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Package detail

openchemlib

cheminfo14kBSD-3-Clause9.2.0TypeScript support: included

Manipulate molecules

chemistry, molecule, molfile, SMILES

readme

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Maintained by Zakodium

OpenChemLib JS

NPM version npm download license DOI

JavaScript port of the OpenChemLib Java library.

Installation

npm install openchemlib

Documentation

Development

To build this project, you need:

Install dependencies

npm ci

Configure directories

Copy config.default.json to config.json and put the path to the GWT classes on your computer.
If you want to use a custom JDK installation, set the "jdk" key to be the path to your JDK directory.

npm scripts

To run one of the scripts, use npm run <scriptName>.
To pass additional options, use npm run <scriptName> -- --option.

build-java

Compile and export the Java API.

copy-openchemlib

Copy the required java files from the openchemlib project.

License

BSD-3-Clause

changelog

Changelog

9.2.0 (2025-05-13)

Features

Bug Fixes

  • use head prepend instead mutate possibly external stylesheet (#290) (f49456d)

9.1.1 (2025-05-01)

Bug Fixes

  • canvas_editor: avoid blurry rendering on hdpi screens (#281) (efd4e5d)

9.1.0 (2025-04-30)

Features

Bug Fixes

  • canvas_editor: open shadow root (cb6c2d2)
  • canvas_editor: optimize draw context (b7868f0)

9.0.1 (2025-04-28)

Bug Fixes

9.0.0 (2025-04-17)

⚠ BREAKING CHANGES

  • openchemlib is now exported as an ESM-only package. This doesn't prevent using it from CommonJS (require('openchemlib')), as long as you are using a supported and up to date Node.js version.
  • The library now exposes only one build. If you were using openchemlib/minimal, openchemlib/core, or openchemlib/full, switch back to openchemlib, which contains everything.
  • Removed the following classes: SVGRenderer, StructureEditor, and StructureView. They were using old and deprecated OpenChemLib java APIs.
    • Instead of the SVGRenderer, molecule.toSVG() can be used.
    • Instead of the StructureEditor, the replacement CanvasEditor can be used.
    • Instead of the StructureView, the replacement CanvasEditor with the readOnly option can be used.
  • Removed the bundled static resources. This allows to reduce the build size by half.
    • Static data can be loaded/registered with these new methods: OCL.Resources.register, OCL.Resources.registerFromUrl, or OCL.Resources.registerFromNodejs.
    • These classes require static resources to be registered before being instantiated: ConformerGenerator, ForceFieldMMFF94, DruglikenessPredictor, ToxicityPredictor.
  • Removed support for Node.js 18, which will be EoL at the end of April 2025.
  • Removed the getOCL method from all classes except Molecule.
  • Renamed some TypeScript types for consistency.

Features

  • rework library packaging and remove deprecated editor (#266) (88cc001)

8.21.0 (2025-04-11)

Features

  • CanvasEditor: add isDestroyed getter (#264) (37065c6)

8.20.2 (2025-04-11)

Bug Fixes

  • expose moleculeChanged method from Java (#262) (6f0057c)

8.20.1 (2025-04-11)

Bug Fixes

  • typo in CanvasEditor removeOnChangeListener method (#260) (270731c)

8.20.0 (2025-04-10)

Features

  • update OCL to v2025.4.0 (97ca346)

Bug Fixes

  • do not use unexposed Java API from JS (#257) (9af170b)

8.19.0 (2025-03-14)

Features

  • CanvasEditorElement: expose the moleculeChanged() method (#250) (d4c1c13)

8.18.1 (2025-02-06)

Bug Fixes

8.18.0 (2025-02-05)

Features

Bug Fixes

  • types: declare ambient types correctly (aea1332)

8.17.0 (2024-11-06)

Features

8.16.0 (2024-10-17)

Features

  • add options to ReactionEncoder.decode and ReactionEncoder.decode (9716b26)
  • create a script to build help (#223) (cc7042f)
  • sync webcomponent props with attributes (#234) (9716b26)
  • update OCL to v2024.10.0 (2cee300)
  • update OCL to v2024.10.1 (#233) (5eb0ed8)

Bug Fixes

8.15.0 (2024-07-25)

Features

Bug Fixes

8.14.0 (2024-06-19)

Features

8.13.0 (2024-05-28)

Features

  • add molecule.getBondQueryFeaturesObject (#210) (2844831)

8.12.0 (2024-05-27)

Features

  • add method Molecule.getAtomQueryFeaturesObject (c1843b8)

8.11.0 (2024-05-17)

Features

  • add experimental support for touch events in editor (#206) (bc41dcc)

8.10.0 (2024-05-13)

Features

Bug Fixes

8.9.0 (2024-02-22)

Features

  • update OCL to v2024.2.1 (afaae1e)

Bug Fixes

  • do not crash when drag-and-drop comes from toolbar (#195) (f10c782)

8.8.1 (2024-02-01)

Bug Fixes

  • only add data-atom-map-no when defined (#190) (567b9d7)

8.8.0 (2024-01-19)

Features

8.7.2 (2023-11-14)

Bug Fixes

  • deal correctly with non matching reactions (#181) (74e337e)

8.7.1 (2023-10-16)

Bug Fixes

8.7.0 (2023-10-13)

Features

  • improve exports for ESM and add shorthand export for the full.pretty build (688aedd)

8.6.0 (2023-10-06)

Features

  • when generating SVG check that coordinates are not all 0 (#174) (eded253)

8.5.0 (2023-08-14)

Features

8.4.0 (2023-08-11)

Features

  • add data-atom-map-no props in the circle of the svg (#170) (ea29871)

Bug Fixes

  • CanonizerUtil with NOSTEREO yielded to a wrong result (#165) (817ec97)

8.3.0 (2023-04-05)

Features

8.2.0 (2023-01-25)

Features

  • add new CANONIZER static options (bd2eca1)

Bug Fixes

  • add getAtomicNoFromLabel second argument (8aa1268)
  • correct and expose all static parameters of JSMolecule (81d7361)

8.1.0 (2023-01-04)

Features

  • expose ReactionEncoder to encode / decode a reaction as a string (0d645c3)
  • expose Reactor (5eb1c26)
  • expose Transformer (e88d2b4)
  • update OCL to v2022.10.2 (64b7d9a)
  • update OCL to v2022.12.4 (#146) (8511629)

8.0.1 (2022-08-15)

Bug Fixes

  • inverted red/blue colors in editor (d8d25a3)

8.0.0 (2022-08-15)

⚠ BREAKING CHANGES

This release updates OpenChemLib to the latest version 2022.8.1. There were a lot of changes since the last update and some of them are breaking. Here's a list of the changes we were able to identify (but there may be more):

  • The setAtomQueryFeature and getAtomQueryFeatures methods were removed from the Molecule class because they now return a long in Java.
  • The addRing, addRingToAtom and addRingToBond methods of the Molecule class now take one additional parameter, called bondLength.
  • The showSymmetryDiastereotopic and showSymmetryEnantiotopic depictor options were removed.
  • The value of computed 3D coordinates may change.
  • Generated conformers may be different (in quantity and their coordinates).
  • It is no longer possible to change ring size in the atom query features dialog of the editor.

We also removed support for Node.js 12. It's still possible that the library works on this version, but it is no longer tested in CI.

Features

  • update GWT to version 2.10 (9eed1ef)
  • update OpenChemLib to v2022.8.1 (1ac3899)
  • Added the following new depictor options (all boolean): showSymmetryStereoHeterotopicity, showSymmetryAny, noColorOnESRAndCIP, noImplicitHydrogen, and drawBondsInGray.

7.5.0 (2022-08-09)

Features

Bug Fixes

  • README link to documentation (77dfc46)
  • types: coordinates can be omitted from fromIDCode (636a73b)

7.4.3 (2021-10-02)

Bug Fixes

  • fromIDCode: pass coordinates option to the IDCodeParser (0b8775e)

7.4.2 (2021-08-05)

Bug Fixes

  • addImplicitHydrogens on 'Cl' (f2cf71f)

7.4.1 (2021-07-27)

Bug Fixes

  • addImplicitHydrogens for NH3 (9e9c353)
  • publish projet on Zenodo (e94ebb7)

7.4.0 (2021-03-24)

Features

  • expose a "getOCL" method on public classes (1879045)

7.3.0 (2021-01-04)

Features

  • update OCL to version 2020.12.1 (bb9c07d)

7.2.3 / 2020-01-10

  • Update OCL to 2020.1.0
  • Fix repaint issue in SVG Toolbar

7.2.2 / 2019-11-07

  • Update OCL to 2019_11_05-15_48_20

7.2.1 / 2019-07-12

  • Fix: work around a bug in Chromium with SVGDepictor when SVG is printed.

7.2.0 / 2019-07-08

  • Add ConformerGenerator class.
  • Add ForceFieldMMFF94 class.

7.1.1 / 2019-07-06

  • Update OCL to 2019_07_04-04_00_27
  • The SVG depictor (Molecule#toSVG) has been improved and its visual output is now more in line with the Java version.

7.1.0 / 2019-06-09

  • Added two new options to the toSVG method:
    • autoCrop: if set to true, the SVG will be automatically crop to fit the bounds of the molecule. This will change the resulting dimensions of the SVG.
    • autoCropMargin: This is the margin (in px) kept around the molecule when autoCrop is true. Default: 5.
  • Update OCL to 2019.6.0
  • Added is3D option to the removeExplicitHydrogens method.

7.0.1 / 2019-05-05

  • fix(types): make all depictor options effectively optional

7.0.0 / 2019-05-03

  • Update OCL to 2019_05_03-16_18_03
  • BREAKING: Node.js 6 is no longer supported
  • BREAKING: The output of Molecule.toSVG has changed: bonds are now identified by the bond id instead of the ids of its two atoms. For example: myId:Bond:0-1 becomes myId:Bond:0.

6.0.1 / 2019-02-08

  • Update OCL to 2019_02_08-04_00_25
  • Add missing return types in TypeScript declarations
  • Support retina displays in StructureEditor

6.0.0 / 2019-01-27

  • Update OCL to 2019_01_26-04_00_26
  • BREAKING: Editor: the StructureEditor constructor now takes a DOM element instead of an id.

5.9.1 / 2018-12-21

  • Update OCL to 2018_12_21-04_00_23
  • Editor: fix bond query feature dialog

5.9.0 / 2018-12-17

  • Update OCL to 2018_12_17-16_27_18
  • Added RXN methods to Reaction class
  • Added more options to bond query features in editor
  • Added getBounds method to Molecule class

5.8.0 / 2018-12-09

  • Update OCL to 2018_12_08-04_00_22
  • Added Reaction class
  • Added TypeScript declaration files
  • Ported the documentation to TypeDoc

5.7.0 / 2018-12-02

  • Update OCL to 2018.12.0
  • Added support for copying and pasting molfiles
  • Added molecule.toIsomericSmiles(includeAtomMapping)
  • Fixed display of query features
  • Fixed emitting change event for modifications coming from dialogs

5.6.1 / 2018-11-06

  • Update OCL to 2018_11_03-04_00_20

5.6.0 / 2018-06-19

  • Update OCL to 2018.6.0
  • feat: expose RingCollection to JS

5.5.2 / 2018-04-27

  • fix(editor): do not consider a mouse move for small movements

5.5.1 / 2018-04-19

  • feat: add factorTextSize option to toSVG

5.5.0 / 2017-11-20

  • Allow to retrieve a JSMolecule from editor

5.4.0 / 2017-11-16

  • Update OCL to 2017_11_14-04_01_01

5.3.0 / 2017-09-22

  • Update OCL to 2017_08_29-04_01_13
  • Fix addMissingChirality

5.2.10 / 2017-07-13

  • Fix H mapping issue

5.2.9 / 2017-07-07

  • Use the X symbol for hydrogens in DiaID

5.2.8 / 2017-07-07

  • Identical to 5.2.7

5.2.7 / 2017-07-07

  • Use isotopes to mark atoms

5.2.6 / 2017-07-07

  • Precalculate X atom number

5.2.5 / 2017-07-06

  • Update to add missing stereochemistry based on parities helper

5.2.4 / 2017-07-06

  • update diastereotopicAtomID not to rely on CIP

5.2.3 / 2017-07-04

  • fix hoseCodeCreator

5.2.2 / 2017-07-03

  • Update OCL to 2017_06_10-04_00_52
  • Update diaID

5.2.1 / 2017-04-24

  • Update OCL to 2017_04_22-04_01_31
  • Fix a bug with the SMILES parser that could enter in a wrong state after parsing an invalid SMILES

5.2.0 / 2017-03-21

  • feat: add fontWeight and strokeWidth options to toSVG

5.1.2 / 2017-03-08

  • fix: Update OCL to 2017_03_03-04_00_41

5.1.1 / 2017-01-30

  • fix: Update OCL to 2017_01_28-04_00_45

5.1.0 / 2017-01-27

  • feat: add mol.toMolfileV3
  • fix: Fixed SVGDepictor setLineWidth() regression.

5.0.0 / 2017-01-13

  • remove viewer build
  • introduce minimal build
  • do not include MoleculeProperties in minimal build

BREAKING CHANGE:

molecule.getProperties() has been removed. new MoleculeProperties(molecule) must be used instead.

4.7.2 / 2017-01-10

  • include full dist directory in npm and add require aliases

4.7.1 / 2017-01-10

  • SVG depictor: compute string width without canvas for Helvetica. This allows the SVG depictor to be used on Node.js

4.7.0 / 2017-01-05

Update public methods of JSMolecule. This adds a few new methods:

  • static double getDefaultAverageBondLength()
  • static void setDefaultAverageBondLength(double defaultAVBL)
  • int suggestBondType(int atom1, int atom2)
  • double calculateTorsion(int[] atom)
  • void setBondOrder(int bond,int order)
  • int getMetalBondedConnAtoms(int atom)
  • int getAllConnAtomsPlusMetalBonds(int atom)
  • int getNonHydrogenNeighbourCount(int atom)
  • int getExcludeGroupValence(int atom)
  • int getLowestFreeValence(int atom)
  • int getExplicitHydrogens(int atom)
  • boolean isPseudoRotatableBond(int bond)
  • boolean isAmideTypeBond(int bond)
  • int getZNeighbour(int connAtom, int bond)
  • int getHelperArrayStatus()

4.6.3 / 2017-01-04

  • update OCL to 2017.1.0

4.6.2 / 2016-11-08

  • AtomQueryFeaturesDialog: added more than 2 Hydrogens on query features
  • Fix SVGDepictor: minimal bond width is now 1

4.6.1 / 2016-11-03

  • fix license issue
  • fix StructureEditor not present in last release

4.6.0 / 2016-10-25

  • add more depictor options and support options in SVG depictor

4.5.1 / 2016-10-25

  • update OCL to 2016_10_25-04_00_46

4.5.0 / 2016-10-19

  • editor: fixed regression in chain placement
  • update OCL to 2016_10_18-04_00_45

4.4.2 / 2016-09-23

  • editor: fix initial placement of new bond/chain/ring
  • editor: fix dialog positions

4.4.1 / 2016-09-23

  • editor: fix structure change notification with keyboard
  • editor: add drag and drop support
  • editor: fix invasive paste issue

4.4.0 / 2016-09-01

  • fix highlighting issues
  • add SVG editor version
  • add compatibility with CouchDB views

4.3.2 / 2016-08-16

  • update openchemlib
  • update GWT compiler

4.3.1 / 2016-07-19

  • update openchemlib

4.3.0 / 2016-05-24

  • update openchemlib
  • add support for exclude group

4.2.2 / 2016-04-25

  • update openchemlib
  • remove sourceURL from dist files

4.2.1 / 2016-04-20

  • toSVG now works correctly in core build
  • warn that toSVG only works in a browser's window

4.2.0 / 2016-04-14

  • add DrugScoreCalculator

4.1.0 / 2016-03-17

  • add new contrib methods to generate HOSE codes and diastereotopic atom IDs
  • do not use global window for core library (still needed for the other builds)
  • this allows to load any number of independant versions of core along with one version of full or viewer
  • viewer will probably be removed in the future, leaving only core and full

4.0.0 / 2016-02-16

  • Major: use property getters for MolecularFormula and MoleculeProperties
  • update openchemlib

3.2.2 / 2015-12-15

  • fix namespace for editor and structure viewer

3.2.1 / 2015-12-15

  • refactor for and recompile with GWT 2.8.0-beta1

3.2.0 / 2015-11-24

  • add auto-generated methods to Molecule

3.1.1 / 2015-11-07

  • Editor: fixed AtomHightlight
  • Editor: working query feature dialogs

3.1.0 / 2015-10-21

  • add ToxicityPredictor
  • add DruglikenessPredictor

3.0.1 / 2015-10-20

  • update openchemlib
  • use GWT 2.8 to fix bug in SSSearcher

3.0.0 / 2015-09-28

  • Make JS API in line with Java API
  • Remove cheminfo-specific methods

3.0.0-beta6 / 2015-06-03

  • Changed prefix from actchem to OCL

3.0.0-beta5 / 2015-06-01

  • Fixed resizing issues in StructureViewer

3.0.0-beta4 / 2015-05-15

  • fix layout and missing images in editor

3.0.0-beta3 / 2015-05-12

  • fix resizing
  • fix toolbar in case of multiple instances
  • fix right click issues

3.0.0-beta2 / 2015-05-11

  • build without fake window

3.0.0-beta1 / 2015-05-11

  • update openchemlib
  • build editor

3.0.0-alpha10 / 2015-04-08

  • update openchemlib

3.0.0-alpha9 / 2015-03-20

  • fix SVG depictor

3.0.0-alpha8 / 2015-03-20

  • add bower.json

3.0.0-alpha7 / 2015-03-20

  • update SVGDepictor
  • expose molecule.getDiastereotopicAtomIDsArray

3.0.0-alpha6 / 2015-03-18

  • fixed build errors for editor (missing class): this prevented exports
  • add SVG output

3.0.0-alpha5 / 2015-02-27

  • update chemlib
  • update gwt exporter (no more globals)
  • add options to Molecule.fromSmiles

3.0.0-alpha4 / 2015-02-06

  • update chemlib
  • fix SMILES parser

3.0.0-alpha3 / 2015-01-26

  • update chemlib
  • Depictor : new flag to allow suppression of stereo problems
  • Depictor : fix superscript locations
  • SMILES parser : @ indicators in smiles don't conflict anymore with implicit hydrogens as in [N@H]
  • SMILES parser : handling of '.' was improved
  • SMILES parser : detection of unusual valences was improved
  • add noStereoProblem option to drawStructure

3.0.0-alpha2 / 2015-01-23

  • add support for displayMode options in javascript

3.0.0-alpha1 / 2015-01-22

  • add StructureViewer

2.0.7 / 2015-01-21

  • ensure invented coordinates are always the same

2.0.6 / 2015-01-19

  • update java library

2.0.5 / 2015-01-15

  • SMILES parser : custom coordinate inventor
  • update java library

2.0.4 / 2015-01-12

  • Update java library

2.0.3 / 2015-01-09

  • Github webhook

2.0.2 / 2014-12-22

  • fix bugs in SMILES parser

2.0.1 / 2014-12-19

  • add molecule.ensureHelperArrays

2.0.0 / 2014-12-05

  • GWT 2.7
  • no more javascript getters
  • initialize molecule with 32 length arrays
  • improve IDCode parser performance

1.2.1 / 2014-11-18

  • add molecule.getIDCodeAndCoordinates()
  • fix bug with SSSearchWithIndex

1.2.0 / 2014-11-11

  • add dependency to actelion-ext project
  • add molecule.getIDCoordinates()
  • add Molecule.fromIDCode(idcode, coordinates)
  • add Molecule.expandHydrogens()
  • add Molecule.getDiastereotopicAtomIDs
  • perf improvement : parsers and other utility classes are created only once and when needed

1.1.0 / 2014-11-05

  • add molecule.getFragmentNumbers() and molecule.getFragments()

1.0.0 / 2014-09-10

  • first release