Epam Indigo Versions Save

Universal cheminformatics toolkit, utilities and database search tools

indigo-1.18.0

2 months ago

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

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.17.0...indigo-1.18.0

indigo-1.17.0

2 months ago

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: https://github.com/epam/Indigo/compare/indigo-1.16.0...indigo-1.17.0

indigo-1.18.0-rc.4

3 months ago

What's Changed

Bugfixes

  • #1589 Apply hydrogens folding/unfolding with respect to selected atoms
  • #1573 Add/Remove explicit hydrogens can't be applied to fullerene C60 - system throws exception
  • #1525 System attach two explicit hydrogens to aromatized ring
  • #1488 Atom Query feature export: System lost "Ring bond count" if value greater that 4 - export to RXN V2000
  • #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)

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.18.0-rc.3...indigo-1.18.0-rc.4

indigo-1.16.0

3 months ago

What's Changed

Features

  • #1185 Macromolecules export from MolV3000 to KET
  • #1381 Macromolecules import from KET

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-rc.1

5 months ago

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: https://github.com/epam/Indigo/compare/indigo-1.16.0-rc.2...indigo-1.17.0-rc.1

indigo-1.16.0-rc.1

6 months ago

Indigo 1.16.0-rc.1

Features

  • #1185 Macromolecules export from MolV3000 to KET
  • #1381 Macromolecules import from KET

Bugs

  • #1395 Class and naturalAnalog of KET monomerTemplate should be optional

indigo-1.14.0

6 months ago

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: https://github.com/epam/Indigo/compare/indigo-1.13.0...indigo-1.14.0

indigo-1.15.0-rc.1

6 months ago

What's Changed

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.14.0-rc.1...indigo-1.15.0-rc.2

indigo-1.13.0

7 months ago

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: https://github.com/epam/Indigo/compare/indigo-1.12.0...indigo-1.13.0

indigo-1.12.0

10 months ago

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: https://github.com/epam/Indigo/compare/indigo-1.11.0...indigo-1.12.0