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jdurrant committed Aug 19, 2021
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2.0 WIP

Major refactor

Before, in calculating close contacts, those less than 2.5 not included in list of less than 4 (no redundancies). Now listed again (so redundancies).

Added output_json option.

Created BINANA.js library, and made web app.

Changed name of development branch to `main`.
1. We have refactored the code to make it more modular. BINANA still works as a
command-line program, but it now also functions as a Python library, allowing
others to import BINANA's various functions into their scripts.
2. BINANA now works with Python3. Python2 is no longer officially supported.
3. BINANA can now output analyses to the JSON format, improving compatibility
with other analysis programs.
4. We have ported the Python codebase to JavaScript using the [Transcrypt
transpiler]( Others can now access the BINANA.js
library from their web apps.
5. To demonstrate JavaScript use, we created a [web
app]( that leverages the BINANA.js library. The
Git repository includes the web-app source code.
6. The BINANA 2.0 interaction criteria are identical to the original version,
except for close and closest contacts. Previously, these two interactions
were mutually exclusive (i.e., those protein/ligand atom pairs that were
close enough to be categorized as "closest" were not also considered to be
"close"). In BINANA 2.0, all closest contacts are also close.
7. We created a [documentation website](
to further improve BINANA usability.
8. We changed the name of the development branch from `master` to `main`.
9. We release BINANA 2.0 under a more permissive license than previous versions
(Apache License, Version 2.0).


1. BINANA is now requires Python3. Python2 support has been discontinued.
1. BINANA now requires Python3. Python2 support has been discontinued.
2. Added documentation files in MarkDown format.
3. Updated code formatting some (using black formatter).
4. Added
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