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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