Releases: epam/Indigo
Releases · epam/Indigo
Indigo-1.28.0
What's Changed
Bugfixes
- #2313 - Indigo functions doesn't work if ambiguous monomer present on the canvas
- #2435 - Export of ambiguous monomers to Sequence/FASTA doesn't work for mixed ambiguous monomers
- #2324 - System loads DNA bases instead of RNA ones during IDT import
- #2387 - After opening a saved HELM file, microstructure name F1 turns into Mod0
- #2062 - HELM loader ignores repeating token
- #2332 - Error message should use "ambiguous monomer" instead of "variant monomer"
- #2338 - System loads HELM inline SMILES phosphate as base (RNA1{R[P%91(O)(O)=O.[*:1]%91 |$;;;;_R1$|]}$$$$V2.0)
- #2436 - System should report an error if we have one or more monomers on the canvas don't have mapping for them in case of export to Sequence/FASTA
- #2427 - Import of unsplit monomers from HELM doesn't work
- #2041 - Monomer could be saved to RXN V3000 format but can't be loaded back - exception
- #2137 - An error occurred while saving the unresolved nucleotides and arrow in the RXN3000 format
- #2195 - Indigo functions doesn't work if query atom and monomer on the canvas at the same time
- #2126 - An error occurred while saving the nucleotide and arrow in the RXN2000 format
- #2330 - Error diagnostic is not clear in case of wrong percent value type
- #2622 - Saving to MOL 3000 cause template data loss that causes wrong export to HELM
- #2361 - Wrong error message if SMILES phosphate has lack of attachemt point
- #2359 - System loads HELM even it it has wrong connection section (PEPTIDE1{[DACys]}|PEPTIDE2{C}$PEPTIDE1,PEPTIDE2,1:R1-1:R2$$$V2.0)
- #2539 - Export of unknown monomer to HELM doesn't work
- Revert "#2657 - Add ES6 options for WASM build (#2658)"
Full Changelog: indigo-1.27.0-rc.1...indigo-1.28.0
Indigo-1.27.0
What's Changed
- #2559 - Read Name and Reaction Conditions from RDF Metadata as a text
- bugfix: indentation errors in docstring description
- #2404 - Save Name and Reaction Conditions to RDF Metadata
- #2654 - Arrow size become 2 bonds length after indigo changed default arrow size to 1
- #2657 - Add ES6 options for WASM build
- #2652 - Skip Name and/or Reaction Conditions metadata fields on save to RDF if no data is available
- #2574 - Support for Collapsed monomers
- #2665 - Margins are missing if no reaction result
- #2664 - Vertical margin for catalyst is wrong
- #2662 - Arrow size is wrong if reaction loaded from SMARTS
- #2653 - Indigo should send to ketcher different bond size for macromolecules
- #2647 - Reaction's name or conditions text wraps incorrectly in specific cases: the last line before truncating, removing of special symbols, empty line instead of "..."
- #2583 - Not correct length of Multi-Tailed and Single arrows for reactions with atoms after loading from RDF or Layout actions
- #2519 - The length of the arrow becomes 2 bonds after layout but should be 1
- #2624 - Elliptic arrow rendered wrong while expotring to PNG in remote mode
- #2497 - Test fail on compare CML file for R-group
Full Changelog: indigo-1.26.0-rc.1...indigo-1.27.0
indigo-1.26.0
What's Changed
- #2491 - Update ketcher to newer version for indigo-service frontend
- #2460 - Load/save hydrogen bonds from/to HELM, KET and MOL
- #2519 - The length of the arrow becomes 2 bonds after layout but should be 1
- #2520 - The length of arrow should be 1 bond after importing reaction from rxn file
- #2575 - Saving atom to monomer connections to Mol and HELM
- #2472 - Support for three letter sequences
- #2458 - The reaction with catalysts is displayed incorrectly with ACS style setting and after layout
- #2681 - Molfile V3000 with SGROUP type DAT fails to load in Ketcher due to missing spaces in FIELDDISP
- #2654 - Arrow size become 2 bonds length after indigo changed default arrow size to 1
Full Changelog: indigo-1.25.0...indigo-1.26.0
indigo-1.25.0
What's Changed
Features
- #2236 - Import/export multi-tails in KET
- #2162 - Add support for rendering embedded SVGs while exporting to PNG
- #2129 - Render Multi-tail Arrows for Pathway Reactions in PNG and SVG
- #2176 - add ACS style reaction layout
- #2209 - SVG image support in CDX/CDXML
- #2237 - Save multi reactions (pathway, single, edge cases) to RDF
- #2175 - Adjust the rendering of PNG and SVG formats for ACS style
Bugfixes and improvements
- #2293 - Export IDT doesn't work for natural ambiguous monomers
- #2383 - update lunasvg
- #2309 - Update layout for pathway reaction on canvas
- #1989 - Convert api does not recognise format during autodetection
- #2070 - Settings for the "attachment point tool" don't update with changed pixel settings
- #2457 - The reaction is not in the center of the picture after saved in png (svg)
- #2444 - The thickness of the arrow is incorrect when saving to png(svg)
- #2447 - single up and single down bonds are displayed incorrect when save to PNG(svg)
- #2257 - Unable to save CHEM SS3 to IDT format
- #2312 - Export of ambiguous monomers doesn't work (error appears) to any export format (even to SVG/PNG) except KET
- #2433 - Issues with Saving and Opening Structures with Multi-Tailed Arrow in CDX and CDXML Formats
- #2512 - Equilibrium Half Arrows are displayed incorrect when saved to PNG (svg) by default size
- #2217 - The wrong direction of the arrows when exporting from CDXML (or CDX, base64 cdx) format and two retrosynthetic arrows
- #2422 - Indigo functions doesn't work prorerly: Aromatize, Dearomatize, Layout, Clean Up, Hydrogens, Auto-Mapping Tool
- #2458 - The reaction with catalysts is displayed incorrect with ACS style setting and after layout
- #2440 - System shouldn't allow user to export alternatives ambiguous monomers to IDT (since only mixtures are supported)
- #2331 - System should throw an error in case of wrong IUBcode
- #2122 - Sugar R should not save in the IDT format
- #2446 - Sub font size is incorrect when save to png (svg)
- #2407 - The ordering of branches of cascade reactions and reactions themselves should be the same on Load/Save from/to RDF
- #2478 - The arrow is displayed incorrect when import from rxn file
- #2603 - Unknown 'a' CIP stereochemistry cause error in CDXML parser
Full Changelog: indigo-1.24.0-rc.1...indigo-1.25.0
indigo-1.24.0
What's Changed
Features
- #2096 - Support retrosynthetic arrows - PNG/SVG rendering
- #2097 - Add retrosynthetic arrow import/export for cdx/cdxml formats
- #2031 - Build a data structure for a reaction tree
- #1619 - Import/export of variant monomers from IDT
- #2052 - Position pathway reaction on canvas
- #2015 - Import/Export of variant monomers from Fasta/Sequence
- #2028 - PNG image support in CDX/CDXML
- #2128 - Add Multi-tail Arrows to Pathway Reactions Loaded from RDF
- #2188 - HELM 2 support: variant monomers
- #2189 - HELM 2 support: support for SMILES
Bugfixes and improvements
- #2232 - System replace arrows of diffrent types with Open Arrow type while loading from PPTX(CDX)
- #2249 - Arrow Open Angle changes to Arrow Filled Triangle after saving and opening in CDX/CDXML
- #2120 - Export the structure for nucleotides 2-Amino-dA does not work correctly
- #2266 - Error message is wrong for missing ratio number (PEPTIDE1{(A:+C:0.1)}$$$$V2.0)
- #2300 - HELM loading doesn't work in remote version
- #2293 - Export IDT doesn't work for natural ambiguous monomers
- #2336 - Ribose sugar doesn't allow to load IDT custom mixed bases
- #2358 - Import of monomer with only one connection point (R2) doesn't work
- #2321 - Export of multi-character monomer IDs inside ambiguous monomer works wrong
- #2375 - Export to IDT doesn't work at all for mixed bases
- #2356 - Library ambiguous peptides loaded as mixtures from FASTA
- #2357 - Export to HELM doesn't work if we connect peptide TO molecule
- #2303 - Import of variant monomers from Sequence doesn't work for RNA and FASTA for RNA/DNA
- #2355 - Import of HELM with fractional ratio mixture values doesn't work - system expects integer
- #2421 - Incorrect stereo-label placement for (E) and (Z) (indigo part)
- #2417 - The layout is incorrect with retrosynthetic arrow
Full Changelog: indigo-1.23.0...indigo-1.24.0
indigo-1.24.0-rc.3
What's Changed
- #2358 - Import of monomer with only one connection point (R2) doesn't work
- #2321 - Export of multi-character monomer IDs inside ambiguous monomer works wrong
- #2341 - Save to Sequence and FASTA doesn't work for monomers loaded from HELM with inline SMILES
- #2375 - Export to IDT doesn't work at all for mixed bases
- #2356 - Library ambiguous peptides loaded as mixtures from FASTA
- #2357 - Export to HELM doesn't work if we connect peptide TO molecule
- #2318 - The reaction with retrosynthetic arrow is displayed not correct after clicking on Aromatize
- #2303 - Import of variant monomers from Sequence doesn't work for RNA and FASTA for RNA/DNA
- #2355 - Import of HELM with fractional ratio mixture values doesn't work - system expects integer
- #2337 - Export of HELM with inline SMILES contains "Mod0" instead of SMILES
Full Changelog: indigo-1.24.0-rc.2...indigo-1.24.0-rc.3
indigo-1.24.0-rc.2
What's Changed
Bugfixes and improvements
- #2300 - HELM loading doesn't work in remote version
- #2293 - Export IDT doesn't work for natural ambiguous monomers
- #2259 - When importing and exporting to/from CDX and CDXML, images are lost
- #2336 - Ribose sugar doesn't allow to load IDT custom mixed bases
- #2339 - Unable to load HELM inline SMILES sugar
- #2333 - cdxml reactions loading fails with ignore stereo
indigo-1.23.0
indigo-1.22.0
What's Changed
Features
- #1912 - Support unresolved IDT monomers (no structure, IDT only)
- #1919 - Support of unsplit nucleotides
- #1188 - HELM ver 1 scope: support multiple sequences and connection tables (import and export)
- #1188 - HELM ver 2.04 support API for ketcher
Bugfixes and improvements
- #877 - api: wasm: indigo-ketcher: prepare 2-files wasm+js package
- #1993 - Micro and macro structures connected through attachment points cannot be opened after save in CDXML format in micro mode
- #1986 - System breaks IDT export line if it is longer than 80 chars by
- #2106 - Export monomer with R2, R3, R4 APs resulted in monomer with R2, R3 if exported to mol v3000
- #2110 - The structure changes when saved in SVG/PNG formats
indigo-1.24.0-rc.1
What's Changed
- #2096 - Support retrosynthetic arrows - PNG/SVG rendering
- #2097: Add retrosynthetic arrow import/export for cdx/cdxml formats
- #2031 - Build a data structure for a reaction tree
- #1619 Import/export of variant monomers from IDT
- #2052 - Position pathway reaction on canvas
- #2015 Import/Export of variant monomers from Fasta/Sequence
- #2028 - PNG image support in CDX/CDXML
- #2232 - System replace arrows of diffrent types with Open Arrow type while loading from PPTX(CDX)
- #2128 - Add Multi-tail Arrows to Pathway Reactions Loaded from RDF
- #2244 CI/CD regress: "RNA/DNA presets loaded from FASTA/Seqeunce positioned wrong at the flex mode canvas (phosphate over sugar)
- #2249 - Arrow Open Angle changes to Arrow Filled Triangle after saving and opening in CDX/CDXML
- #2188 HELM 2 support: variant monomers
- #2259 - Preview: When importing and exporting to/from CDX and CDXML, images are lost
- #2189 HELM 2 support: support for SMILES
- #2120 Export the structure for nucleotides 2-Amino-dA does not work correctly
- #2266 Error message is wrong for missing ratio number (PEPTIDE1{(A:+C:0.1)}$$$$V2.0)
- #2287 Wrong smiles in HELM
Full Changelog: indigo-1.23.0-rc.2...indigo-1.24.0-rc.1