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Updated license notices, etc.
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jdurrant committed Nov 27, 2021
1 parent 9b0ebf6 commit d93c4e0
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Showing 176 changed files with 2,387 additions and 16,231 deletions.
33 changes: 6 additions & 27 deletions CHANGES.md
@@ -1,8 +1,8 @@
Changes
=======

WIP
---
2.1 WIP
-------

1. Can select multiple interactions at once.
2. PNG file included in download from "Save" button. Also, log.txt file, for
Expand Down Expand Up @@ -31,41 +31,20 @@ WIP
19. output_csv option now also prints csv file containing same information as json.
20. Possible to toggle ribbon on and off.
21. Updated documentation.
22. chain and resid now included in output PDB files.
23. Throws a warning when using Python 2. Only Python 3 now offically supported.

TODO:

Hydrogen bonds w/o hydrogens added. Need to be more judicious. Remove certain
bonds per this heuristic:

* For oxygen and sulfur, sum of actual neighbors and hydrogen bonds cannot be >
two. Remember to account for water molecules. Pick based on distance, dihedral
angle. =O not marked as donor, so don't need to worry about that.
* Nitrogen cannot donate to more than actual neighbors + hydrogen bonds > 4, as
above.
* chain and resid now included in output PDB files.

Tests on all operating systems (including mobile).

Be sure to compress javascript

MAke sure not javascript is external.

Clean up examples directory

Tests both python2 and python3

Test should also test version of protein without hydrogens, and make sure you
get all interactions tested. Metal, halogen, hydrogen with S.

finish README.md on file loading component.

PDBQT in webapp looks strange?

*** Makesure can loadin multipleligands. Probably need to rewritecodethat
triggersbinana run. Also, can run if restart.

And you need a message explaining the difference between delete/extract.

Push updated documentation somewhere.

2.0
---

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6 changes: 5 additions & 1 deletion javascript/compile.sh
@@ -1,3 +1,7 @@
# This file is part of BINANA, released under the Apache 2.0 License. See
# LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
# details. Copyright 2021 Jacob D. Durrant.

# This script only works if transcrypt is installed.
# pip install transcrypt

Expand All @@ -7,7 +11,7 @@ rm -rf ../python/__target__/ ./lib/
# Compile the python file.
cd ../python/
# --nomin
transcrypt --build --nomin --ecom --verbose binana.py
transcrypt --build --ecom --verbose binana.py
cd -

# Move the javascript library to the lib directory.
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7 changes: 3 additions & 4 deletions javascript/lib/__future__.js

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91 changes: 10 additions & 81 deletions javascript/lib/binana._cli_params._get_params.js

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