epam/Indigo

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Universal cheminformatics toolkit, utilities and database search tools

Stars: 406
Forks: 134
Open beginner issues: 0
Indexed issues: 712
Avg merge: 2d 3h
Merged PRs (30d): 20

Dominant language: C++
License: Apache-2.0
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 15, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: help wanted

Beginner friendly Everything

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709 open issues indexed

HELM conversion produces an invalid CHEM attachment mapping when an atom from a monomer-uncovered fragment is connected to multiple recognized monomers Open

Difficulty 4/5 3-5 days Newbie friendliness 68/100

epam/Indigo#3917 · Opened Sep 17, 2026
Substructure matching ignores E/Z configuration for query molecules loaded from mol v3000 files Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

epam/Indigo#3914 · Opened Sep 15, 2026
`IndigoException` when handling HELM strings containing the `psiU` monomer Open

Priority: Low

Difficulty 4/5 3-5 days Newbie friendliness 56/100

epam/Indigo#3911 · Opened Sep 9, 2026
Indigo.exactMatch() result depends on molecule arguments order Open

Priority: High

Difficulty 3/5 1-2 days Newbie friendliness 74/100

epam/Indigo#3910 · Opened Sep 9, 2026
Patch Result SVG Glyph IDs Open

epam/Indigo#3882 · 1 assignee · Opened Sep 4, 2026
Use Loaded Fonts to Render Text Using Font Manager Open

epam/Indigo#3881 · 1 assignee · Opened Sep 4, 2026
SubstructureMatcher doesn't see match in a query molecule with ABS stereo-label and the same molecule with AND or OR stereo-label instead of ABS Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

epam/Indigo#3874 · Opened Sep 2, 2026
Aromatization can produce stereochemical SMILES that Indigo cannot reload Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

epam/Indigo#3871 · 1 comment · Opened Sep 2, 2026
Segmentation fault when expanding HELM with comma-separated monomers Open

Priority: Low

Difficulty 4/5 3-5 days Newbie friendliness 62/100

epam/Indigo#3869 · Opened Sep 1, 2026
Change the definition of a chiral center Open

Draft Stereochemistry

Difficulty 5/5 Over a week Newbie friendliness 30/100

epam/Indigo#3853 · Opened Aug 21, 2026
Layout works wrong for unfold hydrogen operation Open

Ljubica found bugs Priority: High Severity: High

Difficulty 3/5 1-2 days Newbie friendliness 55/100

epam/Indigo#3851 · Opened Aug 20, 2026
Render S-group abbreviations in PNG and SVG Open

Draft

Difficulty 4/5 3-5 days Newbie friendliness 55/100

epam/Indigo#3845 · Opened Aug 13, 2026
Provide a support within a layout algorithm for a haptic bond. Open

epam/Indigo#3844 · 1 assignee · Opened Aug 13, 2026
Provide a support for CDX/CDXML to correctly handle haptic bonds during load and/or save operations. Open

epam/Indigo#3843 · 1 comment · 1 assignee · Opened Aug 13, 2026
System ignores Display charge option on export to SVG/PNG Open

Ljubica found bugs Priority: Medium Severity: Medium

Difficulty 3/5 1-2 days Newbie friendliness 55/100

epam/Indigo#3832 · Opened Aug 6, 2026
System loads mirrored version of sence/antisence chain if opened as new project Open

Priority: High Severity: High

Difficulty 4/5 3-5 days Newbie friendliness 38/100

epam/Indigo#3836 · Opened Aug 4, 2026
Support rendering and saving of lone pairs Open

User`s Feedback

Difficulty 5/5 Over a week Newbie friendliness 38/100

epam/Indigo#3827 · Opened Aug 4, 2026
Need to make a transition fo ObjPool<int> to std::vector<int> migration. Open

c++ Core Indigo Service

epam/Indigo#3793 · 1 assignee · Opened Jul 21, 2026
Support Graft, Crosslink, and Modification S-groups Open

Draft

Difficulty 5/5 Over a week Newbie friendliness 35/100

epam/Indigo#3791 · Opened Jul 21, 2026
Support Any Polymer, Mer, Generic, and Monomer S-groups Open

Draft

Difficulty 5/5 Over a week Newbie friendliness 35/100

epam/Indigo#3790 · Opened Jul 21, 2026
Support bold and up aromatic bonds in Indigo import, export and rendering Open

Draft

Difficulty 5/5 Over a week Newbie friendliness 45/100

epam/Indigo#3788 · Opened Jul 21, 2026
Support different S-group bracket types Open

Draft

Difficulty 5/5 Over a week Newbie friendliness 48/100

epam/Indigo#3783 · Opened Jul 20, 2026
Support Dagger and Double Dagger objects Open

Draft

Difficulty 4/5 3-5 days Newbie friendliness 55/100

epam/Indigo#3774 · Opened Jul 15, 2026
Support Component and Mixture S-groups Open

Draft

Difficulty 5/5 Over a week Newbie friendliness 35/100

epam/Indigo#3773 · Opened Jul 14, 2026
Add support for custom fonts in SVG and PNG Open

NFDI

epam/Indigo#3770 · 3 comments · 1 reaction · 1 assignee · Opened Jul 10, 2026
Layout for structures that contain Markush and haptic bonds Open

Draft

Difficulty 5/5 Over a week Newbie friendliness 30/100

epam/Indigo#3767 · Opened Jul 9, 2026
Indigo functions removes wrong valence warning indicator from atom Open

Priority: Medium Severity: Medium

Difficulty 3/5 1-2 days Newbie friendliness 52/100

epam/Indigo#3765 · Opened Jul 7, 2026
Create a flag for ignoring undefined stereocenters Open

epam/Indigo#3756 · 1 assignee · Opened Jun 24, 2026
Merging monomer libraries with different monomer properties Open

Draft

Difficulty 5/5 Over a week Newbie friendliness 20/100

epam/Indigo#3753 · Opened Jun 23, 2026
Exported string chosen for circular backbone is not first alphabetically Open

BILN Priority: Low Severity: Low

Difficulty 4/5 3-5 days Newbie friendliness 52/100

epam/Indigo#3751 · Opened Jun 19, 2026
Multiple backbones are exported in incorrect order Open

BILN Priority: Low Severity: Low

Difficulty 3/5 1-2 days Newbie friendliness 55/100

epam/Indigo#3750 · Opened Jun 19, 2026
Monomers with hyphens in names are loaded incorrectly Open

BILN Priority: High Severity: High

Difficulty 3/5 1-2 days Newbie friendliness 68/100

epam/Indigo#3749 · Opened Jun 19, 2026
String with invalid syntax can be imported Open

BILN Priority: Medium Severity: Medium

Difficulty 3/5 1-2 days Newbie friendliness 55/100

epam/Indigo#3748 · Opened Jun 19, 2026
Inappropriate error message displayed when importing an invalid string Open

BILN Priority: Low Severity: Low

Difficulty 3/5 1-2 days Newbie friendliness 65/100

epam/Indigo#3747 · Opened Jun 19, 2026
Exported string deviates from best practices when exporting previously imported valid input Open

BILN Priority: Medium Severity: Medium

Difficulty 3/5 1-2 days Newbie friendliness 58/100

epam/Indigo#3746 · Opened Jun 19, 2026
Monomers without hyphens in square brackets in BILN string are loaded incorrectly Open

BILN Priority: Medium Severity: Medium

Difficulty 3/5 1-2 days Newbie friendliness 55/100

epam/Indigo#3745 · Opened Jun 18, 2026
CHEMs cannot be imported; system treats them as amino acids Open

BILN Priority: High Severity: High

Difficulty 3/5 1-2 days Newbie friendliness 55/100

epam/Indigo#3744 · Opened Jun 18, 2026
Impossible to import a valid BILN string - error occurs Open

BILN Priority: Medium Severity: Medium

Difficulty 3/5 1-2 days Newbie friendliness 55/100

epam/Indigo#3743 · Opened Jun 18, 2026
getSGroupName() works for any type of S-group Open

Priority: Medium Severity: Medium User`s Feedback

Difficulty 4/5 3-5 days Newbie friendliness 45/100

epam/Indigo#3740 · Opened Jun 17, 2026
It is possible to export amino acid without BILN alias to BILN format Open

BILN Priority: Low Severity: Low

Difficulty 3/5 1-2 days Newbie friendliness 55/100

epam/Indigo#3739 · Opened Jun 17, 2026
Bad layout execution from reaction with salts, when exporting RXN V3000 Open

User`s Feedback

Difficulty 4/5 3-5 days Newbie friendliness 45/100

epam/Indigo#3736 · 1 comment · Opened Jun 16, 2026
Unable to import monomer with asterisk in BILN alias from BILN Open

BILN Priority: Medium Severity: Medium

Difficulty 3/5 1-2 days Newbie friendliness 55/100

epam/Indigo#3732 · Opened Jun 11, 2026
Support for Markush bonds Open

CDX-ChemDraw Export to CDXML Export to MOL Import from CDXML Import from MOL

Difficulty 5/5 Over a week Newbie friendliness 35/100

epam/Indigo#3731 · Opened Jun 11, 2026
Unable to export monomer with hyphen in BILN alias to BILN format Open

BILN Priority: Medium Severity: Medium

Difficulty 3/5 1-2 days Newbie friendliness 58/100

epam/Indigo#3730 · Opened Jun 11, 2026
Function to generate all possible transformations Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

epam/Indigo#3712 · Opened Jun 5, 2026
Get rid of cairo library in WASM build Open

epam/Indigo#3710 · 1 assignee · Opened Jun 5, 2026
InChl generation for cyclical sugars produces incorrect m layer Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

epam/Indigo#3705 · Opened Jun 3, 2026
Add tautomer rule-based index support for bingo Open

epam/Indigo#3704 · 1 assignee · Opened Jun 3, 2026
Indigo getLayeredCode freezes with specific molecule Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

epam/Indigo#3690 · Opened May 28, 2026
Image export - font size issue Open

Export to SVG/PNG Priority: Low Severity: Low User`s Feedback

Difficulty 3/5 1-2 days Newbie friendliness 55/100

epam/Indigo#3689 · 1 comment · Opened May 26, 2026

epam/Indigo

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