DebiChem Project
Summary
The DebiChem Pure Blend contains 113 packages which are grouped by metapackages. Each metapackage will cause the installation of packages for a specific topic. The following table lists the metapackages of DebiChem

Tasks page

This is a list of the Tasks DebiChem is made of:

Table of contents

Analytical biochemistry - DebiChem Analytical BioChemistry

This metapackage will install packages which enable you to:

  • load and convert mass spectrometric data files;
  • edit biopolymer sequences;
  • elaborate complex mass spectrometry workflows;
  • perform protein database searches using tandem-ms data;
  • visualize and explore mass spectrometric data;
  • simulate isotopic clusters;
  • implement proteomics workflows.

Official Debian packages with high relevance

Libmstoolkit-tools
libraries for manipulating mass spectrometry data - tools
Libpwiz-tools
ProteoWizard command line tools
Lutefisk
de novo interpretation of peptide CID spectra
Massxpert
polymer chemistry modelling and mass spectrometry data simulation (runtime)
Minexpert2
MS^n mass spectrometric data visualization and mining (runtime)
Mmass
Mass spectrometry tool for proteomics
Openms
package for LC/MS data management and analysis
Python3-pymzml
mzML mass spectrometric data parsing (Python 3.x)
R-cran-maldiquant
GNU R package for quantitative analysis of mass spectrometry data
R-cran-maldiquantforeign
GNU R package providing import/export routines for MALDIquant
R-cran-mixtools
GNU R tools for analyzing finite mixture models
R-cran-readbrukerflexdata
GNU R package to read Bruker Daltonics *flex format files
R-cran-readmzxmldata
GNU R package to read mass spectrometry data in mzXML format
R-other-amsmercury
efficient calculation of accurate masses and abundances of isotopic peaks
R-other-curvefdp
estimation of confidence levels for peptide identifications
R-other-iwrlars
least angle regression, lasso, positive lasso and forward stagewise
R-other-nitpick
peak identification for mass spectrometry data
Tandem-mass
mass spectrometry software for protein identification
Toppic
Top-down proteoform identification and characterization (programs)
Xtpcpp
Transitional package from xtpcpp to i2masschroq

Official Debian packages with lower relevance

Libisospec++-dev
Isotopic fine structure calculator (C++ development files)
Libpwiz-dev
library to perform proteomics data analyses (devel files)
Libpwizlite-dev
Library to load mzML/mzXML files (dev files)

Packaging has started and developers might try the packaging code in VCS

Biceps
error-tolerant peptide identification

Cheminformatics - DebiChem Cheminformatics

This metapackage will install cheminformatics packages useful for chemists.

Official Debian packages with high relevance

Libcdk-java
Chemistry Development Kit (CDK) Java libraries
Libopenchemlib-java
framework providing cheminformatics core functionality
Libopsin-java
Chemical name to structure converter
Liboscar4-java
automated annotation of chemistry in scientific articles
Openbabel
Chemical toolbox utilities (cli)
Osra
optical structure recognition
Python3-indigo
Organic Chemistry Toolkit (Python module)
Python3-openbabel
Chemical toolbox library (Python bindings)
Python3-rdkit
Collection of cheminformatics and machine-learning software
Smiles-scripts
command line tools to handle SMILES descriptors

Crystallography - DebiChem crystallography

This metapackage will install packages for crystallography which might be useful for chemists.

Official Debian packages with high relevance

Drawxtl
crystal structure viewer
Gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
Gcrystal
lightweight crystal structures visualizer
Python3-fabio
I/O library for images produced by 2D X-ray detector - Python3
Shelxle
graphical user interface for SHELXL
Xcrysden
Crystalline and Molecular Structure Visualizer

C/c++/fortran development - DebiChem C/C++/Fortran Development

This metapackage will install development packages useful for chemists.

Official Debian packages with high relevance

Libblas-dev
Basic Linear Algebra Subroutines 3, static library
Libbtas-dev
Basic Tensor Algebra Subroutines Library (development files)
Libdbcsr-dev
Distributed Block Compressed Sparse Row matrix library
Libelpa-dev
Eigenvalue SoLvers for Petaflop-Applications (Development version)
Libfftw3-dev
Library for computing Fast Fourier Transforms - development
Libga-dev
C++ Library of Genetic Algorithm Components
Libint-dev
Evaluate the integrals in modern atomic and molecular theory (devel)
Libint2-dev
Computation Chemistry Integral Evaluation Library (development files)
Liblapack-dev
Library of linear algebra routines 3 - static version
Libmadness-dev
Numerical Environment for Scientific Simulation (development files)
Libopenmm-dev
C++ header files for the OpenMM library
Libpsi3-dev
Quantum Chemical Program Suite (Development Libraries)
Libsc-dev
Scientific Computing Toolkit (development files)
Libscalapack-mpi-dev
Scalable Linear Algebra Package - Dev files for MPI
Libsymspg-dev
C library for crystal symmetry determination (development files)
Libtiledarray-dev
Block-Sparse Tensor Library (development files)
Libxc-dev
Library of Exchange-Correlation Functionals (development files)
Mpi-default-dev
Standard MPI development files (metapackage)

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.

Official Debian packages with high relevance

Ase
Atomic Simulation Environment
Avogadro
Molecular Graphics and Modelling System
Ballview
free molecular modeling and molecular graphics tool
C2x
converter between DFT electronic structure codes formats
Cclib
Parsers and algorithms for computational chemistry
Gabedit
graphical user interface to Ab Initio packages
Gausssum
parse and display Gaussian, GAMESS, and etc's output
Jmol
Molecular Viewer
Python3-pycifrw
CIF/STAR file support for Python
Travis
trajectory analyzer and visualizer
Viewmol
graphical front end for computational chemistry programs
Xcrysden
Crystalline and Molecular Structure Visualizer

Molecular ab initio calculations - DebiChem Molecular Ab Initio Calculations

This metapackage will install packages doing molecular ab initio calculations which might be useful for chemists.

Official Debian packages with high relevance

Aces3
Advanced Concepts in Electronic Structure III
Bagel
Computational Chemistry Package
Chemps2
Executable to call libchemps2-3 from the command line
Cp2k
Ab Initio Molecular Dynamics
Elk-lapw
All-Electron Density-Functional Electronic Structure Code
Ergo
Quantum chemistry program for large-scale calculations
Mpqc
Massively Parallel Quantum Chemistry Program
Mpqc3
Massively Parallel Quantum Chemistry Program
Nwchem
High-performance computational chemistry software (default MPI)
Openmolcas
Quantum chemistry software package
Psi3
Quantum Chemical Program Suite
Psi4
Quantum Chemical Program Suite

Molecular dynamics - DebiChem Molecular Dynamics

This metapackage will install Molecular Dynamics packages which might be useful for chemists.

Official Debian packages with high relevance

Adun.app
Molecular Simulator for GNUstep (GUI)
Cp2k
Ab Initio Molecular Dynamics
Gromacs
Molecular dynamics simulator, with building and analysis tools
Lammps
Molecular Dynamics Simulator
Nwchem
High-performance computational chemistry software (default MPI)
Votca
Molecular dynamics analysis - coarse-graining and charge transport

Packaging has started and developers might try the packaging code in VCS

Dl-poly-classic
General purpose molecular dynamics simulation package

Molecular modelling - DebiChem 3D Molecular Modelling and Visualization

This metapackage will install 3D Molecular Modelling and Visualization which might be useful for chemists.

Official Debian packages with high relevance

Avogadro
Molecular Graphics and Modelling System
Ballview
free molecular modeling and molecular graphics tool
Ghemical
GNOME molecular modelling environment
Mmb
model the structure and dynamics of macromolecules
Openstructure
Open-Source Computational Structural Biology Framework
Promod3
protein homology modelling engine
Pymol
Molecular Graphics System

No known packages available

Nmoldyn
interactive analysis program for Molecular Dynamics simulations

Periodic ab initio calculations - DebiChem Periodic Ab Initio Calculations

This metapackage will install packages doing periodic ab initio calculations which might be useful for chemists.

Official Debian packages with high relevance

Abinit
package for electronic structure calculations
Cp2k
Ab Initio Molecular Dynamics
Gpaw
DFT and beyond within the projector-augmented wave method
Nwchem
High-performance computational chemistry software (default MPI)
Openmx
package for nano-scale material simulations
Quantum-espresso
Electronic-Structure and Ab-Initio Molecular Dynamics Suite
Wannier90
Maximally Localized Wannier Functions - executables

Semi empirical calculations - DebiChem Semi Empirical

This metapackage will install Semi Empirical which might be useful for chemists.

Official Debian packages with high relevance

Cp2k
Ab Initio Molecular Dynamics
Molds
Semi-empirical electronic structure and molecular dynamics
Mopac
Molecular Orbital PACkage (MOPAC)
Mopac7-bin
Semi-empirical Quantum Chemistry Library (binaries)
Xtb
semiempirical extended tight-binding program package

Chemical formula/structure editors - DebiChem chemical formular/structure editors

This metapackage will install drawers for chemical structures which might be useful for chemists.

Official Debian packages with high relevance

Bkchem
Chemical structures editor
Chemtool
chemical structures drawing program
Easychem
Draw high-quality molecules and 2D chemical formulas
Gchempaint
2D chemical structures editor for the GNOME2 desktop
Osra
optical structure recognition
Xdrawchem
Chemical structures and reactions editor

3d visualization - DebiChem 3D Viewers

This metapackage will install 3D Viewers which might be useful for chemists.

Official Debian packages with high relevance

Adun.app
Molecular Simulator for GNUstep (GUI)
Avogadro
Molecular Graphics and Modelling System
Ballview
free molecular modeling and molecular graphics tool
Cclib
Parsers and algorithms for computational chemistry
Drawxtl
crystal structure viewer
Gabedit
graphical user interface to Ab Initio packages
Gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
Garlic
visualization program for biomolecules
Gausssum
parse and display Gaussian, GAMESS, and etc's output
Gdis
molecular and crystal model viewer
Gdpc
visualiser of molecular dynamic simulations
Jmol
Molecular Viewer
Kalzium
periodic table and chemistry tools
Qutemol
interactive visualization of macromolecules
Rasmol
visualization of biological macromolecules
Raster3d
tools for generating images of proteins or other molecules
Shelxle
graphical user interface for SHELXL
V-sim
Visualize atomic structures
Viewmol
graphical front end for computational chemistry programs
Xbs
3-d models and movies of molecules
Xcrysden
Crystalline and Molecular Structure Visualizer
Xmakemol
program for visualizing atomic and molecular systems