Debian Science Project
Summary
Chemistry
Pakiety z grupy Debian Science Chemistry

Metapakiet, który instaluje pakiety naukowe Debiana związane z chemią. Być może zainteresuje Cię również znacznik field::chemistry oraz, w zależności od osobistych zainteresowań, metapakiet education-chemistry.

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
Symulator molekularny do GNUstep-a (GUI)
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Adun jest symulatorem biomolekularnym, który umożliwia także zarządzanie danymi i ich analizę. Został stworzony przez Computational Biophysics and Biochemistry Laboratory (laboratorium obliczeń biofizycznych i biomedycznych), będące częścią Research Unit on Biomedical Informatics (jednostki badawczej nad informatyką biomedyczną) na UPF.

Pakiet zawiera UL, frontend z graficznym interfejsem użytkownika do symulatora Adun.

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.

This package contains the apbs program and utilities.

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)
atomes
atomic-scale 3D modeling toolbox
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Atomes is a tool box to analyze (physico-chemical properties calculations), visualize (atoms, bonds, colormaps, measurements, coordination polyedra ...) create (crystal builder, molecular library, surface creation and passivation ...) 3D atomistic models. Atomes offers a workspace capable of handling many projects opened simultaneously. The different projects in the workspace can exchange data: analysis results, atomic coordinates... Atomes also provides an advanced input preparation system for further calculations using well known molecular dynamics codes: Classical MD: DLPOLY and LAMMPS

  • ab-initio MD: CPMD and CP2K
  • QM-MM MD: CPMD and CP2K To prepare the input files for these calculations is likely to be the key, and most complicated step towards MD simulations. Atomes offers a user-friendly assistant to help and guide the scientist step by step to achieve this crucial step.

This package provides the binaries.

The package is enhanced by the following packages: atomes-data
avogadro
System do molekularnego modelowania i wizualizacji
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Avogadro jest systemem do molekularnego modelowania oraz wizualizacji cząsteczek i biocząsteczek. Może wizualizować właściwości cząsteczek, takie jak orbitale lub potencjały elektrostatyczne, a ponadto udostępnia intuicyjne narzędzie do budowania cząsteczek.

Podstawowe możliwości:

  • molekularne modelowanie z automatyczną optymalizacją opartą na geometrii pól siłowych;
  • mechanika molekularna obejmująca wyszukiwanie według ograniczeń i konformacji;
  • wizualizacja orbitali molekularnych oraz ogólnych izopowierzchni;
  • wizualizacja drgań i kreślenie widm oscylacyjnych;
  • obsługa krystalograficznych komórek elementarnych;
  • generowanie wejścia dla pakietów chemii kwantowej Gaussian, GAMESS i MOLPRO;
  • elastyczna architektura wtyczek i skryptów Pythona.

Avogadro odczytuje formaty plików takie jak: PDB, XYZ, CML, CIF, Molden oraz dane wyjściowe: Gaussian, GAMESS i MOLPRO.

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)
Registry entries: Bio.tools  SciCrunch 
bkchem
Edytor struktur chemicznych
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BKchem to darmowy program do rysowania chemicznego napisany w języku Python.

Program udostępnia następujące funkcje:

  • Rysowanie (wiązania po wiązaniu; szablonów dla wspólnych pierścieni; rozszerzanie wspólnych grup; rysowanie rodników, ładunków, strzałek; obsługa kolorów itd.).
  • Edycja (nieograniczone możliwości cofania i ponawiania; wyrównywanie; skalowanie; obracanie (2D, 3D) itd.).
  • Eksport/Import (w pełni obsługiwany eksport SVG, OpenOffice.org-Draw, EPS; podstawowa obsługa importu i eksportu CML1 i CML2).
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bodr
Repozytorium danych do Blue Obelisk
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Wspólne repozytorium faktów chemicznych i fizycznych mające na celu poprawę interoperacyjności pomiędzy aplikacjami do chemii.

https://dx.doi.org/10.1021/ci050400b

Please cite: Peter Murray-Rust: The Blue Obelisk (eprint) CDK News 2(2):43-46 (2005)
chemeq
Analizator składu i równowagi chemicznej
Maintainer: Georges Khaznadar
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Program chemeq to podstawowy samodzielny filtr napisany w językach C, Flex i Bison. Wprowadza ciągi takie jak:

 2H2 + O2 ---> 2 H2O
a następnie wysyła kod LaTeX i komunikaty o równowadze reakcji chemicznej.

Przykład: ~/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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The chemical media type and various subtypes have been proposed by Henry Rzepa, Peter-Murray Rust and Benjamin Whitaker in 1996 as an addition to the existing MIME types. The proposal didn't succeed but various applications make use of these MIME/file types. This package adds support to Linux desktops to detect and recognize files of the chemical/* media type.

See also for http://www.ch.ic.ac.uk/chemime/.

chemical-structures
web service providing molecular structures in open formats
Maintainer: Georges Khaznadar
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This web service allows one to browse a rich set of molecular structures provided by the package chemical-structures-data, and eventually have them translated to other open formats, thanks to openbabel.

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chemtool
Program do rysowania struktur chemicznych
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Chemtool to dwuwymiarowy, bazujący na GTK+, edytor struktur chemicznych do X11. Obsługuje wiele typów wiązań, większość rodzajów tekstu potrzebnych do oznaczania składu chemicznego oraz krzywe/łukowe/zakrzywione strzałki.

Rysunki mogą być eksportowane do formatu MOL oraz PDB, SVG lub XFig - do dalszych adnotacji, jako rysunek PiCTeX, bitmapa lub pliki Postscript (kilka z nich przez fig2dev towarzyszący programowi XFig).

Pakiet zawiera również program pomocniczy - cht, do obliczania sumy wzoru i (dokładnej) masy cząsteczkowej z rysunku stworzonego przez Chemtool. Cht może być wywoływany bezpośrednio przez Chemtool lub poprzez konsolę.

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 (SGCP))

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
Wyświetlanie wysokiej jakości cząsteczek i dwuwymiarowych formuł chemicznych
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EasyChem to program, który pomaga tworzyć wysokiej jakości diagramy molekularne i dwuwymiarowe formuły chemiczne, które można eksportować do formatów PDF, PS, LaTeX i FIG.

EasyChem został pierwotnie zaprojektowany w celu tworzenia diagramów do książek związanych z chemią i jest obecnie często wykorzystywany pod tym względem w komercyjnych i niekomercyjnych książkach tego rodzaju.

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feff85exafs
Open Source theoretical EXAFS calculations
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The feff85exafs project aims to provide high quality theoretical standards for EXAFS analysis within an open source, freely re-distributable framework.

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.

slurm-wlm-torque and gridengine-client are workload managers which provide wrappers for PBS commands. Gabedit also allows one to configure it for any other workload manager.

Please cite: Abdul-Rahman Allouche: Gabedit - A graphical user interface for computational chemistry softwares. (eprint) J. Comp. Chem. 32:174-182 (2011)
galculator
Kalkulator naukowy
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Galculator jest kalkulatorem naukowym. Aktualnie obsługuje różne systemy liczbowe (DEC/HEX/OCT/BIN) i jednostki miary kąta (DEG/RAD/GRAD). Program wyposażony jest w szeroką gamę matematycznych (podstawowe operacje arytmetyczne, funkcje trygonometryczne itp.) oraz innych użytecznych funkcji (pamięć itp.). Galculator może być używany w trybie algebraicznym, jak również w odwrotnej notacji polskiej (ang. Reverse Polish Notation - RPN).

gamgi
Ogólny Interfejs Graficzny do Modelowania Atomistycznego
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GAMGI (General Atomistic Modelling Graphic Interface) udostępnia interfejs graficzny do budowania, przeglądania i analizowania struktur atomowych. Program jest skierowany do społeczności naukowej i zawiera interfejs graficzny do badania struktur atomowych i przygotowywania obrazów do prezentacji oraz do nauczania budowy materii atomowej.

The package is enhanced by the following packages: gamgi-data gamgi-doc
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garlic
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)
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gausssum
Analizowanie i wyświetlanie plików wyjściowych Gaussian, GAMESS itd.
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GaussSum analizuje pliki wyjściowe ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar i obliczenia z PC GAMESS, aby zdobyć użyteczne informacje.

GaussSum używa GNUPlot-a do wyświetlenia postępu optymalizacji geometrii, gęstości stanów widma, widma UV-VIS, widma IR, widma Ramana, i map różnic gęstości elektronowej. Może również wyświetlać wszystkie linie zawierające dowolne wyrażenia i nie tylko to.

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
Lekki wizualizator struktur krystalicznych
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GNOME Crystal to lekki wizualizator modeli struktur krystalicznych. Bazuje na GNOME Chemistry Utils (narzędziach chemicznych środowiska GNOME) i powinien wyświetlać modele wszelkiego rodzaju mikroskopijnych struktur kryształów przy użyciu OpenGL.

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gcu-bin
Aplikacje użyteczne w chemii do GNOME (aplikacje pomocnicze)
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GNOME Chemistry Utils dostarcza klasy C++ i 2 widżety GTK+ związane z chemią. Zostaną one wykorzystane w przyszłych wersjach, zarówno gcrystal jak i gchempaint.

Pakiet udostępnia 4 aplikacje:

  • przeglądarkę struktur molekularnych (GChem3D),
  • kalkulator masy molowej (GChemCalc),
  • układ okresowy pierwiastków (GChemTable),
  • przeglądarkę widm (GSpectrum).
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
Wizualizator symulacji dynamiki molekularnej
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Jest to program graficzny gpdc, służący do wizualizacji danych wyjściowych pochodzących z symulacji dynamiki molekularnej. Obsługuje on standardowy format xyz, a także inne formaty jako dane wejściowe oraz formaty plików graficznych JPG i PNG jako dane wyjściowe.

gelemental
Przeglądarka układu okresowego
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gElemental to przeglądarka układu okresowego (oparta na GTK+), która dostarcza szczegółowych informacji na temat pierwiastków chemicznych.

Prezentuje tabelę, która umożliwia tematyczne kolorowanie elementów według kilku właściwości, widok listy z możliwością sortowania i okno dialogowe właściwości elementu, wyświetlające różnorodne informacje, w tym: właściwości historyczne, termodynamiczne, elektrochemiczne oraz krystalograficzne.

Pakiet zawiera główną aplikację.

ghemical
Środowisko modelowania molekularnego do GNOME
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Ghemical jest pakietem oprogramowania stosowanym w chemii obliczeniowej, napisanym w języku C++. Posiada graficzny interfejs użytkownika i obsługuje zarówno modele mechaniki kwantowej (na wpół doświadczalne) jak i modele mechaniki molekularnej. Zapewnia optymalizację geometrii, dynamikę molekularną oraz zawiera duży zestaw narzędzi wizualnych wspieranych przez OpenGL.

Ghemical opiera się na kodzie zewnętrznym, umożliwiającym dokonywanie obliczeń w mechanice kwantowej. Zawiera, pochodzące z pakietu MOPAC7, semiempiryczne metody MNDO, MINDO/3, AM1 i PM3. Pakiet MPQC dostarcza, opartych na teorii Hartree-Focka, metod ab initio, obsługiwanych obecnie w podstawowym zakresie od STO-3G do 6-31G**.

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gperiodic
tablica okresowa pierwiastków
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GPeriodic jest małym programem X napisanym w GTK+, który pozwala na przeszukiwanie tablicy okresowej pierwiastków oraz wyświetlanie szczegółowych informacji o każdym jej elemencie. Obecnie jest obsługiwanych 118 pierwiastków.

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.

This package contains variants both for execution on a single machine, and using the MPI interface across multiple 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)
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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)
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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)
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jmol
Przeglądarka molekularna
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Jmol to przeglądarka molekularna do trójwymiarowych struktur chemicznych, napisana w języku Java. Jmol umożliwia odczytywanie różnych typów plików i danych wyjściowych z programów chemii kwantowej oraz animację plików wieloklatkowych i obliczonych trybów normalnych z tychże programów. Program udostępnia funkcje do chemikaliów, kryształów, materiałów i biomolekuł. Jmol może być przydatny dla studentów, nauczycieli oraz badaczy chemii i biochemii.

Formaty plików odczytywane przez Jmol obejmują: PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton i 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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kalzium
Układ okresowy pierwiastków i narzędzia chemiczne
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Kalzium jest w pełni funkcjonalną aplikacją chemiczną, obejmującą układ okresowy pierwiastków, opis zagadnień z zakresu chemii, rozwiązywanie równań chemicznych oraz podgląd cząsteczek w 3D.

Pakiet jest częścią modułu edukacyjnego KDE.

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katomic
Gra - układanka Atomix
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KAtomic jest grą - układanką, w której gracz przesuwa atomy po planszy w celu połączenia ich w cząsteczki.

Pakiet jest częścią modułu gier KDE.

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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.

mmass
Narzędzie do spektrometrii mas dla proteomiki
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Program mMass to darmowa przeglądarka / analizator widma masowego, w którym można wykonywać następujące zadania związane z proteomiką:

  • Otwierać nieprzetworzony tekst, widma masowe mzXML i mzData.
  • Definiować listy szczytowe.
  • Przeglądać widma masowe (zoom, kursor ...).
  • Rekalibrować dane.
  • Przeprowadzać symulacje tylko na bazie białka.
  • Wyszukiwać oprogramowanie poprzez sieć internetową.

Można łatwo rozszerzyć funkcjonalność oprogramowania dzięki dodatkowym modułom Pythona. Niniejszy pakiet zawiera niezależne od platformy części oprogramowania.

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
Półempiryczna biblioteka chemii kwantowej (pliki binarne)
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MOPAC zapewnia procedury rozwiązywania struktury elektronowej cząsteczek na poziomie półempirycznym. Dostępne metody obejmują: MNDO, MINDO/3, AM1 i PM3.

Pakiet zawiera pliki binarne MOPAC7.

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 perturbation 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.

msxpertsuite
mass spectrometry software suite - metapackage
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msXpertSuite provides programs to model linear (bio-) polymer chemistries, simulate mass spectral data, analyse and data-mine mass. It is the successor of GNU polyXmass, first, and then of massXpert.

The massXpert and mineXpert programs allow the following:

massXpert:

  • making brand new polymer chemistry definitions;
  • using the definitions to perform easy calculations in a desktop calculator-like manner;
  • performing sophisticated polymer sequence editing and simulations;
  • perform m/z list comparisons;

    Chemical simulations encompass cleavage (either chemical or enzymatic), gas-phase fragmentations, chemical modification of any monomer in the polymer sequence, cross-linking of monomers in the sequence, arbitrary mass searches, calculation of the isotopic pattern...

mineXpert:

  • Open mass spectrometry data files (mzML, mzXML, asc, xy, ...);
  • Calculate and display the TIC chromatogram;
  • For mobility data, calculate and display a mz=f(dt) color map;
  • Integrate the data from the TIC chromatogram or color map
  • to mass spectrum;
  • to drift spectrum;
  • back to TIC chromatogram (XIC chromatogram);
  • reverse operations;
  • to single TIC intensity value (for mass spectral intensity comparisons);
  • Model centroids peaks into mass spectra using either the Gaussian model or the Lorentzian model;
  • Export the data to text files;
  • Slice a big initial file into smaller chunks for easier mining;
  • Define how mining activity is recorded on disk for later use;
  • Convert mzML files into a private (albeit open) mass spectrometry format that allows better performance (based on SQLite3).

This package depends on both massXpert and mineXpert packages and thus will install both of them. To install only one of the packages, install the corresponding msxpertsuite-massxpert or msxpertsuite-minexpert package.

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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:

  • obabel: 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
Open source toolbox for Computational Fluid Dynamics (CFD) - binaries
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OpenFOAM is the free, open source CFD software released and developed primarily by OpenCFD Ltd since 2004. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.

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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
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)
psi3
Zestaw programów chemii kwantowej PSI3
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PSI3 jest pakietem programów z zakresu chemii kwantowej wykorzystujących do obliczeń metody ab-initio. Dzięki wysoce korelacyjnym technikom obliczeniowym jest szczególnie użyteczny w zakresie dokładnego określania własności molekuł, tak małych, jak i średniej wielkości.

Pakiet umożliwia obliczanie energii i gradientów następującymi metodami:

  • Hartree-Focka dla powłoki walencyjnej i ogólnej ograniczonej powłoki otwartej (RHF/ROHF) (w tym analityczne hessiany dla RHF),
  • teorii zaburzeń Mollera-Plesseta z zamkniętą powłoką (MP2),
  • metodą zamknięcia przestrzeni aktywnej SCF (CASSCF),
  • klastrowo-złączonych singli i dubletów (CCSD),
  • klastrowo-złączonych singli i dubletów z perturbacyjnymi trypletami (CCSD(T)) (tylko dla nieograniczonych (UHF) referencyjnych funkcji falowych).

Dodatkowo może liczyć energie następującymi metodami:

  • nieograniczonej otwartej powłoki Hartree-Focka (UHF),
  • teorii perturbacji Moellera-Plesseta dla zamkniętej/otwartej powłoki (MP2),
  • teorii MP2 z zamkniętą powłoką wyraźnie skorelowaną (MP2-R12) oraz teorii MP2 skalowanej ze składowymi spinowymi (SCS-MP2),
  • teorii perturbacji Moellera-Plesseta dla zamkniętej powłoki liniowej R12 (MP2-R12),
  • wieloreferencyjnej konfiguracji-interakcji (MRCI),
  • przybliżonych pojedynczych klastrów drugiego/trzeciego rzędu dubletów (CC2/CC3),
  • pojedynczych klastrów sprzężonych z wieloma odniesieniami dubletów (MRCCSD),
  • zamkniętej powłoki i ogólnie ograniczonego równania otwartej powłoki z pojedynczymi klastrami sprzężonymi z równaniem ruchu (EOM-CCSD).

Pozostałe własności pakietu obejmują m.in.:

  • elastyczne, modularne i dopasowane przez użytkownika formaty wejściowe,
  • obliczenia stanów wzbudzonych metodami CC2/CC3, EOM-CCSD, CASSCF, MRCI i MRCCSD,
  • wewnętrzny optymalizator koordynat geometrycznych,
  • obliczenia częstotliwości harmonicznych,
  • własności jednoelektronowe w rodzaju: momenty dipolowe/kwadrupolowe, orbitale naturalne, potencjały elektrostatyczne, stałe parowania hiperfinicznego, czy gęstość spinową,
  • wykorzystywanie molekularnej symetrii grupowo-punktowej do zwiększenia wydajności.
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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
Molekularny system graficzny
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PyMOL jest systemem grafiki molekularnej, ukierunkowanym na średnie i duże biocząsteczki takie jak białka. Potrafi tworzyć wysokiej jakości, gotowe do opublikowania, molekularne grafiki i animacje.

Wśród możliwości:

  • wizualizowanie molekuł, trajektorii molekularnych i powierzchnii danych krystalograficznych lub orbitalnych;
  • budowanie i rzeźbienie molekularne;
  • kreślenie wewnętrznej grafiki i generowanie filmów;
  • pełna rozszerzalność i obsługa skryptów za pośrednictwem interfejsu Pythona.

PyMOL umożliwia odczytywanie następujących formatów plików: PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps i Gaussian cube maps.

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python3-mpiplus
Python GPU framework for alchemical free energy calculations (Python 3)
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GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations.

python3-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.

python3-pymzml
mzML mass spectrometric data parsing (Python 3.x)
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python-pymzml (pymzML) 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 python-pymzml for Python 3.

Please cite: T. Bald, J. Barth, A. Niehues, M. Specht, M. Hippler and C. Fufezan: pymzML - Python module for high throughput bioinformatics on mass spectrometry data. (PubMed,eprint) Bioinformatics, UK 28(7):1052-1053 (2012)
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
visualization of 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
Wizualizacja struktur atomowych
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V_Sim wizualizuje struktury atomowe, takie jak kryształy, granice ziaren, cząsteczki itd. (w formacie binarnym lub w formacie zwykłego tekstu).

Renderowanie odbywa się w pseudo 3D z kulkami (atomami) lub strzałkami (spinami). Użytkownik może wchodzić w interakcje za pomocą wielu funkcji, aby wybrać widok, ustawić powiązania, narysować płaszczyzny cięcia, obliczyć powierzchnie z pól skalarnych, zduplikować węzły, zmierzyć geometrię itd. Ponadto, V_Sim umożliwia eksportowanie widoku jako obrazu w formatach PNG, JPG, PDF (bitmapa), SVG (schemat) i innych formatach. Dostępne są również narzędzia do kolorowania atomów z wartości danych lub do animowania na ekranie wielu plików pozycji.

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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
Trójwymiarowe modelowanie i animacja cząsteczek
Maintainer: Matthew Vernon
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xbs (ball-and-sticks) to program do rysowania. Potrafi tworzyć i wprawiać w ruch trójwymiarowe modele cząsteczek. Udostępnia wyjścia do X11 i do PostScript. Modele cząsteczek mogą być obracane, skalowane itd. Posiada opcje dodawania etykietek, podświetlania, cieniowania i kolorowania.

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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.

This packaged version comes from a fork available at https://gitlab.com/yamanq/xdrawchem, as the previous version was no longer actively maintained. More information about it in the copyright file.

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xmakemol
Program do wizualizacji układów atomowych i molekularnych
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XMakemol jest programem obsługiwanym za pomocą myszki, napisanym przy użyciu zestawu widżetów LessTif, służącym do przeglądania i zarządzania układami atomów oraz innymi chemicznymi układami. XMakemol wczytuje dane wejściowe XYZ i wyświetla atomy, wiązania i wiązania wodorowe.

Do jego funkcji należą:

  • animowanie plików zawierających wiele klatek;
  • interaktywne mierzenie długości wiązań, kątów pomiędzy nimi oraz kątów skręcenia;
  • kontrolowanie rozmiaru atomu/wiązania;
  • eksportowanie do formatów XPM, Encapsulated PostScript oraz XYZ;
  • przełączanie widzialności poszczególnych grup atomów;
  • edytowanie pozycji podzbiorów atomów.
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xmakemol-gl
Program do wizualizacji układów atomowych i molekularnych (OpenGL)
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XMakemol jest programem obsługiwanym za pomocą myszki, napisanym przy użyciu zestawu widżetów LessTif, służącym do przeglądania i zarządzania układami atomów oraz innymi chemicznymi układami. XMakemol wczytuje dane wejściowe XYZ i wyświetla atomy, wiązania i wiązania wodorowe.

Do jego funkcji należą:

  • animowanie plików zawierających wiele klatek;
  • interaktywne mierzenie długości wiązań, kątów pomiędzy nimi oraz kątów skręcenia;
  • kontrolowanie rozmiaru atomu/wiązania;
  • eksportowanie do formatów XPM, Encapsulated PostScript oraz XYZ;
  • przełączanie widzialności poszczególnych grup atomów;
  • edytowanie pozycji podzbiorów atomów.

Jest to pakiet XMakemol z obsługą OpenGL. Obrazy renderowane są przy użyciu prymitywów grafiki 3D i można je eksportować w formacie Xpm; można również tworzyć obrazy stereo w kolorze czerwonym lub niebieskim. Ten pakiet OpenGL zapewnia więcej opcji wyświetlania wraz z lepszą obsługą wyświetlania wektorów. Umożliwia również renderowanie elips.

Official Debian packages with lower relevance

gdpc-examples
Przykładowe pliki do programu gdpc
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Jest to program graficzny gpdc, służący do wizualizacji danych wyjściowych pochodzących z symulacji dynamiki molekularnej. Obsługuje on standardowy format xyz, a także inne formaty jako dane wejściowe oraz formaty plików graficznych JPG i PNG jako dane wyjściowe.

Ten pakiet zawiera przykładowe przykłady, które można wykorzystać w programie gdpc.

libcoordgen-dev
2D coordinate generation for chemical compounds - header files
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This package provides the Open Source release of Schroedinger's routines for the 2D coordinate representation of chemical compounds.

This package provides header files for developing against the API of that library.

libmaeparser-dev
Development files to parse Schrödinger Maestro files
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This package provides header files to develop one's own software that uses a library wth an Open Source parser for Maestro (.mae) files.

libschroedinger-coordgenlibs-dev
2D coordinate generation for chemical compounds - header files
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This package provides the Open Source release of Schroedinger's routines for the 2D coordinate representation of chemical compounds.

This package provides header files for developing against the API of that library.

python-pymzml-doc
mzML mass spectrometric data parsing - documentation
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python-pymzml (pymzML) 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 (processed with sphinx).

Please cite: T. Bald, J. Barth, A. Niehues, M. Specht, M. Hippler and C. Fufezan: pymzML - Python module for high throughput bioinformatics on mass spectrometry data. (PubMed,eprint) Bioinformatics, UK 28(7):1052-1053 (2012)
python3-amp
Atomistic Machine-learning Package (python 3)
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Amp is an open-source package designed to easily bring machine-learning to atomistic calculations. This project is being developed at Brown University in the School of Engineering, primarily by Andrew Peterson and Alireza Khorshidi, and is released under the GNU General Public License. Amp allows for the modular representation of the potential energy surface, allowing the user to specify or create descriptor and regression methods.

Amp is designed to integrate closely with the Atomic Simulation Environment (ASE). As such, the interface is in pure python, although several compute-heavy parts of the underlying code also have fortran versions to accelerate the calculations. The close integration with ASE means that any calculator that works with ASE ─ including EMT, GPAW, DACAPO, VASP, NWChem, and Gaussian ─ can easily be used as the parent method.

This package provides the python 3 modules.

python3-periodictable
Extensible periodic table of the elements (Python 3)
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This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.

Masses, densities and natural abundances come from the NIST Physics Laboratory, but do not represent a critical evaluation by NIST scientists.

Neutron scattering calculations use values collected by the Atomic Institute of the Austrian Universities. These values do corresponding to those from other packages, though there are some differences depending to the tables used. Bound coherent neutron scattering for gold in particular is significantly different from older value: 7.63(6) as measured in 1974 compared to 7.90(7) as measured in 1990.

X-ray scattering calculations use a combination of empirical and theoretical values from the LBL Center for X-ray Optics. These values differ from those given in other sources such as the International Tables for Crystallography, Volume C, and so may give different results from other packages.

This package installs the library for Python 3.

refmac-dictionary
dictionary for macromolecular refinement and model building
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Dictionary of ligands and constituent blocks (e.g. amino acids, nucleic acids, sugars) contains necessary stereochemical information (e.g. bond lengths, angles, torsion angles) about small molecules used in refinement and model building. Values in the dictionary are for an abstract form of monomers, i.e there is no conformational/configurational or environment dependence.

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.

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.
tinker
Software Tools for Molecular Design
Responsible: LI Daobing (LI Daobing)
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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
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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
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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
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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.

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