DebiChem Project
Summary
Cheminformatics
DebiChem Cheminformatics

This metapackage will install cheminformatics packages 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 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
wheezy1.2.10-3all
bullseye1.2.10-7all
sid1.2.10-7all
buster1.2.10-7all
stretch1.2.10-6all
jessie1.2.10-6all
upstream1.4.19
Debtags of package libcdk-java:
devellang:java, library
fieldchemistry
roledevel-lib
Popcon: 0 users (0 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)
Libopsin-java
Chemical name to structure converter
Versions of package libopsin-java
ReleaseVersionArchitectures
stretch1.5.0-1all
buster2.3.1-1all
wheezy1.2.0-1all
sid2.4.0-1all
bullseye2.4.0-1all
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
Chemical toolbox utilities (cli)
Versions of package openbabel
ReleaseVersionArchitectures
wheezy2.3.1+dfsg-4amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
bullseye2.4.1+dfsg-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.4.1+dfsg-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.4.1+dfsg-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch2.3.2+dfsg-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie2.3.2+dfsg-2amd64,armel,armhf,i386
squeeze2.2.3-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Debtags of package openbabel:
fieldchemistry
interfacecommandline
roleprogram
scopeutility
useconverting
Popcon: 72 users (79 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 includes the following utilities:

  • babel: Convert between various chemical file formats
  • obenergy: Calculate the energy for a molecule
  • obminimize: Optimize the geometry, minimize the energy for a molecule
  • obgrep: Molecular search program using SMARTS pattern
  • obgen: Generate 3D coordinates for a molecule
  • obprop: Print standard molecular properties
  • obfit: Superimpose two molecules based on a pattern
  • obrotamer: Generate conformer/rotamer coordinates
  • obconformer: Generate low-energy conformers
  • obchiral: Print molecular chirality information
  • obrotate: Rotate dihedral angle of molecules in batch mode
  • obprobe: Create electrostatic probe grid
Screenshots of package openbabel
Python-chemfp
cheminformatics fingerprints file formats and tools
Versions of package python-chemfp
ReleaseVersionArchitectures
bullseye1.1p1-2.1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
wheezy1.0-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.1p1-2.1amd64,armel,armhf,i386
stretch1.1p1-2.1amd64,armel,i386,mips64el,ppc64el,s390x
buster1.1p1-2.1amd64,armel,i386,mips64el,ppc64el,s390x
sid1.1p1-2.1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 2 users (1 upd.)*
Versions and Archs
License: DFSG free
Svn

Chem-fingerprints is a set of formats and related tools for the storage, exchange, and search of cheminformatics fingerprint data sets.

It translates fingerprints from the OpenBabel and RDKIT and cheminformatics packages (as well as the proprietary OEChem package) into the binary FPS format.

Besides Python modules, it provides the following tools:

  • sdf2fps - Extract fingerprint data from SD tags
  • ob2fps - Use OpenBabel to generate fingerprints from structures
  • rdkit2fps - Use RDKit to generate fingerprints from structures
  • oe2fps - Use OEChem/OEGraphSim to generate fingerprints from structures
  • simsearch - Do threshold or k-nearest neighbor Tanimoto similarity searches between two FPS files
Python-cinfony
Python abstraction layer to cheminformatics toolkits
Versions of package python-cinfony
ReleaseVersionArchitectures
jessie1.2-1all
sid1.2-4all
bullseye1.2-3all
buster1.2-1all
stretch1.2-1all
wheezy1.1-1all
Popcon: 3 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

Cinfony provides a common Python interface to various cheminformatics toolkits. This makes it possible to use the complementary features of cheminformatics toolkits using a common interface. If functionality is provided by more than one toolkit, the Cinfony user can choose the implementation they prefer.

Cinfony supports the following toolkits:

  • OpenBabel
  • RDKit
  • CDK
  • Indigo

Cinfony also includes the Opsin module for translating IUPAC names to chemical data and the Webel web services module.

Please cite: N. M. O'Boyle and G. R. Hutchison: Cinfony - combining Open Source cheminformatics toolkits behind a common interface. (eprint) Chem. Cent. J. 2(1):24 (2008)
Python-fmcs
Find Maximum Common Substructure
Versions of package python-fmcs
ReleaseVersionArchitectures
wheezy1.0-1all
jessie1.0-1all
stretch1.0-1all
buster1.0-1all
sid1.0-1all
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Svn

Fcms finds the maximum common substructure (MCS) of a group (or cluster) of chemical structures and report the result as a SMARTS string.

More specifically, the MCS found is a common edge subgraph, and not a common induced subgraph. Only connected MCSes are found.

Python-indigo
Organic Chemistry Toolkit (Python module)
Versions of package python-indigo
ReleaseVersionArchitectures
stretch1.1.12-2all
sid1.2.3-1all
bullseye1.2.3-1all
jessie1.1.12-1all
buster1.2.3-1all
wheezy1.0.0-2all
Popcon: 0 users (2 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.

Python-openbabel
Chemical toolbox library (python bindings)
Versions of package python-openbabel
ReleaseVersionArchitectures
sid2.4.1+dfsg-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
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
squeeze2.2.3-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
stretch2.3.2+dfsg-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.4.1+dfsg-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.4.1+dfsg-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package python-openbabel:
devellang:python
fieldchemistry
roleshared-lib
Popcon: 45 users (7 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.

Python-rdkit
Collection of cheminformatics and machine-learning software
Versions of package python-rdkit
ReleaseVersionArchitectures
wheezy201203-3amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie201403-1amd64,armel,armhf,i386
stretch201603.5-2amd64,arm64,armel,i386,mips,mips64el,mipsel,ppc64el,s390x
buster201809.1+dfsg-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid201809.1+dfsg-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream201903.4
Popcon: 8 users (2 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 201330