Releases: epam/Indigo
Releases · epam/Indigo
Indigo-1.43.0
Features
- #3526 - Update SDF and KET format to include information about preset phosphate position
- #3525 - Expose ability to calculate fully expanded large molecule into chemical structures
- #3562 – Add api to iterate through attachments points of S-groups of 'SUP' type
- #3554 - Implement multi-threading in Bingo NoSQL substructure search
Bugfixes and improvements
- #3307 - If the selected group is forming an n-agon with 6 or more than 6 points, then the bases should be located inside of the circular structure
- #3308 - If the selected group is forming an n-agon with 12 or more than 12 points, the bases should be located inside of the circular structure
- #3304, #3305 Fixed monomer of cycle on layout should be top left monomer
- #3496 - Fixing the issue during reading of the molecule data and parse it.
- #3301 - System provides invalid SDF content (missing semicolon) on mono…
- #3449 - Bond length become wrong after Arrange as a Ring option applied
- #3329 - Sequential application of “Create cyclic structure” to different segments of one chain leads to overlapping and distorted topology
- #3584 - Deadlock in multithread subsearch.
- #3622 - Fix Bingo-nosql matcher sub tau speed issue
- #3268 - Cyclic layout issues
- #3353 - System ignores Implicit H count value in export to SVG/PNG
- #3303 - Wrong monomer re-layout
Full Changelog: indigo-1.42.0-rc.1...indigo-1.43.0
Indigo-1.42.0
Features
- #3461 - Export/import multi-tailed arrows to/from CDX/CDXML
- Enable tau fingerprints in Bingo NoSQL
Bugfixes and improvements
- #3528 - Bingo NoSQL database format different in Windows and Linux
Full Changelog: indigo-1.41.0-rc.1...indigo-1.42.0
Indigo-1.41.0
Features
- Run sonarqube only by request
Bugfixes and improvements
- #3437 - Turn off specific indigo wrappers using cmake
- #3352 - System should count O and U peptides in Amino Acid natural analog grid
- #3465 - Substructure match: add parameter to limit tautomer chain search only by matched struct
- #3446 - Export to CDXML replaces multi-line text labels to many one-line text labels stacked one over another
Full Changelog: indigo-1.40.0-rc.1...indigo-1.41.0
Indigo-1.40.0
Features
- #3375 - Improve the alignment logic
Bugfixes and improvements
- #3360 - CIP labels aren't added correctly when loading from a cdxml file with no CIP labels
- #3362 - 13C isotope not recognised in molecular formula when loading from cdxml
Full Changelog: indigo-1.39.0-rc.1...indigo-1.40.0
Indigo-1.39.0
Features
- #3211 - Introducing alignment of sense and antisense chains
- #3273 - Circular structures improvement - formation of fused rings
- #3250 - Alignment of sense and antisense strings in AxoLabs format
- #3337 - Bingo NoSQL tautomer substructure search support.
Bugfixes and improvements
- #3282 - Can't use indigo as a git submodule
- #3297 - Random '$$$$V2.0' empty return from conversion to HELM
- #3306 - Saving to HELM doesn't work for cycled structures consist of nucleosides
- #3177 - System can't calculate Calculate properties window values for Amino acids with query bonds
- #3299 - System should set Implicit H value for atoms if the comes without hydrogens from CDXML
- #3343 - Export to Mol v3000 works wrong for stereo bonds between monomers
- #3369 - Bingo NoSQL treat empty flags as NONE instead of ALL
- #3363 - The layout algorithm returns different coordinates on macOS for some tests
- #3342 - Export ot SVG and PNG doesn't work for stereo bond between monomers, system throws an error: pool: access to unused element
- #3343 - Export to Mol v3000 works wrong for stereo bonds between monomers
- #3344 - Export to SVG/PNG works wrong for stereo bonds between monomers
Full Changelog: indigo-1.38.0-rc.1...indigo-1.39.0
Indigo-1.38.0
Features
- #3227 - Introducing Copolymer S-group type
- #3272 - SDF files for library/monomer information
- #3196 - Support formation of circular structures in flex mode - PoC
Bugfixes and improvements
- #3239 - System doesn't save monomer expand/collapse state in Mol v3000 for user created monomers (they always come in collapsed state)
- #3261 - indigoSaveCdxml doesn't support reaction molecules
- #3269 - System ignored HELM alias for bases on monomer load to Library
- #3256 - Metals loaded from cdxml are always represented with hydrogens
- #3237 - Stackoverflow iterate components
- #3277 - System adds broken Preset to the library (part2)
- #3278 - System doesn't allow to add monomers with the same structure but different names (part2)
- #3286 - CHEMBUGS-64 Automapping fails to guard against contradictory reaction center annotation, corrupts future structure export data
- #3297 - Random '$$$$V2.0' empty return from conversion to HELM
- #3293 - Library update works wrong if we use empty SDF file
- #3292 - Save to SDF v2000 works wrong for created monomers
- #3291 - Layout works wrong
- #3267 - Export to sugar monomer to AxoLabs error message is wrong
- #3265 - System should be able to load unknown monomer on any position
- #3338 - System losts stereo bonds on monomer load to Library
- #3247 - SVG/PNG: Export of any atom with Isotope (atomic mass) value set doesn't work
Full Changelog: indigo-1.37.0-rc.1...indigo-1.38.0
Indigo-1.37.0
Features
- #3161 - SDF files for library/monomer information
- #3152 - AxoLabs format support
- #3146 - IDT export: use hardcorded nucleotides instead of standard ones
Bugfixes and improvements
- #2922 - Performing an exact match search results in PostgreSQL termination
- #3193 - Missing valence of 0 in mol file
- #3016 - Valence 0 is not taken into account by Molfile export via API
- #3079 - Export to SVG/PNG doesn't work for molecules with "star" atom. System throws an error: molecule render internal: Query atom type 4 not supported
- #3141 - One time exception on export to RXN: molecule: casting to molecule is invalid
- #3178 - Unable to copy user created monomer, exception: Convert error! molecule: casting to molecule is invalid
- #3070 - Saving to RXN v2000 encloses Polymer labels into double quotes
- #3206 - Export (or import) to (from) Mol v3000 works wrong for CHEM monomers
- #3200 - System allows to export not a purely amino acid to Sequence (3-letter code)
- #3210 - System loads Sequence with numbers in middle
- #3102 - System can't load sugar-phosphate preset from HELM if sugar provided with HELMAlias name
- #3220 - System ignores implicitly provided file format on load content thru Paste From Clipboard way
- #3187 - Export to HELM works wrong for custom monomers imported from HELM with inline SMILES (part 2)
- #3228 - Loading of AxoLabs with last monomer in brackets doesn't work
- #3234 - Unable to add user`s peptide, nucleotide and CHEM to the library
- #3235 - System adds broken Preset to the library
- #3238 - Monomer name is missed if updated from the API
- #3212 - Export to RXN disorganize the reaction
Full Changelog: indigo-1.36.0-rc.1...indigo-1.37.0
Indigo-1.36.0
Features
- #905 - Support for pagination in Bingo Elastic
- #3092 - Avoid overwriting cmake output directories variables
- #3099 - Support dev container
- #2893 - Reaction data support in KET-format
- #3136 - No attachment points check should be performed for terminal CHEMs on IDT import/export
- #3135 - Mark undefined stereocenters using the standardize function
- #3085 - HELM annotations support
Bugfixes and improvements
- #3065 - Indigo build fails when trying to build indigo-depict
- #3060 - CH labels are recognized as pseudo-atoms when parsing cdxml
- #3096 - Expand monomer works wrong with selection
- #3105 - bingo-elastic-python filter broken for exact/substructure
- #3130 - Bingo-postrgress-fingerprints tests are failing
- #3071 - Export to RDF V2000 doesn't work if "star" atom on the canvas. System throws exception: Convert error! std::bad_cast
- #3067 - System can't load HELM with inline SMILES if it has r-site star atom without square brackets
- #3120 - bingo-elastic-python reaction exact search do not use postprocess actions
- #3150 - Exception during molecules loading in test fixture
- #3123 - Unable to paste FASTA content from clipboard
- #3159 - Export to HELM works wrong for custom monomers imported from HELM with inline SMILES
- #3068, #3080, #3082, #3086, #3087, #3088, #3090, #3084 - System can't load atom properties (Charge, Isotope and Valence) in SMARTS with "star" atom. System throws exception.
- #3144, #3147 - Export to IDT baseless preset and modified phosphate
- #3148 - Export to IDT shouldn't work if monomer at the end has no 3' position IDT code
- #3169 - Export to IDT doesn't work if R1-only CHEM stays on five prime position
Full Changelog: indigo-1.35.0-rc.1...indigo-1.36.0
Indigo-1.35.0
Features
- #2894 - Saving expanded monomers into MOL-files
- Update monomer expand to follow Indigo structure
Bugfixes and improvements
- #2900 - CIP labels are always rendered from cdxml
- #3012 - Create IUPAC Compliant Chemical Formula
- #3050, #3047, #3048, #3054, #3051 - Loading monomer chain from SDF file works wrong - bonds between monomers got lost/Export RNA monomers from MOLv3000 doesn't work for ACCLDraw export
- #2928 - Isoelectric Point calculation should take into account occupied leaving groups (exclude them)
- #3053 - Calculate properties doesn't work for "rich" sequences
- #3049 - Stereo labels got missied on export to SVG result
- #3056 - HELM load fails if it contains more than one instance of monomers with aliasHELM property
- #3045 - Adding substituents to reactants breaks chemical property calculations
- #3061, #3062 - System can't recognize single rebose or phosphate if loaded from HELM
- #3069 - Export to RXN doesn't work, system throws exception: Error: memory access out of bounds
- #3094 - Export of expanded CHEMs works wrong (system losts CHEM type)
Full Changelog: indigo-1.34.0-rc.1...indigo-1.35.0
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