Releases: epam/Indigo
Releases · epam/Indigo
Indigo-1.22.0-rc.1
What's Changed
- #1912 Support unresolved IDT monomers (no structure, IDT only)
- #1919 Support of unsplit nucleotides
- #877 api: wasm: indigo-ketcher: prepare 2-files wasm+js package
- #1188 HELM ver 2.04 support multiple sequences and connection tables (import and export)
- #1986 System breaks IDT export line if it is longer than 80 chars
Full Changelog: indigo-1.21.0-rc.3...indigo-1.22.0-rc.1
Indigo-1.20.0
What's Changed
Features
- #1654 - Export of RNA presets to IDT notation (standard IDT monomers)
- #1588 - Import of standard IDT monomers
- #1466 - Export as sequence string for RNA, DNA and PEPTIDEs
Bugs
- #1891 - Bug Report | When building api/http container, it cannot run due to mismatch in pydantic version
- #1598 - Macro: V3000 export: leaving groups are displayed as side chain connections for standard presets added to canvas
- #1579 - Unable to add hydrogens for aromatic bonds outside the ring - system throws exception
- #1910 - Indigo incorrectly calculates RNA coordinates with data from FASTA/Sequence file
- #1950 - Empty headers appear when exporting to FASTA
Improvements
- #1802 - bad performance during the parsing of large sequences
Full Changelog: indigo-1.19.0-rc.3...indigo-1.20.0-rc.1
indigo-1.21.0-rc.1
What's Changed
Features
- #1903 - Introduce IDT alias for monomers and RNA presets in Ket format
- #1901 - Receive monomer library from Ketcher upon import/export IDT notation
- #1900 - Export of modified RNA to IDT notation (modified IDT monomers)
- #1899 - Import of modified IDT monomers
Bugsfixes and improvements
- #1979 - Preview: IDT sequence with leading or trailing spaces will not open.
- #1978 - Preview: Open an IDT file with a "" character if the "" is only between nucleotides (RNA presets or unsplit nucleotides)
- #1976 - Too slow monomer library load
- #1974 - Preview: User can save IDT with 5' phosphate but cannot open this file again.
- #1972 - Can't save KET with nameless superatom
- #1996 - Cannot open IDT with MOE sugar.
- #1960 - Fix error message in the SequenceLoader for an invalid sequence
- #1959 - Preview: Saved in the Ketcher IDT file should be opened
- #1928 - Support monomer to molecule connections type
- #1878 - The structure saved in CML format does not open
- #1843 - FASTA export: 80 chars limit
- #2000 - Exporting a CDX file to ChemDraw loses information about charge on atoms
- #1997 - Export to IDT doesn't work at all for remote indigo
- #1993 - Micro and macro structures connected through attachment points cannot be opened after save in CDXML format in micro mode
- #2004 - Errors occur when trying to save a macro structure connected to a micro structure to MOL V3000
- #1994 - Micro and macro structures connected through attachment points cannot be opened after save in CDX and Base 64CDX format in micro mode
- #1992 - Micro and macro structures connected through attachment points cannot be saved in Extended SMILES format in micro mode
- #1990 - Micro and macro structures connected through attachment points cannot be saved in CML format in micro mode
- #1984 - Error message is wrong if in case if position indicator in IDT code contradicts real position of the monomer in the chain
- #1982 - Cannot open some expected IDT.
Full Changelog: indigo-1.21.0-rc.1...indigo-1.21.0-rc.2
indigo-1.19.0
What's Changed
Features
- #1755 Import and export fasta format for RNA, DNA and PEPTIDES
- #1466 Export as sequence string for RNA, DNA and PEPTIDEs
Bugs
- #1787 Some Bonds from ChemDraw don't open in the Ketcher
- #1776 Cannot add to Canvas saved in the Ketcher CDX file with Bond structures
- #1775 Save to CDX converts triple bond to Single/Double Aromatic bond
- #1774 Save to CDX converts aromatic benzene ring to dashed ring
- #1425 Indexing of a substantial quantity of molecules instigates the indexing process for the entire file.
- #1575 Basic hydrogen layout problem - angles of hydrogens are not perfect
- #1771 Bingo version does not return current tag
- #1761 Can't export sequence with 1 monomer to molv3000
- #1598 Macro: V3000 export: leaving groups are displayed as side chain connections for standard presets added to canvas
- #1477 sequence id calculation for molv3000
- #1563 Unable to load mol file: System throws exception: Convert error! Unexpected token '<', "<!DOCTYPE "... is not valid JSON
- #1852 Macro(Export FASTA): The header 'Sequence N' is missing, and '>' symbol is located at end of the first sequence
- #1822 Fasta: All Peptides should be saved to FASTA format and (use N/X symbol as well).
- #1851 Macro(Import FASTA): The ';' symbol is not recognized as a comment
- #1786 Some bonds from Ketcher don't display correctly in the Ketcher and the ChemDraw for CDXML format.
- #1777 Some bonds don't display correctly in ChemDraw when opening a saved Ketcher CDX file.
- #1849 Macro(Import FASTA): The ' * ' symbol occurring between two letters is not recognized as a break in peptide chain
- #1850 Macro(Import FASTA): The '>' symbol is not recognized as indicating a new sequence
- #1802 bad performance in WASM during the parsing of large sequences
- #1848 Cannot save FASTA using the Remote mode
- #1791 Aromatic is lost from Benzene while save to CDX/base64 CDX formats
- #1774 Save to CDX converts aromatic benzene ring to dashed ring
- #1773 Save to CDX converts plus and arrow into lone pair and line
- #1796 Some bonds from ChemDraw don't display correctly in the Ketcher.
- #1814 Macro: System ignore spaces and line breaks when importing a sequence through Paste from Clipboard
- #1801 No monomer full name when import from a sequence
- #1161 - bingo unable to index on sql server
- #1773 Save to CDX converts plus and arrow into lone pair and line
- #1774 Save to CDX converts aromatic benzene ring to dashed ring
- #1796 Some bonds from ChemDraw don't display correctly in the Ketcher.
- #1881 Macro: Cannot load Peptides from our Library that are not connected by bonds using FASTA file
Full Changelog: indigo-1.18.0...indigo-1.19.0
indigo-1.18.0
What's Changed
Features
- #1436 Expose Fold/Unfold hydrogens function in indigo API
- #1440 Add support for query features in MOL, SDF and RXN formats (Marvin extension)
- #1426 Import sequence format for RNA, DNA and PEPTIDES
- #1589 Apply hydrogens folding/unfolding with respect to selected atoms
Bugs
- #1232 Multi-line reaction cause access violationg exception.
- #1423 Common atoms loaded as aliphatic in SMARTS mode
- Update bug_report.md
- #1458 Failed UT api\indigo_test.py:test_convert_smarts
- #1460 ImplicitH set to zero casue error loading query molecule from ket
- #1446 Dearomatization does not work with query features
- PostgreSQL 11 EOL support
- #1465 Unable to load specific mol-file
- #1484 Query molecule convert implicit/explicit hydrogens cause error
- #1512 Broken string-formats support for wasm
- #1452 Convert from implicit hydrogens change layout
- #1463 Macro: Some molecules are not perfect on preview tooltip
- #1524 Dearomatizing doesn't work for molecula with custom query fetures
- #1568 Wrong molecule nodes enumeration in KET-file
- #1476 Aromatization/Dearomatization wipes out SOME Ring bond count values
- #1478 Dearomatization causes exception in case of Implicit H count query feature set to 4 (i.e. more than 2)
- #1525 System attach two explicit hydrogens to aromatized ring
- #1573 Add/Remove explicit hydrogens can't be applied to fullerene C60 - system throws exception
- #1567 System can't copy atom with custom query feature to clipboard
- #1534 Presence of stand alone H2 molecule on the canvas breaks Add explicit hydrogens feature (it stops working)
- #1468 Valence lost on loading molfile with MRV extension.
- #1472 Dearomatization wipes out Aromaticity query property
- #1504 Molfile MRV extension generated for "H count"
- #1500 Atom Query feature export: System replace "Ring membership" values with "Ring Bond Count" ones for value 0 - export to SDF V2000 file
- #1564 Add/Remove explicit hydrogens wanishes "Chirality" value
- #1598 Macro: V3000 export: leaving groups are displayed as side chain connections for standard presets added to canvas
- #1533 System attach two explicit hydrogens to atoms connected to "any type" bonds
- #1608 convert_explicit_hydrogens response doesn't comply with the ket schema
- #1538 Add/Remove explicit hydrogens feature doesn't work if atom with problem valence present on canvas (crash happens)
- #1614 Adding hydrogens doesn't work for bonds with No center value of Reacting Center
- #1550 Add/Remove explicit hydrogens feature doesn't work for "Any Atom" molecule with valence value set
- #1593 Macro: V3000 import: removed 5' phosphate is displayed in Ketcher
- #1483 Unable to past empty reaction (arrow only) from clipboard to canvas
- #1607 Unable to load large base64 CDX content to canvas if remote indigo used`
- #1536 Add/Remove explicit hydrogens feature doesn't work for reactions on canvas (crash happens)
- #1652 Unfold hydrogens does not select added bonds
- #1640 System adds hydrogens for only one atom among many selected by
- #1634 Add/Remove hydrogens doesn't work for atoms with Radical=Triplete if atom with query feature present on the canvas
- #1629 Add/Rmove hydrogens process should count R-Group attachment point as hydrogen
- #1695 CDX loader failed if object with zero id follow by reaction
- #1697 CDX loader crashed on some files with abbreviations by
- #1684 System put on the canvas two arrows (one above other) per each arrow on target CDX
- #1724 Fold hydrogen in reaction with selection works wrong by
- #1730 UT cano/permutations is too slow by
- #1576 Bad molecule layout after adding hydrogens (Chlorophyll A)
- #1685 System shows attached abbreviation group in wrong position
New Contributors
- @AlexeyGirin made their first contribution in #1434
Full Changelog: indigo-1.17.0...indigo-1.18.0
Contributors
AlexeyGirin
Assets 2
indigo-1.17.0
What's Changed
Features
- #1412 Nucleotide splitting for V3000 molfile SCSR
- #1450 No naturalAnalogShort in KET for basic aminoacids during conversion MOLV3000 -> KET
Bugs
- #1307 Error in DevTool console about memory access out of bound when call 'ketcher.getRxn()'
- #1431 Crash during parsing query mol-file
- #1439 Indigo can't parse KET with R-Site as a leaving group
New Contributors
Full Changelog: indigo-1.16.0...indigo-1.17.0
Contributors
khatymov
Assets 2
Indigo 1.16.0
What's Changed
Features
Bugs
- #1395 Class and naturalAnalog of KET monomerTemplate should be optional
- #1405 Valence is lost for Mol and Rxn files
- #1415 Incorrect S-Group count in MOL V3000 header if ImplicitH is set
- #1346 Extended SMILES: Atropisomer is displayed incorrectly
- #1304 Indigo accepts
[#6]notation in SMILES mode - #1355 Error appears when pressing 'Layout'
- #1330 Implicit H count is not added to the SMARTS file
- #1358 Error while loading
[!#6,!#7,!#8]smarts - #1357 Wrong atom list when paste structure as SMARTS
- #1292 valid SMARTS with cycles cause error in loader
- #1349 Symbol for topology chain is missing in SMARTS file
- #1351 Error returned when try to convert structure with custom query for bond into SMARTS format
- #1283 wrong chirality generated by SMARTS load/save
- #1329 Aromacity is incorrectly marked in the SMARTS file
- #1325 Indigo should return warning for some attributes
- #1328 Chirality is not added to the SMARTS file
- #1281 Support SMARTS "or unspecified" bond property in custom queries
- #1321 When saving a structure with set up Implicit H count and any other atom attribute then an error appears
- #1309 Error appears while trying to save some element with set up H count and implicit H count
- #1319 Directional bonds are encoded incorrectly in SMARTS
- #1183 Support monomer templates import from KET-format
- #1184 Support monomer templates export into KET-format
- #1310 Error appears while opening SMARTS file with query which contains comma
- #1322 Reaction cannon be saved in convert function
- #1303 Return original format from convert and layout function
- #1316 SMARTS saver miss component level grouping
- #1254 SMARTS with component-level grouping saved without '()'
- #1252 SMARTS loader load grouped components as separate molecules
- #1245 Reaction/Molecule autoloaders don't load SMARTS
- #914 Why is the code InChI=123 valid?
- #1224 Different indent after loading reaction from file and after layout it.
- #1221 An empty structure is returned given incorrect InChi string
Improvements
- #1338 Use docker image for building npm packages and apply tags while publish
Indigo 1.17.0
What's Changed
Features
- #1412 Nucleotide splitting for V3000 molfile SCSR
Bugfixes
- #1414 Templates with space in templateId lost after conversion from ket to molv3000
- #1242 SMARTS Component-Level Grouping doesn't work
- #1307 Error in DevTool console about memory access out of bound when call 'ketcher.getRxn()'
- #1393 There is no way to keep the link between modified template and monomer instance
- #1265 The error appears when saving structure with enhanced stereo in the "Daylight SMARTS" file format
- #1231 Cannot load valid reaction smiles with parents
Full Changelog: indigo-1.16.0-rc.2...indigo-1.17.0-rc.1
Indigo 1.16.0
Indigo 1.14.0
Indigo 1.14.0
Released 2023-11-07
Features
- #1217 Support SDF-format for Indigo-Ketcher API
- #1257 Enhanced stereo labels on atropisomers are lost when opening saved Extended SMILES
Bugs
- #887 When saving in PNG and SVG format, files have low resolution when opened (Ketcher Remote)
- #1200 MolfileSaver add Data S-Groups to molecule at saveMolecule()
- #1199 CanonicalSmiles saver contains extended part.
- #1161 Bingo unable to index on SQL Server
- #1040 SMILES/SMARTS import: Files with S-Group Properties cause an error
- #1145 CDX import: letter is duplicate and 'superscript' and 'subscript' become the same size as the letter
- #1191 Bingo-elastic: Cannot search at elastic using custom-index
- #731 Warnings in the Structure Check window doesn't display for molecules with R-Groups
- #1230 Unable to save file if the canvas has a reaction arrow and a Functional Group
- #1249 Incorrect order of aliases in SMILES saver
- #1240 Unable to open the CDX file with an R-Group added to the whole structure
- #1239 CDX: An abbreviation appears in the upper left corner of a Function Group or Salt when opening a saved file
- #1287 New S-Group type Query component level grouping
- #1260 SMARTS saver works incorrectly for non-query entities if atom valence or radical present
- #1300 Stereobond is not preserved after pasting a SMILES structure
- #1277 Atropisomer centers support
- #1347 When pasting Extended SMILES with coordinates enhanced stereochemistry is lost
Improvements
- #1037 Indigo Toolkit information in the 'About' section that is not relevant for the users
- #1197 Migrate indigo-knime nodes to KNIME Analytics Platform 5.1
Full Changelog: indigo-1.13.0...indigo-1.14.0