DebiChem Project
Summary
Cheminformatics
chimio-informatique de DebiChem

Ce métapaquet installe les paquets de chimio-informatique utiles pour les chimistes.

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 Cheminformatics packages

Official Debian packages with high relevance

Libcdk-java
Chemistry Development Kit (CDK) Java libraries
Versions of package libcdk-java
ReleaseVersionArchitectures
squeeze1.0.2-5all
sid2.3.134.g1bb9a64587-2all
wheezy1.2.10-3all
jessie1.2.10-6all
stretch1.2.10-6all
buster1.2.10-7all
bullseye2.3.134.g1bb9a64587-2all
upstream2.5.12.g7c7a2c71c8
Debtags of package libcdk-java:
devellang:java, library
fieldchemistry
roledevel-lib
Popcon: 2 users (8 upd.)*
Newer upstream!
License: DFSG free
Git

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.

Please cite: C. Steinbeck, Y. Han, S. Kuhn, O. Horlacher, E. Luttmann and E. L. Willighagen: The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. (2003)
Libopenchemlib-java
framework providing cheminformatics core functionality
Versions of package libopenchemlib-java
ReleaseVersionArchitectures
bullseye2021.2.0+dfsg-1all
sid2021.2.0+dfsg-1all
upstream2021.5.4
Popcon: 0 users (0 upd.)*
Newer upstream!
License: DFSG free
Git

OpenChemLib is Java based framework providing cheminformatics core functionality and user interface components. Its main focus is on organics chemistry and small molecules. It is built around a StereoMolecule class, which represents a molecule using atom and bond tables, provides atom neighbours, ring and aromaticity information, and supports MDL's concept of enhanced stereo representation. Additional classes provide, 2D-depiction, descriptor calculation, molecular similarity and substructure search, reaction search, property prediction, conformer generation, support for molfile and SMILES formats, energy minimization, ligand-protein interactions, and more. OpenChemLib's idcode represents molecules, fragments or reactions as canonical, very compact string that includes stereo and query features.

Different to other cheminformatics frameworks, OpenChemLib also provides user interface components that allow one to easily embed chemical functionality into Java applications, e.g. to display or edit chemical structures or reactions.

Libopsin-java
Chemical name to structure converter
Versions of package libopsin-java
ReleaseVersionArchitectures
stretch1.5.0-1all
wheezy1.2.0-1all
bullseye2.5.0-1all
sid2.5.0-1all
buster2.3.1-1all
jessie1.5.0-1all
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

OPSIN (Open Parser for Systematic IUPAC Nomenclature) converts IUPAC compound names to semantic chemical information and outputs a structure either as CML (Chemical Markup Language), SMILES, or InChI.

This package contains the Java library.

Openbabel
boîte à outils de chimie – interface en ligne de commande
Versions of package openbabel
ReleaseVersionArchitectures
stretch2.3.2+dfsg-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze2.2.3-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy2.3.1+dfsg-4amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie2.3.2+dfsg-2amd64,armel,armhf,i386
buster2.4.1+dfsg-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye3.1.1+dfsg-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid3.1.1+dfsg-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package openbabel:
fieldchemistry
interfacecommandline
roleprogram
scopeutility
useconverting
Popcon: 84 users (32 upd.)*
Versions and Archs
License: DFSG free
Git

Open Babel est une boite à outils dans le domaine de la chimie. Elle a été conçue pour prendre en charge les nombreux langages des données chimiques. Elle permet de rechercher, convertir, analyser ou bien stocker les données de modélisation moléculaire, de chimie, de matériaux solides, de biochimie ou de domaines connexes. Les fonctionnalités comprennent :

 − ajout ou suppression d'hydrogène ;
 − gestion de la dynamique moléculaire ;
 − gestion de la syntaxe de reconnaissance moléculaire SMARTS ;
 − perception automatique des propriétés (cycles, liaisons,
    hybridation ou aromaticité) ;
 − typage flexible des atomes et perception des liaisons multiples
    d'après les coordonnées atomiques ;
 − calcul de charge partielle de Gasteiger-Marsili.

Les formats de fichiers traités par Open Babel comprennent : PDB, XYZ, CIF, CML, SMILES, MDL, Molfile, ChemDraw, Gaussian, GAMESS, MOPAC et MPQC.

Ce paquet comprend les utilitaires suivants :

 – obabel : conversion entre divers formats de fichiers de chimie ;
 – obenergy : calcul de l'énergie d'une molécule ;
 – obminimize : optimisation de la géométrie, minimisation de l'énergie
                d'une molécule ;
 – obgrep : programme de recherche moléculaire utilisant le modèle
            SMARTS ;
 – obgen : génération des coordonnées en 3D d'une molécule ;
 – obprop : affichage des propriétés standard d'une molécule ;
 – obfit : superposition de deux molécules à partir d'un modèle ;
 – obrotamer : génération de coordonnées de conformères ou rotamères ;
 – obconformer : génération de conformères de faible énergie ;
 – obchiral : affichage des informations de chiralité moléculaire ;
 – obrotate : notation d’angle dièdre de molécules en mode automatique
              (batch) ;
 – obprobe : création d’une grille de sonde électrostatique.
Screenshots of package openbabel
Python3-indigo
Organic Chemistry Toolkit (Python module)
Versions of package python3-indigo
ReleaseVersionArchitectures
sid1.2.3-3.1all
bullseye1.2.3-3.1all
Popcon: 0 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

Indigo is a C++ based organic chemistry and cheminformatics software environment. Features Include:

  • Molecule and reaction rendering including SVG support
  • Automatic layout for SMILES-represented molecules and reactions
  • Canonical (isomeric) SMILES computation
  • Exact matching, substructure matching, SMARTS matching
  • Matching of tautomers and resonance structures
  • Molecule fingerprinting, molecule similarity computation
  • Fast enumeration of SSSR rings, subtrees, and edge sugraphs
  • Molecular weight, molecular formula computation
  • R-Group deconvolution and scaffold detection
  • Computation of the exact maximum common substructure for an arbitrary amount of input structures
  • Combinatorial chemistry
  • Plugin support in the API

File formats Indigo support include MDL Mol, SDF, RDF, CML, SMILES and SMARTS.

This package contains the Python modules.

Python3-openbabel
Chemical toolbox library (Python bindings)
Versions of package python3-openbabel
ReleaseVersionArchitectures
sid3.1.1+dfsg-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.1.1+dfsg-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 0 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Python3-rdkit
Collection of cheminformatics and machine-learning software
Versions of package python3-rdkit
ReleaseVersionArchitectures
sid202009.5-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye202009.4-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream202103.2
Popcon: 8 users (1 upd.)*
Newer upstream!
License: DFSG free
Git

RDKit is a Python/C++ based cheminformatics and machine-learning software environment. Features Include:

  • Chemical reaction handling and transforms
  • Substructure searching with SMARTS
  • Canonical SMILES
  • Molecule-molecule alignment
  • Large number of molecular descriptors, including topological, compositional, EState, SlogP/SMR, VSA and Feature-map vectors
  • Fragmentation using RECAP rules
  • 2D coordinate generation and depiction, including constrained depiction
  • 3D coordinate generation using geometry embedding
  • UFF and MMFF94 forcefields
  • Chirality support, including calculation of (R/S) stereochemistry codes
  • 2D pharmacophore searching
  • Fingerprinting, including Daylight-like, atom pairs, topological torsions, Morgan algorithm and MACCS keys
  • Calculation of shape similarity
  • Multi-molecule maximum common substructure
  • Machine-learning via clustering and information theory algorithms
  • Gasteiger-Marsili partial charge calculation

File formats RDKit supports include MDL Mol, PDB, SDF, TDT, SMILES and RDKit binary format.

Registry entries: SciCrunch  OMICtools 
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 203033