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Recent Releases of mortar

mortar - MORTAR v1.4.0

Change notes

  • Adds stereo chemistry support to MORTAR; for details, see the new tutorial section
  • Improves settings menu layout
  • Replaces the anthraquinone tutorial data set with the BIOFACQUIM natural products collection
  • Updates the Chemistry Development Kit (CDK) dependency from 2.10 to 2.11
  • Solve issue that open valences in imported MOL/SD files were not fixed correctly
  • Solves issue with toggle switch warnings

What's Changed (auto-generated release notes)

  • fix: sets cdk-fragment version to general 2.11-SNAPSHOT version by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/161
  • Adds stereochemistry to MORTAR by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/163
  • Updates CDK from 2.10 to 2.11 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/168
  • fixes ToggleSwitch skin property issue #150 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/169
  • Fixes issue that radicals imported from MOL files are not saturated at import by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/172
  • Issue 118 nicer settings display by @ToLeWeiss in https://github.com/FelixBaensch/MORTAR/pull/175
  • Preparations for MORTAR v1.4 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/173
  • MORTAR v1.4 release by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/176
  • fixes two SonarCloud issues to pass quality check by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/177
  • Sonar issues fix by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/178

New Contributors

  • @ToLeWeiss made their first contribution in https://github.com/FelixBaensch/MORTAR/pull/175

Full Changelog: https://github.com/FelixBaensch/MORTAR/compare/v1.3.0...v1.4.0

- Java
Published by JonasSchaub 8 months ago

mortar - MORTAR v1.3.0

Change notes

  • Improvements to parallel fragmentation routine; MORTAR is more responsive now while a fragmentation is being executed and error reporting from parallel computation threads has been improved
  • Fixes bug in items tab that occurred when only a subset of imported molecules has been fragmented (https://github.com/FelixBaensch/MORTAR/issues/151)
  • Update CDK from v2.9 to v2.10
    • this makes new aromaticity models available to use
  • Replaces ErtlFunctionalGroupsFinder and Sugar Removal Utility implementations with the new ones available directly from CDK now
    • NOTE, there is a slight behaviour change for the ErtlFunctionalGroupsFinder fragmenter: environmental carbon atoms on extracted functional groups are duplicated now, i.e. they will appear in the functional group fragment and in the alkyl remnants fragments. To suppress this, you have to use the "no environment" setting for functional group environments.
  • Update OpenPDF from 1.3.26 to 2.0.3
  • License update to 2025

What's Changed (auto-generated release notes)

  • Issues 152 and 153 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/154
  • Fix bug #151; by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/156
  • Update licenses to 2025 and change Felix mail address; by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/155
  • Updates CDK from 2.9 to 2.10 and replaces SRU and EFGF artifacts with the new CDK-own implementations by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/158
  • MORTAR v1.3 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/159

Full Changelog: https://github.com/FelixBaensch/MORTAR/compare/v1.2.2...v1.3.0

- Java
Published by JonasSchaub about 1 year ago

mortar - MORTAR v1.2.2

Change notes

  • Support for native app menu bar on MacOS now implemented
  • Debian package (.deb) distribution for Ubuntu now available

What's Changed (auto-generated release notes)

  • System native menu bar on Mac by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/144
  • Debian package (.deb) distribution for Ubuntu by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/145
  • Native menu bar on macOS and DEB deployment for Ubuntu by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/146
  • MORTAR v1.2.2 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/147

Full Changelog: https://github.com/FelixBaensch/MORTAR/compare/v1.2.1...v1.2.2

- Java
Published by JonasSchaub over 1 year ago

mortar - MORTAR v1.2.1

Change notes

  • New toggle switch control for settings (@ZeynepDagtekin)
  • Fix bug in right-click menu copy functionality of fragments tab (#135)(@FelixBaensch)
  • More installation options for macOS (#122)(@JonasSchaub)

What's Changed (auto-generated release notes)

  • Make gradle build badge point to main branch by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/124
  • Fix bug 135: Copying parent molecule instead of fragment by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/136
  • Additions to IMoleculeFragmenter interface documentation about how to add new fragmentation classes by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/134
  • Toogle switch for boolean settings by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/90
  • Merge production into main by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/139
  • MORTAR v1.2.1 release by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/137

Full Changelog: https://github.com/FelixBaensch/MORTAR/compare/v1.2.0.0...v1.2.1

- Java
Published by JonasSchaub over 1 year ago

mortar - MORTAR v1.2.0.0

Change notes

  • Settings menus now have proper option strings in drop-down boxes and every option has a specific tooltip
  • Minor GUI rework concerning button and other control sizes
  • Switched licence to MIT
  • Now using GitHub pages: https://felixbaensch.github.io/MORTAR/
  • Updated ErtlFunctionalGroupsFinder (https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder) to v1.3 which has some new functionality and less input restrictions (https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder/releases/tag/V1.3.0.0)
  • Updated from Java 17 to Java 21
  • SDF and SMILES import routines improved and augmented
  • Changed CSV export separator char from being set directly to an enum constant defining the character
  • New fragmentation option in ScaffoldGeneratorFragmenter to dissect a scaffold into its single rings
  • A few changes and additions in headers of exported files
  • Added MORTAR icon to all alerts and dialogs
  • Revision of exception handling at import
  • Fixed import without adding implicit hydrogen atoms
  • Separator character is now replaced with _ in molecule names when items tab is exported to CSV
  • New row added in pipeline settings view is now pre-set to selected fragmenter and other issues fixed there
  • Keep last fragment setting for pipeline was removed since the fragmentation algorithms can be configured in this regard now
  • Fixed bug with file extension on export for Linux
  • Fixed issue https://github.com/FelixBaensch/MORTAR/issues/56 that coordinates were not generated for fragments exported to separate SD files
  • Added drag and drop feature for file import (issue https://github.com/FelixBaensch/MORTAR/issues/33)
  • Fixed issue https://github.com/FelixBaensch/MORTAR/issues/72 that parent structures overview of fragments resulting from a pipeline fragmentation showed only one parent structure
  • Added ".tsv" as accepted import file extension (issue https://github.com/FelixBaensch/MORTAR/issues/81)
  • Fixed issue https://github.com/FelixBaensch/MORTAR/issues/86 that "data will be lost" dialogue appeared two times
  • Fixed issue https://github.com/FelixBaensch/MORTAR/issues/88 regarding pipeline settings dialogue
  • Changed arrangement of fragments tab (issue https://github.com/FelixBaensch/MORTAR/issues/84)
  • Fixed unnecessary scroll bars in molecules tab
  • Added note to tutorial about forwarding MORTAR from a remote server using X (https://github.com/FelixBaensch/MORTAR/issues/85)
  • Added more tooltips to fragments tab
  • Fixed issue https://github.com/FelixBaensch/MORTAR/issues/108, a major problem with the deployment on Windows by restructuring the automatically created start scripts (batch files)
  • Fixed issue https://github.com/FelixBaensch/MORTAR/issues/100, the unnecessary scroll bar in the items tab
  • Multiple other small bug fixes
  • Code only:
    • Now using the spotless plugin for automatic code formatting
    • Now using SonarCloud for automatics code analysis
    • Copied source files from ErtlFunctionalGroupsFinder, Scaffold Generator (now CDK-Scaffold), and Sugar Removal Utility were replaced with their artifacts taken from Maven Central
    • Updated Gradle to v8.5, CDK to v2.9, JavaFx to 21.0.1, and spotless to v6.25
    • Updated JavaFx Gradle plugin (0.0.14 -> 0.1.0) (issue https://github.com/FelixBaensch/MORTAR/issues/23)
    • Conducted general code base review guided by SonarCloud analysis (https://sonarcloud.io/project/issues?resolved=false&types=CODESMELL&id=FelixBaenschMORTAR)
    • Introduced a configuration properties file to read paths to icons and other resource files from
    • Fixed all the "bugs" that SonarCloud reported (https://sonarcloud.io/summary/overall?id=FelixBaensch_MORTAR): putting readers and writers in try-with-resources blocks, logic error in PreferenceContainer.addWithoutChecks(), retrieval of example parent molecule in FragmentDataModel, preventing possible division by zero in FragmentationService, better handling of InterruptedExceptions at ExecutorService shutdown
    • Most strings like log messages are now formatted correctly instead of using string concatenation
    • Improved casting and typing in most places
    • Throwing defined exception types instead of general ones in some places
    • Manual code linting and additional documentation
    • Overhaul of exporter, mostly exception treatment (more is passed on to export thread now, so that it fails properly)
    • Introduced separate display names for settings (general and for fragmenters)
    • Added SimpleIDisplayEnumConstantProperty as new JavaFX property that wraps an enum constant with associated display name and tooltip to be used in the GUI and replaced all SimpleEnumConstantNameProperty settings with SimpleIDisplayEnumConstantProperty settings
    • Reduced duplication by moving translation of preferences to properties and check of properties for preference restrictions to PreferenceUtil for SettingsContainer, FragmentationService, and ViewToolsManager
    • Added separate display names to fragmenters for usage in GUI
    • Changed integer and double filters of settings view text fields to positive value filter including zero
    • Collection util rework

What's Changed (auto-generated release notes)

  • Gradle build in GitHub actions on push to master; spotless code formatting plugin; DOI badge in readme by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/9
  • Replaced copied ScaffoldGenerator source files with cdk-scaffold artifact by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/14
  • Replaced SRU source files with maven artifact by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/17
  • EFGF artifact integration and dependency updates by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/25
  • Update readme by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/34
  • Update README.md by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/37
  • Readme update by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/39
  • Updated EFGF to v1.3 and make adjustments in fragmenter class by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/35
  • Update of ErtlFunctionalGroupsFinder v1.2 to v1.3 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/42
  • Changed licence to MIT in source code file headers and in licence files by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/41
  • Licence change to MIT by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/43
  • Update LICENSE by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/44
  • Fixed SD files not being imported completely by @SamuelBehr in https://github.com/FelixBaensch/MORTAR/pull/12
  • SDF import fix by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/45
  • Smiles import minor adaptions by @SamuelBehr in https://github.com/FelixBaensch/MORTAR/pull/13
  • Smiles importer test for improvements by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/31
  • Collection util rework by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/53
  • Fixed some SonarCloud issues from the complete code analysis by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/49
  • Fixed copy and paste error in SettingsContainer by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/60
  • Separator character is now replaced with _ in molecule names when items tab is exported to CSV by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/64
  • Issue 54 button sizes by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/65
  • Export fixes by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/62
  • Issue 36 query bonds import by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/63
  • Issue 59 pipeline settings view by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/69
  • Marked keepLastFragmentSetting for pipelines as deprecated and removed… by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/70
  • Preparations for v1.2, adjusted version numbers, updated gradle wrapper, … by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/73
  • Check for file extension on export; by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/76
  • Add drag'n'drop feature by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/74
  • Fix for issue 72, only one parent molecule for each fragment after pipeline by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/78
  • Adding .tsv file extension to accepted import file types by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/89
  • Making shell code in readme directly copyable by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/92
  • Update javafxplugin according to its readme; by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/95
  • Issue 86 by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/91
  • Update copyright year to 2024 in about view by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/96
  • Fix for issue 88 that fragmenter settings in pipeline reflect back to fragmentation settings in main view by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/97
  • Added paragraph about X11 forwarding to the tutorial by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/101
  • Issue 84 column swap by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/99
  • Issue 100 scroll bar by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/109
  • Removing "if defined JAVA_HOME" from the batch files to fix the issue… by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/110
  • MORTAR v1.2-beta.2 preparations by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/111
  • MORTAR v1.2.0.0 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/119

Full Changelog: https://github.com/FelixBaensch/MORTAR/compare/v1.1.1.0...v1.2.0.0

- Java
Published by JonasSchaub almost 2 years ago

mortar - MORTAR v1.2.0.0-beta.2

Change notes

  • Added more tooltips to fragments tab
  • Fixed issue #108, a major problem with the deployment on Windows by restructuring the automatically created start scripts (batch files)
  • Fixed issue #100, the unnecessary scroll bar in the items tab

What's Changed (according to GitHub pull requests)

  • Gradle build in GitHub actions on push to master; spotless code formatting plugin; DOI badge in readme by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/9
  • Replaced copied ScaffoldGenerator source files with cdk-scaffold artifact by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/14
  • Replaced SRU source files with maven artifact by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/17
  • EFGF artifact integration and dependency updates by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/25
  • Update readme by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/34
  • Update README.md by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/37
  • Readme update by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/39
  • Updated EFGF to v1.3 and make adjustments in fragmenter class by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/35
  • Update of ErtlFunctionalGroupsFinder v1.2 to v1.3 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/42
  • Changed licence to MIT in source code file headers and in licence files by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/41
  • Licence change to MIT by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/43
  • Update LICENSE by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/44
  • Fixed SD files not being imported completely by @SamuelBehr in https://github.com/FelixBaensch/MORTAR/pull/12
  • Smiles import minor adaptions by @SamuelBehr in https://github.com/FelixBaensch/MORTAR/pull/13
  • Smiles importer test for improvements by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/31
  • Collection util rework by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/53
  • Fixed some SonarCloud issues from the complete code analysis by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/49
  • Fixed copy and paste error in SettingsContainer by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/60
  • Separator character is now replaced with _ in molecule names when items tab is exported to CSV by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/64
  • Issue 54 button sizes by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/65
  • Export fixes by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/62
  • Issue 36 query bonds import by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/63
  • Issue 59 pipeline settings view by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/69
  • Marked keepLastFragmentSetting for pipelines as deprecated and removed… by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/70
  • Preparations for v1.2, adjusted version numbers, updated gradle wrapper, … by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/73
  • Check for file extension on export; by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/76
  • Add drag'n'drop feature by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/74
  • Fix for issue 72, only one parent molecule for each fragment after pipeline by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/78
  • Adding .tsv file extension to accepted import file types by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/89
  • Making shell code in readme directly copyable by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/92
  • Update javafxplugin according to its readme; by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/95
  • Issue 86 by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/91
  • Update copyright year to 2024 in about view by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/96
  • Fix for issue 88 that fragmenter settings in pipeline reflect back to fragmentation settings in main view by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/97
  • Added paragraph about X11 forwarding to the tutorial by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/101
  • Issue 84 column swap by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/99
  • Issue 100 scroll bar by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/109
  • Removing "if defined JAVA_HOME" from the batch files to fix the issue… by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/110
  • MORTAR v1.2-beta.2 preparations by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/111

Full Changelog: https://github.com/FelixBaensch/MORTAR/compare/v1.1.1.0...v1.2.0.0-beta.2

- Java
Published by JonasSchaub almost 2 years ago

mortar - MORTAR v1.2.0.0-beta.1

Change notes

  • Added drag and drop feature for file import (issue #33)
  • Fixed issue #72 that parent structures overview of fragments resulting from a pipeline fragmentation showed only one parent structure
  • Added ".tsv" as accepted import file extension (issue #81)
  • Fixed issue #86 that "data will be lost" dialogue appeared two times
  • Updated JavaFx Gradle plugin (0.0.14 -> 0.1.0) (issue #23)
  • Fixed issue #88 regarding pipeline settings dialogue
  • Changed arrangement of fragments tab (issue #84)
  • Fixed unnecessary scroll bars in molecules tab
  • Added note about forwarding MORTAR from a remote server using X (#85)

What's Changed (according to GitHub pull requests)

  • Gradle build in GitHub actions on push to master; spotless code formatting plugin; DOI badge in readme by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/9
  • Replaced copied ScaffoldGenerator source files with cdk-scaffold artifact by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/14
  • Replaced SRU source files with maven artifact by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/17
  • EFGF artifact integration and dependency updates by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/25
  • Update readme by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/34
  • Update README.md by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/37
  • Readme update by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/39
  • Updated EFGF to v1.3 and make adjustments in fragmenter class by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/35
  • Update of ErtlFunctionalGroupsFinder v1.2 to v1.3 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/42
  • Changed licence to MIT in source code file headers and in licence files by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/41
  • Licence change to MIT by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/43
  • Update LICENSE by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/44
  • Fixed SD files not being imported completely by @SamuelBehr in https://github.com/FelixBaensch/MORTAR/pull/12
  • Smiles import minor adaptions by @SamuelBehr in https://github.com/FelixBaensch/MORTAR/pull/13
  • Smiles importer test for improvements by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/31
  • Collection util rework by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/53
  • Fixed some SonarCloud issues from the complete code analysis by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/49
  • Fixed copy and paste error in SettingsContainer by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/60
  • Separator character is now replaced with _ in molecule names when items tab is exported to CSV by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/64
  • Issue 54 button sizes by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/65
  • Export fixes by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/62
  • Issue 36 query bonds import by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/63
  • Issue 59 pipeline settings view by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/69
  • Marked keepLastFragmentSetting for pipelines as deprecated and removed… by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/70
  • Preparations for v1.2, adjusted version numbers, updated gradle wrapper, … by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/73
  • Check for file extension on export; by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/76
  • Add drag'n'drop feature by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/74
  • Fix for issue 72, only one parent molecule for each fragment after pipeline by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/78
  • Adding .tsv file extension to accepted import file types by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/89
  • Making shell code in readme directly copyable by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/92
  • Update javafxplugin according to its readme; by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/95
  • Issue 86 by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/91
  • Update copyright year to 2024 in about view by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/96
  • Fix for issue 88 that fragmenter settings in pipeline reflect back to fragmentation settings in main view by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/97
  • Added paragraph about X11 forwarding to the tutorial by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/101
  • Issue 84 column swap by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/99

Full Changelog: https://github.com/FelixBaensch/MORTAR/compare/v1.1.1.0...v1.2.0.0-beta.1

- Java
Published by JonasSchaub almost 2 years ago

mortar - MORTAR v1.2.0.0-beta

Change notes

  • Settings menus now have proper option strings in drop-down boxes and every option has a specific tooltip
  • Minor GUI rework concerning button and other control sizes
  • Switched licence to MIT
  • Now using GitHub pages: https://felixbaensch.github.io/MORTAR/ (not updated for this beta release)
  • Updated ErtlFunctionalGroupsFinder (https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder) to v1.3 which has some new functionality and less input restrictions (https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder/releases/tag/V1.3.0.0)
  • Updated from Java 17 to Java 21
  • SDF and SMILES import routines improved and augmented
  • Changed CSV export separator char from being set directly to an enum constant defining the character
  • New fragmentation option in ScaffoldGeneratorFragmenter to dissect a scaffold into its single rings
  • A few changes and additions in headers of exported files
  • Added MORTAR icon to all alerts and dialogs
  • Revision of exception handling at import
  • Fixed import without adding implicit hydrogen atoms
  • Separator character is now replaced with _ in molecule names when items tab is exported to CSV
  • New row added in pipeline settings view is now pre-set to selected fragmenter and other issues fixed there
  • Keep last fragment setting for pipeline was removed since the fragmentation algorithms can be configured in this regard now
  • Fixed bug with file extension on export for Linux
  • Fixed issue #56 that coordinates were not generated for fragments exported to separate SD files
  • Multiple other small bug fixes
  • Code only:
    • Now using the spotless plugin for automatic code formatting
    • Now using SonarCloud for automatics code analysis
    • Copied source files from ErtlFunctionalGroupsFinder, Scaffold Generator (now CDK-Scaffold), and Sugar Removal Utility were replaced with their artifacts taken from Maven Central
    • Updated Gradle to v8.5, CDK to v2.9, JavaFx to 21.0.1, and spotless to v6.25
    • Conducted general code base review guided by SonarCloud analysis (https://sonarcloud.io/project/issues?resolved=false&types=CODESMELL&id=FelixBaenschMORTAR)
    • Introduced a configuration properties file to read paths to icons and other resource files from
    • Fixed all the "bugs" that SonarCloud reported (https://sonarcloud.io/summary/overall?id=FelixBaensch_MORTAR): putting readers and writers in try-with-resources blocks, logic error in PreferenceContainer.addWithoutChecks(), retrieval of example parent molecule in FragmentDataModel, preventing possible division by zero in FragmentationService, better handling of InterruptedExceptions at ExecutorService shutdown
    • Most strings like log messages are now formatted correctly instead of using string concatenation
    • Improved casting and typing in most places
    • Throwing defined exception types instead of general ones in some places
    • Manual code linting and additional documentation
    • Overhaul of exporter, mostly exception treatment (more is passed on to export thread now, so that it fails properly)
    • Introduced separate display names for settings (general and for fragmenters)
    • Added SimpleIDisplayEnumConstantProperty as new JavaFX property that wraps an enum constant with associated display name and tooltip to be used in the GUI and replaced all SimpleEnumConstantNameProperty settings with SimpleIDisplayEnumConstantProperty settings
    • Reduced duplication by moving translation of preferences to properties and check of properties for preference restrictions to PreferenceUtil for SettingsContainer, FragmentationService, and ViewToolsManager
    • Added separate display names to fragmenters for usage in GUI
    • Changed integer and double filters of settings view text fields to positive value filter including zero
    • Collection util rework

What's Changed (according to GitHub pull requests)

  • Gradle build in GitHub actions on push to master; spotless code formatting plugin; DOI badge in readme by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/9
  • Replaced copied ScaffoldGenerator source files with cdk-scaffold artifact by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/14
  • Replaced SRU source files with maven artifact by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/17
  • EFGF artifact integration and dependency updates by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/25
  • Update readme by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/34
  • Update README.md by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/37
  • Readme update by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/39
  • Updated EFGF to v1.3 and make adjustments in fragmenter class by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/35
  • Update of ErtlFunctionalGroupsFinder v1.2 to v1.3 by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/42
  • Changed licence to MIT in source code file headers and in licence files by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/41
  • Licence change to MIT by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/43
  • Update LICENSE by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/44
  • Fixed SD files not being imported completely by @SamuelBehr in https://github.com/FelixBaensch/MORTAR/pull/12
  • Smiles import minor adaptions by @SamuelBehr in https://github.com/FelixBaensch/MORTAR/pull/13
  • Smiles importer test for improvements by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/31
  • Collection util rework by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/53
  • Fixed some SonarCloud issues from the complete code analysis by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/49
  • Fixed copy and paste error in SettingsContainer by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/60
  • Separator character is now replaced with _ in molecule names when items tab is exported to CSV by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/64
  • Issue 54 button sizes by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/65
  • Export fixes by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/62
  • Issue 36 query bonds import by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/63
  • Issue 59 pipeline settings view by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/69
  • Marked keepLastFragmentSetting for pipelines as deprecated and removed… by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/70
  • Preparations for v1.2, adjusted version numbers, updated gradle wrapper, … by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/73
  • Check for file extension on export; by @FelixBaensch in https://github.com/FelixBaensch/MORTAR/pull/76

Full Changelog: https://github.com/FelixBaensch/MORTAR/compare/v1.1.1.0...v1.2.0.0-beta

- Java
Published by JonasSchaub almost 2 years ago

mortar - MORTAR v1.1.1.0

Change notes

  • GUI:
    • Settings of histogram view and overview view are now persisted during a session and between sessions
  • Code:
    • Histogram view and overview view functionalities are now more unified and more encapsulated via IViewToolController interface and ViewToolsManager class
    • Extensive restructuring of HistogramViewController and OverviewViewController
    • ListUtil class was renamed to CollectionUtil and extended
    • Junit updated v4.13 to 5.9.3 with some minor adaptions of the test classes
    • Bug fix in pipeline fragmenter depersistence
    • Central SMILES code parsing method added to ChemUtil class

What's Changed

  • Rework of HashMap initialisations by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/5
  • Histogram unification by @B-s123 in https://github.com/FelixBaensch/MORTAR/pull/8
  • Unifying view tools, histogram and overview, to some extend and persisting their settings within and between sessions by @JonasSchaub in https://github.com/FelixBaensch/MORTAR/pull/6

Full Changelog: https://github.com/FelixBaensch/MORTAR/compare/v1.1.0.0...v1.1.1.0

- Java
Published by FelixBaensch over 2 years ago

mortar - MORTAR v1.1.0.0

  • Added overview feature as an alternative, grid-based visualization of molecular structures
  • Bug in the mapping of the "parent molecules" for the fragments has been fixed
  • Minor bug fixes

- Java
Published by FelixBaensch about 3 years ago

mortar - MORTAR v1.0.6.0

  • Invalid Java version alert is now a warning that can be dismissed and is suppressed when MORTAR is started from the automatically generated batch files on Windows (in response to a bug that was reported)
  • Updated Scaffold Generator to v1.0.3
  • Changed default fragmentation of Scaffold Generator to Schuffenhauer fragmentation
  • Adjustments of (re-)sizing behavior of some dialogues

- Java
Published by FelixBaensch over 3 years ago

mortar - MORTAR v1.0.5.0

Fixed a NullPointerException;

- Java
Published by FelixBaensch over 3 years ago

mortar - MORTAR v1.0.4.0

Updated CDK to version 2.8; Updated integrated fragmentation algorithms to CDK v2.8; Changed DefaultChemObjectBuilder objects to SilentChemObjectBuilder objects; If installed on Windows via installer batch files now have a MORTAR icon in start menu;

- Java
Published by FelixBaensch over 3 years ago

mortar - MORTAR v1.0.3.0

MORTAR now supports x64 on Windows, Linux and MacOS and offers a specific "fat jar" for AArch64 on Linux and MacOS;

- Java
Published by FelixBaensch over 3 years ago

mortar - MORTAR v1.0.2.0

MORTAR now supports AArch64 architecture on Mac and Linux; Fixed bug that identical fragments were not recorded as the same;

- Java
Published by FelixBaensch over 3 years ago

mortar - MORTAR v1.0.1.0

Deployment adjustments for MacOS and Linux; Updated to Java v17.0.4+8; Updated to JavaFX v17.0.2; Updated to Gradle v7.3; Minor changes in GUI;

- Java
Published by FelixBaensch over 3 years ago

mortar - MORTAR v1.0.0.0

Initial release of the MOlecule fRagmenTAtion fRamework (MORTAR) v1.0.0.0

- Java
Published by FelixBaensch over 3 years ago