CHANGES.md 3.36 KB
Newer Older
1
2
3
Changes
=======

4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
WIP
---

1. Can select multiple interactions at once.
2. PNG file included in download from "Save" button. Also, log.txt file, for those not comfortable with JSON.
3. Bonds now color coded.
4. Certain interactions turned on by default.
5. Clear button changed to "Reset" because resets to default value.
6. No more coloring by molecule, interaction, etc. Too confusing.
7. JSZip now dynamic import.
8. zip download now includes vmd state directory.
9. Vmd state file centers on ligand automatically.
10. changed hydrogen_bond_dist_cutoff and hydrogen_bond_angle_cutoff parameter names to hydrogen_halogen_bond_dist_cutoff
hydrogen_halogen_bond_angle_cutoff
11. Removed ability to toggle on and off cylinder interactions, to simplify UI. Always on for those interaction where appropriate.
12. Some interactions are shown as spheres, others as bonds. Keeps it simplier.
20
21
22
13. Improved ability to detect salt bridges even if protein and ligand models do not have hydrogen atoms. TODO: Try to detect hydrogen bonds too.

TODO:
23
24
25
26

Halogen bonds mention in all documentation?
Halogen bonds counted twice? Good to check. In the chart in log file.

27
28
29
30
31
32
33
34
35
36
37
38
CAPTURE WARNINGS. Also, move no-hydrogen warning to below table to be less
obtrusive.

Consider "S" as donor/acceptors? Need to investigate.

Much of hydrogen-bond detecting code should go into mol. Also, use protein
definitions where possible, like you do for electrostatics. But in case of
hydrogen bonds detecvt only on the ffly (otherwise too many).


Test should also test version of protein without hydrogens

jdurrant's avatar
jdurrant committed
39
40
2.0
---
jdurrant's avatar
jdurrant committed
41

jdurrant's avatar
jdurrant committed
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
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](https://www.transcrypt.org/). Others can now access the BINANA.js
   library from their web apps.
5. To demonstrate JavaScript use, we created a [web
   app](http://durrantlab.com/binana/) 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](http://durrantlab.com/apps/binana/docs/)
   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). 
jdurrant's avatar
jdurrant committed
64

65
66
67
1.3
---

jdurrant's avatar
jdurrant committed
68
1. BINANA now requires Python3. Python2 support has been discontinued.
69
70
2. Added documentation files in MarkDown format.
3. Updated code formatting some (using black formatter).
71
72
73
4. Added README.md.
5. Added roadmap.
6. Updated example files, now located at `examples/`.
74
75
76
77
78
79

1.2.0
-----

1. The version previously hosted on
   [SourceForge](https://sourceforge.net/projects/binana/).