/
README
65 lines (53 loc) · 2.94 KB
/
README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
╭━━╮╱╱╱╭╮╱╭╮╱╭╮╱╱╱╭━━╮╱╱╱╱╱╱╭╮
┃╭╮┃╱╱╱┃┃╱┃┃╱┃┃╱╱╱┃╭╮┃╱╱╱╱╱╭╯╰╮
┃╰╯╰┳╮╭┫╰━┫╰━┫┃╭━━┫╰╯╰┳╮╭┳━┻╮╭╋━━┳━╮
┃╭━╮┃┃┃┃╭╮┃╭╮┃┃┃┃━┫╭━╮┃┃┃┃━━┫┃┃┃━┫╭╯
┃╰━╯┃╰╯┃╰╯┃╰╯┃╰┫┃━┫╰━╯┃╰╯┣━━┃╰┫┃━┫┃
╰━━━┻━━┻━━┻━━┻━┻━━┻━━━┻━━┻━━┻━┻━━┻╯
********
***** *****
**** ****
****\\ ****
**** \\ ****
*** \\ ***
*** ......\\................... ***
*** .......\\........H.....H... ***
*** ........\\........\.../.... ***
*** ......\\........C=C..... ***
*** ......\\....../...\.... ***
** .......\\....H.....H... **
** ........\\............. **
** ..........\\............ **
** ............\\........... **
** ...............\\.......... **
** ................\\......... **
*** .................\\........ ***
*** ..................\\....... ***
*** ...................\\...... ***
*** \\ ***
*** \\ ***
**** \\ ****
**** ****
**** ****
***** *****
*********
# Bubblebuster
Bubblebuster is a Python Library for detecting water box bubbles in structural
files used in molecular simulations.
## Installation
Use the package manager [pip](https://pip.pypa.io/en/stable/) to install bubblebuster.
```bash
pip install bubblebuster
```
## Usage
```python
import bubblebuster
structure_box_properties = bubblebuster.periodic_box_properties(
"trypsin_benzamidine.pdb", #system's structural filename
"triclinic" #system's periodic box type
)
# Returns True if the system's water box has a bubble
structure_box_properties.has_bubble
```
## License
[MIT](https://choosealicense.com/licenses/mit/)