Tasks page

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

Table of contents

• Analytical biochemistry
• Cheminformatics
• Crystallography
• C/c++/fortran development
• Input preparation and output processing
• Molecular ab initio calculations
• Molecular dynamics
• Molecular modelling
• Periodic ab initio calculations
• Semi empirical calculations
• Chemical formula/structure editors
• 3d visualization

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

Comet-ms

Tandem mass spectrometry (MS/MS) search engine

Freesasa

Solvent Accessible Surface Area of biomolecules

Libmstoolkit-tools

libraries for manipulating mass spectrometry data - tools

Libpwiz-tools

ProteoWizard command line tools

Lutefisk

de novo interpretation of peptide CID spectra

Massxpert

transitional package for massxpert -> massxpert2

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

C++ version of X!TandemPipeline

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

Libchemicaltagger-java

tool for semantic text-mining in chemistry

Libinchi-bin

International Chemical Identifier (InChI) algorithm (executable)

Libjni-inchi-java

Java Native Interface wrapper for InChI

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

Gemmi

library for structural biology - executable

Libmmtf-java

Java API for macromolecular transmission format encoder/decoder

Pdb-tools

tools for manipulating and editing PDB files

Python3-fabio

I/O library for images produced by 2D X-ray detector - Python3

Python3-phonopy

phonon calculations at harmonic and quasi-harmonic levels (Python 3)

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

Libsimtkmolmodel-dev

C++ API for creating molecular models for SimTK (development files)

Libsymspg-dev

C library for crystal symmetry determination (development files)

Libtiledarray-dev

Block-Sparse Tensor Library (development files)

Libtrexio-dev

TREX I/O library for efficient data I/O in quantum chemistry.

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

??? missing short description for package aces3 :-(

Bagel

Computational Chemistry Package

Chemps2

Executable to call libchemps2-3t64 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

??? missing short description for package nwchem :-(

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

Cpptraj

fast, parallelized molecular dynamics trajectory data analysis

Gromacs

Molecular dynamics simulator, with building and analysis tools

Lammps

Molecular Dynamics Simulator

Nwchem

??? missing short description for package nwchem :-(

Python3-parmed

parameter and topology file editor and molecular mechanical simulator

Python3-prody

Python package for protein dynamics analysis

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

??? missing short description for package nwchem :-(

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