get all min dist pairs

[jamesmkrieger]

This is the right one now

fixes #2107

Now we get 57 hydrophobic interactions instead of 30 for this pdb and the pair of interest is included:

In [1]: from prody import *

In [2]: ag = parsePDB('DE_pd_15_0_dldesign_2_merged_af2pred.pdb')
@> 1637 atoms and 1 coordinate set(s) were parsed in 0.02s.

In [3]: x = calcHydrophobic(ag)
...
@> VAL35 A CG2_56914s <---> LEU54 A CD1_856 3.5 8.4
...
@> Number of detected hydrophobic interactions: 57.

In [5]: interactions = Interactions()

In [6]: all_ints = interactions.calcProteinInteractions(ag)
...
@> Number of detected hydrophobic interactions: 57.
@> Lack of cysteines in the structure.
@> Number of detected disulfide bonds: 0.

In [7]: interactions.getInteractions(selection='resid 54', selection2='resid 35')
Out[7]:
[[],
[],
[],
[],
[],
[['VAL35', 'CG2_569', 'A', 'LEU54', 'CD1_856', 'A', 3.494, 8.4201]],
[]]

[jamesmkrieger]

The tests need to be updated to have the new results

[jamesmkrieger]

The tests need to be updated to have the new results

all good now!

[karolamik13]

Works fine.
Thank you, James.

In [1]: from prody import *

In [2]: p = parsePDB('DE_pd_15_0_dldesign_2_merged_af2pred.pdb')

In [3]: HPh = calcHydrophobic(p)

In [4]: HPh[0:10]
Out[4]:
[['LEU51', 'CD1_811', 'A', 'ILE9', 'CD1_146', 'A', 2.7584, 31.8842],
['PHE93', 'CZ_1491', 'A', 'LEU70', 'CD1_1103', 'A', 2.8553, 33.053],
['TYR74', 'CE1_1192', 'A', 'LEU83', 'CD2_1325', 'A', 3.0261, 45.6964],
['LEU7', 'CD2_105', 'A', 'ALA17', 'CB_259', 'A', 3.1304, 20.4302],
['LEU64', 'CD2_1011', 'A', 'VAL35', 'CG1_568', 'A', 3.1482, 33.2354],
['PHE93', 'CE1_1489', 'A', 'VAL61', 'CG2_975', 'A', 3.1741, 23.8432],
['TYR74', 'OH_1195', 'A', 'LEU91', 'CD1_1461', 'A', 3.277, 23.8169],
['ALA33', 'CB_546', 'A', 'TYR24', 'OH_400', 'A', 3.3265, 19.5246],
['LEU30', 'CD1_497', 'A', 'TYR24', 'CD2_396', 'A', 3.3289, 26.8882],
['ALA77', 'CB_1227', 'A', 'LEU57', 'CG_910', 'A', 3.3466, 36.183]]

In [5]: interactions = Interactions()

In [6]: all_ints = interactions.calcProteinInteractions(p)

In [7]: interactions.getInteractions(selection='resid 54', selection2='resid 35')
Out[7]:
[[],
[],
[],
[],
[],
[['LEU54', 'CD1_856', 'A', 'VAL35', 'CG2_569', 'A', 3.494, 8.4201]],
[]]

[jamesmkrieger]

Great. Can you try it on another system where you can check other interactions too?

[karolamik13]

Sure. I will check it today.

[karolamik13]

I sent a message with the tests to your email.

[jamesmkrieger]

So, in summary, this fix works and can be merged, but there's something else that needs fixing in the hpb module that Xin will fix next month or something like that.