def test_msd():
analyzer = ba.BilayerAnalyzer(structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.print_analysis_protocol()
analyzer.run_analysis()
msd_dat_a = analyzer.get_analysis_data('msd_1')
print("MSD from BilayerAnalyzer:")
print(msd_dat_a)
u = mda.Universe('../pybilt/sample_bilayer/sample_bilayer.psf', '../pybilt/sample_bilayer/sample_bilayer_10frames.dcd')
bilayer_sel = u.select_atoms("resname POPC DOPE TLCL2")
ct = comtraj.COMTraj(u.trajectory,bilayer_sel)
msd_dat_b = ct.calc_msd()
print("MSD from COMTraj:")
print(msd_dat_b)
print(("BilayerAnalyzer and COMTraj match: {}".format(np.isclose(msd_dat_a, msd_dat_b, rtol=0.001))))
#redo bilayer_anlayzer calc, but use the iterator looper
analyzer = ba.BilayerAnalyzer(structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.print_analysis_protocol()
for _frame in analyzer:
pass
msd_dat_c = analyzer.get_analysis_data('msd_1')
print("MSD from BilayerAnalyzer obtained using iterator:")
print(msd_dat_c)
print(("matches first BilayerAnalyzer comp: {}".format(np.isclose(msd_dat_a, msd_dat_b, rtol=0.001))))
def test_lipid_collinearity():
analyzer = ba.BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
#remove the default msd analysis
analyzer.remove_analysis('msd_1')
analyzer.add_analysis(
"lipid_collinearity lc leaflet lower resname_1 POPC resname_2 DOPE style order"
)
analyzer.adjust_rep_setting(
'vector_frame', 'ref_atoms', {
'DOPE': {
'start': ['C218', 'C318'],
'end': 'P'
},
'POPC': {
'start': ['C218', 'C316'],
'end': 'P'
},
'TLCL2': {
'start': ['CA18', 'CB18', 'CC18', 'CD18'],
'end': ['P1', 'P3']
}
})
analyzer.run_analysis()
lc_dat = analyzer.get_analysis_data('lc')
print('Lipid Collinearities (vs time):')
print(lc_dat)
def test_leaflet_update_interval():
analyzer = ba.BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.remove_analysis('msd_1')
analyzer.add_analysis(
'nnf nnf_a resname_1 DOPE resname_2 POPC leaflet upper n_neighbors 6')
analyzer.add_analysis(
'nnf nnf_b resname_1 DOPE resname_2 DOPE leaflet upper n_neighbors 4')
analyzer.add_analysis(
'nnf nnf_c resname_1 DOPE resname_2 TLCL2 leaflet upper n_neighbors 8')
print("Default Rep Settings:")
analyzer.print_rep_settings()
analyzer.adjust_rep_setting('leaflets', 'update_interval', 2)
print("\nAdjusted Rep Settings:")
analyzer.print_rep_settings()
analyzer.print_analysis_protocol()
analyzer.run_analysis()
print(analyzer.get_analysis_data('nnf_a'))
print(" ")
print(analyzer.get_analysis_data('nnf_b'))
print(" ")
print(analyzer.get_analysis_data('nnf_c'))
def test_vector_frame():
analyzer = ba.BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
#remove the default msd analysis
analyzer.remove_analysis('msd_1')
analyzer.add_analysis("lipid_length ll leaflet upper resname TLCL2")
analyzer.adjust_rep_setting(
'vector_frame', 'ref_atoms', {
'DOPE': {
'start': ['C218', 'C318'],
'end': 'P'
},
'POPC': {
'start': ['C218', 'C316'],
'end': 'P'
},
'TLCL2': {
'start': ['CA18', 'CB18', 'CC18', 'CD18'],
'end': ['P1', 'P3']
}
})
analyzer.run_analysis()
ll_dat = analyzer.get_analysis_data('ll')
print('Lipid Lengths (vs time):')
print(ll_dat)
def test_ndcorr():
analyzer = ba.BilayerAnalyzer(structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.add_analysis('ndcorr ndcorr_a')
analyzer.remove_analysis('msd_1')
analyzer.print_analysis_protocol()
#use the phosphorous atoms instead of full lipid center of mass
analyzer.run_analysis()
print((analyzer.get_analysis_data('ndcorr_a')))
def test_ba_ap_dispveccorravg():
analyzer = ba.BilayerAnalyzer(structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.remove_analysis('msd_1')
analyzer.add_analysis('disp_vec_corr_avg disp_vec_corr_avg leaflet upper interval 2')
analyzer.print_analysis_protocol()
analyzer.run_analysis()
print(analyzer.get_analysis_data('disp_vec_corr_avg'))
return
def test_halperin_nelson():
analyzer = ba.BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.remove_analysis('msd_1')
analyzer.add_analysis('halperin_nelson hn leaflet upper')
analyzer.print_analysis_protocol()
analyzer.run_analysis()
print(analyzer.get_analysis_data('hn'))
def test_ba_ap_dispveccorravg():
analyzer = ba.BilayerAnalyzer(structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.remove_analysis('msd_1')
analyzer.add_analysis('spatial_velocity_corr spatial_velocity_corr leaflet lower interval 3 n_bins 120 range_outer 60.0 resname_1 POPC resname_2 POPC')
analyzer.print_analysis_protocol()
analyzer.run_analysis()
bins, averages = analyzer.get_analysis_data('spatial_velocity_corr')
plt.plot(bins, averages)
#plt.show()
return
def test_flip_flop():
analyzer = ba.BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory=
'../pybilt/sample_bilayer/sample_bilayer_10frames_flipflop.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.remove_analysis('msd_1')
analyzer.add_analysis('flip_flop flip_flop')
analyzer.print_analysis_protocol()
analyzer.run_analysis()
print(analyzer.get_analysis_data('flip_flop'))
return
def test_msd_multi():
analyzer = ba.BilayerAnalyzer(structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
#analyzer.remove_analysis('msd_1')
analyzer.add_analysis('msd_multi msd_multi_1 resname all leaflet both n_tau 10 n_sigma 10')
analyzer.add_analysis('msd_multi msd_multi_2 resname all leaflet both n_tau 3 n_sigma 3')
analyzer.print_analysis_protocol()
analyzer.run_analysis()
print(analyzer.get_analysis_data('msd_multi_1'))
print(analyzer.get_analysis_data('msd_1'))
print(analyzer.get_analysis_data('msd_multi_2'))
return
def test_com_frame_multi_bead():
analyzer = ba.BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.remove_analysis('msd_1')
analyzer.rep_settings['com_frame']['name_dict'] = {
'DOPE': ['C2'],
'POPC': ['C2'],
'TLCL2': ['C13', 'C32']
}
analyzer.rep_settings['com_frame']['multi_bead'] = True
analyzer.add_analysis(
'halperin_nelson halperin_nelson_upper leaflet upper')
analyzer.run_analysis()
com_halp = analyzer.get_analysis_data('halperin_nelson_upper')
nbeads = len(analyzer.reps['com_frame'])
print(("There are {} COM beads.".format(nbeads)))
print(com_halp)
def test_com_frame_sub_selection():
analyzer = ba.BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.run_analysis()
com_msd = analyzer.get_analysis_data('msd_1')
#reset
analyzer.reset()
#use the phosphorous atoms instead of full lipid center of mass
analyzer.rep_settings['com_frame']['name_dict'] = {
'DOPE': ['P'],
'POPC': ['P'],
'TLCL2': ['P1', 'P3']
}
analyzer.run_analysis()
analyzer.get_analysis_data('msd_1')
phospho_msd = analyzer.get_analysis_data('msd_1')
#reset
analyzer.reset()
#use the phosphorous and nitrogen atoms instead of full lipid center of mass -- TLCL2 has no nitrogen
analyzer.rep_settings['com_frame']['name_dict'] = {
'DOPE': ['P', 'N'],
'POPC': ['P', 'N'],
'TLCL2': ['P1', 'P3']
}
analyzer.run_analysis()
PN_msd = analyzer.get_analysis_data('msd_1')
print('Center of Mass MSD:')
print(com_msd)
print('Phosphorous MSD:')
print(phospho_msd)
print('Phosphorous and Nitrogen MSD:')
print(PN_msd)
def test_ba_ap_dv_stm():
analyzer = ba.BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.remove_analysis('msd_1')
analyzer.add_analysis(
'disp_vec disp_vec interval 5 wrapped True leaflet upper scale_to_max True'
)
analyzer.add_analysis(
'disp_vec disp_vec_b interval 1 wrapped True leaflet upper scale_to_max True'
)
analyzer.print_analysis_protocol()
analyzer.run_analysis()
output = analyzer.get_analysis_data('disp_vec')
dv_res = output[0]
pgf.plot_step_vectors(dv_res,
save=False,
show=False,
scaled=True,
wrapped=True)
dv_res = output[len(output) - 1]
pgf.plot_step_vectors(dv_res,
save=False,
show=False,
scaled=True,
wrapped=True)
output = analyzer.get_analysis_data('disp_vec_b')
pgf.plot_step_vectors_stroboscopic(output,
index=0,
scaled=True,
wrapped=True,
save=False,
show=False)
def test_nnf():
analyzer = ba.BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.remove_analysis('msd_1')
analyzer.add_analysis(
'nnf nnf_a resname_1 DOPE resname_2 POPC leaflet upper n_neighbors 6')
analyzer.add_analysis(
'nnf nnf_b resname_1 DOPE resname_2 DOPE leaflet upper n_neighbors 4')
analyzer.add_analysis(
'nnf nnf_c resname_1 DOPE resname_2 TLCL2 leaflet upper n_neighbors 8')
analyzer.print_analysis_protocol()
analyzer.run_analysis()
print analyzer.get_analysis_data('nnf_a')
print " "
print analyzer.get_analysis_data('nnf_b')
print " "
print analyzer.get_analysis_data('nnf_c')
#Same protocol as sample_script_1 without using the input setup file.
import pybilt.bilayer_analyzer.bilayer_analyzer as ba
analyzer = ba.BilayerAnalyzer(
structure='../../sample_bilayer/sample_bilayer.psf',
trajectory='../../sample_bilayer/sample_bilayer_10frames.dcd',
selection='resname POPC DOPE TLCL')
analyzer.add_analysis('msd msd_1')
analyzer.add_analysis('msd msd_2 leaflet upper resname POPC')
analyzer.add_plot('msd msd_p msd_1 DOPE-U msd_2 POPC-U')
analyzer.run_analysis()
analyzer.show_plot('msd_p')
#Setup using an input file
import pybilt.bilayer_analyzer.bilayer_analyzer as ba
analyzer = ba.BilayerAnalyzer(input_file='../sample_input_script/sample_1.in')
analyzer.run_analysis()
analyzer.show_plot('msd_p')
