DebiChem Project
Summary
Cheminformatics
DebiChem - Cheminformatics

Denne metapakke vil installere cheminformatics-pakker nyttige for kemikere.

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

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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)
Libopenchemlib-java
framework providing cheminformatics core functionality
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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
Kemisk navn til struktur-konverteringsprogram
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OPSIN (Open Parser for Systematic IUPAC Nomenclature) konverterer IUPAC-forbindelsesnavne til semantik kemisk information og viser en struktur enten som CML (Chemical Markup Language), SMILES eller InChi.

Denne pakke indeholder Javabiblioteket.

Openbabel
Redskaber til kemisk værktøjskasse - kommandolinje
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roleprogram
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Open Babel er en kemisk værktøjskasse, som er designet til at tale mange kemiske data-sprog. Den tillader søgning, konvertering, analyse eller lagring af data fra molekylær modellering, kemi, faste materialer, biokemi eller beslægtede områder. Egenskaber inkluderer:

  • Indsættelse og fjernelse af hydrogen
  • Understøttelse af molekylær-mekanik
  • Understøttelse af SMARTS molekylære syntaks-sammenligninger
  • Automatisk registrering af egenskaber (ringe, bånd, hybridisering, aromaticitet)
  • Fleksibel bestemmelse af atomtyper og registrering af atomare koordinater med flere bånd
  • Gasteiger-Marsili-beregning af delvis ladning

Filformater som Open Babel understøtter inkluderer PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC og MPQC.

Denne pakke inkluderer følgende redskaber:

  • obabel: Konverter mellem forskellige kemiske filformater
  • obenergy: Beregn energien for et molekyle
  • obminimize: Optimer geometrien, minimer energien for et molekyle
  • obgrep: Molekylært søgeprogram som anvender mønstre fra SMARTS
  • obgen: Opret 3D-koordinater for et molekyle
  • obprop: Udskriv standardegenskaber for molekyler
  • obfit: Læg to molekyler oveni hinanden baseret på et mønster
  • obrotamer: Opret konformer/rotamer-koordinater
  • obconformer: Opret konformere med lavt energiniveau
  • obchiral: Udskriv informationer om molekylær kiralitet
  • obrotate: Roter torsionsvinkel for molekyler i stakkevis tilstand
  • obprobe: Opret elektrostatisk sondegitter
Screenshots of package openbabel
Python3-indigo
Organic Chemistry Toolkit - Pythonmodul
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Indigo er et C++-baseret programmiljø for organisk kemi og kemiinformatik. Inkluderede funktioner:

  • Molekyle- og reaktionsoptegning inklusive SVG-understøttelse
  • Automatisk layout for SMILES-repræsenterede molekyler og reaktioner
  • Kanonisk (isomerisk) SMILES-beregning
  • Præcis matchning, matchning af understruktur, SMARTS-matchning
  • Matchning af tautomerer og resonansstrukturer
  • Molekylefingeraftryk, beregning af molekylelighed
  • Hurtig enumeration af SSSR-ringe, undertræer og kant-sugraphs
  • Molekylær vægt, molekylær formelberegning
  • R-Group dekonvolution og scaffold-detektion
  • Beregning af den præcise maksimale fælles understruktur for en arbitrær mængde af inddatastrukturer
  • Kombinatorisk kemi
  • Understøttelse af udvidelsesmoduler i API'en

Filformater som Indigo understøtter inkluderer MDL Mol, SDF, RDF, CML, SMILES og SMARTS.

Denne pakke indeholder Pythonmodulerne.

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
Program til indsamling af cheminformatics og maskinlæring
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RDKit er et programmiljø baseret på Python/C++ cheminformatics og maskinlæring. Funktioner omfatter:

  • Kemisk reaktionshåndtering og -transformationer
  • Underkonstruktionssøgning med SMARTS
  • Kanoniske SMILES
  • Molekyle-molekyle tilpasning
  • Stort antal molekylære deskriptorer, herunder topologiske, kompositoriske, Estate-, SlogP/SMR-, VSA- og Feature-map-vektorer
  • Fragmentering via RECAP-regler
  • 2D-koordinatoprettelse og skildring, herunder begrænset skildring
  • 3D-koordinatoprettelse via geometriindlejring
  • UFF- og MMFF94-kraftfelter
  • Chiralitet-understøttelse, herunder beregning af (R/S)-stereokemikoder
  • 2D-farmakoforsøgning
  • Fingeraftryk, herunder Daylight-lignende, atompar, topologiske vridninger, Morganalogritme og MACCS-nøgler
  • Beregning af formlighed
  • Fler-molekyle maksimum for fælles understruktur
  • Maskinlæring via klyngedannelse og informationsteorialgoritmer
  • Delvis Gasteiger-Marsili-opladningsberegning

Filformater som RDKit understøtter inkluderer de binære formater MDL Mol, FBF, SDF, TDT, SMILES og RDKit.

Registry entries: SciCrunch  OMICtools 
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