>
> *GeometryTools* "@deprecated use {@link *GeometryUtil*} moved for
> dependency reorganisation"Specifically Java awt I think was the issue, so GeometryUtil should provide like for like and more and is in cdk-standard module *MoleculeFactory* "@deprecated Old CDK class primarily for testing, for CDK > Tests please use *TestMoleculeFactory* in cdk-data." We were reoragnising and decoupling tests SMARTS is a bit more complicated because the entire API stack was redesigned. Fortunately the doc should be good on these. The parser (and generator) is now just "Smarts" http://cdk.github.io/cdk/latest/docs/api/index.html?org/openscience/cdk/smarts/Smarts.html Then for the Atom/Bond matchers, this is now handled by an expression tree rather than let Java do dynamic dispatches on lots of different classes. The key class is "Expr"(ression) and you can set/get expression on QueryAtom|Bond.setExpression(expr). http://cdk.github.io/cdk/latest/docs/api/index.html?org/openscience/cdk/isomorphism/matchers/Expr.html For matching http://cdk.github.io/cdk/latest/docs/api/index.html?org/openscience/cdk/smarts/SmartsPattern.html (when from SMARTS string) or http://cdk.github.io/cdk/latest/docs/api/index.html?org/openscience/cdk/isomorphism/DfPattern.html (when building an IAtomContainer up for matching) The key challenge here is for some of these APIs you may need to make sure all molecule creation is done via the factories and not "new AtomContainer()", that will be less important in future but might be an issue here. Further reading: - https://github.com/cdk/cdk/wiki/AtomContainer2 - SMARTS API release notes: https://github.com/cdk/cdk/wiki/2.2-Release-Notes#core On Tue, 16 Aug 2022 at 07:38, Uli Fechner <u...@pending.ai> wrote: > I did a backward dependency analysis of the cdk-legacy module for the > ambit2 library. > > These are the classes in cdk-legacy that are used by ambit2: > > geometry/GeometryTools.class > isomorphism/matchers/smarts/AliphaticAtom.class > isomorphism/matchers/smarts/AliphaticSymbolAtom.class > isomorphism/matchers/smarts/AnyAtom.class > isomorphism/matchers/smarts/AnyOrderQueryBond.class > isomorphism/matchers/smarts/AromaticAtom.class > isomorphism/matchers/smarts/AromaticQueryBond.class > isomorphism/matchers/smarts/LogicalOperatorAtom.class > isomorphism/matchers/smarts/OrderQueryBond.class > isomorphism/matchers/smarts/SMARTSAtom.class > isomorphism/matchers/smarts/SMARTSBond.class > smiles/smarts/parser/SMARTSParser.class > smiles/smarts/SMARTSQueryTool.class > templates/MoleculeFactory.class > > All of the classes listed above are used by both classes in main and in > source of the ambit2 library with the exception of AliphaticSymbolAtom, > LogicalOperatorAtom and SMARTSParser that are used by classes in test only. > > Best > Uli > > On Tue, Aug 16, 2022 at 4:18 PM John Mayfield <john.wilkinson...@gmail.com> > wrote: > >> Do you consider it a problem that the library (heavily) depends on the >>> cdk-legacy module? In other words, will the cdk-legacy module potentially >>> be removed in an upcoming CDK 3 release? >> >> >> Fine for now but it needs someone to go through and put in the new API >> calls. Most of the stuff in legacy (with the exception of SMSD) there >> should be a better way to do it now, SMSD there is a new >> independent version (we tried to merge but ultimately it's a lot of code >> and works well as a standalone app). If you give me the errors that occur >> (class not found) when you remove cdk-legacy I can probably give the list >> of what to use instead. Since you already have a local Ambit version >> shouldn't be a problem to try them out. >> >> John >> >> On Tue, 16 Aug 2022 at 03:36, Uli Fechner <u...@pending.ai> wrote: >> >>> Thank you John for the helpful information. >>> >>> The <dependencyManagement> declarations seem like an elegant solution. >>> In my understanding, this only works if the project itself and its >>> dependent projects are maven-based, i.e. there is no mix-and-match between >>> maven-based and gradle-based projects here. >>> >>> My solution then was to compile the library of the maven-based project >>> (ambit2), deploy the resultant jars to our internal maven repository, and >>> pull those jars from the internal repository for the gradle-based project. >>> I'd be happy to know if there is an easier way to do this...? >>> >>> Do you consider it a problem that the library (heavily) depends on the >>> cdk-legacy module? In other words, will the cdk-legacy module potentially >>> be removed in an upcoming CDK 3 release? >>> >>> On Mon, Aug 15, 2022 at 9:07 PM John Mayfield < >>> john.wilkinson...@gmail.com> wrote: >>> >>>> Do you import via gradle/maven repos? Or are you using local paths? I >>>> didn't actually know the public release was still on CDK 1.4.11 but >>>> anyways. >>>> >>>> It sounds like you've maybe got it working but basically in Maven you >>>> would do something like this with the publically released projects: >>>> >>>> <pom> >>>>> ... >>>>> <dependency> >>>>> <groupId>ambit</groupId> >>>>> <artifactId>ambit2-core</artifactId> >>>>> <version>2.4.9</version> >>>>> </dependency> >>>>> <dependencyManagement> >>>>> <dependency> >>>>> <groupId>org.opensicence.cdk</groupId> >>>>> <artifactId>cdk-core</artifactId> >>>>> <version>2.7.1</version> >>>>> </dependency> >>>>> >>>> <dependency> >>>>> <groupId>org.opensicence.cdk</groupId> >>>>> <artifactId>cdk-isomorphism</artifactId> >>>>> <version>2.7.1</version> >>>>> </dependency> >>>> >>>> ... etc etc >>>> >>>> </dependencyManagement> >>>>> </pom> >>>> >>>> >>>> The dependencyManagement section basically says if any dependencies >>>> (ambit in this case) that use CDK, rather than using the version they >>>> declare you should v2.7.1. You would need to do this for all the modules it >>>> uses. I tried to find the equivalent in gradle but no luck. >>>> However you should be able to do something like this where you just >>>> declare everything and the build tool will use the version you declare: >>>> >>>> dependencies { >>>> implementation 'ambit:ambit2-core:2.4.9' >>>> implementation 'org.openscience.cdk:cdk-core:2.7.1' >>>> implementation 'org.openscience.cdk:cdk-isomorphism:2.7.1' >>>> ... etc etc >>>> } >>>> >>>> On Mon, 15 Aug 2022 at 06:58, Uli Fechner <u...@pending.ai> wrote: >>>> >>>>> It has been a while since I have used maven, so I am not quite sure if >>>>> I understand correctly what you are referring to with the usage of >>>>> <depdencencyManagement>. The project I want to use the ambit2 library as a >>>>> dependency with uses gradle; at the moment, it directly depends on the >>>>> jars >>>>> that I compiled from the modified ambit library version. >>>>> >>>>> Here is a text export of the backward dependency analysis of the >>>>> cdk-legacy jar: >>>>> >>>>> <root isBackward="true"> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/geometry/GeometryTools.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-jchempaint/src/main/java/ambit2/jchempaint/editor/MoleculeEditAction.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/isomorphism/matchers/smarts/AliphaticAtom.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/smirks/SmartsMatch.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-sln/src/main/java/ambit2/sln/io/SLN2ChemObject.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsHelper.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsParser.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/isomorphism/matchers/smarts/AliphaticSymbolAtom.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/test/java/ambit2/smarts/test/TestUtilities.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/smirks/SmartsMatch.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/test/java/ambit2/smarts/test/TestUtilities.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-sln/src/main/java/ambit2/sln/io/SLN2ChemObject.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsHelper.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsParser.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/smirks/SmartsMatch.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-sln/src/main/java/ambit2/sln/io/SLN2ChemObject.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsHelper.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsParser.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsManager.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/smirks/SmartsMatch.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-sln/src/main/java/ambit2/sln/io/SLN2ChemObject.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsHelper.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsParser.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/smirks/SmartsMatch.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsHelper.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsToChemObject.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsParser.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsManager.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorAtom.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/test/java/ambit2/smarts/test/AutomaticTestUtilities.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/isomorphism/matchers/smarts/OrderQueryBond.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/smirks/SmartsMatch.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/test/java/ambit2/smarts/test/TestUtilities.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-sln/src/main/java/ambit2/sln/io/SLN2ChemObject.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsHelper.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsToChemObject.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsParser.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-tautomers/src/main/java/ambit2/tautomers/RuleStateBondDistribution.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsManager.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-sln/src/main/java/ambit2/sln/SLNAtom.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/smirks/SmartsMatch.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsAtomExpression.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-sln/src/main/java/ambit2/sln/io/SLN2ChemObject.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsHelper.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/AromaticSymbolQueryAtom.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/smirks/SmartsIsomorphismTester.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsManager.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/AliphaticSymbolQueryAtom.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/IsomorphismTester.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SymbolQueryAtomAromaticityNotSpecified.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/TripleBondAromaticityNotSpecified.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SingleOrAromaticBond.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/RingQueryBond.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsBondExpression.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsHelper.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SingleNonAromaticBond.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SingleBondAromaticityNotSpecified.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsManager.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/smirks/SmartsMatch.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/DoubleBondAromaticityNotSpecified.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/SmartsParser.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/DoubleNonAromaticBond.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-sln/src/main/java/ambit2/sln/SLNBond.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/IsomorphismTester.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/test/java/ambit2/smarts/test/AutomaticTestUtilities.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-descriptors/src/main/java/ambit2/descriptors/fingerprints/PubChemFingerprinterAmbitSmarts.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/main/java/ambit2/smarts/query/SmartsPatternCDK.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smarts/src/test/java/ambit2/smarts/processors/StructureKeysBitSetGeneratorTest.java" >>>>> /> >>>>> </file> >>>>> <file >>>>> path="$MAVEN_REPOSITORY$/org/openscience/cdk/cdk-legacy/2.7.1/cdk-legacy-2.7.1.jar!/org/openscience/cdk/templates/MoleculeFactory.class"> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-db/src/test/java/ambit2/db/processors/test/DbDescriptorWriterTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-core/src/test/java/ambit2/core/processors/test/InchiProcessorTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-db/src/test/java/ambit2/db/search/test/QuerySimilarityBitSetTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-ui/src/test/java/ambit2/ui/test/QueryBrowserTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-rendering/src/test/java/ambit2/rendering/RendererTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-apps/ambit2-www/src/test/java/ambit2/rest/test/similarity/SimilarityResourceTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-namestructure/src/test/java/ambit2/namestructure/test/Name2StructureProcessorTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-smi23d/src/test/java/ambit2/smi23d/test/CommandShellTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-db/src/test/java/ambit2/db/search/test/QuerySimilarityStructureTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-core/src/test/java/ambit2/core/processors/test/HydrogenAdderProcessorTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-model/src/test/java/ambit2/similarity/measure/test/AtomEnvironmentDistanceTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-core/src/test/java/ambit2/core/processors/test/AtomConfiguratorProcessorTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-db/src/test/java/ambit2/db/search/test/QueryCombinedTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-core/src/test/java/ambit2/core/external/test/CommandShellTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-apps/ambit2-www/src/test/java/ambit2/rest/test/query/SmartsResourceTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-tautomers/src/test/java/ambit2/tautomers/test/TautomersVisualisationTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-core/src/test/java/ambit2/core/obabel/test/TestOpenBabelShell.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-db/src/test/java/ambit2/db/processors/test/DbDescriptorValuesWriterTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-balloon/src/test/java/ambit2/balloon/test/BalloonShellTest.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-apps/ambit2-dbcli/src/main/java/ambit2/dbcli/AmbitPipeline.java" >>>>> /> >>>>> <dependency >>>>> path="$PROJECT_DIR$/ambit2-all/ambit2-model/src/test/java/ambit2/similarity/measure/test/AtomEnvironmentHammingDistanceTest.java" >>>>> /> >>>>> </file> >>>>> </root> >>>>> >>>>> On Fri, Jul 22, 2022 at 11:41 PM John May <john.wilkinson...@gmail.com> >>>>> wrote: >>>>> >>>>>> Which parts does it depend on? A better way to do the versioning is >>>>>> to use the “<dependencyManagment>” in maven - no need to modify the ambit >>>>>> props >>>>>> >>>>>> - John >>>>>> >>>>>> On 22 Jul 2022, at 09:26, Uli Fechner <u...@pending.ai> wrote: >>>>>> >>>>>> >>>>>> Thank you for your reply, John. >>>>>> >>>>>> I bumped the cdk dependency in the POM of ambit by changing the >>>>>> property <cdk.version> from 2.1.1 to 2.7.1. >>>>>> >>>>>> I also had to change two dependency configurations in the POM of >>>>>> ambit2-smarts to get it to compile: >>>>>> - the scope test of the dependency org.openscience.cdk:cdk-legacy >>>>>> was removed (effectively changing >>>>>> <https://maven.apache.org/guides/introduction/introduction-to-dependency-mechanism.html#Dependency_Scope> >>>>>> the scope from test to the default scope compile) >>>>>> - the dependency >>>>>> org.openscience.cdk:cdk-jniinchi-support:${cdk.version} was added >>>>>> >>>>>> It seems like ambit2 quite heavily depends on the cdk-legacy package, >>>>>> so I guess this will all break at one point if the ambit2 package isn't >>>>>> updated... >>>>>> >>>>>> Best >>>>>> Uli >>>>>> >>>>>> On Tue, Jul 19, 2022 at 11:00 PM John Mayfield < >>>>>> john.wilkinson...@gmail.com> wrote: >>>>>> >>>>>>> There "should" not be any breaking change 2.2.1 -> 2.7.1. If there >>>>>>> is try including the cdk-legacy module. >>>>>>> >>>>>>> Best regards >>>>>>> John >>>>>>> >>>>>>> On Tue, 19 Jul 2022 at 08:14, Uli Fechner <u...@pending.ai> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> I want to apply a SMIRKS pattern to a molecule and get the products >>>>>>>> as a result. My understanding is that CDK does not support this at the >>>>>>>> moment. Is that correct? >>>>>>>> >>>>>>>> The ambit-smirks package by IdeaConsult seems to offer the >>>>>>>> functionality I am looking for. However, it declares a dependency on >>>>>>>> cdk >>>>>>>> 2.2.1 in its latest pom ( >>>>>>>> https://github.com/ideaconsult/ambit-mirror/blob/master/ambit2-all/pom.xml). >>>>>>>> We use cdk 2.71 and I don't want to downgrade. Does anyone have any >>>>>>>> experience with bumping the cdk version in ambit and compiling it >>>>>>>> yourself? >>>>>>>> >>>>>>>> Any help is much appreciated. >>>>>>>> >>>>>>>> Best >>>>>>>> Uli >>>>>>>> _______________________________________________ >>>>>>>> Cdk-user mailing list >>>>>>>> Cdk-user@lists.sourceforge.net >>>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>>>>> >>>>>>>
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