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Add test trajectories #45

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f4699e5
Add 3 test trajectories with same protein and different number of sam…
rjoshi44 Jul 29, 2025
0c2b647
3 test trajectories with same protein and different lipid number with…
rjoshi44 Jul 30, 2025
9b36385
add PAPE datafiles
rjoshi44 Sep 2, 2025
f058cf0
removed subdirectories and kept all the xtc and pdb files in tests/da…
rjoshi44 Sep 18, 2025
b7e782f
Add trajectory files
rjoshi44 Dec 3, 2025
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -13,3 +13,4 @@ basicrta-*/

# macOS garbage
.DS_Store
build/
Binary file added basicrta/tests/data/prestin/test_pdb/protein_pape1.pdb.bz2
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@orbeckst orbeckst Sep 12, 2025

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The pdbs and trajectories should be inside the tests/data/prestin directory and not in subdirectories (see datafiles.py).

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Binary file added basicrta/tests/data/prestin/test_pdb/protein_pape2.pdb.bz2
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@orbeckst orbeckst Sep 12, 2025

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The pdbs and trajectories should be inside the tests/data/prestin directory and not in subdirectories (see datafiles.py).

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Binary file added basicrta/tests/data/prestin/test_pdb/protein_pape3.pdb.bz2
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@orbeckst orbeckst Sep 12, 2025

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The pdbs and trajectories should be inside the tests/data/prestin directory and not in subdirectories (see datafiles.py).

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Binary file added basicrta/tests/data/prestin/test_trajectories/pape1_20ns.xtc
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@orbeckst orbeckst Sep 12, 2025

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The pdbs and trajectories should be inside the tests/data/prestin directory and not in subdirectories (see datafiles.py).

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Binary file added basicrta/tests/data/prestin/test_trajectories/pape2_20ns.xtc
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@orbeckst orbeckst Sep 12, 2025

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The pdbs and trajectories should be inside the tests/data/prestin directory and not in subdirectories (see datafiles.py).

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Binary file added basicrta/tests/data/prestin/test_trajectories/pape3_20ns.xtc
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@orbeckst orbeckst Sep 12, 2025

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The pdbs and trajectories should be inside the tests/data/prestin directory and not in subdirectories (see datafiles.py).

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@orbeckst orbeckst Sep 12, 2025

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This file is 18 MB – why is this so much bigger? Is there a way to make it smaller??

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@rjoshi44 rjoshi44 Sep 18, 2025

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I have removed subdirectories and put all the pdb and xtc files in tests/data/prestin.

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@rjoshi44 rjoshi44 Sep 18, 2025

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The file pape3_20ns.xtc was larger than the others because its output was saved every 10 ps. I reduced the size for this file.

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9 changes: 9 additions & 0 deletions basicrta/tests/datafiles.py
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Expand Up @@ -30,6 +30,15 @@
times = np.load((_data_ref / 'times.npy').as_posix())
PDB = (_data_ref / 'prot_chol.pdb').as_posix()
XTC = (_data_ref / 'prot_chol.xtc').as_posix()
PDB_PAPE_1 = (_data_ref / 'prestin' /'protein_pape1.pdb.bz2').as_posix()
XTC_PAPE_1 = (_data_ref / 'prestin' /'pape1_20ns.xtc').as_posix()
PDB_PAPE_2 = (_data_ref / 'prestin' /'protein_pape2.pdb.bz2').as_posix()
XTC_PAPE_2 = (_data_ref / 'prestin' /'pape2_20ns.xtc').as_posix()
PDB_PAPE_3 = (_data_ref / 'prestin' /'protein_pape3.pdb.bz2').as_posix()
XTC_PAPE_3 = (_data_ref / 'prestin' /'pape3_20ns.xtc').as_posix()



# This should be the last line: clean up namespace
del resources

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