epam/Indigo

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Universal cheminformatics toolkit, utilities and database search tools

Stars: 406
Forks: 134
Open beginner issues: 0
Indexed issues: 710
Avg merge: 1d 22h
Merged PRs (30d): 23

Dominant language: C++
License: Apache-2.0
Last GitHub push: Sep 9, 2026
Latest indexed: Sep 15, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: help wanted

Open All

710 open issues indexed

create atom count skip option for bingo indexing Open

Bingo Improvement Indigo API

epam/Indigo#7 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create bingo batch processing in API Open

epam/Indigo#13 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Fix indigo pka model API. Remove static model Open

Improvement Indigo API

epam/Indigo#14 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Reorganize Indigo plugins Open

Improvement Indigo API

epam/Indigo#20 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Find why Indigo NoSQL and Bingo gives different number of search results Open

epam/Indigo#25 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Consider improvement of canonicalization speed Open

Improvement Indigo API

epam/Indigo#26 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Layout structure changes data s-group position Open

epam/Indigo#43 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve canonicalSmiles for multicomponent systems Open

Improvement Indigo API

epam/Indigo#46 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Change substructure matching rules for aromatic<->single,double bonds embeddings Open

Improvement

epam/Indigo#59 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Unnecessary layout during selective layout Open

Layout

epam/Indigo#63 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Session could be changed by garbage collector Open

Core Indigo API

epam/Indigo#69 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Unsafe strcmp usage in molecule gross formula and mass composition Open

Indigo API

epam/Indigo#71 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Add option to calculate properties only for highlighted structure Open

Improvement Indigo API

epam/Indigo#72 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add possibility to iterate errors on each atom and bond Open

Improvement Indigo API

epam/Indigo#73 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add new method check() to Indigo to verify object properties Open

Improvement Indigo API

epam/Indigo#74 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add function for rewind iterator Open

Improvement Indigo API

epam/Indigo#76 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Name To Structure: add support for spiro compounds Open

Improvement Indigo API

epam/Indigo#77 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Name To Structure: add support for bridged compounds Open

Improvement Indigo API

epam/Indigo#78 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Name To Structure: implement suffix-based lexeme stream analysis Open

Improvement Indigo API

epam/Indigo#79 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Name To Structure: construct a resulting Molecule in-place Open

Improvement Indigo API

epam/Indigo#80 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Name To Structure: investigate a feasibility of FSM-based parser for IUPAC grammar Open

Improvement Indigo API

epam/Indigo#81 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Name To Structure: add support for acids Open

Improvement Indigo API

epam/Indigo#82 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Name To Structure: add support for structures based on trivial names Open

Improvement Indigo API

epam/Indigo#83 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Triggering rendering option "render-superatom-mode" to "collapse" causes crash Open

Indigo API

epam/Indigo#85 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Add reactions support for bingo lucene Open

Bingo Improvement

epam/Indigo#87 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
InChI molecule with amide groups is rendered incorrectly Open

Indigo API

epam/Indigo#90 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Polymer rendering breaks in new version Open

Indigo API

epam/Indigo#91 · 7 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
automap mapping oxygen to carbon atom Open

Indigo API

epam/Indigo#93 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Can't serialize smarts query object (python) Open

Indigo API

epam/Indigo#94 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
move load_moldata Open

Improvement Indigo API

epam/Indigo#97 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Bingo tanimoto similarity can be over 1? Open

Bingo

epam/Indigo#112 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Certain concurrent queries crash Bingo Open

Bingo

epam/Indigo#113 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Bingo PgSQL checkMolecule function doesn't check implicit hydrogen count Open

Bingo

epam/Indigo#115 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add support of "ignore error" flags into cmf loader Open

Improvement Indigo API

epam/Indigo#118 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Add external fingerprint packing to Bingo NoSql Open

Improvement Indigo API

epam/Indigo#119 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Add new option for control stereo configuration interpretation Open

Improvement Indigo API Priority: Medium

epam/Indigo#120 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Add option `similarity-type` to Bingo Oracle Open

Bingo Improvement

epam/Indigo#123 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add option `similarity-type` to Bingo MS SqlServer Open

Bingo Improvement Priority: Low

epam/Indigo#124 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
inaccurate explicit/implicit hydrogen handling in fingerprints Open

Bingo Priority: High

epam/Indigo#127 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Interested in resolving issues from the SMILES benchmark? Open

Core Priority: Medium question

epam/Indigo#129 · 10 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Bingo PostgreSQL Extension Open

Bingo Improvement

epam/Indigo#133 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Substructure Reaction Bingo/PostgreSQL (Explicit H issue) Open

Bingo

epam/Indigo#134 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Bingo 1.8x PostgreSQL install bug Open

Bingo Priority: Medium

epam/Indigo#137 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Official Conda package for Python bindings? Open

CI Improvement Indigo API Priority: Medium

epam/Indigo#138 · 5 comments · 4 reactions · 1 assignee · Indexed Sep 15, 2026
implement ketcher in jupyter nodebooks Open

epam/Indigo#374 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
automap: IndigoException: array: memory to reserve is large than allowed threshold Open

AAM Priority: Medium

epam/Indigo#156 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
it takes long time to add map for the reaction? Open

AAM Priority: Medium

epam/Indigo#157 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
different reactants order generate different atommap results Open

AAM Indigo API Priority: Medium

epam/Indigo#158 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
some atoms in the product was not mapped for the reaction Open

AAM Priority: Medium

epam/Indigo#160 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
indigo.createDecomposer changes R-group passed as query Open

Indigo API Priority: Medium

epam/Indigo#171 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

epam/Indigo

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