Delete of micromolecules bonds works wrong (or doesn't work) #5949

AlexeyGirin · 2024-11-08T13:57:57Z

Steps to Reproduce

Go to Macro - Flex
Load from file: Delete of micromolecules bonds works wrong (or doesn't work).zip
Delete few bonds

Actual behavior
Bonds between micro and macro - remain in place and atoms are selected

if you switch to Micro and back - all bonds got recovered

Expected behavior
Bonds between micro and macro - got deleted

Versions

Ketcher Version 2.27.0-rc.1 Build at 2024-11-05; 14:55:18
Indigo Toolkit Version 1.26.0-rc.1.0-g904d2d992-wasm32-wasm-clang-19.0.0
Chrome Version 130.0.6723.117 (Official Build) (64-bit)
Win10

Issue found while testing: #5359

- added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes

…6110) - added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes

- reworked bonds/atoms deletion logic - moved post execution logic from renderer to command

…sn't work) (#6119) * #5949 - Delete of micromolecules bonds works wrong (or doesn't work) (#6110) - added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command

…sn't work) (#6124) * #5949 - Delete of micromolecules bonds works wrong (or doesn't work) - added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command

…6135) - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command

commit 8862787 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 23:06:58 2024 +0100 Backmerge: #5949 - Delete of micromolecules bonds works wrong (or doesn't work) (#6124) * #5949 - Delete of micromolecules bonds works wrong (or doesn't work) - added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command commit dc4cfdc Author: Igor Kostrubin <kostrubin@bk.ru> Date: Wed Dec 11 20:54:17 2024 +0100 #5796 - Indigo functions doesn't work if monomer on micro canvas - system throws an error: Error: Cannot deserialize input JSON. (#6130) commit 014472b Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 17:50:13 2024 +0100 #5317 - Some side chain bonds are not shown in Sequence mode for bases, CHEMs, phosphates and sugars (#6054) commit b236964 Author: Maksim Labovich <lumihis+github@gmail.com> Date: Wed Dec 11 18:55:54 2024 +0300 #5476 - Copy/Cut and Paste using Ctrl+C/X and Ctrl+V doesn't work for static elements in Mozilla Firefox (#6121) * #5476 - save to text/plain in KET format instead of RXN - Firefox doesn't support MIME types other than text/plain in ClipboardItem, and RXN format saved by default to text/plain supports only chemical elements * #5476 - added comment, added stringify for data object to avoid [object Object] in console commit fa13b99 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:48:24 2024 +0100 #6086 - Unable to create antisense chains for ambiguous monomers from the library (#6113) (#6118) - added antisense creation for chains with ambiguous bases commit 668758d Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:34:37 2024 +0100 #6096 - Antisense creation works wrong in case of partial selection (#6122) (#6123) - fixed creation of antisense for partial selection by several pieces in one chain commit 89f5ce6 Author: Ruslan <117785539+Guch1g0v@users.noreply.github.com> Date: Wed Dec 11 13:14:21 2024 +0500 #6127 - Hover mouse over ambiguous monomer on Micromolecules canvas causes app crash (#6128) commit cca5f90 Author: Anrei Menshikov <95479023+Drimodaren@users.noreply.github.com> Date: Wed Dec 11 12:05:35 2024 +0400 #5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots (#6059) * 5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots * Refactoring * fix test * add new metod bondHoverablePath after review * createBondHoverablePath new logic * add type,const and refctoring createBondHoverablePath * commit TODO for mouseEvents * add ?? operand --------- Co-authored-by: Andrey Menshikov <andrey.menshikov@bostongene.com> commit 932ed0f Author: Roman Rodionov <roman_rodionov@epam.com> Date: Tue Dec 10 12:49:17 2024 +0100 Backmerge: #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6111) * #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6099) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6080 - System doesn't flip chain if connected to monomer but not to base (3) #6081 - Smaller chain should be at the bottom #6087 - Antisense layout is wrong for any ambiguouse base from the library #6077 - H-bond is not alligned to Snake mode view in some cases #6076 - Two-to-one base H-bond connection layouted wrong #6075 - In case of multipal H-bonds system should arrange antisence chain to first base of bottom chain #6070 - System doesn't flip chain if connected to monomer but not to base #6067 - Two chains connected by H-bond arranged wrong if third bond present on the canvas #6061 - RNA chain remain flipped after hydrogen bond removal - reworked antisense chains calculation * - fixed flacky test

commit 42a2a6c Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:29:11 2024 +0100 #6109 - Antisense of layout doesn't work on flex mode after load (#6114) (#6138) * #6109 - Antisense of layout doesn't work on flex mode after load - applied snake layout in flex mode if open/paste file with antisense chain - fixed open file implementation * #6083 - Creation of antisense chain causes monomer re-arrangement on the flex canvas - applied zoom to left top corner of the structures after antisense chains creation - updated ketcher version to 2.28.0-rc.2 commit 6c4a38b Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:28:28 2024 +0100 #6107 - Create Antisense Strand doesn't work in some cases (#6116) (#6120) - changed implementation of searching first monomers in selection (in this case monomer can be in the middle of the chain and does not have free r1 attachment point) - changed antisense base for Adenine commit c7d3f22 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:27:46 2024 +0100 #5032 - Selection of monomers should disappear when the user moves the cursor (#6136) commit 8862787 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 23:06:58 2024 +0100 Backmerge: #5949 - Delete of micromolecules bonds works wrong (or doesn't work) (#6124) * #5949 - Delete of micromolecules bonds works wrong (or doesn't work) - added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command commit dc4cfdc Author: Igor Kostrubin <kostrubin@bk.ru> Date: Wed Dec 11 20:54:17 2024 +0100 #5796 - Indigo functions doesn't work if monomer on micro canvas - system throws an error: Error: Cannot deserialize input JSON. (#6130) commit 014472b Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 17:50:13 2024 +0100 #5317 - Some side chain bonds are not shown in Sequence mode for bases, CHEMs, phosphates and sugars (#6054) commit b236964 Author: Maksim Labovich <lumihis+github@gmail.com> Date: Wed Dec 11 18:55:54 2024 +0300 #5476 - Copy/Cut and Paste using Ctrl+C/X and Ctrl+V doesn't work for static elements in Mozilla Firefox (#6121) * #5476 - save to text/plain in KET format instead of RXN - Firefox doesn't support MIME types other than text/plain in ClipboardItem, and RXN format saved by default to text/plain supports only chemical elements * #5476 - added comment, added stringify for data object to avoid [object Object] in console commit fa13b99 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:48:24 2024 +0100 #6086 - Unable to create antisense chains for ambiguous monomers from the library (#6113) (#6118) - added antisense creation for chains with ambiguous bases commit 668758d Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:34:37 2024 +0100 #6096 - Antisense creation works wrong in case of partial selection (#6122) (#6123) - fixed creation of antisense for partial selection by several pieces in one chain commit 89f5ce6 Author: Ruslan <117785539+Guch1g0v@users.noreply.github.com> Date: Wed Dec 11 13:14:21 2024 +0500 #6127 - Hover mouse over ambiguous monomer on Micromolecules canvas causes app crash (#6128) commit cca5f90 Author: Anrei Menshikov <95479023+Drimodaren@users.noreply.github.com> Date: Wed Dec 11 12:05:35 2024 +0400 #5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots (#6059) * 5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots * Refactoring * fix test * add new metod bondHoverablePath after review * createBondHoverablePath new logic * add type,const and refctoring createBondHoverablePath * commit TODO for mouseEvents * add ?? operand --------- Co-authored-by: Andrey Menshikov <andrey.menshikov@bostongene.com> commit 932ed0f Author: Roman Rodionov <roman_rodionov@epam.com> Date: Tue Dec 10 12:49:17 2024 +0100 Backmerge: #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6111) * #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6099) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6080 - System doesn't flip chain if connected to monomer but not to base (3) #6081 - Smaller chain should be at the bottom #6087 - Antisense layout is wrong for any ambiguouse base from the library #6077 - H-bond is not alligned to Snake mode view in some cases #6076 - Two-to-one base H-bond connection layouted wrong #6075 - In case of multipal H-bonds system should arrange antisence chain to first base of bottom chain #6070 - System doesn't flip chain if connected to monomer but not to base #6067 - Two chains connected by H-bond arranged wrong if third bond present on the canvas #6061 - RNA chain remain flipped after hydrogen bond removal - reworked antisense chains calculation * - fixed flacky test

commit ebb65a9 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 20:17:51 2024 +0100 #6129 - Undo operation creates unremovable bonds on the canvas (clear canvas doesn't help) (#6131) (#6141) commit 42a2a6c Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:29:11 2024 +0100 #6109 - Antisense of layout doesn't work on flex mode after load (#6114) (#6138) * #6109 - Antisense of layout doesn't work on flex mode after load - applied snake layout in flex mode if open/paste file with antisense chain - fixed open file implementation * #6083 - Creation of antisense chain causes monomer re-arrangement on the flex canvas - applied zoom to left top corner of the structures after antisense chains creation - updated ketcher version to 2.28.0-rc.2 commit 6c4a38b Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:28:28 2024 +0100 #6107 - Create Antisense Strand doesn't work in some cases (#6116) (#6120) - changed implementation of searching first monomers in selection (in this case monomer can be in the middle of the chain and does not have free r1 attachment point) - changed antisense base for Adenine commit c7d3f22 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:27:46 2024 +0100 #5032 - Selection of monomers should disappear when the user moves the cursor (#6136) commit 8862787 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 23:06:58 2024 +0100 Backmerge: #5949 - Delete of micromolecules bonds works wrong (or doesn't work) (#6124) * #5949 - Delete of micromolecules bonds works wrong (or doesn't work) - added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command commit dc4cfdc Author: Igor Kostrubin <kostrubin@bk.ru> Date: Wed Dec 11 20:54:17 2024 +0100 #5796 - Indigo functions doesn't work if monomer on micro canvas - system throws an error: Error: Cannot deserialize input JSON. (#6130) commit 014472b Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 17:50:13 2024 +0100 #5317 - Some side chain bonds are not shown in Sequence mode for bases, CHEMs, phosphates and sugars (#6054) commit b236964 Author: Maksim Labovich <lumihis+github@gmail.com> Date: Wed Dec 11 18:55:54 2024 +0300 #5476 - Copy/Cut and Paste using Ctrl+C/X and Ctrl+V doesn't work for static elements in Mozilla Firefox (#6121) * #5476 - save to text/plain in KET format instead of RXN - Firefox doesn't support MIME types other than text/plain in ClipboardItem, and RXN format saved by default to text/plain supports only chemical elements * #5476 - added comment, added stringify for data object to avoid [object Object] in console commit fa13b99 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:48:24 2024 +0100 #6086 - Unable to create antisense chains for ambiguous monomers from the library (#6113) (#6118) - added antisense creation for chains with ambiguous bases commit 668758d Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:34:37 2024 +0100 #6096 - Antisense creation works wrong in case of partial selection (#6122) (#6123) - fixed creation of antisense for partial selection by several pieces in one chain commit 89f5ce6 Author: Ruslan <117785539+Guch1g0v@users.noreply.github.com> Date: Wed Dec 11 13:14:21 2024 +0500 #6127 - Hover mouse over ambiguous monomer on Micromolecules canvas causes app crash (#6128) commit cca5f90 Author: Anrei Menshikov <95479023+Drimodaren@users.noreply.github.com> Date: Wed Dec 11 12:05:35 2024 +0400 #5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots (#6059) * 5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots * Refactoring * fix test * add new metod bondHoverablePath after review * createBondHoverablePath new logic * add type,const and refctoring createBondHoverablePath * commit TODO for mouseEvents * add ?? operand --------- Co-authored-by: Andrey Menshikov <andrey.menshikov@bostongene.com> commit 932ed0f Author: Roman Rodionov <roman_rodionov@epam.com> Date: Tue Dec 10 12:49:17 2024 +0100 Backmerge: #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6111) * #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6099) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6080 - System doesn't flip chain if connected to monomer but not to base (3) #6081 - Smaller chain should be at the bottom #6087 - Antisense layout is wrong for any ambiguouse base from the library #6077 - H-bond is not alligned to Snake mode view in some cases #6076 - Two-to-one base H-bond connection layouted wrong #6075 - In case of multipal H-bonds system should arrange antisence chain to first base of bottom chain #6070 - System doesn't flip chain if connected to monomer but not to base #6067 - Two chains connected by H-bond arranged wrong if third bond present on the canvas #6061 - RNA chain remain flipped after hydrogen bond removal - reworked antisense chains calculation * - fixed flacky test

…elper functions part 2 (#6117) * changing the zoom in in specs * changing the zoom in in specs * changing the zoom in specs * changing the zoom in specs * changing the zoom in specs * changing the zoom in specs * changing the zoom in specs * changing the zoom in specs * changing the zoom in specs * fixes * Squashed commit of the following: commit 8862787 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 23:06:58 2024 +0100 Backmerge: #5949 - Delete of micromolecules bonds works wrong (or doesn't work) (#6124) * #5949 - Delete of micromolecules bonds works wrong (or doesn't work) - added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command commit dc4cfdc Author: Igor Kostrubin <kostrubin@bk.ru> Date: Wed Dec 11 20:54:17 2024 +0100 #5796 - Indigo functions doesn't work if monomer on micro canvas - system throws an error: Error: Cannot deserialize input JSON. (#6130) commit 014472b Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 17:50:13 2024 +0100 #5317 - Some side chain bonds are not shown in Sequence mode for bases, CHEMs, phosphates and sugars (#6054) commit b236964 Author: Maksim Labovich <lumihis+github@gmail.com> Date: Wed Dec 11 18:55:54 2024 +0300 #5476 - Copy/Cut and Paste using Ctrl+C/X and Ctrl+V doesn't work for static elements in Mozilla Firefox (#6121) * #5476 - save to text/plain in KET format instead of RXN - Firefox doesn't support MIME types other than text/plain in ClipboardItem, and RXN format saved by default to text/plain supports only chemical elements * #5476 - added comment, added stringify for data object to avoid [object Object] in console commit fa13b99 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:48:24 2024 +0100 #6086 - Unable to create antisense chains for ambiguous monomers from the library (#6113) (#6118) - added antisense creation for chains with ambiguous bases commit 668758d Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:34:37 2024 +0100 #6096 - Antisense creation works wrong in case of partial selection (#6122) (#6123) - fixed creation of antisense for partial selection by several pieces in one chain commit 89f5ce6 Author: Ruslan <117785539+Guch1g0v@users.noreply.github.com> Date: Wed Dec 11 13:14:21 2024 +0500 #6127 - Hover mouse over ambiguous monomer on Micromolecules canvas causes app crash (#6128) commit cca5f90 Author: Anrei Menshikov <95479023+Drimodaren@users.noreply.github.com> Date: Wed Dec 11 12:05:35 2024 +0400 #5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots (#6059) * 5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots * Refactoring * fix test * add new metod bondHoverablePath after review * createBondHoverablePath new logic * add type,const and refctoring createBondHoverablePath * commit TODO for mouseEvents * add ?? operand --------- Co-authored-by: Andrey Menshikov <andrey.menshikov@bostongene.com> commit 932ed0f Author: Roman Rodionov <roman_rodionov@epam.com> Date: Tue Dec 10 12:49:17 2024 +0100 Backmerge: #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6111) * #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6099) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6080 - System doesn't flip chain if connected to monomer but not to base (3) #6081 - Smaller chain should be at the bottom #6087 - Antisense layout is wrong for any ambiguouse base from the library #6077 - H-bond is not alligned to Snake mode view in some cases #6076 - Two-to-one base H-bond connection layouted wrong #6075 - In case of multipal H-bonds system should arrange antisence chain to first base of bottom chain #6070 - System doesn't flip chain if connected to monomer but not to base #6067 - Two chains connected by H-bond arranged wrong if third bond present on the canvas #6061 - RNA chain remain flipped after hydrogen bond removal - reworked antisense chains calculation * - fixed flacky test * Squashed commit of the following: commit 42a2a6c Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:29:11 2024 +0100 #6109 - Antisense of layout doesn't work on flex mode after load (#6114) (#6138) * #6109 - Antisense of layout doesn't work on flex mode after load - applied snake layout in flex mode if open/paste file with antisense chain - fixed open file implementation * #6083 - Creation of antisense chain causes monomer re-arrangement on the flex canvas - applied zoom to left top corner of the structures after antisense chains creation - updated ketcher version to 2.28.0-rc.2 commit 6c4a38b Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:28:28 2024 +0100 #6107 - Create Antisense Strand doesn't work in some cases (#6116) (#6120) - changed implementation of searching first monomers in selection (in this case monomer can be in the middle of the chain and does not have free r1 attachment point) - changed antisense base for Adenine commit c7d3f22 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:27:46 2024 +0100 #5032 - Selection of monomers should disappear when the user moves the cursor (#6136) commit 8862787 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 23:06:58 2024 +0100 Backmerge: #5949 - Delete of micromolecules bonds works wrong (or doesn't work) (#6124) * #5949 - Delete of micromolecules bonds works wrong (or doesn't work) - added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command commit dc4cfdc Author: Igor Kostrubin <kostrubin@bk.ru> Date: Wed Dec 11 20:54:17 2024 +0100 #5796 - Indigo functions doesn't work if monomer on micro canvas - system throws an error: Error: Cannot deserialize input JSON. (#6130) commit 014472b Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 17:50:13 2024 +0100 #5317 - Some side chain bonds are not shown in Sequence mode for bases, CHEMs, phosphates and sugars (#6054) commit b236964 Author: Maksim Labovich <lumihis+github@gmail.com> Date: Wed Dec 11 18:55:54 2024 +0300 #5476 - Copy/Cut and Paste using Ctrl+C/X and Ctrl+V doesn't work for static elements in Mozilla Firefox (#6121) * #5476 - save to text/plain in KET format instead of RXN - Firefox doesn't support MIME types other than text/plain in ClipboardItem, and RXN format saved by default to text/plain supports only chemical elements * #5476 - added comment, added stringify for data object to avoid [object Object] in console commit fa13b99 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:48:24 2024 +0100 #6086 - Unable to create antisense chains for ambiguous monomers from the library (#6113) (#6118) - added antisense creation for chains with ambiguous bases commit 668758d Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:34:37 2024 +0100 #6096 - Antisense creation works wrong in case of partial selection (#6122) (#6123) - fixed creation of antisense for partial selection by several pieces in one chain commit 89f5ce6 Author: Ruslan <117785539+Guch1g0v@users.noreply.github.com> Date: Wed Dec 11 13:14:21 2024 +0500 #6127 - Hover mouse over ambiguous monomer on Micromolecules canvas causes app crash (#6128) commit cca5f90 Author: Anrei Menshikov <95479023+Drimodaren@users.noreply.github.com> Date: Wed Dec 11 12:05:35 2024 +0400 #5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots (#6059) * 5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots * Refactoring * fix test * add new metod bondHoverablePath after review * createBondHoverablePath new logic * add type,const and refctoring createBondHoverablePath * commit TODO for mouseEvents * add ?? operand --------- Co-authored-by: Andrey Menshikov <andrey.menshikov@bostongene.com> commit 932ed0f Author: Roman Rodionov <roman_rodionov@epam.com> Date: Tue Dec 10 12:49:17 2024 +0100 Backmerge: #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6111) * #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6099) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6080 - System doesn't flip chain if connected to monomer but not to base (3) #6081 - Smaller chain should be at the bottom #6087 - Antisense layout is wrong for any ambiguouse base from the library #6077 - H-bond is not alligned to Snake mode view in some cases #6076 - Two-to-one base H-bond connection layouted wrong #6075 - In case of multipal H-bonds system should arrange antisence chain to first base of bottom chain #6070 - System doesn't flip chain if connected to monomer but not to base #6067 - Two chains connected by H-bond arranged wrong if third bond present on the canvas #6061 - RNA chain remain flipped after hydrogen bond removal - reworked antisense chains calculation * - fixed flacky test * fix * Squashed commit of the following: commit ebb65a9 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 20:17:51 2024 +0100 #6129 - Undo operation creates unremovable bonds on the canvas (clear canvas doesn't help) (#6131) (#6141) commit 42a2a6c Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:29:11 2024 +0100 #6109 - Antisense of layout doesn't work on flex mode after load (#6114) (#6138) * #6109 - Antisense of layout doesn't work on flex mode after load - applied snake layout in flex mode if open/paste file with antisense chain - fixed open file implementation * #6083 - Creation of antisense chain causes monomer re-arrangement on the flex canvas - applied zoom to left top corner of the structures after antisense chains creation - updated ketcher version to 2.28.0-rc.2 commit 6c4a38b Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:28:28 2024 +0100 #6107 - Create Antisense Strand doesn't work in some cases (#6116) (#6120) - changed implementation of searching first monomers in selection (in this case monomer can be in the middle of the chain and does not have free r1 attachment point) - changed antisense base for Adenine commit c7d3f22 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Thu Dec 12 11:27:46 2024 +0100 #5032 - Selection of monomers should disappear when the user moves the cursor (#6136) commit 8862787 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 23:06:58 2024 +0100 Backmerge: #5949 - Delete of micromolecules bonds works wrong (or doesn't work) (#6124) * #5949 - Delete of micromolecules bonds works wrong (or doesn't work) - added invertAfterAllOperations method to atom and bonds operations to allow renderers rely on final state of model before rendering - added deleting of atoms and bonds from molecules struct to synchronize molecules and macromolecules modes - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command commit dc4cfdc Author: Igor Kostrubin <kostrubin@bk.ru> Date: Wed Dec 11 20:54:17 2024 +0100 #5796 - Indigo functions doesn't work if monomer on micro canvas - system throws an error: Error: Cannot deserialize input JSON. (#6130) commit 014472b Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 17:50:13 2024 +0100 #5317 - Some side chain bonds are not shown in Sequence mode for bases, CHEMs, phosphates and sugars (#6054) commit b236964 Author: Maksim Labovich <lumihis+github@gmail.com> Date: Wed Dec 11 18:55:54 2024 +0300 #5476 - Copy/Cut and Paste using Ctrl+C/X and Ctrl+V doesn't work for static elements in Mozilla Firefox (#6121) * #5476 - save to text/plain in KET format instead of RXN - Firefox doesn't support MIME types other than text/plain in ClipboardItem, and RXN format saved by default to text/plain supports only chemical elements * #5476 - added comment, added stringify for data object to avoid [object Object] in console commit fa13b99 Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:48:24 2024 +0100 #6086 - Unable to create antisense chains for ambiguous monomers from the library (#6113) (#6118) - added antisense creation for chains with ambiguous bases commit 668758d Author: Roman Rodionov <roman_rodionov@epam.com> Date: Wed Dec 11 15:34:37 2024 +0100 #6096 - Antisense creation works wrong in case of partial selection (#6122) (#6123) - fixed creation of antisense for partial selection by several pieces in one chain commit 89f5ce6 Author: Ruslan <117785539+Guch1g0v@users.noreply.github.com> Date: Wed Dec 11 13:14:21 2024 +0500 #6127 - Hover mouse over ambiguous monomer on Micromolecules canvas causes app crash (#6128) commit cca5f90 Author: Anrei Menshikov <95479023+Drimodaren@users.noreply.github.com> Date: Wed Dec 11 12:05:35 2024 +0400 #5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots (#6059) * 5978-entire-element-bounding-box-should-be-clickable-not-only-black-dots * Refactoring * fix test * add new metod bondHoverablePath after review * createBondHoverablePath new logic * add type,const and refctoring createBondHoverablePath * commit TODO for mouseEvents * add ?? operand --------- Co-authored-by: Andrey Menshikov <andrey.menshikov@bostongene.com> commit 932ed0f Author: Roman Rodionov <roman_rodionov@epam.com> Date: Tue Dec 10 12:49:17 2024 +0100 Backmerge: #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6111) * #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) (#6099) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong) #6074 - System doesn't flip chain if connected to monomer but not to base (2) #6080 - System doesn't flip chain if connected to monomer but not to base (3) #6081 - Smaller chain should be at the bottom #6087 - Antisense layout is wrong for any ambiguouse base from the library #6077 - H-bond is not alligned to Snake mode view in some cases #6076 - Two-to-one base H-bond connection layouted wrong #6075 - In case of multipal H-bonds system should arrange antisence chain to first base of bottom chain #6070 - System doesn't flip chain if connected to monomer but not to base #6067 - Two chains connected by H-bond arranged wrong if third bond present on the canvas #6061 - RNA chain remain flipped after hydrogen bond removal - reworked antisense chains calculation * - fixed flacky test * screenshots update * screenshots update * fix * fixes * fix * fix * removed import --------- Co-authored-by: Konstantin_Nadonenko <konstantin_nadonenko@epam.com>

AlexeyGirin · 2024-12-25T11:54:42Z

Verified.

Ketcher Version 2.27.0-rc.3 Build at 2024-12-25; 10:08:04
Indigo Version 1.26.0-rc.5.0-g42ee8510b-wasm32-wasm-clang-19.0.0
Chrome Version 131.0.6778.205 (Official Build) (64-bit)
Win10

AlexeyGirin added bug Priority: High Flex mode Bucket: Flex canvas related mode Micro-Macro Bucket: Bugs related to Micro structures on Macro mode labels Nov 8, 2024

AlexeyGirin added this to the Ketcher 2.27.0-rc.2 milestone Nov 8, 2024

rrodionov91 modified the milestones: Ketcher 2.27.0-rc.2, Ketcher 2.27.0-rc.3 Nov 12, 2024

rrodionov91 self-assigned this Dec 4, 2024

rrodionov91 linked a pull request Dec 9, 2024 that will close this issue

#5949 - Delete of micromolecules bonds works wrong (or doesn't work) #6110

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rrodionov91 linked a pull request Dec 10, 2024 that will close this issue

Backmerge: #5949 - Delete of micromolecules bonds works wrong (or doesn't work) #6119

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9 tasks

rrodionov91 linked a pull request Dec 10, 2024 that will close this issue

Backmerge: #5949 - Delete of micromolecules bonds works wrong (or doesn't work) #6124

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rrodionov91 added a commit that referenced this issue Dec 11, 2024

#5949 - Delete of micromolecules bonds works wrong (or doesn't work)

e58ef14

- reworked bonds/atoms deletion logic - moved post execution logic from renderer to command

rrodionov91 added a commit that referenced this issue Dec 11, 2024

#5949 - Delete of micromolecules bonds works wrong (or doesn't work)

0fc2679

- reworked bonds/atoms deletion logic - moved post execution logic from renderer to command

rrodionov91 added a commit that referenced this issue Dec 11, 2024

#5949 - Delete of micromolecules bonds works wrong (or doesn't work)

297ea8a

- reworked bonds/atoms deletion logic - moved post execution logic from renderer to command

rrodionov91 linked a pull request Dec 11, 2024 that will close this issue

#5949 - Delete of micromolecules bonds works wrong (or doesn't work) #6135

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9 tasks

rrodionov91 closed this as completed in #6124 Dec 11, 2024

rrodionov91 added a commit that referenced this issue Dec 11, 2024

#5949 - Delete of micromolecules bonds works wrong (or doesn't work) (#…

bcc6b94

…6135) - reworked bonds/atoms deletion logic - moved post execution logic from renderer to command

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Delete of micromolecules bonds works wrong (or doesn't work) #5949

Delete of micromolecules bonds works wrong (or doesn't work) #5949

AlexeyGirin commented Nov 8, 2024 •

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AlexeyGirin commented Dec 25, 2024

Delete of micromolecules bonds works wrong (or doesn't work) #5949

Delete of micromolecules bonds works wrong (or doesn't work) #5949

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AlexeyGirin commented Nov 8, 2024 • edited Loading

AlexeyGirin commented Dec 25, 2024

AlexeyGirin commented Nov 8, 2024 •

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