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test core_def_all_beads added. [Issue #27] #31

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merged 11 commits into from
Jun 25, 2021
Merged

test core_def_all_beads added. [Issue #27] #31

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3e9a08f
test core_def_all_bedas added.
Jun 18, 2021
ba2ace4
Function def_all_beads changed to select PO4 beads only.
Jun 20, 2021
54a3da1
Added datafiles for testing in small, med and big toy model systems.
Jun 21, 2021
f2b35d7
Tests added for small med big systems
Jun 21, 2021
d9ca9af
Added xfail for non sequential indexes in leaflets.
Jun 20, 2021
c7f3276
pep8 fixed
Jun 20, 2021
0561449
Test files of small system with 9 lipids
Jun 24, 2021
1a08caa
Test of small system added. core_fast, core_fast_leaflet and test_all…
Jun 24, 2021
cee1883
Temporarily removed med and big files
Jun 24, 2021
f5adf5e
minor changes
Jun 24, 2021
59bc610
minor changes
Jun 24, 2021
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5 changes: 1 addition & 4 deletions membrane_curvature/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,7 @@
Handles the primary functions
"""

from .lib.mods import dict2pickle, core_fast, curvature
import sys
import os
from .lib.mods import dict2pickle, core_fast, curvature, def_all_beads
import time
import mdtraj as md
import MDAnalysis as mda
Expand All @@ -16,7 +14,6 @@
__author__ = "Estefania Barreto-Ojeda"
version = 0.1

sys.path.append('lib/')

def main():

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13 changes: 13 additions & 0 deletions membrane_curvature/data/test_po4_inverted_indexes.gro
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
Test file 10 lipids in grid with indexes inverted. Correct form is: Index 1 belongs to lower leaflet and index 10 belong to upper leaflet.
10
3000POPE PO4 1 0.639 1.402 12.078
2054POPC PO4 2 0.704 2.229 15.981
2298POPE PO4 3 0.956 1.559 16.059
2337POPE PO4 4 0.707 0.736 15.711
2622POPC PO4 5 1.451 0.382 11.752
2702POPC PO4 6 0.081 0.610 11.835
2708POPC PO4 7 0.678 2.233 11.825
2713POPC PO4 8 0.988 0.554 11.838
2999POPE PO4 9 1.371 1.989 12.027
1923POPC PO4 10 1.361 0.630 16.101
2.60167 2.60167 32.07157
12 changes: 12 additions & 0 deletions membrane_curvature/data/test_po4_small.gro
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
Test file 9 lipids in grid
9
1923POPC PO4 1 0.000 0.000 15.000
2054POPC PO4 2 1.000 0.000 15.000
2298POPC PO4 3 2.000 0.000 15.000
2337POPC PO4 4 0.000 1.000 15.000
2622POPC PO4 5 1.000 1.000 12.000
2702POPC PO4 6 2.000 1.000 12.000
2708POPC PO4 7 0.000 2.000 12.000
2713POPC PO4 8 1.000 2.000 12.000
2999POPC PO4 9 2.000 2.000 12.000
3.00000 3.00000 3.00000
Binary file added membrane_curvature/data/test_po4_small.xtc
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27 changes: 7 additions & 20 deletions membrane_curvature/lib/mods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,24 +30,12 @@ def def_all_beads(lipid_types, leaflets, head_list, topology):
print('==== Lipid types in membrane ==== ')
for lt in lipid_types:
print('====>', lt)
dic_all_beads['upper'][lt] = np.concatenate((topology.select('resname ' +
lt +
' and index ' +
str(head_list[0]) +
' to ' +
str(head_list[1]) +
' and name PO4'), topology.select('resname ' +
lt +
' and index ' +
str(head_list[0]) +
' to ' +
str(head_list[1]) +
' and name GM1'))).astype(int).tolist()
dic_all_beads['lower'][lt] = np.concatenate((topology.select(
'resname ' + lt + ' and index ' + str(head_list[1] + 1) + ' to ' + str(head_list[2]) + ' and name PO4'),
topology.select(
'resname ' + lt + ' and index ' + str(head_list[1] + 1) + ' to ' + str(head_list[2]) + ' and name GM1'))).astype(int).tolist()

dic_all_beads['upper'][lt] = topology.select(
'resname ' + lt + ' and index ' + str(head_list[0])
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Do you know about f-strings, @ojeda-e? It might be more readable to do this?

f"resname {lt} and index {head_list[0]} to {head_list[1]} and name PO4"

As a side note, maybe you shouldn't hard-code the name of the bead / atom in in the refactor :)

+ ' to ' + str(head_list[1]) + ' and name PO4').astype(int).tolist()
dic_all_beads['lower'][lt] = topology.select(
'resname ' + lt + ' and index ' + str(head_list[1] + 1)
+ ' to ' + str(head_list[2]) + ' and name PO4').astype(int).tolist()
print("upper", len(dic_all_beads['upper'][lt]))
print("lower", len(dic_all_beads['lower'][lt]))

Expand Down Expand Up @@ -75,8 +63,7 @@ def dict2pickle(name, dict_):
pickle.dump(dict_, pk, protocol=pickle.HIGHEST_PROTOCOL)


def core_fast(traj, jump, n_cells, leaflets, lipid_types, lipid_ref,
box_size, max_width, prefix):
def core_fast(traj, jump, n_cells, leaflets, lipid_types, lipid_ref, max_width, prefix):
"""
Runs core_fast_leaflet for each leaflet

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21 changes: 19 additions & 2 deletions membrane_curvature/tests/datafiles.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,14 +10,31 @@
"""

__all__ = [
# From lower to higher complexity
"GRO_PO4_SMALL", # Gromacs file of PO4 beads in POPC POPE membrane with 10 lipids
"XTC_PO4_SMALL", # Gromacs traj file of PO4 beacs in POPC POPE membrane with 10 lipids with indexes inverted.
"GRO_PO4_INVERTED_ID",
"GRO_PO4_MED", # Gromacs file of PO4 beads in POPC POPE membrane with 25 lipids
"GRO_PO4_BIG", # Gromacs file of PO4 beads in POPC POPE membrane with 50 lipids
"GRO_PO4", # Gromacs file of PO4 beads in POPC POPE membrane with 914 lipids
"XTC_PO4", # Gromacs trajectory of GRO_PO4
"GRO_MEMBRANE_PROTEIN", # Gromacs file of POPC POPE CHOL membrane
"XTC_MEMBRANE_PROTEIN" # Gromacs trajectory of 10 frames.
"XTC_MEMBRANE_PROTEIN", # Gromacs trajectory of 10 frames.
]

from pkg_resources import resource_filename

# Membrane protein systems
GRO_MEMBRANE_PROTEIN = resource_filename(__name__, '../data/test_curvature_abca1.gro')
GRO_PO4 = resource_filename(__name__, '../data/test_curvature_po4_only.gro')
XTC_MEMBRANE_PROTEIN = resource_filename(__name__, '../data/test_curvature_abca1.xtc')
# PO4 beads only
GRO_PO4 = resource_filename(__name__, '../data/test_curvature_po4_only.gro')
XTC_PO4 = resource_filename(__name__, '../data/test_curvature_po4_only.xtc')
# Smaler systems derived from
GRO_PO4_SMALL = resource_filename(__name__, '../data/test_po4_small.gro')
XTC_PO4_SMALL = resource_filename(__name__, '../data/test_po4_small.xtc')
GRO_PO4_MED = resource_filename(__name__, '../data/test_po4_med.gro')
GRO_PO4_BIG = resource_filename(__name__, '../data/test_po4_big.gro')
# Inverted indexes
GRO_PO4_INVERTED_ID = resource_filename(__name__, '../data/test_po4_inverted_indexes.gro')
del resource_filename
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