Flatten 19 sub-packages into parents: 28 → 9 packages

Moved all files from sub-packages into their parent packages:
- mapping/{container,graph,helper,algorithm/checks} → mapping/ and mapping/algorithm/
- mechanism/{helper,interfaces} → mechanism/
- tools/{labelling,matrix,rxnfile} → tools/
- stereo/ → mechanism/
- smsd/{algorithm/matchers,filters,tools} → smsd/

Package structure now: aamtool, fingerprints, mapping, mapping/algorithm,
mechanism, signature, tools, smsd, cdk/smiles (9 packages total).

139 files, 135/135 tests pass. Zero functionality changes.

Co-Authored-By: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>

Author: asad

src/main/java/com/bioinceptionlabs/aamtool/Annotator.java

@@ -49,7 +49,7 @@
 import com.bioinceptionlabs.reactionblast.mechanism.BondChangeCalculator;
 import com.bioinceptionlabs.reactionblast.mechanism.MappingSolution;
 import com.bioinceptionlabs.reactionblast.mechanism.ReactionMechanismTool;
-import com.bioinceptionlabs.reactionblast.mechanism.helper.MoleculeMoleculePair;
+import com.bioinceptionlabs.reactionblast.mechanism.MoleculeMoleculePair;
 import static com.bioinceptionlabs.reactionblast.tools.ReactionSimilarityTool.getSimilarity;
 import com.bioinceptionlabs.reactionblast.tools.StandardizeReaction;
 

src/main/java/com/bioinceptionlabs/aamtool/ChemicalFormatParser.java

@@ -43,8 +43,8 @@
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
-import org.openscience.smsd.tools.ExtAtomContainerManipulator;
-import com.bioinceptionlabs.reactionblast.tools.rxnfile.MDLRXNV2000Reader;
+import org.openscience.smsd.ExtAtomContainerManipulator;
+import com.bioinceptionlabs.reactionblast.tools.MDLRXNV2000Reader;
 
 /**
  * @contact Syed Asad Rahman, BioInception.

src/main/java/com/bioinceptionlabs/aamtool/Helper.java

@@ -33,7 +33,7 @@
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 import com.bioinceptionlabs.reactionblast.tools.ImageGenerator;
-import com.bioinceptionlabs.reactionblast.tools.rxnfile.MDLV2000RXNWriter;
+import com.bioinceptionlabs.reactionblast.tools.MDLV2000RXNWriter;
 
 /**
  * @contact Syed Asad Rahman, BioInception.

src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/ReactionFingerprinter.java

@@ -32,7 +32,7 @@
 import org.openscience.cdk.tools.ILoggingTool;
 import static org.openscience.cdk.tools.LoggingToolFactory.createLoggingTool;
 import static org.openscience.smsd.MoleculeInitializer.initializeMolecule;
-import static org.openscience.smsd.tools.ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID;
+import static org.openscience.smsd.ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID;
 import static com.bioinceptionlabs.reactionblast.fingerprints.FingerprintGenerator.getFingerprinterSize;
 import com.bioinceptionlabs.reactionblast.fingerprints.IPatternFingerprinter;
 

src/main/java/com/bioinceptionlabs/reactionblast/mapping/AbstractGraphMatching.java

@@ -23,7 +23,7 @@
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IReaction;
 import com.bioinceptionlabs.reactionblast.mapping.algorithm.Holder;
-import com.bioinceptionlabs.reactionblast.mapping.container.ReactionContainer;
+import com.bioinceptionlabs.reactionblast.mapping.ReactionContainer;
 
 /**
  * @contact Syed Asad Rahman, BioInception.

…last/mapping/helper/AbstractReactor.java …actionblast/mapping/AbstractReactor.javasrc/main/java/com/bioinceptionlabs/reactionblast/mapping/helper/AbstractReactor.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/mapping/AbstractReactor.java src/main/java/com/bioinceptionlabs/reactionblast/mapping/helper/AbstractReactor.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/mapping/AbstractReactor.java

@@ -16,7 +16,7 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
  * MA 02110-1301  USA
  */
-package com.bioinceptionlabs.reactionblast.mapping.helper;
+package com.bioinceptionlabs.reactionblast.mapping;
 
 import java.io.IOException;
 import java.util.List;

…apping/container/BestMatchContainer.java …ionblast/mapping/BestMatchContainer.javasrc/main/java/com/bioinceptionlabs/reactionblast/mapping/container/BestMatchContainer.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/mapping/BestMatchContainer.java src/main/java/com/bioinceptionlabs/reactionblast/mapping/container/BestMatchContainer.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/mapping/BestMatchContainer.java

@@ -16,7 +16,7 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
  * MA 02110-1301  USA
  */
-package com.bioinceptionlabs.reactionblast.mapping.container;
+package com.bioinceptionlabs.reactionblast.mapping;
 
 //~--- JDK imports ------------------------------------------------------------
 import java.io.IOException;
@@ -29,7 +29,7 @@
 import org.openscience.cdk.tools.ILoggingTool;
 import static org.openscience.cdk.tools.LoggingToolFactory.createLoggingTool;
 import org.openscience.smsd.AtomAtomMapping;
-import com.bioinceptionlabs.reactionblast.mapping.container.Key;
+import com.bioinceptionlabs.reactionblast.mapping.Key;
 import com.bioinceptionlabs.reactionblast.mapping.BestMatch;
 import com.bioinceptionlabs.reactionblast.mapping.IKey;
 

…apping/container/CDKReactionBuilder.java …ionblast/mapping/CDKReactionBuilder.javasrc/main/java/com/bioinceptionlabs/reactionblast/mapping/container/CDKReactionBuilder.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/mapping/CDKReactionBuilder.java src/main/java/com/bioinceptionlabs/reactionblast/mapping/container/CDKReactionBuilder.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/mapping/CDKReactionBuilder.java

@@ -16,7 +16,7 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
  * MA 02110-1301  USA
  */
-package com.bioinceptionlabs.reactionblast.mapping.container;
+package com.bioinceptionlabs.reactionblast.mapping;
 
 import java.io.IOException;
 import java.io.Serializable;
@@ -45,19 +45,19 @@
 import org.openscience.cdk.tools.ILoggingTool;
 import static org.openscience.cdk.tools.LoggingToolFactory.createLoggingTool;
 import org.openscience.smsd.Substructure;
-import org.openscience.smsd.algorithm.matchers.AtomBondMatcher;
-import org.openscience.smsd.algorithm.matchers.AtomMatcher;
-import org.openscience.smsd.algorithm.matchers.BondMatcher;
+import org.openscience.smsd.AtomBondMatcher;
+import org.openscience.smsd.AtomMatcher;
+import org.openscience.smsd.BondMatcher;
 import com.bioinceptionlabs.reactionblast.fingerprints.FingerprintGenerator;
 import com.bioinceptionlabs.reactionblast.fingerprints.IFingerprintGenerator;
 import static com.bioinceptionlabs.reactionblast.fingerprints.Similarity.getTanimotoSimilarity;
 import com.bioinceptionlabs.reactionblast.tools.AtomContainerSetComparator;
 import com.bioinceptionlabs.reactionblast.tools.BasicDebugger;
-import static org.openscience.smsd.tools.ExtAtomContainerManipulator.aromatizeMolecule;
-import static org.openscience.smsd.tools.ExtAtomContainerManipulator.cloneWithIDs;
-import static org.openscience.smsd.tools.ExtAtomContainerManipulator.fixDativeBonds;
-import static org.openscience.smsd.tools.ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms;
-import static org.openscience.smsd.tools.ExtAtomContainerManipulator.removeHydrogens;
+import static org.openscience.smsd.ExtAtomContainerManipulator.aromatizeMolecule;
+import static org.openscience.smsd.ExtAtomContainerManipulator.cloneWithIDs;
+import static org.openscience.smsd.ExtAtomContainerManipulator.fixDativeBonds;
+import static org.openscience.smsd.ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms;
+import static org.openscience.smsd.ExtAtomContainerManipulator.removeHydrogens;
 
 /**
  * @contact Syed Asad Rahman, BioInception.

src/main/java/com/bioinceptionlabs/reactionblast/mapping/CallableAtomMappingTool.java

@@ -47,7 +47,7 @@
 import static com.bioinceptionlabs.reactionblast.mapping.IMappingAlgorithm.MIN;
 import static com.bioinceptionlabs.reactionblast.mapping.IMappingAlgorithm.MIXTURE;
 import static com.bioinceptionlabs.reactionblast.mapping.IMappingAlgorithm.RINGS;
-import com.bioinceptionlabs.reactionblast.tools.rxnfile.MDLV2000RXNWriter;
+import com.bioinceptionlabs.reactionblast.tools.MDLV2000RXNWriter;
 
 /**
  *

…tionblast/mapping/graph/Combination.java …s/reactionblast/mapping/Combination.javasrc/main/java/com/bioinceptionlabs/reactionblast/mapping/graph/Combination.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/mapping/Combination.java src/main/java/com/bioinceptionlabs/reactionblast/mapping/graph/Combination.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/mapping/Combination.java

@@ -16,7 +16,7 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
  * MA 02110-1301  USA
  */
-package com.bioinceptionlabs.reactionblast.mapping.graph;
+package com.bioinceptionlabs.reactionblast.mapping;
 
 import java.io.Serializable;
 import java.util.Comparator;