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
>>>>>>>>>
>>>>>>>>
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