying a variety of information, including historical, thermodynamic, electrochemical, and crystallographic properties.

This package contains the main application.

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Ghemical
GNOME molecular modelling environment
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Ghemical is a computational chemistry software package written in C++. It has a graphical user interface and it supports both quantum- mechanics (semi-empirical) models and molecular mechanics models. Geometry optimization, molecular dynamics and a large set of visualization tools using OpenGL are currently available.

Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the package. The MPQC package is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**.

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Gperiodic
periodic table application
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GPeriodic is a small X/GTK+-based program which allows you to browse through a periodic table of chemical elements, and view somewhat detailed information on each of the elements. 118 elements are currently listed.

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Gromacs
Molecular dynamics simulator, with building and analysis tools
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GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers.

Please cite: Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. (eprint) J. Chem. Theory Comput. 4(3):435-447 (2008)
Jmol
Molecular Viewer
Maintainer: Debichem Team (Ximin Luo)
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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.

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Kalzium
periodic table and chemistry tools
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Kalzium is a full-featured chemistry application, including a Periodic Table of Elements, chemical reference, chemical equation solver, and 3D molecule viewer.

This package is part of the KDE education module.

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Katomic
atomix puzzle game
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KAtomic is a puzzle game in which the player slides atoms around the board to assemble a molecule.

This package is part of the KDE games module.

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Libcdk-java
Chemistry Development Kit (CDK) Java libraries
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The CDK is a library of Java classes used in computational and information chemistry and in bioinformatics. It includes renderers, file IO, SMILES generation/parsing, maximal common substructure algorithms, fingerprinting and much, much more.

Massxpert
transitional package
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This is a transitional package. It can safely be removed.

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Mmass
Mass spectrometry tool for proteomics
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mMass is a free mass spectrum viewer/analyzer in which the following proteomics-related tasks can be performed:

  • Open raw text, mzXML and mzData mass spectra;
  • Define peak lists;
  • Powerful mass spectrum viewer (zoom, cursor...);
  • Data recalibration;
  • Protein-only simulations;
  • Online Mascot searches.

The software can be easily extended by additional Python modules. This package contains the platform-independent parts of the software.

Please cite: Martin Strohalm, Daniel Kavan, Petr Novák, Michael Volný and Vladimír Havlíček: mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data. (PubMed,eprint) Analytical chemistry (ACS) 82(11):4648-4651 (2010)
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Mmass-modules
Mass spectrometry tool for proteomics - extension modules
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mMass is a free mass spectrum viewer/analyzer in which the following proteomics-related tasks can be performed:

  • Open raw text, mzXML and mzData mass spectra;
  • Define peak lists;
  • Powerful mass spectrum viewer (zoom, cursor...);
  • Data recalibration;
  • Protein-only simulations;
  • Online Mascot searches.

The software can be easily extended by additional Python modules. This package contains the platform-dependent parts of the software.

Please cite: Martin Strohalm, Daniel Kavan, Petr Novák, Michael Volný and Vladimír Havlíček: mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data. (PubMed,eprint) Analytical chemistry (ACS) 82(11):4648-4651 (2010)
Mopac7-bin
Semi-empirical Quantum Chemistry Library (binaries)
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MOPAC provides routines to solve the electronic structure of molecules on a semi-empirical level. Available methods include MNDO, MINDO/3, AM1 and PM3.

This package contains the MOPAC7 binaries.

Please cite: James J. P. Stewart: MOPAC: A semiempirical molecular orbital program. (eprint) J. Comput.-Aided Mol. Design 4(1):1-103 (1990)
Mpqc
Massively Parallel Quantum Chemistry Program
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MPQC is an ab-inito quantum chemistry program. It is especially designed to compute molecules in a highly parallelized fashion.

It can compute energies and gradients for the following methods:

  • Closed shell and general restricted open shell Hartree-Fock (HF)
  • Density Functional Theory (DFT)
  • Closed shell second-order Moeller-Plesset pertubation theory (MP2)

Additionally, it can compute energies for the following methods:

  • Open shell MP2 and closed shell explicitly correlated MP2 theory (MP2-R12)
  • Second order open shell pertubation theory (OPT2[2])
  • Z-averaged pertubation theory (ZAPT2)

It also includes an internal coordinate geometry optimizer.

MPQC is built upon the Scientific Computing Toolkit (SC).

Mpqc-support
Massively Parallel Quantum Chemistry Program (support tools)
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MPQC is an ab-inito quantum chemistry program. It is especially designed to compute molecules in a highly parallelized fashion.

This package includes Perl modules to parse the output, Emacs-modes to facilitate editing mpqc files and molrender, a program to output the molecules in OOGL-format.

Openbabel
Chemical toolbox utilities (cli)
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Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows one to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

  • Hydrogen addition and deletion
  • Support for Molecular Mechanics
  • Support for SMARTS molecular matching syntax
  • Automatic feature perception (rings, bonds, hybridization, aromaticity)
  • Flexible atom typer and perception of multiple bonds from atomic coordinates
  • Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package includes the following utilities:

  • babel: Convert between various chemical file formats
  • obenergy: Calculate the energy for a molecule
  • obminimize: Optimize the geometry, minimize the energy for a molecule
  • obgrep: Molecular search program using SMARTS pattern
  • obgen: Generate 3D coordinates for a molecule
  • obprop: Print standard molecular properties
  • obfit: Superimpose two molecules based on a pattern
  • obrotamer: Generate conformer/rotamer coordinates
  • obconformer: Generate low-energy conformers
  • obchiral: Print molecular chirality information
  • obrotate: Rotate dihedral angle of molecules in batch mode
  • obprobe: Create electrostatic probe grid
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Openfoam
Set of programs for Computational Fluid Dynamics (CFD). Binaries
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OpenFOAM is the leading free, open source software for computational fluid dynamics (CFD), owned by the OpenFOAM Foundation and distributed exclusively under the General Public Licence (GPL).

Package contains binaries.

Pdb2pqr
Preparation of protein structures for electrostatics calculations
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PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include:

  • Adding a limited number of missing heavy atoms to biomolecular structures
  • Determining side-chain pKas
  • Placing missing hydrogens
  • Optimizing the protein for favorable hydrogen bonding
  • Assigning charge and radius parameters from a variety of force fields

This package also includes PropKa, a tool to modify the protonation state of protein structures in the Protein Data Bank (PDB) format to match a given pKa value. It can also be used to refine NMR structures, which often yield inaccurate pKa values for some residues.

Please cite: Todd J Dolinsky, Paul Czodrowski, Hui Li, Jens E Nielsen, Jan H Jensen, Gerhard Klebe and Nathan A Baker: PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. (PubMed,eprint) Nucleic Acids Research 35:W522-5 (2007)
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Psi3
Quantum Chemical Program Suite
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PSI3 is an ab-initio quantum chemistry program. It is especially designed to accurately compute properties of small to medium molecules using highly correlated techniques.

It can compute energies and gradients for the following methods:

  • Closed shell and general restricted open shell Hartree-Fock (RHF/ROHF) (including analytical hessians for RHF)
  • Closed shell Moeller-Plesset pertubation theory (MP2)
  • Complete active space SCF (CASSCF)
  • Coupled-cluster singles doubles (CCSD)
  • Coupled-cluster singles doubles with pertubative triples (CCSD(T)) (only for unrestricted (UHF) reference wavefunctions)

Additionally, it can compute energies for the following methods:

  • Unrestricted open shell Hartree-Fock (UHF)
  • Closed/open shell Moeller-Plesset pertubation theory (MP2)
  • Closed shell explicitly correlated MP2 theory (MP2-R12) and spin-component scaled MP2 theory (SCS-MP2)
  • Multireference configuration-interaction (MRCI)
  • Coupled-cluster singles doubles with pertubative triples (CCSD(T))
  • Second/third-order approximate coupled-cluster singles doubles (CC2/CC3)
  • Multireference coupled-cluster singles doubles (MRCCSD)
  • Closed shell and general restricted open shell equation-of-motion coupled- cluster singles doubles (EOM-CCSD)

Further features include:

  • Flexible, modular and customizable input format
  • Excited state calculations with the CC2/CC3, EOM-CCSD, CASSCF, MRCI and MRCCSD methods
  • Internal coordinate geometry optimizer
  • Harmonic frequencies calculations
  • One-electron properties like dipole/quadrupole moments, natural orbitals, electrostatic potential, hyperfine coupling constants or spin density
  • Utilization of molecular point-group symmetry to increase efficiency
Please cite: T. Daniel Crawford, C. David Sherrill, Edward F. Valeev, Justin T. Fermann, Rollin A. King, Matthew L. Leininger, Shawn T. Brown, Curtis L. Janssen, Edward T. Seidl, Joseph P. Kenny and Wesley D. Allen: PSI3: An open-source Ab Initio electronic structure package. (eprint) J. Comp. Chem. 28(9):1610-1616 (2007)
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Pyfai
Fast Azimuthal Integration scripts
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PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis.

As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on "powder rings" of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D.

PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer.

Pymol
Molecular Graphics System
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PyMOL is a molecular graphics system targeted at medium to large biomolecules like proteins. It can generate high-quality publication-ready molecular graphics images and animations.

Features include:

  • Visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals
  • Molecular builder and sculptor
  • Internal raytracer and movie generator
  • Fully extensible and scriptable via a Python interface

File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps.

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Python-mmtk
molecular modeling toolkit
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The Molecular Modeling Toolkit (MMTK) is a library for molecular simulation applications. It provides the most common methods in molecular simulations (molecular dynamics, energy minimization, normal mode analysis) and several force fields used for biomolecules (Amber 94, Amber 99, several elastic network models). MMTK also serves as a code basis that can be easily extended and modified to deal with non-standard situations in molecular simulations.

Python-mzml
mzML mass spectrometric data parsing
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python-mzml is an extension to Python that offers:

  • easy access to mass spectrometry (MS) data that allows the rapid development of tools;
  • a very fast parser for mzML data, the standard in mass spectrometry data format;
  • a set of functions to compare or handle spectra.
Python-openbabel
Chemical toolbox library (python bindings)
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Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows one to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

  • Hydrogen addition and deletion
  • Support for Molecular Mechanics
  • Support for SMARTS molecular matching syntax
  • Automatic feature perception (rings, bonds, hybridization, aromaticity)
  • Flexible atom typer and perception of multiple bonds from atomic coordinates
  • Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package contains the Python binding.

Qutemol
interactive visualization of macromolecules
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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.

Qutemol uses advanced OpenGL techniques and might not work correctly with all video cards and drivers.

Features QuteMol offers include:

  • Real time ambient occlusion
  • Depth aware silhouette enhancement
  • Ball-and-stick, space-filling and liquorice visualization modes
  • High resolution antialiased snapshots for creating publication quality renderings
  • Automatic generation of animated gifs of rotating molecules for web page animations
  • Interactive rendering of macromolecules (>100k atoms)

QuteMol reads PDB files as input.

Please cite: Marco Tarini, Paolo Cignoni and Claudio Montani: Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization. (eprint) IEEE Transactions on Visualization and Computer Graphics 12(5):1237-1244 (2006)
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Rasmol
Visualize biological macromolecules
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RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

Supported input file formats include Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files.

This package installs two versions of RasMol, rasmol-gtk has a modern GTK-based user interface and rasmol-classic is the version with the old Xlib GUI.

The package is enhanced by the following packages: rasmol-doc
Please cite: Roger A. Sayle and E. James Milner-White: RasMol: Biomolecular graphics for all. (PubMed) Trends in Biochemical Sciences (TIBS) 20(9):374 (1995)
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Tandem-mass
mass spectrometry software for protein identification
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X! Tandem can match tandem mass spectra with peptide sequences, in a process that is commonly used to perform protein identification.

This software has a very simple, unsophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. The output file format is described at http://www.thegpm.org/docs/X_series_output_form.pdf.

Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found here. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used.

V-sim
Visualize atomic structures
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V_Sim visualizes atomic structures such as crystals, grain boundaries, molecules and so on (either in binary format, or in plain text format).

The rendering is done in pseudo-3D with spheres (atoms) or arrows (spins). The user can interact through many functions to choose the view, set the bindings, draw cutting planes, compute surfaces from scalar fields, duplicate nodes, measure geometry... Moreover V_Sim allows one to export the view as images in PNG, JPG, PDF (bitmap), SVG (scheme) and other formats. Some tools are also available to colorize atoms from data values or to animate on screen many position files.

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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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Xbs
3-d models and movies of molecules
Maintainer: Matthew Vernon
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xbs ball-and-sticks plotting program can create still and moving three dimensional models of molecules. X11 and PostScript output are available. Models can be rotated, scaled, etc. Various labeling, shading, lighting, coloring options are available.

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Xdrawchem
Chemical structures and reactions editor
Maintainer: Georges Khaznadar
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Xdrawchem is a 2D editor for chemical structures and reactions. It mirrors the abilities of the commercial ChemDraw suite and has file compatibility with it as well as other chemical formats through OpenBabel.

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Xmakemol-gl
program for visualizing atomic and molecular systems (OpenGL)
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XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.

Features include:

  • Animating multiple frame files
  • Interactive measurement of bond lengths, bond angles and torsion angles
  • Control over atom/bond sizes
  • Exporting to Xpm, Encapsulated PostScript and XYZ formats
  • Toggling the visibility of groups of atoms
  • Editing the positions of subsets of atoms

This is the OpenGL-enabled XMakemol package. The images are rendered using true 3D graphics primitives, and can be exported using the Xpm format; red/blue stereo images can also be produced. The OpenGL package provides more display options, along with better support for displaying vectors. Ellipses can also be rendered.

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Gdpc-examples
example files for the gdpc program
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gpdc is a graphical program for visualising output data from molecular dynamics simulations. It reads input in the standard xyz format, as well as other custom formats, and can output pictures of each frame in JPG or PNG format.

This package contains examples to be used by the gdpc program.

Gromacs-mpich
Molecular dynamics sim, binaries for MPICH parallelization
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GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers.

This package contains only the core simulation engine with parallel support using the MPICH (v3) interface. It is suitable for nodes of a processing cluster, or for multiprocessor machines.

Please cite: Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. (eprint) J. Chem. Theory Comput. 4(3):435-447 (2008)
Gromacs-openmpi
Molecular dynamics sim, binaries for OpenMPI parallelization
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GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers.

This package contains only the core simulation engine with parallel support using the OpenMPI interface. It is suitable for nodes of a processing cluster, or for multiprocessor machines.

Please cite: Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. (eprint) J. Chem. Theory Comput. 4(3):435-447 (2008)
Python-mzml-doc
mzML mass spectrometric data parsing - documentation
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python-mzml is an extension to Python that offers:

  • easy access to mass spectrometry (MS) data that allows the rapid development of tools;
  • a very fast parser for mzML data, the standard in mass spectrometry data format;
  • a set of functions to compare or handle spectra.

This package contains the documentation in PDF and HTML format, along with the text sources (process with sphinx).

Xmakemol
program for visualizing atomic and molecular systems
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XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.

Features include:

  • Animating multiple frame files
  • Interactive measurement of bond lengths, bond angles and torsion angles
  • Control over atom/bond sizes
  • Exporting to Xpm, Encapsulated PostScript and XYZ formats
  • Toggling the visibility of groups of atoms
  • Editing the positions of subsets of atoms
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Packaging has started and developers might try the packaging code in VCS

Fdmnes
calculates spectra of different spectroscopies
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FDMNES calculates the spectra of different spectroscopies related to the real or virtual absorption of x-ray in material. It gives the absorption cross sections of photons around the ionization edge, that is in the energy range of XANES in the EXAFS. The calculation is performed with all conditions of rectilinear or circular polarization. In the same way, it calculates the structure factors and intensities of anomalous or resonant diffraction spectra (DAFS or RXD). FDMNES also allows the comparison of the simulated spectra to experimental ones with the help of objective criteria.

Please cite: O. Bunău and Y. Joly: Self-consistent aspects of x-ray absorption calculations. (eprint) J. Phys.: Condens. Matter 21:345501 (2009)
Molden
processing program of molecular and electronic structure
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MOLDEN is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the MOLDEN Format. MOLDEN reads all the required information from the GAMESS / GAUSSIAN outputfile. MOLDEN is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. MOLDEN supports contour plots, 3-d grid plots with hidden lines and a combination of both. It can write a variety of graphics instructions; postscript, X, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. The X version of MOLDEN is also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files and lots of other formats. It also can animate reaction paths and molecular vibrations. It can calculate and display the true or Multipole Derived Electrostatic Potential and atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface. MOLDEN has a powerful Z-matrix editor which give full control over the geometry and allows you to build molecules from scratch, including polypeptides. MOLDEN was also submitted to the QCPE (QCPE619), allthough the X version is considerably running behind on the current one.

Molekel
Advanced Interactive 3D-Graphics for Molecular Sciences
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Molekel is an open-source multi-platform molecular visualization program.

Some of the features are:

  • Different methods to speed-up rendering of molecules with support for billboards and view-dependent level of detail techniques
  • Programmable shaders; standard shaders to enhance rendering quality, outline contours and perform sketch-like renderings are provided
  • Visualization of residues (ribbon or schematic)
  • Complete control over the generation of molecular surfaces (bounding box and resolution)
  • Visualization of the following surfaces:
  • Orbitals
  • Iso-surface from density matrix
  • Iso-surface from Gaussian cube grid data
  • SAS
  • SES
  • Van der Waals
  • Animation of molecular surfaces
  • Animation of vibrational modes
  • Export high resolution images for 300+ DPI printing
  • Export to PostScript and PDF
  • Export animation
  • Plane widget to visualize a scalar field: the plane can be freely moved in 3d space and the points on the plane surface will be colored according to the value of the scalar field: a cursor can be moved on the plane surface to show the exact value of the field at a specific point in space.

Unofficial packages built by somebody else

Tinker
Software Tools for Molecular Design
Responsible: LI Daobing
License: non-free

The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases.

The TINKER package includes a variety of novel algorithms such as a new distance geometry metrization method that has greater speed and better sampling than standard methods, Elber's reaction path methods, several of our Potential Smoothing and Search (PSS) methods for global optimization, an efficient potential surface scanning procedure, a flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, a selection of continuum solvation treatments including several variants of the generalized Born (GB/SA) model, an efficient truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, velocity Verlet stochastic dynamics, an improved spherical energy cutoff method, Particle Mesh Ewald summation for partial charges and regular Ewald for polarizable multipoles, a novel reaction field treatment of long range electrostatics, and more....

No known packages available but some record of interest (WNPP bug)

Libegad - wnpp
rational protein design library
Responsible: LI Daobing
License: LGPL
Debian package not available

The EGAD Library is a modular, object oriented approach to rational protein design. It is platform-independent, written in C++ and, most importantly, free. Its raison d'etre is to serve as a tool for building protein design applications. It can also be used as a test-bed for the comparison of different energy functions and minimization algorithms under the same physical model.

Citations of EGAD Library should reference the paper in the Journal of Computational Chemistry. doi:10.1002/jcc.20727

Libint - wnpp
Evaluate the integrals in modern atomic and molecular theory
Responsible: Daniel Leidert
License: GPL
Debian package not available

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).

Libint has been utilized to implement methods such as Hartree-Fock (HF) and Kohn-Sham density functional theory (KS DFT), second-order Moller-Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD) method, as well as explicitly correlated R12 methods. The following software packages use Libint:

Improves mpqc (#409025) and psi3.

No known packages available

Openchrom
process chromatographic and mass spectrometric data
License: EPL
Debian package not available

OpenChrom is an open source software for chromatography based on the Eclipse Rich Client Platform (RCP). Its focus is to handle mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files natively. OpenChrom is able to import binary and textual chromatographic data files, such as *.D chromatograms from Agilent Technologies or NetCDF. Moreover, it offers a nice graphical user interface and is available for various operating systems, e.g. Windows, Linux, Solaris and Mac OSX. A basis set of methods to detect baselines, peaks and to integrate peaks in a chromatogram are implemented. Preprocessing steps, e.g. to remove certain mass fragments (m/z) such as nitrogen (28) or water (18), are supported by applying filter on the chromatogram or mass spectrum. Extensions are welcome, as OpenChrom is open source and uses a flexible approach, which allows others to implement their own methods, algorithms, filters, detectors or integrators. Therefore, OpenChrom shall be an efficiently system to process chromatographic and mass spectrometric data using an extensible and flexible plugin approach.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 203532