I summarized the information we exchanged here and opened an issue in the ambit2 repo.
https://sourceforge.net/p/ambit/feature-requests/103/ On Wed, Aug 17, 2022 at 12:46 PM Uli Fechner <u...@pending.ai> wrote: > Thank you so much for your very helpful message! > > I will contact the authors of the ambit2 library and provide them with > this information. > > On Wed, Aug 17, 2022 at 6:56 AM John Mayfield <john.wilkinson...@gmail.com> > wrote: > >> *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 >>>>>>>>>> >>>>>>>>>
_______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
