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
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devellang:java, library
fieldchemistry
roledevel-lib
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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
Maintainer: Debichem Team
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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
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bullseye3.1.1+dfsg-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
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buster2.4.1+dfsg-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package openbabel:
fieldchemistry
interfacecommandline
roleprogram
scopeutility
useconverting
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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:

  • obabel: 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
Python3-indigo
Organic Chemistry Toolkit (Python module)
Maintainer: Debichem Team
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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)
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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
Maintainer: Debichem Team (Adrian Bunk)
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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 
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