Releases: epam/Indigo
Releases · epam/Indigo
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
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
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
indigo-1.15.0
What's Changed
- #1221 An empty structure is returned given incorrect InChi string by @Wadym in #1228
- #1224 Different indent after loading reaction from file and after layout it by @AliaksandrDziarkach in #1227
- #914 Why is the code InChI=123 valid by @Wadym in #1229
- Revert: #1033 CDXML: expanded abbreviation opens as contracted from .cdxm files by @even1024 in #1234
- #1245 Reaction/Molecule autoloaders don't load SMARTS by @AliaksandrDziarkach in #1243
- #1252 SMARTS loader load grouped components as separate molecules by @AliaksandrDziarkach in #1255
- #1254 SMARTS with component-level grouping saved without '()' by @AliaksandrDziarkach in #1266
- #1282 SMARTS load/save errors in Indigo. by @AliaksandrDziarkach in #1284
- #1285 Add new query properties support to KET format by @AliaksandrDziarkach in #1286
- #1287 New S-Group type Query component level grouping by @AliaksandrDziarkach in #1288
- #1278 Indigo-service. Remove Mithril library dependency from UI module by @bodyangug in #1275
- #1302 Pylint cause error "too many arguments" by @AliaksandrDziarkach in #1301
- #1296 Add "customQuery" option support to ket format by @AliaksandrDziarkach in #1297
- #1316 SMARTS saver miss component level grouping by @AliaksandrDziarkach in #1317
- #1303 Return original format by @AliaksandrDziarkach in #1315
- #1310 Error while opening SMARTS contains comma by @AliaksandrDziarkach in #1327
- #1184 Support monomer templates export into KET-format by @even1024 in #1251
- #1183 Support monomer templates import from KET-format by @even1024 in #1335
- #1319 Directional bonds not work with SMARTS by @AliaksandrDziarkach in #1326
- #1338 Use docker image for building npm packages and apply tags while publish by @AlexanderSavelyev in #1339
- #1309 Error appears while trying to save some element with set up H count and implicit H count by @AliaksandrDziarkach in #1336
- #1281 Support SMARTS "or unspecified" bond property by @AliaksandrDziarkach in #1341
- #1328 Chirality is not added to the SMARTS file by @AliaksandrDziarkach in #1343
- #1325 Indigo should return warning for some attributes by @AliaksandrDziarkach in #1344
- #1331 Ring bond count 'As drawn' saved wrong by @AliaksandrDziarkach in #1352
- #1351 Error returned when try to convert structure with custom query… by @AliaksandrDziarkach in #1353
- #1349 Symbol for topology chain is missing in SMARTS file by @AliaksandrDziarkach in #1354
- #1292 valid SMARTS with cycles cause error in loader by @AliaksandrDziarkach in #1356
- #1358 Error while loading [!#6,!#7,!#8] smarts by @AliaksandrDziarkach in #1361
- #1330 Implicit H count is not added to the SMARTS file by @AliaksandrDziarkach in #1365
- #1355 Error appears when pressing 'Layout" by @AliaksandrDziarkach in #1364
- #1304 Indigo accepts [#6] notation in SMILES mode by @AliaksandrDziarkach in #1363
- #1360 Wrong ordering of atoms in atom list by @AliaksandrDziarkach in #1368
- #1337 List of atoms from custom query is converted into SMARTS filу without aliphatic attribute by @AliaksandrDziarkach in #1373
- #1332 Aromatic atom list is not recognized in SMARTS query by @AliaksandrDziarkach in #1370
- #1376 SMARTS file is paste into Ketcher as SMILES file by @AliaksandrDziarkach in #1375
- #1362 Valence is not added to the SMARTS file by @AliaksandrDziarkach in #1379
- #1371 Chirality symbol is added to the SMARTS when 'single up/down' or 'double cis/trans' bond type is set up by @AliaksandrDziarkach in #1382
- #1372 Wildcard symbol ('any') with logical operators at custom query for bond is missing at SMARTS by @AliaksandrDziarkach in #1386
Full Changelog: indigo-1.14.0-rc.1...indigo-1.15.0-rc.2
Indigo 1.13.0
What's Changed
Bugfixes
- #1205 Reagent located at the bottom of the arrow when opening the RXN V2000 and V3000 files are located on top of the arrow
- #1168 Error message when trying to save structure with Multiple Group type applied to entire structure
- #1166 CDX: file with R-Group label saved in Ketcher opens without part of structure
- #1159 [CDX] IndigoException: stoi when reading USPTO CDX file
- #1155 [CDX] Indigo header files doesn't appear in msvc solution.
- #1152 No module named tzdata while running indigo service
- #1139 core dumped when reading CDX file downloaded from USPTO
- #1113 RXN 3000 import: When importing, the structure becomes unreadable
- #1094 Structure with R-Group isn't opened correctly from v3000 mol file
- #1061 [Bingo-Elastic] Cannot create custom index in python bingo-elastic
- #1026 [Bingo-Elastic] SVG/PNG: Contracted 'Functional Groups' and 'Salts and Solvents' are rendered expanded when saved
- #926 CDXML import: 'superscript' and 'subscript' appears below the letter
Features
- #1182 Enhanced stereo labels on atropisomers are lost when opening molfiles
- #1158 Ketcher needs to correctly serialize/deserialize attachment point information for super atoms for mol v3000 & ket format
Improvements
- #1111 api: add method for copying RGroups for Java and .NET
- #1124 SMILES format does not store alias information
Full Changelog: indigo-1.12.0...indigo-1.13.0
Indigo 1.12.0
What's Changed
Bugfixes
- #965 MDL Molfile v3000: when opening files containing 'Salts an Solvents', names are truncated and abbreviation is expanded
- #1036 SMILES import: general chiral specification labels (TH, AL, SP, TB, OH ) don't work
- #1051 Opening file with a superatom label saved in RXN v3000 format only the first part of the label is displayed
- #1114 Atoms of Benzene ring become Monoradicals when opened from file saved in Daylight SMARTS
- #1132 SMILES loader uninitialized heap fix
- #1102 When pasting Extended SMILES structure with stereochemistry there are two &1 centers instead of an ABS and an &1
- #1135 C library macro - va_end() is missing before return statement.
- #1126 Segfault when iterating CDX file from USPTO downloads
- #1144 Unable to save the structure after clicking 'Save', an error appears
Improvements
- #1098 api: add method for copying RGroups
Full Changelog: indigo-1.11.0...indigo-1.12.0