Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / cdk/cdk issues and pull requests

#1034 - Fix a minor issue from sonarcloud, we check the counts elsewhere so t…

Pull Request - State: closed - Opened by johnmay 10 months ago - 2 comments

#1033 - Symmetry calculation may fail.

Pull Request - State: closed - Opened by johnmay 10 months ago - 1 comment

#1032 - First pass at aligned depictions API.

Pull Request - State: closed - Opened by johnmay 10 months ago - 5 comments

#1031 - Make sure Sgroups attached to reactions get passed through and emitte…

Pull Request - State: closed - Opened by johnmay 11 months ago - 1 comment

#1030 - Fix a minor issue with an abbreviation like -NnButBu. Currently this …

Pull Request - State: closed - Opened by johnmay 11 months ago - 2 comments

#1029 - italics in labels nButBu

Issue - State: closed - Opened by IngvarLa 11 months ago

#1028 - Fix and issue with contraction on terminal attachment points.

Pull Request - State: closed - Opened by johnmay 12 months ago - 1 comment

#1027 - Fix for non-deterministic CIP designation bug

Pull Request - State: closed - Opened by tylerperyea 12 months ago - 5 comments

#1026 - Updated dependencies

Pull Request - State: closed - Opened by egonw 12 months ago - 4 comments

#1025 - Fixes #1024 - we should perhaps rework the CDK radical representation…

Pull Request - State: closed - Opened by johnmay about 1 year ago - 1 comment

#1024 - Generated MDL misses radical

Issue - State: closed - Opened by michael-striewe about 1 year ago - 3 comments

#1023 - Efficient algorithm to generate an isotope distribution

Issue - State: open - Opened by ctapobep about 1 year ago - 9 comments

#1022 - IMolecularFormula remove

Issue - State: open - Opened by lukasmur13 about 1 year ago - 4 comments

#1021 - FragmentUtils protected

Issue - State: closed - Opened by lukasmur13 about 1 year ago - 2 comments

#1020 - Fixed the OSGi meta data export

Pull Request - State: closed - Opened by Mailaender about 1 year ago - 6 comments

#1019 - Added an API for fatal IO errors

Pull Request - State: closed - Opened by egonw about 1 year ago - 1 comment

#1018 - Code cleanup

Pull Request - State: closed - Opened by egonw about 1 year ago - 1 comment

#1017 - Question regarding Signature and Lingo fingerprint

Issue - State: closed - Opened by Jnelen about 1 year ago - 2 comments

#1015 - Fixes https://github.com/cdk/depict/issues/76. We do not like -C=CO a…

Pull Request - State: closed - Opened by johnmay about 1 year ago - 1 comment

#1014 - Java21

Pull Request - State: closed - Opened by johnmay about 1 year ago - 4 comments

#1013 - stereo information unavailable when generating SMILES from IAtomcontainer

Issue - State: open - Opened by biotech7 about 1 year ago - 9 comments

#1012 - Read the atom-atom mapping info from a V3000 file.

Pull Request - State: closed - Opened by johnmay about 1 year ago - 4 comments

#1011 - Fix the CDK C.plus atom type, there was already comment in the test t…

Pull Request - State: closed - Opened by johnmay about 1 year ago - 1 comment

#1010 - When atoms/bonds are aware of the container they are in - it is usefu…

Pull Request - State: closed - Opened by johnmay about 1 year ago - 3 comments

#1009 - Redo @parit's changes for net/undirected reaction depiction on the ne…

Pull Request - State: closed - Opened by johnmay about 1 year ago - 5 comments

#1008 - Parit undir reaction

Pull Request - State: closed - Opened by johnmay about 1 year ago

#1007 - Smiles 0 isotope

Pull Request - State: closed - Opened by johnmay about 1 year ago - 1 comment

#1006 - Incomplete OSGi metadata

Issue - State: open - Opened by Mailaender about 1 year ago - 12 comments

#1005 - MACCS (166bit) Fingerprint returns fingerprint of length 192

Issue - State: closed - Opened by al-pi314 over 1 year ago - 2 comments

#1004 - CMLXOM 4.6

Pull Request - State: closed - Opened by egonw over 1 year ago

#1002 - Bug

Issue - State: open - Opened by johnmay over 1 year ago

#1001 - Sonar settings for aggregated test coverage.

Pull Request - State: closed - Opened by johnmay over 1 year ago - 1 comment

#1000 - SonarCloud is not reporting test coverage correctly because it was no…

Pull Request - State: closed - Opened by johnmay over 1 year ago - 2 comments

#999 - Add a "loose" SMILES writer mode

Issue - State: open - Opened by johnmay over 1 year ago

#998 - Fix - avoid placing a wedge on the right-angled bond when a centre is…

Pull Request - State: closed - Opened by johnmay over 1 year ago - 1 comment

#997 - Quality of life API interfaces. The IAtomContainerSet and IReaction c…

Pull Request - State: closed - Opened by johnmay over 1 year ago - 2 comments

#996 - Improved the abbreviation handling over atom sets, this is useful for…

Pull Request - State: closed - Opened by johnmay over 1 year ago - 4 comments

#994 - ReactionEnumerator

Issue - State: open - Opened by markfortner over 1 year ago - 7 comments

#993 - Sonarcloud bug cleanup

Pull Request - State: closed - Opened by johnmay over 1 year ago - 1 comment

#992 - Abbreviations rebased

Pull Request - State: closed - Opened by johnmay over 1 year ago - 3 comments

#991 - Improved Abbreviation Handling

Pull Request - State: closed - Opened by johnmay over 1 year ago - 6 comments

#990 - Sonarcloud wants J17 now

Pull Request - State: closed - Opened by egonw over 1 year ago - 1 comment

#989 - Sonarcloud wants to use Java 17

Issue - State: closed - Opened by egonw over 1 year ago - 1 comment
Labels: dependencies, bug

#988 - SDG rotation selection

Pull Request - State: closed - Opened by johnmay over 1 year ago - 1 comment

#987 - Fix a slight issue with the bounds/resizing calculations of reaction …

Pull Request - State: closed - Opened by johnmay over 1 year ago - 1 comment

#986 - SMILES extension and depiction of multipart reactions

Pull Request - State: closed - Opened by johnmay over 1 year ago - 6 comments

#985 - Updates of a few dependencies

Pull Request - State: closed - Opened by egonw over 1 year ago - 3 comments

#984 - Update documentation on PubChem fingerprinter.

Pull Request - State: closed - Opened by johnmay over 1 year ago - 1 comment

#983 - Question: How to use PubchemFingerprinter?

Issue - State: closed - Opened by Kohulan over 1 year ago - 8 comments

#982 - fix needed to get the latest CDK main compiling

Pull Request - State: closed - Opened by egonw over 1 year ago - 1 comment

#981 - added a new reaction type to allow drawing '=' sign for a Net reaction

Pull Request - State: closed - Opened by parit over 1 year ago - 11 comments

#980 - Propogating molecule id in svg to the corresponding title element

Pull Request - State: closed - Opened by parit over 1 year ago - 1 comment

#979 - Turn on the large molecules flag in InChI Universal SMILES numbers.

Pull Request - State: closed - Opened by johnmay over 1 year ago - 7 comments

#978 - Molecule alignment setting in org.openscience.cdk.depict.DepictionGenerator

Issue - State: closed - Opened by parit over 1 year ago - 1 comment

#977 - added test case for initial cycles oom

Pull Request - State: open - Opened by uli-f over 1 year ago - 4 comments

#976 - OOM in InitialCycles when applying aromaticity

Issue - State: open - Opened by uli-f over 1 year ago - 8 comments

#975 - Molecule titles as Bounds

Issue - State: open - Opened by parit over 1 year ago - 3 comments

#974 - InChi LargeMolecules Switch

Issue - State: closed - Opened by cubbardo over 1 year ago

#973 - Improved PubChem Fingerprinter through comparission to the CACTVS_SUB…

Pull Request - State: closed - Opened by johnmay over 1 year ago - 2 comments

#972 - More consistent MOLfile/SDfile property handling.

Pull Request - State: open - Opened by johnmay over 1 year ago - 11 comments

#971 - differences in processing V2000/V3000 tag data

Issue - State: open - Opened by adalke over 1 year ago - 2 comments

#969 - Kekulization / hydrogen adder problem

Issue - State: open - Opened by JonasSchaub over 1 year ago - 3 comments

#968 - Upgrade to BEAM 1.3.5 - Fix aromatic phosphorus "https://github.com/j…

Pull Request - State: closed - Opened by johnmay over 1 year ago - 5 comments

#967 - Scaffold generator integration

Pull Request - State: closed - Opened by egonw over 1 year ago - 7 comments

#966 - Updates of code and build dependencies

Pull Request - State: closed - Opened by egonw over 1 year ago - 1 comment

#965 - merge CML code into a single module

Issue - State: open - Opened by egonw over 1 year ago - 5 comments
Labels: feature request

#964 - Fix IteratingSdfReader - Ensure extra empty lines don't affect the pr…

Pull Request - State: closed - Opened by johnmay over 1 year ago - 2 comments

#963 - unexpected not reading of properties in ChEMBL SDFs

Issue - State: closed - Opened by egonw over 1 year ago - 6 comments

#962 - How to handle MDL files with aromatic bonds?

Issue - State: closed - Opened by StaffanArvidsson over 1 year ago - 6 comments

#961 - Invalid SMILES

Issue - State: closed - Opened by johnmay over 1 year ago

#960 - Error in AtomTools with reference heteroatoms

Issue - State: open - Opened by RamiManaf over 1 year ago

#959 - Absolute SMILES Generation fails for reactions

Issue - State: open - Opened by mrwns almost 2 years ago - 3 comments

#958 - Not working on Android

Issue - State: closed - Opened by tivewsalaeharad almost 2 years ago - 6 comments

#957 - Reproducibility of SMILES parsing

Issue - State: closed - Opened by hechth almost 2 years ago - 7 comments

#956 - More minor dep updates

Pull Request - State: closed - Opened by mjw99 almost 2 years ago

#955 - Various dep updates

Pull Request - State: closed - Opened by mjw99 almost 2 years ago - 1 comment

#954 - only return atoms within sphere=1 layer during generating HOSE code

Issue - State: open - Opened by biotech7 almost 2 years ago - 4 comments

#953 - QueryAtomContainer.create() should have option ignore query atoms/bonds

Issue - State: open - Opened by johnmay almost 2 years ago
Labels: feature request

#952 - merge MDL V2000/V3000 readers

Issue - State: open - Opened by adalke almost 2 years ago

#951 - IO Parsing should have warning, error, and fatal

Issue - State: open - Opened by egonw almost 2 years ago
Labels: feature request

#950 - Bounds check before access the atoms for a bond, this is a fatal erro…

Pull Request - State: closed - Opened by johnmay almost 2 years ago - 1 comment

#949 - ArrayOutOfBoundsException in MDLV2000Reader

Issue - State: closed - Opened by uli-f almost 2 years ago - 1 comment

#948 - added test case for MDLV2000Reader that gives rise to ArrayIndexOutOf…

Pull Request - State: closed - Opened by uli-f almost 2 years ago - 5 comments

#947 - added maven plugin to generate checksum for bundle uber-jar

Pull Request - State: closed - Opened by uli-f almost 2 years ago - 6 comments

#946 - checksum for jar from release page

Issue - State: closed - Opened by uli-f almost 2 years ago - 10 comments

#945 - Removes the Xerces and Xalan dependencies

Pull Request - State: closed - Opened by egonw almost 2 years ago - 3 comments

#944 - Support non-sequential atom index ins MDL V3000 inputs, fixes #943.

Pull Request - State: closed - Opened by johnmay almost 2 years ago - 1 comment

#943 - V3K molfile: Error while parsing index atom X in bond

Issue - State: closed - Opened by rapodaca almost 2 years ago - 1 comment

#942 - Rdfile reader

Pull Request - State: open - Opened by uli-f almost 2 years ago - 19 comments

#941 - Compilation error

Issue - State: closed - Opened by rapodaca almost 2 years ago - 9 comments

#940 - added test cases to BasicMoleculeHashGeneratorTest; added javadoc to …

Pull Request - State: closed - Opened by uli-f almost 2 years ago

#939 - Preliminary support for MRV Data Sgroup tags.

Pull Request - State: open - Opened by johnmay about 2 years ago - 1 comment

#938 - Query bond funcs

Pull Request - State: closed - Opened by johnmay about 2 years ago - 2 comments

#937 - A new contributor

Pull Request - State: closed - Opened by egonw about 2 years ago

#936 - Inchi mass table

Pull Request - State: closed - Opened by johnmay about 2 years ago - 3 comments

#935 - BFS paths, when we update our paths here we need to overwrite the num…

Pull Request - State: closed - Opened by johnmay about 2 years ago - 1 comment

#934 - Added auto-generated OSGi metadata

Pull Request - State: closed - Opened by Mailaender about 2 years ago - 11 comments