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Title: Groovy Cheminformatics with the Chemistry Development Kit | cdkbook

Open Graph Title: Groovy Cheminformatics with the Chemistry Development Kit

X Title: Groovy Cheminformatics with the Chemistry Development Kit

Description: Groovy Cheminformatics with the Chemistry Development Kit

Open Graph Description: Groovy Cheminformatics with the Chemistry Development Kit

Opengraph URL: https://egonw.github.io/cdkbook/

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direct link

Domain: egonw.github.io

Hey, it has json ld scripts: 
{"@context":"https://schema.org","@type":"WebSite","description":"Groovy Cheminformatics with the Chemistry Development Kit","headline":"Groovy Cheminformatics with the Chemistry Development Kit","name":"cdkbook","url":"https://egonw.github.io/cdkbook/"}
 
{
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  "@type":"CreativeWork",
  "about":"This text book describes how to write cheminformatics software with Groovy and the Chemistry Development Kit.",
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    "@type":"URL","url":"http://edamontology.org/topic_2258"
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  "name":"Groovy Cheminformatics with the Chemistry Development Kit",
  "author":[{
    "@type":"Person",
    "name":"Egon Willighagen",
    "identifier":"0000-0001-7542-0286"
  }],
  "keywords":"cheminformatics, chemoinformatics, java, Groovy, Chemistry Development Kit, CDK",
  "license":"CC BY-SA 4.0",
  "url": "https://egonw.github.io/cdkbook/",
  "version":"2.11-2"
}
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Links:

cdkbookhttps://egonw.github.io/cdkbook/
https://zenodo.org/badge/latestdoi/163004968
1https://egonw.github.io/cdkbook/#citeref1
herehttps://github.com/cdk/cdkbook/issues
GitHub repositoryhttps://github.com/cdk/cdkbook/
this repositoryhttps://cdk.github.io/chempyformatics/
file a request herehttps://github.com/cdk/chempyformatics/issues
Introductionhttps://egonw.github.io/cdkbook/introduction.html
Writing CDK Applicationshttps://egonw.github.io/cdkbook/writingApps.html
A (Very) Basic Java Applicationhttps://egonw.github.io/cdkbook/writingApps.html#a-(very)-basic-java-application
Groovyhttps://egonw.github.io/cdkbook/writingApps.html#groovy
Closureshttps://egonw.github.io/cdkbook/writingApps.html#closures
Grabbing dependencieshttps://egonw.github.io/cdkbook/writingApps.html#grabbing-dependencies
Pythonhttps://egonw.github.io/cdkbook/writingApps.html#python
Other environmentshttps://egonw.github.io/cdkbook/writingApps.html#other-environments
Bioclipsehttps://egonw.github.io/cdkbook/writingApps.html#bioclipse
Cinfonyhttps://egonw.github.io/cdkbook/writingApps.html#cinfony
Rhttps://egonw.github.io/cdkbook/writingApps.html#r
Cheminformaticshttps://egonw.github.io/cdkbook/cheminfo.html
Molecular Representationshttps://egonw.github.io/cdkbook/cheminfo.html#molecular-representations
Chemical Graphshttps://egonw.github.io/cdkbook/cheminfo.html#chemical-graphs
Quantum Chemistryhttps://egonw.github.io/cdkbook/cheminfo.html#quantum-chemistry
Numerical Representationshttps://egonw.github.io/cdkbook/cheminfo.html#numerical-representations
Chemometricshttps://egonw.github.io/cdkbook/cheminfo.html#chemometrics
Atoms, Bonds and Moleculeshttps://egonw.github.io/cdkbook/atomsbonds.html
Atomshttps://egonw.github.io/cdkbook/atomsbonds.html#atoms
IElementhttps://egonw.github.io/cdkbook/atomsbonds.html#ielement
IIsotopehttps://egonw.github.io/cdkbook/atomsbonds.html#iisotope
IAtomTypehttps://egonw.github.io/cdkbook/atomsbonds.html#iatomtype
Coordinateshttps://egonw.github.io/cdkbook/atomsbonds.html#coordinates
Bondshttps://egonw.github.io/cdkbook/atomsbonds.html#bonds
Electron countshttps://egonw.github.io/cdkbook/atomsbonds.html#electron-counts
Bond stereochemistryhttps://egonw.github.io/cdkbook/atomsbonds.html#bond-stereochemistry
Moleculeshttps://egonw.github.io/cdkbook/atomsbonds.html#molecules
Iterating over atoms and bondshttps://egonw.github.io/cdkbook/atomsbonds.html#iterating-over-atoms-and-bonds
Neighboring atoms and bondshttps://egonw.github.io/cdkbook/atomsbonds.html#neighboring-atoms-and-bonds
Molecular Formulahttps://egonw.github.io/cdkbook/atomsbonds.html#molecular-formula
Implicit and Explicit Hydrogenshttps://egonw.github.io/cdkbook/atomsbonds.html#implicit-and-explicit-hydrogens
Chemical Objectshttps://egonw.github.io/cdkbook/atomsbonds.html#chemical-objects
Ringshttps://egonw.github.io/cdkbook/atomsbonds.html#rings
Stereochemistryhttps://egonw.github.io/cdkbook/stereo.html
Stereochemistry in a flat worldhttps://egonw.github.io/cdkbook/stereo.html#stereochemistry-in-a-flat-world
Tetrahedral chiralityhttps://egonw.github.io/cdkbook/stereo.html#tetrahedral-chirality
Salts and other disconnected structureshttps://egonw.github.io/cdkbook/salts.html
Saltshttps://egonw.github.io/cdkbook/salts.html#salts
Crystalshttps://egonw.github.io/cdkbook/salts.html#crystals
Paired and unpaired electronshttps://egonw.github.io/cdkbook/unpairedelectrons.html
Lone Pairshttps://egonw.github.io/cdkbook/unpairedelectrons.html#lone-pairs
Unpaired electronshttps://egonw.github.io/cdkbook/unpairedelectrons.html#unpaired-electrons
Protein and DNAhttps://egonw.github.io/cdkbook/protein.html
Protein From Filehttps://egonw.github.io/cdkbook/protein.html#protein-from-file
Protein From Sequencehttps://egonw.github.io/cdkbook/protein.html#protein-from-sequence
Strands and Monomershttps://egonw.github.io/cdkbook/protein.html#strands-and-monomers
Reactionshttps://egonw.github.io/cdkbook/reaction.html
A single reactionhttps://egonw.github.io/cdkbook/reaction.html#a-single-reaction
Reaction from Filehttps://egonw.github.io/cdkbook/reaction.html#reaction-from-file
MDL RXN fileshttps://egonw.github.io/cdkbook/reaction.html#mdl-rxn-files
CMLReact fileshttps://egonw.github.io/cdkbook/reaction.html#cmlreact-files
From IChemObject to IChemFilehttps://egonw.github.io/cdkbook/chemobject.html
IAtomContainerSethttps://egonw.github.io/cdkbook/chemobject.html#iatomcontainerset
IReactionSet and IRingSethttps://egonw.github.io/cdkbook/chemobject.html#ireactionset-and-iringset
IChemModelhttps://egonw.github.io/cdkbook/chemobject.html#ichemmodel
IChemSequencehttps://egonw.github.io/cdkbook/chemobject.html#ichemsequence
IChemFilehttps://egonw.github.io/cdkbook/chemobject.html#ichemfile
IChemObjectBuildershttps://egonw.github.io/cdkbook/builders.html
Implementationshttps://egonw.github.io/cdkbook/builders.html#implementations
The Default Builderhttps://egonw.github.io/cdkbook/builders.html#the-default-builder
The Debug Builderhttps://egonw.github.io/cdkbook/builders.html#the-debug-builder
The Silent Builderhttps://egonw.github.io/cdkbook/builders.html#the-silent-builder
Input/Outputhttps://egonw.github.io/cdkbook/io.html
File Format Detectionhttps://egonw.github.io/cdkbook/io.html#file-format-detection
Custom format matchershttps://egonw.github.io/cdkbook/io.html#custom-format-matchers
Reading from Readers and InputStreamshttps://egonw.github.io/cdkbook/io.html#reading-from-readers-and-inputstreams
Example: Downloading Domoic Acid from PubChemhttps://egonw.github.io/cdkbook/io.html#example:-downloading-domoic-acid-from-pubchem
Input Validationhttps://egonw.github.io/cdkbook/io.html#input-validation
Reading modeshttps://egonw.github.io/cdkbook/io.html#reading-modes
Validationhttps://egonw.github.io/cdkbook/io.html#validation
Gzipped fileshttps://egonw.github.io/cdkbook/io.html#gzipped-files
Iterating Readershttps://egonw.github.io/cdkbook/io.html#iterating-readers
MDL SD fileshttps://egonw.github.io/cdkbook/io.html#mdl-sd-files
PubChem Compounds XML fileshttps://egonw.github.io/cdkbook/io.html#pubchem-compounds-xml-files
Customizing the Outputhttps://egonw.github.io/cdkbook/io.html#customizing-the-output
Setting Propertieshttps://egonw.github.io/cdkbook/io.html#setting-properties
Example: creating unit tests for atom type perceptionhttps://egonw.github.io/cdkbook/io.html#example:-creating-unit-tests-for-atom-type-perception
Line Notationshttps://egonw.github.io/cdkbook/io.html#line-notations
SMILEShttps://egonw.github.io/cdkbook/io.html#smiles
Recipeshttps://egonw.github.io/cdkbook/io.html#recipes
MDL molfile (V2000)https://egonw.github.io/cdkbook/io.html#mdl-molfile-(v2000)
SDF files with propertieshttps://egonw.github.io/cdkbook/io.html#sdf-files-with-properties
Atom typeshttps://egonw.github.io/cdkbook/atomtype.html
The CDK atom type modelhttps://egonw.github.io/cdkbook/atomtype.html#the-cdk-atom-type-model
Hybridization Typeshttps://egonw.github.io/cdkbook/atomtype.html#hybridization-types
Atom type perceptionhttps://egonw.github.io/cdkbook/atomtype.html#atom-type-perception
Single atomshttps://egonw.github.io/cdkbook/atomtype.html#single-atoms
Full moleculeshttps://egonw.github.io/cdkbook/atomtype.html#full-molecules
Configuring the Atomhttps://egonw.github.io/cdkbook/atomtype.html#configuring-the-atom
No atom type perceived?!https://egonw.github.io/cdkbook/atomtype.html#no-atom-type-perceived?!
Sybyl atom typeshttps://egonw.github.io/cdkbook/atomtype.html#sybyl-atom-types
Graph Propertieshttps://egonw.github.io/cdkbook/graph.html
Partitioninghttps://egonw.github.io/cdkbook/graph.html#partitioning
Spanning Treehttps://egonw.github.io/cdkbook/graph.html#spanning-tree
Ring countshttps://egonw.github.io/cdkbook/graph.html#ring-counts
Smallest Ringshttps://egonw.github.io/cdkbook/graph.html#smallest-rings
All Ringshttps://egonw.github.io/cdkbook/graph.html#all-rings
Graph matriceshttps://egonw.github.io/cdkbook/graph.html#graph-matrices
Adjacency matrixhttps://egonw.github.io/cdkbook/graph.html#adjacency-matrix
Distance matrixhttps://egonw.github.io/cdkbook/graph.html#distance-matrix
Atom Numbershttps://egonw.github.io/cdkbook/graph.html#atom-numbers
Morgan Atom Numbershttps://egonw.github.io/cdkbook/graph.html#morgan-atom-numbers
InChI Atom Numbershttps://egonw.github.io/cdkbook/graph.html#inchi-atom-numbers
Missing Informationhttps://egonw.github.io/cdkbook/missing.html
Element and Isotope informationhttps://egonw.github.io/cdkbook/missing.html#element-and-isotope-information
Elementshttps://egonw.github.io/cdkbook/missing.html#elements
Isotopeshttps://egonw.github.io/cdkbook/missing.html#isotopes
Reconnecting Atomshttps://egonw.github.io/cdkbook/missing.html#reconnecting-atoms
Missing Bond Ordershttps://egonw.github.io/cdkbook/missing.html#missing-bond-orders
Missing Hydrogenshttps://egonw.github.io/cdkbook/missing.html#missing-hydrogens
Implicit Hydrogenshttps://egonw.github.io/cdkbook/missing.html#implicit-hydrogens
Explicit Hydrogenshttps://egonw.github.io/cdkbook/missing.html#explicit-hydrogens
2D Coordinateshttps://egonw.github.io/cdkbook/missing.html#2d-coordinates
Unknown Molecular Formulahttps://egonw.github.io/cdkbook/missing.html#unknown-molecular-formula
Depictionhttps://egonw.github.io/cdkbook/depiction.html
Moleculeshttps://egonw.github.io/cdkbook/depiction.html#molecules
Scalable Vector Graphicshttps://egonw.github.io/cdkbook/depiction.html#scalable-vector-graphics
Background colorhttps://egonw.github.io/cdkbook/depiction.html#background-color
Coloring selectionshttps://egonw.github.io/cdkbook/depiction.html#coloring-selections
Parametershttps://egonw.github.io/cdkbook/depiction.html#parameters
Reactionshttps://egonw.github.io/cdkbook/depiction.html#reactions
Substructure Searchinghttps://egonw.github.io/cdkbook/substructure.html
Exact Searchhttps://egonw.github.io/cdkbook/substructure.html#exact-search
Substructureshttps://egonw.github.io/cdkbook/substructure.html#substructures
Matching Substructureshttps://egonw.github.io/cdkbook/substructure.html#matching-substructures
SMARTS matchinghttps://egonw.github.io/cdkbook/substructure.html#smarts-matching
Unique matcheshttps://egonw.github.io/cdkbook/substructure.html#unique-matches
Fingerprintshttps://egonw.github.io/cdkbook/substructure.html#fingerprints
MACCS Fingerprintshttps://egonw.github.io/cdkbook/substructure.html#maccs-fingerprints
ECFP and FCFP Fingerprintshttps://egonw.github.io/cdkbook/substructure.html#ecfp-and-fcfp-fingerprints
Molecular Propertieshttps://egonw.github.io/cdkbook/properties.html
Molecular Masshttps://egonw.github.io/cdkbook/properties.html#molecular-mass
Implicit Hydrogenshttps://egonw.github.io/cdkbook/properties.html#implicit-hydrogens
LogPhttps://egonw.github.io/cdkbook/properties.html#logp
Total Polar Surface Areahttps://egonw.github.io/cdkbook/properties.html#total-polar-surface-area
Van der Waals Volumehttps://egonw.github.io/cdkbook/properties.html#van-der-waals-volume
Aromaticityhttps://egonw.github.io/cdkbook/properties.html#aromaticity
Molecular Descriptorshttps://egonw.github.io/cdkbook/descriptor.html
Descriptors and Specificationshttps://egonw.github.io/cdkbook/descriptor.html#descriptors-and-specifications
IImplementationSpecificationhttps://egonw.github.io/cdkbook/descriptor.html#iimplementationspecification
IDescriptorhttps://egonw.github.io/cdkbook/descriptor.html#idescriptor
IMolecularDescriptorhttps://egonw.github.io/cdkbook/descriptor.html#imoleculardescriptor
IDescriptorResulthttps://egonw.github.io/cdkbook/descriptor.html#idescriptorresult
Counting Nitrogens and Oxygenshttps://egonw.github.io/cdkbook/descriptor.html#counting-nitrogens-and-oxygens
InChIhttps://egonw.github.io/cdkbook/inchi.html
Layershttps://egonw.github.io/cdkbook/inchi.html#layers
Fixed Hydrogenshttps://egonw.github.io/cdkbook/inchi.html#fixed-hydrogens
Stereoisomerismhttps://egonw.github.io/cdkbook/inchi.html#stereoisomerism
Chemistry Toolkit Rosettahttps://egonw.github.io/cdkbook/ctr.html
Heavy atom counts from an SD filehttps://egonw.github.io/cdkbook/ctr.html#heavy-atom-counts-from-an-sd-file
Depict a compound as an imagehttps://egonw.github.io/cdkbook/ctr.html#depict-a-compound-as-an-image
Working with SD tag datahttps://egonw.github.io/cdkbook/ctr.html#working-with-sd-tag-data
Migrationhttps://egonw.github.io/cdkbook/migration.html
CDK 2.9 to 2.10https://egonw.github.io/cdkbook/migration.html#cdk-29-to-210
IChemObjectReaderErrorHandlerhttps://egonw.github.io/cdkbook/migration.html#ichemobjectreadererrorhandler
CDK 2.6 to 2.7https://egonw.github.io/cdkbook/migration.html#cdk-26-to-27
InChI functionalityhttps://egonw.github.io/cdkbook/migration.html#inchi-functionality
CDK 2.0 to 2.3https://egonw.github.io/cdkbook/migration.html#cdk-20-to-23
CDK 1.4 to 2.0https://egonw.github.io/cdkbook/migration.html#cdk-14-to-20
Removed classeshttps://egonw.github.io/cdkbook/migration.html#removed-classes
Renamed classes and methodshttps://egonw.github.io/cdkbook/migration.html#renamed-classes-and-methods
Changed behaviorhttps://egonw.github.io/cdkbook/migration.html#changed-behavior
Constructors that now require a builderhttps://egonw.github.io/cdkbook/migration.html#constructors-that-now-require-a-builder
Static methods that are no longerhttps://egonw.github.io/cdkbook/migration.html#static-methods-that-are-no-longer
IsotopeFactoryhttps://egonw.github.io/cdkbook/migration.html#isotopefactory
IFingerPrinterhttps://egonw.github.io/cdkbook/migration.html#ifingerprinter
SMILESGeneratorhttps://egonw.github.io/cdkbook/migration.html#smilesgenerator
Aromaticity calculationshttps://egonw.github.io/cdkbook/migration.html#aromaticity-calculations
Indexhttps://egonw.github.io/cdkbook/indexList.html
Appendix Ahttps://egonw.github.io/cdkbook/appatomtypes.html
CDK Atom Typeshttps://egonw.github.io/cdkbook/appatomtypes.html#cdk-atom-types
Sybyl Atom Typeshttps://egonw.github.io/cdkbook/appatomtypes.html#sybyl-atom-types
Appendix Bhttps://egonw.github.io/cdkbook/appisotopes.html
Isotope Listhttps://egonw.github.io/cdkbook/appisotopes.html
Appendix Chttps://egonw.github.io/cdkbook/appmoldescs.html
Molecular Descriptorshttps://egonw.github.io/cdkbook/appmoldescs.html#molecular-descriptors
Atomic Descriptorshttps://egonw.github.io/cdkbook/appmoldescs.html#atomic-descriptors
Atom-Pair Descriptorshttps://egonw.github.io/cdkbook/appmoldescs.html#atom-pair-descriptors
Bond Descriptorshttps://egonw.github.io/cdkbook/appmoldescs.html#bond-descriptors
Protein Descriptorshttps://egonw.github.io/cdkbook/appmoldescs.html#protein-descriptors
Appendix Dhttps://egonw.github.io/cdkbook/appfileformats.html
Readers and Writershttps://egonw.github.io/cdkbook/appfileformats.html#the-readers-and-writers
10.6084/M9.FIGSHARE.2057790.V1https://doi.org/10.6084/M9.FIGSHARE.2057790.V1
Scholiahttps://scholia.toolforge.org/doi/10.6084/M9.FIGSHARE.2057790.V1
Improve this pagehttps://github.com/egonw/cdkbook/edit/main/index.md

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