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
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Debian Science Chemistry packages
Official Debian packages with high relevance
adun.app
Symulator molekularny do GNUstep-a (GUI)
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Versions of package adun.app |
Release | Version | Architectures |
trixie | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.81-6 | amd64,armel,armhf,i386 |
stretch | 0.81-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.81-13 | amd64,arm64,armhf,i386 |
bullseye | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package adun.app: |
field | biology, biology:structural |
interface | x11 |
role | program |
scope | application |
suite | gnustep |
uitoolkit | gnustep |
use | analysing, organizing, viewing |
works-with | 3dmodel, db |
x11 | application |
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License: DFSG free
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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.
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apbs
Adaptive Poisson Boltzmann Solver
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Versions of package apbs |
Release | Version | Architectures |
bookworm | 3.4.1-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.4-1 | amd64,arm64,armhf,i386 |
stretch | 1.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.4-1 | amd64,armel,armhf,i386 |
bullseye | 3.0.0+dfsg1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.4.1-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package apbs: |
field | chemistry |
interface | commandline |
role | program |
scope | utility |
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License: DFSG free
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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.
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atomes
atomic-scale 3D modeling toolbox
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Versions of package atomes |
Release | Version | Architectures |
bookworm-backports | 1.1.14-1.1~bpo12+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.1.15-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.1.15-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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
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avogadro
System do molekularnego modelowania i wizualizacji
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Versions of package avogadro |
Release | Version | Architectures |
stretch | 1.2.0-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.97.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.93.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.3-10.1 | amd64,armel,armhf,i386 |
sid | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.2.0-4 | amd64,arm64,armhf,i386 |
Debtags of package avogadro: |
field | chemistry |
role | program |
uitoolkit | qt |
use | viewing |
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License: DFSG free
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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.
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bkchem
Edytor struktur chemicznych
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Versions of package bkchem |
Release | Version | Architectures |
stretch | 0.13.0-5 | all |
jessie | 0.13.0-4 | all |
buster | 0.13.0-6 | all |
bookworm | 0.14.0~pre4+git20211228-3 | all |
trixie | 0.14.0~pre4+git20211228-5 | all |
sid | 0.14.0~pre4+git20211228-5 | all |
Debtags of package bkchem: |
field | chemistry |
role | program |
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License: DFSG free
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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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Versions of package bodr |
Release | Version | Architectures |
bookworm | 10-2 | all |
stretch | 10-1 | all |
buster | 10-1 | all |
sid | 10-3 | all |
jessie | 10-1 | all |
bullseye | 10-2 | all |
trixie | 10-3 | all |
Debtags of package bodr: |
role | app-data |
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License: DFSG free
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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)
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chemeq
Analizator składu i równowagi chemicznej
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Versions of package chemeq |
Release | Version | Architectures |
jessie | 2.12-1 | amd64,armel,armhf,i386 |
bullseye | 2.19-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.23-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.18-1 | amd64,arm64,armhf,i386 |
sid | 3.6-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.6-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.12-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package chemeq: |
devel | interpreter |
field | chemistry |
interface | commandline |
role | program |
scope | utility |
use | calculating, learning, text-formatting, typesetting |
works-with | text |
works-with-format | tex |
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License: DFSG free
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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
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chemical-mime-data
chemical MIME and file type support for desktops
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Versions of package chemical-mime-data |
Release | Version | Architectures |
sid | 0.1.94-7.2 | all |
trixie | 0.1.94-7.2 | all |
bookworm | 0.1.94-7.2 | all |
bullseye | 0.1.94-7.1 | all |
buster | 0.1.94-7 | all |
stretch | 0.1.94-6 | all |
jessie | 0.1.94-6 | all |
Debtags of package chemical-mime-data: |
field | biology, chemistry |
role | app-data |
use | organizing |
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License: DFSG free
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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/.
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chemical-structures
web service providing molecular structures in open formats
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Versions of package chemical-structures |
Release | Version | Architectures |
sid | 2.2.dfsg.0-20 | all |
trixie | 2.2.dfsg.0-20 | all |
bullseye | 2.2.dfsg.0-18 | all |
bookworm | 2.2.dfsg.0-20 | all |
buster | 2.2.dfsg.0-13 | all |
stretch | 2.2.dfsg.0-12 | all |
jessie | 2.2.dfsg.0-12 | all |
Debtags of package chemical-structures: |
field | biology, biology:bioinformatics, chemistry |
interface | commandline, web |
role | data, program |
science | visualisation |
use | comparing, converting, learning, viewing |
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License: DFSG free
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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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Versions of package chemtool |
Release | Version | Architectures |
bookworm | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.6.14-1 | amd64,armel,armhf,i386 |
stretch | 1.6.14-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.6.14-3 | amd64,arm64,armhf,i386 |
bullseye | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package chemtool: |
field | chemistry |
interface | x11 |
role | program |
scope | application |
uitoolkit | gtk |
use | editing, learning |
works-with | image, image:vector |
works-with-format | svg |
x11 | application |
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License: DFSG free
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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.
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cp2k
Ab Initio Molecular Dynamics
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Versions of package cp2k |
Release | Version | Architectures |
sid | 2023.2-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
bookworm | 2023.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 6.1-2 | amd64,arm64,armhf,i386 |
jessie | 2.5.1-3 | amd64,armel,armhf,i386 |
stretch | 4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 8.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2024.3 |
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License: DFSG free
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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).
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drawxtl
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Versions of package drawxtl |
Release | Version | Architectures |
bookworm | 5.5-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 5.5-6.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 5.5-3 | amd64,armel,armhf,i386 |
stretch | 5.5-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 5.5-3 | amd64,arm64,armhf,i386 |
bullseye | 5.5-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 5.5-6.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package drawxtl: |
interface | x11 |
role | program |
uitoolkit | glut |
x11 | application |
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License: DFSG free
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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.
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easychem
Wyświetlanie wysokiej jakości cząsteczek i dwuwymiarowych formuł chemicznych
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Versions of package easychem |
Release | Version | Architectures |
jessie | 0.6-8 | amd64,armel,armhf,i386 |
bookworm | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.6-8 | amd64,arm64,armhf,i386 |
sid | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.6-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package easychem: |
field | chemistry |
interface | x11 |
role | program |
uitoolkit | gtk |
use | editing, learning, viewing |
x11 | application |
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License: DFSG free
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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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Versions of package feff85exafs |
Release | Version | Architectures |
trixie | 0.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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.
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gabedit
graphical user interface to Ab Initio packages
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Versions of package gabedit |
Release | Version | Architectures |
sid | 2.5.1+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.5.1~20200828-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.8-3 | amd64,arm64,armhf,i386 |
stretch | 2.4.8-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.8-1 | amd64,armel,armhf,i386 |
bookworm | 2.5.1+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package gabedit: |
field | chemistry |
role | program |
uitoolkit | gtk |
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License: DFSG free
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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.
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galculator
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Versions of package galculator |
Release | Version | Architectures |
sid | 2.1.4-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.1.4-1.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.1.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.3-1 | amd64,armel,armhf,i386 |
trixie | 2.1.4-1.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.1.4-1 | amd64,arm64,armhf,i386 |
bookworm | 2.1.4-1.2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package galculator: |
field | mathematics |
interface | x11 |
role | program |
scope | utility |
uitoolkit | gtk |
x11 | application |
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License: DFSG free
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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).
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gamgi
Ogólny Interfejs Graficzny do Modelowania Atomistycznego
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Versions of package gamgi |
Release | Version | Architectures |
buster | 0.17.3-2 | amd64,arm64,armhf,i386 |
jessie | 0.17.1-1 | amd64,armel,armhf,i386 |
stretch | 0.17.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.17.3-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.17.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.17.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package gamgi: |
role | program |
uitoolkit | gtk |
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License: DFSG free
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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.
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garlic
visualization program for biomolecules
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Versions of package garlic |
Release | Version | Architectures |
bookworm | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.6-1.1 | amd64,armel,armhf,i386 |
stretch | 1.6-1.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.6-3 | amd64,arm64,armhf,i386 |
bullseye | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package garlic: |
field | biology, chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | xlib |
use | viewing |
x11 | application |
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License: DFSG free
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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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Versions of package gausssum |
Release | Version | Architectures |
jessie | 2.2.6.1-1 | all |
sid | 3.0.2-2 | all |
trixie | 3.0.2-2 | all |
bookworm | 3.0.2-2 | all |
bullseye | 3.0.2-2 | all |
buster | 3.0.2-1 | all |
stretch | 3.0.1.1-1 | all |
Debtags of package gausssum: |
field | chemistry |
role | program |
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License: DFSG free
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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.
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gchempaint
2D chemical structures editor for the GNOME2 desktop
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Versions of package gchempaint |
Release | Version | Architectures |
jessie | 0.14.9-1 | amd64,armel,armhf,i386 |
bookworm | 0.14.17-6.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.14.17-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.14.17-1.1 | amd64,arm64,armhf,i386 |
sid | 0.14.17-6.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.14.15-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package gchempaint: |
field | chemistry |
interface | x11 |
role | program |
suite | gnome |
uitoolkit | gtk |
use | editing, learning |
x11 | application |
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License: DFSG free
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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.
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gcrystal
Lekki wizualizator struktur krystalicznych
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Versions of package gcrystal |
Release | Version | Architectures |
jessie | 0.14.9-1 | amd64,armel,armhf,i386 |
stretch | 0.14.15-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.14.17-1.1 | amd64,arm64,armhf,i386 |
bullseye | 0.14.17-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.14.17-6.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.14.17-6.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package gcrystal: |
field | chemistry |
interface | x11 |
role | program |
uitoolkit | gtk |
x11 | application |
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License: DFSG free
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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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Versions of package gcu-bin |
Release | Version | Architectures |
stretch | 0.14.15-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.14.17-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.14.17-1.1 | amd64,arm64,armhf,i386 |
bookworm | 0.14.17-6.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.14.9-1 | amd64,armel,armhf,i386 |
sid | 0.14.17-6.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package gcu-bin: |
role | program |
uitoolkit | gtk |
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License: DFSG free
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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).
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gcu-plugin
??? missing short description for package gcu-plugin :-(
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Versions of package gcu-plugin |
Release | Version | Architectures |
jessie | 0.14.9-1 | amd64,armel,armhf,i386 |
Debtags of package gcu-plugin: |
field | chemistry |
role | plugin |
uitoolkit | gtk |
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License: DFSG free
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gdis
molecular and crystal model viewer
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Versions of package gdis |
Release | Version | Architectures |
jessie | 0.90-5 | amd64,armel,armhf,i386 |
stretch | 0.90-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.90-5 | amd64,arm64,armhf,i386 |
bookworm | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package gdis: |
field | chemistry |
interface | 3d, x11 |
role | program |
uitoolkit | gtk |
use | editing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
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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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Versions of package gdpc |
Release | Version | Architectures |
bookworm | 2.2.5-15 | amd64,arm64,mips64el,ppc64el |
jessie | 2.2.5-3 | amd64,armel,armhf,i386 |
sid | 2.2.5-16 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 2.2.5-16 | amd64,arm64,mips64el,ppc64el,riscv64 |
stretch | 2.2.5-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.2.5-9 | amd64,arm64,armhf,i386 |
bullseye | 2.2.5-14 | amd64,arm64,mips64el,ppc64el |
Debtags of package gdpc: |
field | biology, biology:structural, chemistry, physics |
interface | x11 |
role | program |
scope | application |
uitoolkit | gtk |
use | viewing |
works-with | 3dmodel, image, video |
works-with-format | jpg, png |
x11 | application |
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License: DFSG free
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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.
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gelemental
Przeglądarka układu okresowego
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Versions of package gelemental |
Release | Version | Architectures |
trixie | 2.0.2-1.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.0.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.0.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.0.2-1.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.2.0-12 | amd64,arm64,armhf,i386 |
stretch | 1.2.0-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.2.0-9 | amd64,armel,armhf,i386 |
Debtags of package gelemental: |
field | chemistry |
interface | x11 |
role | program |
uitoolkit | gtk |
use | viewing |
x11 | application |
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License: DFSG free
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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.
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ghemical
Środowisko modelowania molekularnego do GNOME
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Versions of package ghemical |
Release | Version | Architectures |
buster | 3.0.0-4 | amd64,arm64,armhf,i386 |
stretch | 3.0.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
bookworm | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package ghemical: |
field | chemistry |
interface | 3d, x11 |
role | program |
suite | gnome |
uitoolkit | gtk |
use | editing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
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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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Versions of package gperiodic |
Release | Version | Architectures |
sid | 3.0.3-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 3.0.3-1 | amd64,arm64,armhf,i386 |
trixie | 3.0.3-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.0.10-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.0.10-7 | amd64,armel,armhf,i386 |
bookworm | 3.0.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.0.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package gperiodic: |
field | chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | gtk |
use | learning, viewing |
x11 | application |
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License: DFSG free
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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.
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gromacs
Molecular dynamics simulator, with building and analysis tools
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Versions of package gromacs |
Release | Version | Architectures |
jessie | 5.0.2-1 | amd64,armel,armhf,i386 |
stretch | 2016.1-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2019.1-1 | amd64,arm64,armhf,i386 |
bookworm | 2022.5-2 | amd64,arm64,mips64el,ppc64el,s390x |
bullseye | 2020.6-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2024.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 2024.4-1 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 2025.0~beta |
Debtags of package gromacs: |
field | biology, biology:structural, chemistry |
interface | commandline, x11 |
role | program |
uitoolkit | xlib |
x11 | application |
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License: DFSG free
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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.
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gromacs-mpich
Molecular dynamics sim, binaries for MPICH parallelization
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Versions of package gromacs-mpich |
Release | Version | Architectures |
bullseye | 2020.6-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2016.1-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 5.0.2-1 | amd64,armel,armhf,i386 |
buster | 2019.1-1 | amd64,arm64,armhf,i386 |
upstream | 2025.0~beta |
Debtags of package gromacs-mpich: |
devel | lang:c, library |
field | biology, chemistry |
interface | commandline |
role | devel-lib, program |
scope | utility |
works-with | software:package |
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License: DFSG free
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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.
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gromacs-openmpi
Molecular dynamics sim, binaries for OpenMPI parallelization
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Versions of package gromacs-openmpi |
Release | Version | Architectures |
stretch | 2016.1-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2020.6-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 5.0.2-1 | amd64,armel,armhf,i386 |
buster | 2019.1-1 | amd64,arm64,armhf,i386 |
upstream | 2025.0~beta |
Debtags of package gromacs-openmpi: |
devel | lang:c, library |
field | biology, chemistry |
interface | commandline |
role | devel-lib, program |
scope | utility |
works-with | software:package |
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License: DFSG free
|
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.
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jmol
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Versions of package jmol |
Release | Version | Architectures |
trixie | 16.2.33+dfsg-1 | all |
sid | 16.2.33+dfsg-1 | all |
jessie | 12.2.32+dfsg2-1 | all |
buster | 14.6.4+2016.11.05+dfsg1-4 | all |
stretch | 14.6.4+2016.11.05+dfsg1-3 | all |
bookworm | 14.32.83+dfsg-2 | all |
bullseye | 14.6.4+2016.11.05+dfsg1-4 | all |
upstream | 16.2.37 |
Debtags of package jmol: |
field | chemistry |
role | program |
scope | utility |
use | viewing |
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License: DFSG free
|
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.
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kalzium
Układ okresowy pierwiastków i narzędzia chemiczne
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Versions of package kalzium |
Release | Version | Architectures |
buster | 17.08.3-1 | amd64,arm64,armhf,i386 |
trixie | 23.08.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 23.08.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
experimental | 24.08.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 4.14.2-1 | amd64,armel,armhf,i386 |
bookworm | 22.12.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 20.12.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 16.08.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 24.08.3 |
Debtags of package kalzium: |
field | chemistry |
interface | 3d, x11 |
role | program |
suite | kde |
uitoolkit | qt |
use | browsing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
|
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
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Versions of package katomic |
Release | Version | Architectures |
bullseye | 20.12.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 4.12.4-1 | amd64,armel,armhf,i386 |
buster | 18.04.1-1 | amd64,arm64,armhf,i386 |
stretch | 16.08.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
experimental | 24.08.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 22.12.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 22.12.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 22.12.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 24.08.3 |
Debtags of package katomic: |
game | puzzle |
interface | x11 |
role | program |
suite | kde |
uitoolkit | qt |
use | gameplaying |
x11 | application |
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License: DFSG free
|
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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Versions of package libcdk-java |
Release | Version | Architectures |
bookworm | 2.8-2 | all |
trixie | 2.9-2 | all |
sid | 2.9-2 | all |
bullseye | 2.3.134.g1bb9a64587-2 | all |
stretch | 1.2.10-6 | all |
jessie | 1.2.10-6 | all |
buster | 1.2.10-7 | all |
Debtags of package libcdk-java: |
devel | lang:java, library |
field | chemistry |
role | devel-lib |
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License: DFSG free
|
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.
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mmass
Narzędzie do spektrometrii mas dla proteomiki
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Versions of package mmass |
Release | Version | Architectures |
jessie | 5.5.0-4 | all |
buster | 5.5.0-5 | all |
stretch | 5.5.0-5 | all |
Debtags of package mmass: |
field | biology, chemistry |
interface | x11 |
role | program |
science | plotting, visualisation |
scope | application |
uitoolkit | gtk, wxwidgets |
use | analysing |
works-with | biological-sequence, db |
works-with-format | xml |
x11 | application |
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License: DFSG free
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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.
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mmass-modules
Mass spectrometry tool for proteomics - extension modules
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Versions of package mmass-modules |
Release | Version | Architectures |
stretch | 5.5.0-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 5.5.0-5 | amd64,arm64,armhf,i386 |
jessie | 5.5.0-4 | amd64,armel,armhf,i386 |
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License: DFSG free
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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.
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mopac7-bin
Półempiryczna biblioteka chemii kwantowej (pliki binarne)
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Versions of package mopac7-bin |
Release | Version | Architectures |
stretch | 1.15-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.15-6 | amd64,arm64,armhf,i386 |
bullseye | 1.15-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.15-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.15-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.15-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.15-6 | amd64,armel,armhf,i386 |
Debtags of package mopac7-bin: |
field | chemistry |
role | program |
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License: DFSG free
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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.
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mpqc
Massively Parallel Quantum Chemistry Program
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Versions of package mpqc |
Release | Version | Architectures |
buster | 2.3.1-19 | amd64,arm64,armhf,i386 |
sid | 2.3.1-22 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.3.1-22 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.3.1-21 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.3.1-18+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.3.1-16 | amd64,armel,armhf,i386 |
Debtags of package mpqc: |
field | chemistry, physics |
interface | commandline, x11 |
role | program |
scope | utility |
uitoolkit | gtk |
x11 | application |
|
License: DFSG free
|
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).
Please cite:
The Massively Parallel Quantum Chemistry Program (MPQC), Version 2.3.1, Curtis L. Janssen, Ida B. Nielsen, Matt L. Leininger, Edward F. Valeev, Joseph P. Kenny, Edward T. Seidl, Sandia National Laboratories, Livermore, CA.
(2008)
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mpqc-support
Massively Parallel Quantum Chemistry Program (support tools)
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Versions of package mpqc-support |
Release | Version | Architectures |
jessie | 2.3.1-16 | amd64,armel,armhf,i386 |
buster | 2.3.1-19 | amd64,arm64,armhf,i386 |
bullseye | 2.3.1-21 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.3.1-22 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.3.1-22 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.3.1-18+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package mpqc-support: |
field | chemistry, physics |
interface | commandline, x11 |
role | program |
scope | utility |
suite | emacs |
uitoolkit | tk |
x11 | application |
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License: DFSG free
|
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.
Please cite:
The Massively Parallel Quantum Chemistry Program (MPQC), Version 2.3.1, Curtis L. Janssen, Ida B. Nielsen, Matt L. Leininger, Edward F. Valeev, Joseph P. Kenny, Edward T. Seidl, Sandia National Laboratories, Livermore, CA.
(2008)
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msxpertsuite
mass spectrometry software suite - metapackage
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Versions of package msxpertsuite |
Release | Version | Architectures |
bullseye | 5.8.9-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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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Versions of package openbabel |
Release | Version | Architectures |
trixie | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.1.1+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.3.2+dfsg-2 | amd64,armel,armhf,i386 |
bullseye | 3.1.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.3.2+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.4.1+dfsg-3 | amd64,arm64,armhf,i386 |
Debtags of package openbabel: |
field | chemistry |
interface | commandline |
role | program |
scope | utility |
use | converting |
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License: DFSG free
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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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Versions of package openfoam |
Release | Version | Architectures |
stretch | 4.1+dfsg1-1 | amd64,arm64,armhf,i386,ppc64el,s390x |
buster | 1812+dfsg1-2 | amd64,arm64,armhf,i386 |
bullseye | 1912.200626-1 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1912.200626-1 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1912.200626-3 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
sid | 1912.200626-3 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
upstream | 2406 |
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License: DFSG free
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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.
Package contains binaries.
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pdb2pqr
Preparation of protein structures for electrostatics calculations
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Versions of package pdb2pqr |
Release | Version | Architectures |
trixie | 3.6.1+dfsg-1 | all |
buster | 2.1.1+dfsg-5 | amd64,arm64,armhf,i386 |
jessie | 1.9.0+dfsg-1 | amd64,armel,armhf,i386 |
bullseye | 2.1.1+dfsg-7+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.5.2+dfsg-3 | all |
stretch | 2.1.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 3.6.1+dfsg-1 | all |
upstream | 3.6.2 |
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License: DFSG free
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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
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psi3
Zestaw programów chemii kwantowej PSI3
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Versions of package psi3 |
Release | Version | Architectures |
bullseye | 3.4.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.4.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.4.0-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 3.4.0-6 | amd64,arm64,armhf,i386 |
jessie | 3.4.0-5 | amd64,armel,armhf,i386 |
stretch | 3.4.0-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package psi3: |
field | chemistry, physics |
interface | commandline |
role | program |
science | calculation |
scope | suite |
use | calculating |
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License: DFSG free
|
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
|
Versions of package pyfai |
Release | Version | Architectures |
stretch-backports | 0.15.0+dfsg1-1~bpo9+1 | all |
buster-backports | 0.19.0+dfsg1-3~bpo10+1 | all |
bookworm | 0.21.3+dfsg1-4 | all |
jessie | 0.10.2-1 | amd64,armel,armhf,i386 |
bookworm-backports | 2023.9.0-1~bpo12+1 | all |
trixie | 2024.05-3 | all |
stretch | 0.13.0+dfsg-1 | all |
sid | 2024.05-3 | all |
bullseye | 0.20.0+dfsg1-3 | all |
buster | 0.17.0+dfsg1-3 | all |
upstream | 2024.09 |
|
License: DFSG free
|
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.
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|
pymol
Molekularny system graficzny
|
Versions of package pymol |
Release | Version | Architectures |
jessie | 1.7.2.1-1 | amd64,armel,armhf,i386 |
sid | 3.0.0+dfsg-1 | all |
trixie | 3.0.0+dfsg-1 | all |
bookworm | 2.5.0+dfsg-1 | all |
bullseye | 2.4.0+dfsg-2 | all |
buster | 2.2.0+dfsg-4 | all |
stretch | 1.8.4.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package pymol: |
field | biology:structural, chemistry |
interface | 3d, x11 |
role | program |
scope | utility |
uitoolkit | tk |
use | learning, viewing |
works-with | image |
x11 | application |
|
License: DFSG free
|
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)
|
Versions of package python3-mpiplus |
Release | Version | Architectures |
sid | 0.0.2+ds-1 | all |
trixie | 0.0.2+ds-1 | all |
bookworm | 0.0.1-2 | all |
|
License: DFSG free
|
GPU-accelerated Python framework for exploring algorithms for alchemical free
energy calculations.
|
|
python3-openbabel
Chemical toolbox library (Python bindings)
|
Versions of package python3-openbabel |
Release | Version | Architectures |
sid | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.1.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.1.1+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
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.
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|
python3-pymzml
mzML mass spectrometric data parsing (Python 3.x)
|
Versions of package python3-pymzml |
Release | Version | Architectures |
bullseye | 2.4.7-3 | all |
stretch | 0.7.6-dfsg-4 | all |
sid | 2.5.10+repack1-1 | all |
trixie | 2.5.10+repack1-1 | all |
bookworm | 2.5.2+repack1-1 | all |
|
License: DFSG free
|
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.
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qutemol
interactive visualization of macromolecules
|
Versions of package qutemol |
Release | Version | Architectures |
stretch | 0.4.1~cvs20081111-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.4.1~cvs20081111-3.2 | amd64,armel,armhf,i386 |
bookworm | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.4.1~cvs20081111-12 | amd64,arm64,armhf,i386 |
bullseye | 0.4.1~cvs20081111-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package qutemol: |
interface | x11 |
role | program |
uitoolkit | glut, wxwidgets |
x11 | application |
|
License: DFSG free
|
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.
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rasmol
visualization of biological macromolecules
|
Versions of package rasmol |
Release | Version | Architectures |
bullseye | 2.7.6.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.7.5.2-2 | amd64,armel,armhf,i386 |
stretch | 2.7.5.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,s390x |
buster | 2.7.6.0-1 | amd64,arm64,armhf,i386 |
Debtags of package rasmol: |
field | chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | gtk |
use | learning, viewing |
x11 | application |
|
License: DFSG free
|
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
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tandem-mass
mass spectrometry software for protein identification
|
Versions of package tandem-mass |
Release | Version | Architectures |
buster | 201702011-1 | amd64,arm64,armhf,i386 |
bullseye | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2013.09.01-2 | amd64,armel,armhf,i386 |
stretch | 20151215-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
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v-sim
Wizualizacja struktur atomowych
|
Versions of package v-sim |
Release | Version | Architectures |
bookworm | 3.7.2-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 3.7.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.7.2-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.7.2-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package v-sim: |
field | chemistry, physics |
interface | x11 |
role | program |
science | visualisation |
scope | application |
uitoolkit | gtk |
use | viewing |
x11 | application |
|
License: DFSG free
|
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
|
Versions of package viewmol |
Release | Version | Architectures |
buster | 2.4.1-25 | amd64,arm64,armhf,i386 |
stretch | 2.4.1-24 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.1-22 | amd64,armel,armhf,i386 |
Debtags of package viewmol: |
field | chemistry |
interface | 3d, x11 |
role | program |
uitoolkit | motif |
use | learning, viewing |
x11 | application |
|
License: DFSG free
|
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
|
Versions of package xbs |
Release | Version | Architectures |
sid | 0-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0-8 | amd64,armel,armhf,i386 |
buster | 0-10 | amd64,arm64,armhf,i386 |
stretch | 0-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 0-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package xbs: |
field | chemistry |
interface | 3d |
role | program |
scope | application |
uitoolkit | xlib |
use | printing, viewing |
works-with | text |
works-with-format | postscript |
x11 | application |
|
License: DFSG free
|
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
Edytor struktur i reakcji chemicznych
|
Versions of package xdrawchem |
Release | Version | Architectures |
jessie | 2.0-3 | amd64,armel,armhf,i386 |
buster | 1.10.2.1-2 | amd64,arm64,armhf,i386 |
bullseye | 1.11.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.11.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.11.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.11.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 2.0-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package xdrawchem: |
field | chemistry |
interface | x11 |
role | program |
uitoolkit | qt |
use | editing, learning, viewing |
x11 | application |
|
License: DFSG free
|
Xdrawchem jest edytorem 2D dla struktur i reakcji chemicznych. Program
odzwierciedla możliwości komercyjnego pakietu ChemDraw i jest zgodny z
nim, a także z innymi formatami chemicznymi poprzez OpenBabel.
Ta spakowana wersja wywodzi się z oryginalnego projektu dostępnego
pod adresem: https://gitlab.com/yamanq/xdrawchem, ponieważ poprzednia
wersja nie była już aktywnie utrzymywana. Więcej informacji na ten
temat znajduje się w pliku dotyczącym praw autorskich.
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xmakemol
Program do wizualizacji układów atomowych i molekularnych
|
Versions of package xmakemol |
Release | Version | Architectures |
bullseye | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 5.16-9 | amd64,arm64,armhf,i386 |
sid | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 5.16-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 5.16-7 | amd64,armel,armhf,i386 |
bookworm | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package xmakemol: |
field | chemistry |
hardware | input, input:mouse |
interface | x11 |
role | program |
scope | application |
uitoolkit | motif |
use | editing, viewing |
x11 | application |
|
License: DFSG free
|
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)
|
Versions of package xmakemol-gl |
Release | Version | Architectures |
bullseye | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 5.16-7 | amd64,armel,armhf,i386 |
bookworm | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 5.16-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 5.16-9 | amd64,arm64,armhf,i386 |
Debtags of package xmakemol-gl: |
uitoolkit | motif |
|
License: DFSG free
|
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.
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|
Official Debian packages with lower relevance
gdpc-examples
Przykładowe pliki do programu gdpc
|
Versions of package gdpc-examples |
Release | Version | Architectures |
buster | 2.2.5-9 | all |
jessie | 2.2.5-3 | all |
sid | 2.2.5-16 | all |
trixie | 2.2.5-16 | all |
bookworm | 2.2.5-15 | all |
bullseye | 2.2.5-14 | all |
stretch | 2.2.5-6 | all |
Debtags of package gdpc-examples: |
field | biology, biology:structural, chemistry, physics |
role | documentation |
|
License: DFSG free
|
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.
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libcoordgen-dev
2D coordinate generation for chemical compounds - header files
|
Versions of package libcoordgen-dev |
Release | Version | Architectures |
bookworm | 3.0.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.0.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.4.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
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libmaeparser-dev
Development files to parse Schrödinger Maestro files
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Versions of package libmaeparser-dev |
Release | Version | Architectures |
sid | 1.3.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.3.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.3.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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libschroedinger-coordgenlibs-dev
2D coordinate generation for chemical compounds - header files
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Versions of package libschroedinger-coordgenlibs-dev |
Release | Version | Architectures |
buster | 1.1-3 | amd64,arm64,armhf,i386 |
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License: DFSG free
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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.
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python-pymzml-doc
mzML mass spectrometric data parsing - documentation
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Versions of package python-pymzml-doc |
Release | Version | Architectures |
stretch | 0.7.6-dfsg-4 | all |
bullseye | 2.4.7-3 | all |
trixie | 2.5.10+repack1-1 | all |
sid | 2.5.10+repack1-1 | all |
bookworm | 2.5.2+repack1-1 | all |
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License: DFSG free
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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).
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python3-amp
Atomistic Machine-learning Package (python 3)
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Versions of package python3-amp |
Release | Version | Architectures |
bookworm | 0.6.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.6.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.6.1-1 | amd64,arm64,armhf,i386 |
bullseye | 0.6.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 4878fc892f2cbc5cd9f29f7a367d7b05bdeb6ee9 |
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License: DFSG free
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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.
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python3-periodictable
Extensible periodic table of the elements (Python 3)
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Versions of package python3-periodictable |
Release | Version | Architectures |
bookworm | 1.6.0-1 | all |
sid | 2.0.1-1 | all |
buster | 1.5.0-7 | all |
bullseye | 1.5.3-1 | all |
trixie | 1.7.1-1 | all |
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License: DFSG free
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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.
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refmac-dictionary
dictionary for macromolecular refinement and model building
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Versions of package refmac-dictionary |
Release | Version | Architectures |
trixie | 5.41-3 | all |
bullseye | 5.41-2 | all |
sid | 5.41-3 | all |
buster | 5.41-1 | all |
bookworm | 5.41-2 | all |
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License: DFSG free
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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.
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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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Versions of package fdmnes |
Release | Version | Architectures |
VCS | 0.0.20120607-1 | all |
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License: To-be-clarified
Version: 0.0.20120607-1
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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.
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molden
processing program of molecular and electronic structure
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Versions of package molden |
Release | Version | Architectures |
VCS | 5.2-1 | all |
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License: non-free
Debian package not available
Version: 5.2-1
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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.
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molekel
Advanced Interactive 3D-Graphics for Molecular Sciences
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Versions of package molekel |
Release | Version | Architectures |
VCS | 5.4-1 | all |
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License: free
Debian package not available
Version: 5.4-1
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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.
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tinker
Software Tools for Molecular Design
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Versions of package tinker |
Release | Version | Architectures |
VCS | 4.2-5~dev | all |
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License: free
Debian package not available
Version: 4.2-5~dev
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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....
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No known packages available but some record of interest (WNPP bug)
rational protein design library
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License: LGPL
Debian package not available
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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
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Evaluate the integrals in modern atomic and molecular theory
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License: GPL
Debian package not available
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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.
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No known packages available
openchrom
process chromatographic and mass spectrometric data
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License: EPL
Debian package not available
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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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