Releases: epam/Indigo
Releases · epam/Indigo
Indigo-1.34.0
Features
- #2899 - Peptide sequence should be auto-deceted at insert
- #2958 - Map molfile monomers onto library monomers on import
- #2967 - Support for marking of nucleotide components
- #2952 - Expand c api to return CIP labels
Bugfixes and improvements
- #2929 - Isoelectric Point calculation formula seems to be wrong
- #2964 - System loads base as sugar
- #2985 - Incorrect Implementation of PKA calculation
- #2926 - Atom weights in indigo should be updated according to last IUPAC data
- #2936 - System doesn't calculate melting temperature for mix of nucleotides/nucleosides and unsplit nucleotides/unsplit nucleosides
- #2965 - System shouldn't allow to export molecules to 3-letter sequence format
- #2989 - Export (and import) of sequence of nucleosides to HELM works wrong (doesn't work for import)
- #2993 - System shouldn't consider closing bracket as part of name
- #2998 - Input fields for ion concentration and oligonucleotides become inactive after entering excessively long number
- #2970 - Rendering CIP labels breaks the generated svg for firefox
- #3014 - Wrong bingo-postgres-linux version
Full Changelog: indigo-1.33.0-rc.1...indigo-1.34.0
Indigo-1.33.0
Features
- #2890 - Conda support
- #2835 - Loading HELM with monomers with multi-character IDs without brackets
- #2836 - Loading monomer NOT from the library as Unknown monomers (in the same manner as it works in IDT)
Bugfixes and improvements
- #2933 - Melting temperature calculation works wrong
- #2748 - Substituents are displayed backwards if appearing on the left of the molecule
- #2934 - Melting temperature should not be defined for one RNA/DNA nucleotide chain lenght
- #2927 - Molecule formula atom order wrong
- #522 - core: replace Obj with standard smart pointer
- #2937 - System doesn't calculate melting temperature for mix of nucleotides/nucleosides and phosphates
- #2720 - Reaction SMILES lossily handles enhanced stereochemistry
- #2968 - Melting temperature calculation works wrong
- #2969 - Export of unknown for Ketcher monomers works wrong
- #2923 - System doesn't substract from mass of monomer mass of leaving group atom(s) if an attachment point is occupied
- #2966 - Load from HELM doesn't work for two side chain connected sequences
- #2986 - Don't calculate Melting temperature for one pair of double stranded DNA/RNA nucleotides
Full Changelog: indigo-1.32.0-rc.1...indigo-1.33.0
Indigo-1.32.0
Features
- #2767 - Add support for Postgres 17
- #1970 - New text entities in KET-format
- #2843 - Support of "HELM alias" property for monomers
- #2844 - Support for "Modification Type" property of monomers
- #2870 - Add suuport for flip expanded monomer
- #2840 - Add InChI key method to cpp api
Bugfixes and improvements
- #2805 - Saving of 3:3 reaction to SDF v2000 causes exception: Convert error! core: <reaction> is not a base molecule
- #2781 - Ketcher fails to save structure in MOL V3000 format when encountering custom attachment labels like “Ch”
- #2851 - Macromolecule property Molecular mass wrong calculation
- #2772 - Saving monomers to SDF v3000 works wrong - system saves every monomer template for every monomer on the canvas
- #2860 - Copy to clipboard doesn't work if Multi-Tailed Arrow present on the canvas
- #2858 - Export to any format doesn't work. System throw exception
- #2047 - Saved Ellipse and Line Shapes in CDX, CDXML, Base 64 CDX formats are not correctly displayed after opening
- #2868 - Indigo use wrong rotate parameter name KET files
- #2867 - API calculateMacroProperties does not allow to pass parameters for UPC and NAC
- #2859 - System wrongly reverse reaction order on Calculated Values dialog (and thus - values are wrong)
- #2462 - Can't save a reaction with Multi-Tailed Arrow to Daylight SMARTS format
- #2892 - API calculateMacroProperties does not work if only molecule passed as a parameter without monomers
- #2888 - Unable to export single expanded monomer to SVG Image, system throws error: array: invalid index 0
- #1679 - System ignores carrige return in text blocks in loaded CDX
- #1683 - System shifts text label to the right
- #2897 - Calculated Values doesn't work if reaction arrow overlaps reactant bounding box
- #2931 - Calculated values doesn't work for "rich" monomer chain
- #2917 - Molecular mass and Molecular formula are not calculated for Molecule (custom CHEM)
- #2939 - System doesn't calculate melting temperature for GC nucleotides pair
- #2930 - System shouldn't count bases that are not part of a nucleotide/nucleoside as RNA/DNA
- #2947 - System "caches" PNG/SVG of canvas and stops reflect rotation/flip chanages if any
- #2987 - Melting temperature value missed if UPC or NAC value set to zero
- #2946 - Non-standard connections cause chain break in macromolecule properties calculation
- #2902 - Indigo does not calculate properties for Peptides tab if Phosphate is missing in mixed chain
- #2903 - Indigo fails to calculate properties when two chains are connected via a microstructure
- #2904 - Indigo fails to calculate properties when two chains are connected via a CHEM
- #2905 - Incorrect Calculate Properties result when monomers are connected via not a R2-R1
Full Changelog: indigo-1.31.0-rc.1...indigo-1.32.0
Indigo-1.31.0
Features
- #2788 - Support for PNG/SVG export of expanded monomers
Bugfixes and improvements
- #2150 - Can't save a schema with some elements from Periodic Table in PNG and SVG format
- #425 - Smiles with attachment points is not read correctly (valences are wrong)
- #2747 - Incorrect substituent position
- #1680 - System can't load CDX with (unsupported) brackets inside
- #1631 - Add/Remove hydrogens changes Radical value from Diradical (triplet) to Diradical (singlet)
- #2755 - Error occurs on click of "Remove Explicit Hydrogens" in reaction
- #1686 - System shows positive charge modificator as extra + in addition to charge modified molecule
- #2810 - Unnecessary rearrangment of cdxml reaction
- #2807 - Missing label from cdxml
- #2801 - Can't render reactions which contain brackets
- #2778 - Can't render fragments with multiple external connections
- #2815 - CIP labels are not rendered
- #2591 - Reagents are repositioned above the reaction arrow after saving and loading RXN V2000/V3000 files
- #2832 - Load from clipboard ignores RNA/DNA/PEP switcher and always loads DNA ambiguous bases even if RNA mode switched on
- #2845 - Export to PNG/SVG works wrong for labels
- #2722 - Monomer could be saved to RDF V3000 format but can't be loaded back - exception
Full Changelog: indigo-1.30.0-rc.1...indigo-1.31.0
indigo-1.32.0-rc.1
What's Changed
- #2868 Indigo use wrong rotate parameter name KET files
- #2867 API calculateMacroProperties does not allow to pass parameters for UPC and NAC
- #2860 Copy to clipboard doesn't work if Multi-Tailed Arrow present on the canvas
- #2859 System wrongly reverse reaction order on Calculated Values dialog (and thus - values are wrong)
- #2858 Export to any format doesn't work. System throw exception
- #2851 Macromolecule property Molecular mass wrong calculation
- #2844 Support for "Modification Type" property of monomers
- #2843 Support of "HELM alias" property for monomers
- #2840 Add InChI key method to cpp api
- #2805 Saving of 3:3 reaction to SDF v2000 causes exception: Convert error! core: is not a base molecule
- #2781 Ketcher fails to save structure in MOL V3000 format when encountering custom attachment labels like “Ch”
- #2772 Saving monomers to SDF v3000 works wrong - system saves every monomer template for every monomer on the canvas (geometry progression)
- #2767 - Add support for Postgres 17
- #2462 Can't save a reaction with Multi-Tailed Arrow to Daylight SMARTS format
- #2047 Saved Ellipse and Line Shapes in CDX, CDXML, Base 64 CDX formats are not correctly displayed after opening
- #1970 - New text entities in KET-format
- #1686 System shows positive charge modificator as extra + in addition to charge modified molecule
- #1683 System shifts text label to the right
- #1679 System ignores carrige return in text blocks in loaded CDX
- #2870 Add support for flip expanded monomer
Full Changelog: indigo-1.31.0-rc.2...indigo-1.32.0-rc.1
indigo-1.31.0-rc.2
What's Changed
- #2591 Reagents are repositioned above the reaction arrow after saving and loading RXN V2000/V3000
- #2832 Load from clipboard ignores RNA/DNA/PEP switcher and always loads DNA ambiguous bases even if RNA mode switched on by
- #2845 Export to PNG/SVG works wrong for labels
- #2722 Monomer could be saved to RDF V3000 format but can't be loaded back - exception
Full Changelog: indigo-1.31.0-rc.1...indigo-1.31.0-rc.2
indigo-1.30.1
Indigo 1.30.1
Released 2025-04-17
Features
- 2790 Support of "expanded" monomer option
Bugfixes and improvements
- 2513 Elliptical arrows can not be saved to the png
- 2412 User can't correctly save (or make a layout) to RDF/RXN reaction several products or with separate positioned molecules
- 2746 Incorrect phosphorus valence
- 2708 Export to SMILES works wrong if loaded from MOL
- 2707 Atom Query feature export: System lost MOST "Substitution count" values
- 2702 Export molecule which contains atom with five neighbors and stereo-bond cause error
- 2704 System losts one stereo label if load from MOL
- 2699 R Group logic condition is wrong if loaded from MOL
- 2816 Format recognition order of content from clipboard should be changed for Sequence mode canvas
- 2818 Library ambiguius RNA bases loaded from HELM as bases with % label
- 2826 Unable to load ambiguous RNA and ambiguous DNA monomers with same name from HELM
Full Changelog: indigo-1.29.0...indigo-1.30.1
indigo-1.30.0
What's Changed
Features
- #2790 - Support of "expanded" monomer option
Bugfixes and improvements
- #2741 - Image missing stereochemistry information when using abbreviations
- #2513 - Elliptical arrows can not be saved to the png by
- #2412 - User can't correctly save (or make a layout) to RDF/RXN reaction several products or with separate positioned molecules
- #2746 - Incorrect phosphorus valence
- #2708 - Export to SMILES works wrong if loaded from MOL
- #2707 - Atom Query feature export: System lost MOST "Substitution count" values
- #2702 - Export molecule which contains atom with five neighbors and stereo-bond cause error
- #2704 - System losts one stereo label if load from MOL
- #2699 - R Group logic condition is wrong if loaded from MOL
- #2816 - Format recognition order of content from clipboard should be changed for Sequence mode canvas
- #2818 - Library ambiguius RNA bases loaded from HELM as bases with % label
- #2826 - Unable to load ambiguous RNA and ambiguous DNA monomers with same name from HELM
Full Changelog: indigo-1.29.0...indigo-1.30.0
indigo-1.29.0
What's Changed
Features
- #1844 - Implement GenBank/GenPept sequences import
- #2552 - "Calculate Properties" for macromolecules
- #2713 - Support for the star atom (*)
Bugfixes and improvements
- #2739 - Wrong stereochemistry when reading cdxml reaction
- #2744 - Indigo ignores alternate name for templates in MOL v3000
- #2716 - Valid CXSMILES rejected
- #2732 - V2000 Mol file loader skips essential SGroup line in certain cases
- #2589 - Jump on uninitialised value
- #2763 - System should ignore spaces before line indexes on GenBank/GenPept sequences import
- #2798 - Peptide sequence not pasting directly on canvas
Full Changelog: indigo-1.28.0-rc.1...indigo-1.29.0
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