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more Parallel InSty fixes #2017

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more Parallel InSty fixes #2017

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jamesmkrieger
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karolamik13
karolamik13 approved these changes Dec 18, 2024
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Works fine.

PDB ensemble:
In [1]: from prody import *
In [2]: atoms2 = parsePDB('2k39')
In [3]: interactionsTrajectory = InteractionsTrajectory('trajectory')
In [4]: interactionsTrajectory.calcProteinInteractionsTrajectory(atoms2, stop_frame=5)
Out[4]:
[[43, 52, 53, 50, 49, 50],
[3, 6, 2, 4, 5, 6],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[16, 19, 16, 18, 20, 17],
[0, 0, 0, 0, 0, 0]]

In [5]: interactionsTrajectory.calcProteinInteractionsTrajectory(atoms2, stop_frame=5)
Out[5]:
[[43, 52, 53, 50, 49, 50],
[3, 6, 2, 4, 5, 6],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[16, 19, 16, 18, 20, 17],
[0, 0, 0, 0, 0, 0]]

In [6]: interactionsTrajectory.calcProteinInteractionsTrajectory(atoms2, stop_frame=5)
Out[6]:
[[43, 52, 53, 50, 49, 50],
[3, 6, 2, 4, 5, 6],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[16, 19, 16, 18, 20, 17],
[0, 0, 0, 0, 0, 0]]

In [7]: interactionsTrajectory.getInteractions()
Out[7]:
[[[['GLN49', 'NE2_784', 'A', 'GLU51', 'OE2_820', 'A', 2.5853, 16.2407],
['LYS11', 'NZ_175', 'A', 'GLU34', 'OE1_547', 'A', 2.6141, 7.0039],
['GLY10', 'N_160', 'A', 'THR7', 'O_116', 'A', 2.6801, 19.8254],
['ARG72', 'N_1149', 'A', 'GLN40', 'O_624', 'A', 2.6883, 21.0779],
['ARG72', 'NH1_1158', 'A', 'GLN40', 'OE1_628', 'A', 2.7336, 7.4598],
..

I also tested calcXX, where XX is the interaction type.

In [10]: rib = calcRepulsiveIonicBondingTrajectory(atoms2)

In [11]: rib
Out[11]:
[[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[['ARG72', 'NH1_1158_1159', 'A', 'ARG74', 'NH1_1201_1202', 'A', 4.1822]],
[],
[['ASP52', 'OD1_833_834', 'A', 'GLU24', 'OE1_378_379', 'A', 4.0632]],
[],
[],
[],
..
..

Trajectory:
In [16]: PDBfile = "5kqm_all_sci.pdb"
...: Trajectoryfile = 'NAMD_D2.dcd'
...: atoms = parsePDB(PDBfile)
...: dcd = Trajectory(Trajectoryfile)
...:
...: dcd.link(atoms)
...: dcd.setCoords(atoms)

In [17]: interactionsTrajectory2 = InteractionsTrajectory('trajectory2')
In [18]: interactionsTrajectory2.calcProteinInteractionsTrajectory(atoms, dcd, start_frame=5, stop_frame=10)
Out[18]:
[[119, 123, 125, 125, 120, 126],
[15, 16, 15, 16, 15, 14],
[0, 0, 0, 0, 0, 0],
[1, 3, 3, 2, 3, 3],
[3, 2, 4, 3, 3, 3],
[34, 37, 36, 36, 33, 33],
[0, 0, 0, 0, 0, 0]]

@jamesmkrieger
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I think we were getting the wrong number of frames being read and maybe this is now fixed

@karolamik13
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start_frame=5, stop_frame=10 -> As a result, we have 6 computed frames because we are counting in the 5th, 6th, 7th, 8th, 9th, and 10th frames. I mentioned about it last week. That it might be confusing.

@jamesmkrieger
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I think it makes sense. We start with and include frame 5 and continue until we have included frame 10 and then stop. So, yes, we get frames 5, 6, 7, 8, 9 and 10. These are actually the 6th, 7th, 8th, 9th, 10th and 11th frames because python starts at 0.

@jamesmkrieger
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Your results from the last tests are actually not doing that. For example, the last one has 7 frames

1 [[119, 123, 125, 125, 120, 126],
2 [15, 16, 15, 16, 15, 14],
3 [0, 0, 0, 0, 0, 0],
4 [1, 3, 3, 2, 3, 3],
5 [3, 2, 4, 3, 3, 3],
6 [34, 37, 36, 36, 33, 33],
7 [0, 0, 0, 0, 0, 0]]

@karolamik13
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Your results from the last tests are actually not doing that. For example, the last one has 7 frames

1 [[119, 123, 125, 125, 120, 126], 2 [15, 16, 15, 16, 15, 14], 3 [0, 0, 0, 0, 0, 0], 4 [1, 3, 3, 2, 3, 3], 5 [3, 2, 4, 3, 3, 3], 6 [34, 37, 36, 36, 33, 33], 7 [0, 0, 0, 0, 0, 0]]

Frame 5 6 7 8 9 10
HBs [[119, 123, 125, 125, 120, 126],
SBs [15, 16, 15, 16, 15, 14],
RIB [0, 0, 0, 0, 0, 0],
PiCat [1, 3, 3, 2, 3, 3],
PiStack [3, 2, 4, 3, 3, 3],
HPh [34, 37, 36, 36, 33, 33],
Disu [0, 0, 0, 0, 0, 0]]

@jamesmkrieger
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oh, yeah. I forgot it worked like that. Sorry

@karolamik13
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Yes, it might be confusing, but it is easier to extract things.

@jamesmkrieger
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That wasn't the part that needed checking now. I've now been fixing the single interactions cases

@jamesmkrieger
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For example, this one:

In [1]: from prody.tests.proteins.test_insty import TestInteractions

In [2]: from prody import *

In [3]: self = TestInteractions()

In [4]: self.setUp()
@> 1231 atoms and 15 coordinate set(s) were parsed in 0.03s.
@> 1231 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> 12793 atoms and 1 coordinate set(s) were parsed in 0.09s.

In [5]: self.data_sbs = calcSaltBridgesTrajectory(self.ATOMS, stop_frame=13)
@> Model: 0
@> Model: 1
@> Model: 2
@> Model: 3
@> Model: 4
@> Model: 5
@> Calculating salt bridges.
@> Calculating salt bridges.
@> Calculating salt bridges.
@> Calculating salt bridges.
@>      LYS27    A          NZ_424  <--->      ASP52    A     OD1_833_834     2.9
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     3.2
@>      LYS33    A          NZ_526  <--->      ASP32    A     OD1_512_513     3.4
@>      GLU51    A     OE1_819_820  <--->      ARG54    A     NH1_855_856     4.1
@>      LYS29    A          NZ_456  <--->      ASP21    A     OD1_332_333     4.9
@> Number of detected salt bridges: 5.
@> Calculating salt bridges.
@>      LYS33    A          NZ_526  <--->      GLU16    A     OE1_262_263     2.7
@>      GLU64    A   OE1_1026_1027  <--->      LYS63    A         NZ_1005     2.9
@>      ARG72    A   NH1_1158_1159  <--->      ASP39    A     OD1_615_616     3.3
@>      LYS29    A          NZ_456  <--->      ASP21    A     OD1_332_333     4.2
@>      LYS29    A          NZ_456  <--->      GLU16    A     OE1_262_263     4.8
@> Number of detected salt bridges: 5.
@>      LYS27    A          NZ_424  <--->      GLU24    A     OE1_378_379     3.0
@>      LYS29    A          NZ_456  <--->      ASP21    A     OD1_332_333     3.1
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     3.1
@>      LYS33    A          NZ_526  <--->      ASP32    A     OD1_512_513     3.4
@>      GLU64    A   OE1_1026_1027  <--->      LYS63    A         NZ_1005     3.5
@>      ARG74    A   NH1_1201_1202  <--->      ASP39    A     OD1_615_616     3.7
@>      ARG72    A   NH1_1158_1159  <--->      ASP39    A     OD1_615_616     4.7
@> Number of detected salt bridges: 7.
@> Calculating salt bridges.
@>      GLU64    A   OE1_1026_1027  <--->      LYS63    A         NZ_1005     2.9
@>      LYS27    A          NZ_424  <--->      ASP52    A     OD1_833_834     3.8
@>      GLU51    A     OE1_819_820  <--->      ARG54    A     NH1_855_856     4.0
@>      LYS29    A          NZ_456  <--->      ASP21    A     OD1_332_333     4.7
@> Number of detected salt bridges: 4.
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     2.5
@>      ARG72    A   NH1_1158_1159  <--->      ASP39    A     OD1_615_616     2.5
@>      LYS27    A          NZ_424  <--->      ASP52    A     OD1_833_834     2.7
@>      GLU64    A   OE1_1026_1027  <--->      LYS63    A         NZ_1005     2.9
@>      LYS33    A          NZ_526  <--->      ASP32    A     OD1_512_513     3.7
@>      LYS29    A          NZ_456  <--->      ASP21    A     OD1_332_333     4.2
@> Number of detected salt bridges: 6.
@>      LYS27    A          NZ_424  <--->      ASP52    A     OD1_833_834     3.0
@>      LYS29    A          NZ_456  <--->      ASP21    A     OD1_332_333     3.1
@>      GLU51    A     OE1_819_820  <--->      ARG54    A     NH1_855_856     3.9
@> Number of detected salt bridges: 3.
@> Model: 6
@> Model: 7
@> Model: 8
@> Model: 9
@> Model: 10
@> Model: 11
@> Calculating salt bridges.
@> Calculating salt bridges.
@> Calculating salt bridges.
@> Calculating salt bridges.
@> Calculating salt bridges.
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     2.8
@>      LYS29    A          NZ_456  <--->      ASP21    A     OD1_332_333     2.9
@>      GLU51    A     OE1_819_820  <--->      ARG54    A     NH1_855_856     4.0
@> Number of detected salt bridges: 3.
@>      LYS33    A          NZ_526  <--->      GLU16    A     OE1_262_263     2.7
@>      LYS27    A          NZ_424  <--->      ASP52    A     OD1_833_834     2.8
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     3.0
@>      LYS29    A          NZ_456  <--->      GLU16    A     OE1_262_263     3.6
@> Number of detected salt bridges: 4.
@>      LYS27    A          NZ_424  <--->      ASP52    A     OD1_833_834     2.5
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     3.3
@>      LYS29    A          NZ_456  <--->      ASP21    A     OD1_332_333     3.4
@>      LYS33    A          NZ_526  <--->      ASP32    A     OD1_512_513     3.5
@>      ASP58    A     OD1_920_921  <--->      ARG54    A     NH1_855_856     4.8
@> Number of detected salt bridges: 5.
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     2.5
@>      LYS29    A          NZ_456  <--->      ASP21    A     OD1_332_333     2.7
@>      LYS27    A          NZ_424  <--->      ASP52    A     OD1_833_834     3.0
@>      LYS33    A          NZ_526  <--->      ASP32    A     OD1_512_513     3.5
@>      ASP58    A     OD1_920_921  <--->      ARG54    A     NH1_855_856     4.1
@>      ARG72    A   NH1_1158_1159  <--->      ASP39    A     OD1_615_616     4.2
@>      GLU51    A     OE1_819_820  <--->      ARG54    A     NH1_855_856     4.8
@> Number of detected salt bridges: 7.
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     3.0
@>      LYS29    A          NZ_456  <--->      ASP21    A     OD1_332_333     4.9
@> Number of detected salt bridges: 2.
@> Calculating salt bridges.
@>      GLU64    A   OE1_1026_1027  <--->      LYS63    A         NZ_1005     2.6
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     2.8
@>      GLU51    A     OE1_819_820  <--->      ARG54    A     NH1_855_856     5.0
@> Number of detected salt bridges: 3.
@> Model: 12
@> Calculating salt bridges.
@>      LYS27    A          NZ_424  <--->      ASP52    A     OD1_833_834     3.2
@>      ASP58    A     OD1_920_921  <--->      ARG54    A     NH1_855_856     3.9
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     4.2
@>      GLU51    A     OE1_819_820  <--->      ARG54    A     NH1_855_856     4.8
@> Number of detected salt bridges: 4.
@> Model: 13
@> Calculating salt bridges.
@>      LYS27    A          NZ_424  <--->      ASP52    A     OD1_833_834     2.6
@>      LYS11    A          NZ_175  <--->      GLU34    A     OE1_547_548     2.6
@>      GLU64    A   OE1_1026_1027  <--->      LYS63    A         NZ_1005     3.2
@>      LYS33    A          NZ_526  <--->      ASP32    A     OD1_512_513     3.5
@>      GLU51    A     OE1_819_820  <--->      ARG54    A     NH1_855_856     4.3
@> Number of detected salt bridges: 5.

In [6]: [len(x) for x in self.SBS_INTERACTIONS]
Out[6]: [7, 5, 5, 4, 3, 6, 3, 4, 2, 7, 5, 3, 4, 5]

In [7]: [len(x) for x in self.data_sbs]
Out[7]: [5, 5, 7, 4, 6, 3, 3, 4, 5, 7, 2, 3, 4, 5]

@jamesmkrieger
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Oh, I have a fix for this problem that’s making the tests fail now. I just need to commit and push it

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@karolamik13 karolamik13 karolamik13 approved these changes

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