Groovy Cheminformatics with the Chemistry Development Kit

Edition 2.9-2

Egon L. Willighagen PhD
Long time CDK developer

License: CC-BY-SA 4.0 International

Dependencies

Groovy
nodejs and npm
citation-js (see doi:10.7717/peerj-cs.214)
CDK (see doi:10.1186/S13321-017-0220-4)

About

Further information: https://chem-bla-ics.linkedchemistry.info/

E.L. Willighagen [email protected]

Name	Name	Last commit message	Last commit date
Latest commit johnmay Update README.md Mar 11, 2025 9ee9d97 · Mar 11, 2025 History 266 Commits
code	code	Added a modern way of creating atoms	Jul 30, 2024
images	images	Added a missing hierarchy figure	Apr 28, 2019
.gitignore	.gitignore	Don't ignore the .i.md source files	Jun 16, 2024
LICENSE.gplv3.md	LICENSE.gplv3.md	Added the missing copyright/license info	Dec 25, 2018
LICENSE.md	LICENSE.md	Create LICENSE.md	Dec 24, 2018
Makefile	Makefile	Reabled citations	Jan 18, 2025
README.md	README.md	Update README.md	Mar 11, 2025
appatomtypes.i.md	appatomtypes.i.md	Many small fixes	Apr 21, 2019
appfileformats.i.md	appfileformats.i.md	Added a missing section	May 21, 2022
appisotopes.i.md	appisotopes.i.md	Fixed the description	Aug 20, 2022
appmoldescs.i.md	appmoldescs.i.md	Fixed HTML and bold column headers	Feb 19, 2019
atomsbonds.i.md	atomsbonds.i.md	Added a modern way of creating atoms	Jul 30, 2024
atomtype.i.md	atomtype.i.md	Many small fixes	Apr 21, 2019
builders.i.md	builders.i.md	Many small fixes	Apr 21, 2019
cheminfo.i.md	cheminfo.i.md	New Scholia URL	Jun 13, 2020
chemobject.i.md	chemobject.i.md	Many small fixes	Apr 21, 2019
classinfo.tsv	classinfo.tsv	Some more files for the new Depiction chapter	Jun 16, 2024
createMarkdown.groovy	createMarkdown.groovy	Updated to CDK 2.7.1	May 21, 2022
ctr.i.md	ctr.i.md	Added another CTR task: SD tag data	Mar 26, 2023
depiction.i.md	depiction.i.md	Removed the section, as I first need to rewrite the code base	Jul 30, 2024
descriptor.i.md	descriptor.i.md	A number of small fixes	Apr 28, 2019
findCitations.groovy	findCitations.groovy	Integrated getting the references into the main build system	Dec 27, 2018
findClasses.groovy	findClasses.groovy	Updated to CDK 2.7.1	May 21, 2022
findFigures.groovy	findFigures.groovy	Updated to CDK 2.7.1	May 21, 2022
findScripts.groovy	findScripts.groovy	Added the stereo chapter (in draft)	Dec 28, 2018
findSections.groovy	findSections.groovy	Updated to CDK 2.7.1	May 21, 2022
findTopics.groovy	findTopics.groovy	Updated to CDK 2.7.1	May 21, 2022
foo.sh	foo.sh	Lookup package and module info from source repo (location in foo.sh)	Jan 7, 2019
graph.i.md	graph.i.md	Many small fixes	Apr 21, 2019
inchi.i.md	inchi.i.md	Fixed the xref	Dec 25, 2019
index.i.md	index.i.md	Bumped the year	Jan 16, 2025
introduction.i.md	introduction.i.md	Updated the link: main is now the main branch	Jun 16, 2024
io.i.md	io.i.md	Added another CTR task: SD tag data	Mar 26, 2023
makeIndex.groovy	makeIndex.groovy	Group links	Jan 9, 2019
makeToC.groovy	makeToC.groovy	Updated to CDK 2.7.1	May 21, 2022
migration.i.md	migration.i.md	Mention the JNI 2 JNA update for the InChI functionality	Jan 16, 2025
missing.i.md	missing.i.md	Updated the pointers for structure generators	Aug 23, 2022
numberScripts.groovy	numberScripts.groovy	Updated to CDK 2.7.1	May 21, 2022
order.txt	order.txt	Some more files for the new Depiction chapter	Jun 16, 2024
properties.i.md	properties.i.md	New Scholia URL	Jun 13, 2020
protein.i.md	protein.i.md	Two more scripts linked again	Dec 24, 2019
reaction.i.md	reaction.i.md	Various small fixes	Apr 16, 2019
references.extra.dat	references.extra.dat	Point to the new blog	Aug 6, 2024
references.js	references.js	Reabled citations	Jan 18, 2025
salts.i.md	salts.i.md	A few fixes	Apr 14, 2019
sitemap.xml	sitemap.xml	Fixed to the canonical link	Aug 9, 2023
stereo.i.md	stereo.i.md	A few fixes	Apr 14, 2019
substructure.i.md	substructure.i.md	Some corrections	Jan 23, 2019
unpairedelectrons.i.md	unpairedelectrons.i.md	Fixed the syntax	Apr 17, 2019
updateClassInfo.groovy	updateClassInfo.groovy	Lookup package and module info from source repo (location in foo.sh)	Jan 7, 2019
wrap.groovy	wrap.groovy	More space online; wrap at 80 chars	Mar 26, 2023
writingApps.i.md	writingApps.i.md	Better structuring	May 9, 2024

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Groovy Cheminformatics with the Chemistry Development Kit

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Groovy Cheminformatics with the Chemistry Development Kit

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