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

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

Description

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

DebiChem Input preparation and output processing packages

Official Debian packages with high relevance

Ase
Atomic Simulation Environment
Versions of package ase
ReleaseVersionArchitectures
buster3.17.0-2all
bullseye3.20.1-1all
sid3.20.1-1all
Popcon: 18 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

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

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

This package provides the executable scripts.

Avogadro
sistema de modelagem e gráficos moleculares
Versions of package avogadro
ReleaseVersionArchitectures
jessie1.0.3-10.1amd64,armel,armhf,i386
stretch1.2.0-1+deb9u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.2.0-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.93.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze1.0.1-3amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy1.0.3-5amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
sid1.93.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package avogadro:
fieldchemistry
roleprogram
uitoolkitqt
useviewing
Popcon: 90 users (23 upd.)*
Versions and Archs
License: DFSG free
Git

Avogadro é um sistema de modelagem e gráficos moleculares para moléculas e biomoléculas. Pode visualizar propriedades como orbitais moleculares ou potenciais eletrostáticos e tem um construtor molecular intuitivo.

Inclui os seguintes recursos:

  • Modelador molecular com otimização automática de geometria baseada em campo de força;

  • Mecânica molecular incluindo restrições e buscas de confórmeros;

  • Visualização de orbitais moleculares e isosuperfícies gerais;
  • Visualização de vibrações e plotagem de espectro vibracional;
  • Suporte para células unitárias cristalográficas;
  • Geração de entrada para os pacotes de química quântica Gaussian, GAMESS e MOLPRO;

  • Arquitetura de extensões flexível e scripts em Python.

Os formatos de arquivos que o Avogadro pode ler incluem PDB, XYZ, CML, CIF, Molden, assim como a saída dos pacotes Gaussian, GAMESS e MOLPRO.

Please cite: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison: Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. (eprint) J. Cheminf. 4:17 (2012)
Registry entries: Bio.tools  SciCrunch  OMICtools 
Other screenshots of package avogadro
VersionURL
1.0.1-3+b1https://screenshots.debian.net/screenshots/000/008/025/large.png
Screenshots of package avogadro
Ballview
ferramenta livre de modelagem e gráficos moleculares
Versions of package ballview
ReleaseVersionArchitectures
wheezy1.4.1+20111206-4amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
stretch1.4.3~beta1-3amd64,arm64,armel,armhf,i386,mips,ppc64el,s390x
buster1.5.0+git20180813.37fc53c-3amd64,arm64,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.5.0+git20180813.37fc53c-6amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x
sid1.5.0+git20180813.37fc53c-6amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x
squeeze1.3.2-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie1.4.2+20140406-1amd64,armel,armhf,i386
Debtags of package ballview:
interfacex11
roleprogram
uitoolkitqt
x11application
Popcon: 10 users (17 upd.)*
Versions and Archs
License: DFSG free
Git

Visualização rápida baseada em OpenGL de estruturas moleculares, métodos de mecânica molecular (minimização, simulação MD usando os campos de força Amber, Charmm e MMFF94), cálculo e visualização de propriedades eletrostáticas (FDPB) e recursos de edição molecular.

Pode ser considerada uma interface gráfica de usuário construída sobre o Ball (Biochemical Algorithms Library, Biblioteca de Algoritmos Bioquímicos), com foco nas demandas mais comuns de químicos proteicos e biofísicos em particular. Foi desenvolvido nos grupos Hans-Peter Lenhof (Universidade Saarland, Saarbruecken, Alemanha) e Oliver Kohlbacher (Universidade de Tübingen, Alemanha). O Ball é uma infraestrutura em C++ especificamente projetada para desenvolvimento rápido de programas de modelagem molecular e Biologia molecular computacional. Fornece um conjunto amplo de estruturas de dados e classes para Mecânica molecular, métodos avançados de solvatação, comparação e análise de estruturas proteicas, importação/exportação de arquivos e visualização.

Please cite: Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof and Oliver Kohlbacher: BALLView: a tool for research and education in molecular modeling. (PubMed,eprint) Bioinformatics 22(3):365-366 (2006)
Registry entries: SciCrunch  OMICtools 
Screenshots of package ballview
Cclib
Parsers and algorithms for computational chemistry
Versions of package cclib
ReleaseVersionArchitectures
stretch1.3.1-1all
buster1.6-1all
bullseye1.6.2-2all
sid1.6.2-2all
wheezy1.0.1-2all
jessie1.1-1all
upstream1.6.4
Popcon: 14 users (4 upd.)*
Newer upstream!
License: DFSG free
Git

A Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner.

This package contains helper scripts for end users.

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

Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. (eprint) J. Comp. Chem. 29(5):839-845 (2008)
Gabedit
graphical user interface to Ab Initio packages
Versions of package gabedit
ReleaseVersionArchitectures
jessie2.4.8-1amd64,armel,armhf,i386
squeeze2.2.12-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
sid2.5.1~20200828-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye2.5.1~20200828-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.4.8-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy2.4.2-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
stretch2.4.8-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package gabedit:
fieldchemistry
roleprogram
uitoolkitgtk
Popcon: 19 users (13 upd.)*
Versions and Archs
License: DFSG free
Git

Gabedit is a graphical user interface to computational chemistry packages like:

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

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

Please cite: Abdul-Rahman Allouche: Gabedit - A graphical user interface for computational chemistry softwares. (eprint) J. Comp. Chem. 32:174-182 (2011)
Gausssum
parse and display Gaussian, GAMESS, and etc's output
Versions of package gausssum
ReleaseVersionArchitectures
buster3.0.2-1all
sid3.0.2-2all
squeeze2.2.4-1all
wheezy2.2.5-2all
jessie2.2.6.1-1all
stretch3.0.1.1-1all
bullseye3.0.2-2all
Debtags of package gausssum:
fieldchemistry
roleprogram
Popcon: 15 users (4 upd.)*
Versions and Archs
License: DFSG free
Git

GaussSum parses the output files of ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar and PC GAMESS calculations to extract useful information.

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

Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. J. Comp. Chem. 29(5):839-845 (2008)
Jmol
visualizador molecular
Versions of package jmol
ReleaseVersionArchitectures
buster14.6.4+2016.11.05+dfsg1-4all
wheezy12.2.32+dfsg2-1all
jessie12.2.32+dfsg2-1all
stretch14.6.4+2016.11.05+dfsg1-3all
bullseye14.6.4+2016.11.05+dfsg1-4all
sid14.6.4+2016.11.05+dfsg1-4all
Debtags of package jmol:
fieldchemistry
roleprogram
scopeutility
useviewing
Popcon: 74 users (45 upd.)*
Versions and Archs
License: DFSG free
Git

Jmol é um visualizador molecular desenvolvido em Java para estruturas químicas tridimensionais. Seus recursos incluem a leitura de uma variedade de tipos de arquivos, a saída de programas de química quântica, animação de arquivos multi-quadro e modos normais calculados a partir de programas quânticos. Inclui recursos para produtos químicos, cristais, materiais e biomoléculas. Jmol pode ser útil para estudantes, professores e pesquisadores em química e bioquímica.

Os formatos de arquivos lidos pelo Jmol incluem PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton e VASP.

Please cite: A. Herráez: Biomolecules in the computer: Jmol to the rescue. (PubMed,eprint) Biochem Mol Biol Educ. 34(4):255-261 (2006)
Registry entries: SciCrunch  OMICtools 
Screenshots of package jmol
Travis
trajectory analyzer and visualizer
Versions of package travis
ReleaseVersionArchitectures
jessie140902-1amd64,armel,armhf,i386
sid200504+hf2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye200504+hf2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster190101-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch161013-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 5 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

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

Static (time independent) Functions:

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

Dynamic (time dependent) Functions:

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

Spectroscopic Functions:

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

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

Please cite: Martin Brehm and Barbara Kirchner: TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories. (eprint) J. Chem. Inf. Model. 51(8):2007-2023 (2011)
Viewmol
graphical front end for computational chemistry programs
Versions of package viewmol
ReleaseVersionArchitectures
squeeze2.4.1-15amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc
sid2.4.1-26amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.4.1-25amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch2.4.1-24amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie2.4.1-22amd64,armel,armhf,i386
wheezy2.4.1-18amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package viewmol:
fieldchemistry
interface3d, x11
roleprogram
uitoolkitmotif
uselearning, viewing
x11application
Popcon: 32 users (10 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Registry entries: SciCrunch  OMICtools 
Screenshots of package viewmol
Xcrysden
visualizador de estrutura molecular e cristalina
Versions of package xcrysden
ReleaseVersionArchitectures
jessie1.5.60-1amd64,armel,armhf,i386
stretch1.5.60-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy1.5.53-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
bullseye1.6.2-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.6.2-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream1.6.3~rc1
Popcon: 14 users (2 upd.)*
Newer upstream!
License: DFSG free
Git

XCrySDen é um programa de visualização de estrutura molecular e cristalina que tem o objetivo de exibir isosuperfícies e contornos, que podem ser sobrepostos em estruturas cristalinas e interativamente rotacionadas e manipuladas. Ele pode ser executado na maioria das plataformas UNIX sem quaisquer requisitos especiais de hardware.

XCrySDen permite a captura em tempo real de exibição. Vários codificadores de filme são suportados, em particular são necessários para conversão de GIF animado (imagemagick), gifsicle ou whirlgif. É necessário para AVI/MPEG mencoder ou ppmtompeg (netpbm). Precisa estar presente para a janela de *dumps", imagemagick ou xwd (x11-apps).

Screenshots of package xcrysden
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 200793