Summary
Input Preparation and Output Processing
DebiChem input preparation and output processing
This metapackage will install graphical frontends and input generators/output
processors for computational chemistry packages which might be useful for
chemists.
Description
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 DebiChem
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the DebiChem mailing list
Links to other tasks
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DebiChem Input Preparation and Output Processing packages
Official Debian packages with high relevance
ase
Atomic Simulation Environment
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Versions of package ase |
Release | Version | Architectures |
buster | 3.17.0-2 | all |
sid | 3.23.0-1 | all |
trixie | 3.23.0-1 | all |
bookworm | 3.22.1-3 | all |
bullseye | 3.21.1-2 | all |
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License: DFSG free
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ASE is an Atomic Simulation Environment written in the Python programming
language with the aim of setting up, stearing, and analyzing atomic
simulations. ASE is part of CAMPOS, the CAMP Open Source project.
ASE contains Python interfaces to several different electronic structure
codes including Abinit, Asap, Dacapo, Elk, GPAW and SIESTA.
This package provides the executable scripts.
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avogadro
Molecular Graphics and Modelling System
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Versions of package avogadro |
Release | Version | Architectures |
sid | 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 |
trixie | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.0.3-10.1 | amd64,armel,armhf,i386 |
stretch | 1.2.0-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,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 is a molecular graphics and modelling system targeted at molecules
and biomolecules. It can visualize properties like molecular orbitals or
electrostatic potentials and features an intuitive molecular builder.
Features include:
- Molecular modeller with automatic force-field based geometry optimization
- Molecular Mechanics including constraints and conformer searches
- Visualization of molecular orbitals and general isosurfaces
- Visualization of vibrations and plotting of vibrational spectra
- Support for crystallographic unit cells
- Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry
packages
- Flexible plugin architecture and Python scripting
File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as
Gaussian, GAMESS and MOLPRO output.
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ballview
free molecular modeling and molecular graphics tool
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Versions of package ballview |
Release | Version | Architectures |
stretch | 1.4.3~beta1-3 | amd64,arm64,armel,armhf,i386,mips,ppc64el,s390x |
buster | 1.5.0+git20180813.37fc53c-3 | amd64,arm64,i386 |
bullseye | 1.5.0+git20180813.37fc53c-6 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.5.0+git20180813.37fc53c-11 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.5.0+git20180813.37fc53c-11 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.4.2+20140406-1 | amd64,armel,armhf,i386 |
upstream | 1.5.0+git20220524.d85d2dd |
Debtags of package ballview: |
interface | x11 |
role | program |
uitoolkit | qt |
x11 | application |
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License: DFSG free
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BALLView provides fast OpenGL-based visualization of molecular structures,
molecular mechanics methods (minimization, MD simulation using the
AMBER, CHARMM, and MMFF94 force fields), calculation and visualization
of electrostatic properties (FDPB) and molecular editing features.
BALLView can be considered a graphical user interface on the basis of
BALL (Biochemical Algorithms Library) with a focus on the most common
demands of protein chemists and biophysicists in particular. It is
developed in the groups of Hans-Peter Lenhof (Saarland University,
Saarbruecken, Germany) and Oliver Kohlbacher (University of Tuebingen,
Germany). BALL is an application framework in C++ that has been
specifically designed for rapid software development in Molecular
Modeling and Computational Molecular Biology. It provides an extensive
set of data structures as well as classes for Molecular Mechanics,
advanced solvation methods, comparison and analysis of protein
structures, file import/export, and visualization.
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c2x
converter between DFT electronic structure codes formats
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Versions of package c2x |
Release | Version | Architectures |
bookworm | 2.40.e+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.35a+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.41.b+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.41.b+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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This program should convert CASTEP's .check, .castep_bin, orbitals and .cell
to various other formats, particularly so that they can be visualised with
Jmol, XCrysDen, gnuplot and other programs. It can extract charge and spin
densities, wavefunctions, symmetry operations, and much else besides. It also
interfaces with Abinit, Quantum Espresso, Siesta, VASP, and other electronic
structure codes.
The code can also manipulate .cell and .pdb files, building supercells,
performing shifts, adding vacuum and rolling nanotubes.
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cclib
Parsers and algorithms for computational chemistry
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Versions of package cclib |
Release | Version | Architectures |
bookworm | 1.6.2-2 | all |
bullseye | 1.6.2-2 | all |
buster | 1.6-1 | all |
stretch | 1.3.1-1 | all |
jessie | 1.1-1 | all |
trixie | 1.8-1 | all |
sid | 1.8-1 | all |
upstream | 1.8.1 |
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License: DFSG free
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A Python library that provides parsers for computational
chemistry log files. It also provides a platform to implement
algorithms in a package-independent manner.
This package contains helper scripts for end users.
If you are looking for the unit tests and data files managed by cclib,
they are distributed separately as in non-free package cclib-data.
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gabedit
graphical user interface to Ab Initio packages
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Versions of package gabedit |
Release | Version | Architectures |
bookworm | 2.5.1+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.8-1 | amd64,armel,armhf,i386 |
stretch | 2.4.8-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.8-3 | amd64,arm64,armhf,i386 |
bullseye | 2.5.1~20200828-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.5.1+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,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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gausssum
化学工具,解析和显示 Gaussian、GAMESS 等输出结果
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Versions of package gausssum |
Release | Version | Architectures |
bullseye | 3.0.2-2 | all |
jessie | 2.2.6.1-1 | all |
stretch | 3.0.1.1-1 | all |
buster | 3.0.2-1 | all |
bookworm | 3.0.2-2 | all |
trixie | 3.0.2-2 | all |
sid | 3.0.2-2 | all |
Debtags of package gausssum: |
field | chemistry |
role | program |
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License: DFSG free
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GaussSum 可以分析 ADF、GAMESS、GAMESS-UK、Gaussian、Jaguar 和 PC-GAMESS 的输出,
提取和计算有用的信息。
GaussSum 使用 GNUPlot 来显示结构优化过程、态密度谱图、UV-Vis谱图、IR/Raman谱图、原子
电荷密度变化图。它还能显示包含某一关键词的所有行,以及更多有用的功能。
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jmol
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Versions of package jmol |
Release | Version | Architectures |
bullseye | 14.6.4+2016.11.05+dfsg1-4 | all |
buster | 14.6.4+2016.11.05+dfsg1-4 | all |
jessie | 12.2.32+dfsg2-1 | all |
stretch | 14.6.4+2016.11.05+dfsg1-3 | all |
sid | 16.2.33+dfsg-1 | all |
trixie | 16.2.33+dfsg-1 | all |
bookworm | 14.32.83+dfsg-2 | all |
upstream | 16.2.37 |
Debtags of package jmol: |
field | chemistry |
role | program |
scope | utility |
use | viewing |
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License: DFSG free
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Jmol is a Java molecular viewer for three-dimensional chemical structures.
Features include reading a variety of file types and output from quantum
chemistry programs, and animation of multi-frame files and computed normal
modes from quantum programs. It includes with features for chemicals,
crystals, materials and biomolecules. Jmol might be useful for students,
educators, and researchers in chemistry and biochemistry.
File formats read by Jmol include PDB, XYZ, CIF, CML, MDL Molfile, Gaussian,
GAMESS, MOPAC, ABINIT, ACES-II, Dalton and VASP.
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python3-pycifrw
CIF/STAR file support for Python
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Versions of package python3-pycifrw |
Release | Version | Architectures |
bookworm | 4.4.4-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 4.4.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 4.4-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 4.4.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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PyCIFRW provides support for reading and writing CIF (Crystallographic
Information Format) files using Python.
The specifications found in Vol G of the International Tables for
Crystallography were used as a reference for CIF 1.0/1.1 syntax.
http://dx.doi.org/10.1107/S1600576715021871 was used as the CIF 2.0
reference.
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travis
trajectory analyzer and visualizer
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Versions of package travis |
Release | Version | Architectures |
bullseye | 200504+hf2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 220729-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 220729-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 220729-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 140902-1 | amd64,armel,armhf,i386 |
stretch | 161013-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 190101-1 | amd64,arm64,armhf,i386 |
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License: DFSG free
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TRAVIS (Trajectory Analyzer and Visualizer) is a free tool for analyzing
and visualizing trajectories from all kinds of Molecular Dynamics or
Monte Carlo simulations. The aim of TRAVIS is to collect as many analyses
as possible in one program, creating a powerful tool and making it
unnecessary to use many different programs for evaluating simulations.
This should greatly rationalize and simplify the workflow of analyzing
trajectories. The following analysis functions are available:
Static (time independent) Functions:
- Radial, Angular, Dihedreal or Combined Distribution Function
- Point-Plane or Point-Line Distance Distribution
- Plane Projection Distribution
- Fixed Plane Density Profile
- Density, Spatial or Dipole Distribution Function
Dynamic (time dependent) Functions:
- Velocity Distribution Function
- Mean Square Displacement / Diffusion Coefficients
- Velocity Autocorrelation Functions
- Vector Reorientation Dynamics
- Van Hove Correlation Function
- Aggregation Functions (DACF, DLDF, DDisp)
Spectroscopic Functions:
- Calculate Power Spectrum
- Calculate IR Spectrum
- Calculate Raman Spectrum
TRAVIS can read trajectory files in XYZ, PDB, LAMMPS or DLPOLY format.
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viewmol
graphical front end for computational chemistry programs
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Versions of package viewmol |
Release | Version | Architectures |
jessie | 2.4.1-22 | amd64,armel,armhf,i386 |
buster | 2.4.1-25 | amd64,arm64,armhf,i386 |
stretch | 2.4.1-24 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package viewmol: |
field | chemistry |
interface | 3d, x11 |
role | program |
uitoolkit | motif |
use | learning, viewing |
x11 | application |
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License: DFSG free
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Viewmol is able to graphically aid in the generation of molecular
structures for computations and to visualize their results.
At present Viewmol includes input filters for Discover, DMol3, Gamess,
Gaussian 9x/03, Gulp, Mopac, PQS, Turbomole, and Vamp outputs as well as
for PDB files. Structures can be saved as Accelrys' car-files, MDL files,
and Turbomole coordinate files. Viewmol can generate input files for
Gaussian 9x/03. Viewmol's file format has been added to OpenBabel so that
OpenBabel can serve as an input as well as an output filter for
coordinates.
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xcrysden
Crystalline and Molecular Structure Visualizer
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Versions of package xcrysden |
Release | Version | Architectures |
jessie | 1.5.60-1 | amd64,armel,armhf,i386 |
stretch | 1.5.60-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 1.6.3~rc2 |
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License: DFSG free
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XCrySDen is a crystalline and molecular structure visualisation
program, which aims at display of isosurfaces and contours, which can
be superimposed on crystalline structures and interactively rotated
and manipulated. It can run on most UNIX platforms, without any
special hardware requirements.
XCrySDen allows for real-time capture of display. Several movie encoders
are supported, in particular for Animated-GIF convert (imagemagick),
gifsicle, or whirlgif are necessary. For AVI/MPEG mencoder or
ppmtompeg (netpbm) is required. For window dumps either imagemagick or
xwd (x11-apps) needs to be present.
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