Activity for AMBIT:Chemical Structure DB&Web Service
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Nikolay Kochev committed [a1037b] on Code
Improvement in MoleculeTools.convertExplicitHAtomsToImplicit(): handle doubel bond stereo elements with explict H atoms connected - now the stereo is not lost
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Added debug code to track doboble bond stereo loss within MoleculeTools.convertExplicitHAtomsToImplicit(mol)
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Debug printing of SMILES info
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Small bug fix on handling not applicable reactions. Added a new test case 101B for not applicable reaction
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Restoreed stereo SMIRKS test104() which is now working; added two new modifications: 104B and 104C
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Improved function checkReactionResult(): handling of not applicable reactions
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Fixed a bug: stereo utils code moved from FlagAromaticityTransformation section to FlagApplyStereoTransformation section
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Added test helper function getIsomericSmiles()
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Commented out debug printing code
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Added a check for valid stereo element
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Code update in order to use STEREO_ELEMENTS_PROPERTY instead of CDK mol.stereoElements() container
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Commented out an older function for storing stereo as atom/bond properties
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Updated stereo chem utils to use STEREO_ELEMENTS_PROPERTY instead of container.stereoElements()
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Added basic functionality for handling stereo elements stored as property
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Added test fix with (stChange.isValidStereoElement()
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Fixed a stereo transfotmation bug by checking for appearence of new valid stero elements stored in variable: newValidEl. Added debug printing code.
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Added debug printing
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debug print
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Added function dublicateStereoElement()
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Some debug printing
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in TestSMIRKSStereo: added FlagPrintProducts
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Commented out a junit test with non parsable smiles: n1=cc=cn=c1
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Improvements in IChemObjectReaderErrorHandler interface anonymous instantiation
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Even more IChemObjectReaderErrorHandler fixes
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More IChemObjectReaderErrorHandler fixes
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IChemObjectReaderErrorHandler problem fix: added needed function implementation
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Top level POM files update: changed cdk.version to 2.11
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Added Java pointer info to the StereoChange string
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Added new stereo util function getStereoChangesAsString()
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Fixed junit metabolism test
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Fixed failed junit test due to changes of xlogp model values
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Fixed a failed junit test: query molecule smiles replaced with simple [Fe]
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Fixed a failed jaunit test: png expected size must be > 0
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Added maven dependency in ambit-rest pom for log4j v.2.20.0
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Improved SMIRKSReaction.toString(): added info about stereo double bond and chiral atom transformations. Implemented function StereoChiralAtTransformation.toString()
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Commented out call to AtomConfigurator.process(). This resolves most of the junit fails and errors
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Added new flag FlagLogoutProductSmiles
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Added maven dependency commons-cli
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Migrated opsin version to 2.7.0
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Added check for InChI generation problem
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Replaced inchi options list with a string
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Direct LogingTool usage replaced with LoginToolFactory
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Direct LogingTool usage replaced with LoginToolFactory
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Migrated to cdk 2.8. Added cdk-jniinchi-support dependency. Temporary cdk-legacy depedency scope is changed
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Chnanged maven artifact version to 5.0.0-SNAPSHOT
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In GCMPredictCli: added new option --quiet (-q). Fixed option -v
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Added new cli option -v (verbose) and implemented output of correction factors
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Added getter getCurrentCalculationObject()
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Added new option --max_combinations (-M) in SLNCli. Changed default value maxNumberOfCombinations = 100000
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Code refactoring: system ouput replaced with function outputLine()
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Added new output functionality
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Added functions for handling output. Refactoring: runSLN()-->runSLNApp()
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Implemented basic functions for handling out file writer
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Improved function matchesUserDefinedAttributes(): numerical molecular properties comparison is handled correctly
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Fixed a subtke bug: wrong flag replaced with FlagMatchMolecularProperties
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Implemented function validateSLNContainer()
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Small bug fix in function Expander.getNewAtomWhichIsValenceConection()
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Added FlagSLNContainerValidation
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Added function getValencePosIndex() and implemented handling of valence positions setting via atom attribute 'v'
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Fixed a bug when converting SLN atom expression to SMARTS in mode convert_as_value_list: values are separated with OR logical operation
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Improved valence points array usage and fixed possible 'index out of bounds' exception
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Nina Jeliazkova committed [c2f400] on Code
студъ цонфигс
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Stereo elements are handled via STEREO_ELEMENTS_PROPERTY instead of CDK iterator
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Refactoring to fix small typo
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Added some comments. Refactoring: checkStereoElementsProperty() --> checkStereoElementsStoredAsProperty()
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Un-commented function cloneAndCheckStereo() - it is used in ambit-tautomer module
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One additional comment
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Added comment for using CDK stereo elements iterator
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Refactoring: setSteroElementsAsProperties() --> setSteroElementsAsAtomAndBondProperties()
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Stereo elements are handled via molecule property instead of immutable CDK stereoElements() list
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Commented out unused function cloneAndCheckStereo()
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Implemented function checkStereoElementsProperty()
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Added new function setStereoElementsListAsProperty(). Refactoeing: getStereoElementsFromProperty() --> extractStereoElementsFromProperty()
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Added else clause for empty stereo element list
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Added functions handling stereo elements as molecule property
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Added debug info for target stereo elements at the end of function handleStereoOnBondChange()
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Extended debug log
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Debug log changes. TreeMap usage cause different exception
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study display config
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Added debug printing to trace stereo changes
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Added Java pointer info to the StereoChange string
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Added new stereo util function getStereoChangesAsString()
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cleanuprecords is in the substancestudyvalidator
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Fixed junit metabolism test
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Fixed failed junit test due to changes of xlogp model values
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Fixed a failed junit test: query molecule smiles replaced with simple [Fe]
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Fixed a failed jaunit test: png expected size must be > 0
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Added maven dependency in ambit-rest pom for log4j v.2.20.0
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Improved SMIRKSReaction.toString(): added info about stereo double bond and chiral atom transformations. Implemented function StereoChiralAtTransformation.toString()
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Commented out call to AtomConfigurator.process(). This resolves most of the junit fails and errors
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Added new flag FlagLogoutProductSmiles
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Added maven dependency commons-cli
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Migrated opsin version to 2.7.0
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Added check for InChI generation problem
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Replaced inchi options list with a string
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Direct LogingTool usage replaced with LoginToolFactory
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Direct LogingTool usage replaced with LoginToolFactory
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Migrated to cdk 2.8. Added cdk-jniinchi-support dependency. Temporary cdk-legacy depedency scope is changed
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Chnanged maven artifact version to 5.0.0-SNAPSHOT
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fixed serialisation bug
