def test_lipid_grid_surface_area():
name_dict = {'DOPE': ['P'], 'POPC': ['P'], 'TLCL2': ['P1', 'P3']}
analyzer = 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'] = name_dict
analyzer._analysis_protocol.use_objects['lipid_grid'] = True
# adjust the number of bins for gridding
nbins = 100
analyzer.rep_settings['lipid_grid']['n_xbins'] = nbins
analyzer.rep_settings['lipid_grid']['n_ybins'] = nbins
analyzer.set_frame_range(0, 1, 1)
for _frame in analyzer:
sa_upper, sa_lower = analyzer.reps['lipid_grid'].surface_area(
filter_sigma=5.0)
print(("surface for upper leaflet: {} lower leaflet {}".format(
sa_upper, sa_lower)))
box_area = analyzer.reps['current_mda_frame'].dimensions[0:2].prod()
print(("box area: {}".format(box_area)))
area_diff = (sa_upper + sa_lower) - (2.0 * box_area)
print(area_diff)
area_ratio = (sa_upper + sa_lower) / (2.0 * box_area)
print(area_ratio)
kc = (scicon.k * 303.15 * np.log(300.0)) / (8.0 * np.pi *
(area_ratio - 1.0))
print(kc)
return
def test_analysis_iterator():
print("testing the analysis iterator...")
# initialize analyzer with keyword options--and default analysis
sel_string = "segid MEMB"
ba = BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection=sel_string,
)
# add analysis by string input
ba.add_analysis('msd msd_2 leaflet upper resname POPC')
print('Doing analysis iteration...')
for _frame in ba:
print(ba.reps['com_frame'])
print(" ")
def test_analysis_defaults():
print("testing the default settings of all analysis protocols...")
sel_string = "segid MEMB"
ba = BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection=sel_string,
)
for key in valid_analysis:
analysis_in = [key, key+"_t", dict()]
ba.add_analysis(analysis_in)
ba.settings['print_interval'] = 1
ba.print_analysis_protocol()
ba.run_analysis()
print("outputs:")
for key in valid_analysis:
a_id = key+"_t"
print(a_id+":")
print(ba.get_analysis_data(a_id))
def test_lipid_grid_pdb_writer():
sel_string = "resname POPC DOPE TLCL2"
name_dict = {'DOPE': ['P'], 'POPC': ['P'], 'TLCL2': ['P1', 'P3']}
analyzer = 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'] = name_dict
analyzer._analysis_protocol.use_objects['lipid_grid'] = True
# adjust the number of bins for gridding
nbins = 75
analyzer.rep_settings['lipid_grid']['n_xbins'] = nbins
analyzer.rep_settings['lipid_grid']['n_ybins'] = nbins
analyzer.set_frame_range(0, 5, 1)
i = 0
zgrid = None
for _frame in analyzer:
if i == 0:
zgrid = analyzer.reps['lipid_grid'].leaf_grid['upper'].lipid_grid_z
else:
zgrid += analyzer.reps['lipid_grid'].leaf_grid[
'upper'].lipid_grid_z
i += 1
zgrid /= i
analyzer.reps['lipid_grid'].write_pdb('lipid_grid_t0.pdb',
leaflet='both',
beta_grid_upper=zgrid)
analyzer.reps['lipid_grid'].write_pdb('lipid_grid_t1.pdb',
leaflet='upper',
z_grid_upper=zgrid)
analyzer.reps['lipid_grid'].write_pdb('lipid_grid_t2.pdb',
leaflet='both',
use_gaussian_filter=True,
filter_sigma=5.0)
return
def test_lipid_grid_curvature():
sel_string = "resname POPC DOPE TLCL2"
name_dict = {'DOPE': ['P'], 'POPC': ['P'], 'TLCL2': ['P1', 'P3']}
analyzer = 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'] = name_dict
analyzer._analysis_protocol.use_objects['lipid_grid'] = True
# adjust the number of bins for gridding
nbins = 75
analyzer.rep_settings['lipid_grid']['n_xbins'] = nbins
analyzer.rep_settings['lipid_grid']['n_ybins'] = nbins
analyzer.set_frame_range(0, 1, 1)
i = 0
zgrid = None
for _frame in analyzer:
if i == 0:
zgrid = analyzer.reps['lipid_grid'].leaf_grid['upper'].lipid_grid_z
else:
zgrid += analyzer.reps['lipid_grid'].leaf_grid[
'upper'].lipid_grid_z
i += 1
zgrid_i = zgrid / float(i)
zgrid_i_f = gaussian_filter(zgrid_i, 5.0, mode="nearest")
x_vals = analyzer.reps['lipid_grid'].leaf_grid['upper'].x_centers
y_vals = analyzer.reps['lipid_grid'].leaf_grid['upper'].y_centers
curvature_grids_i = grid_curvature(x_vals, y_vals, zgrid_i_f)
xyzc_mean = analyzer.reps['lipid_grid'].get_xyzc(
leaflet='upper', color_grid=curvature_grids_i[0])['upper']
#xyzc_u_mean_i = (x_vals, y_vals, x_vals, curvature_grids_i[0].flatten())
pgf.plot_grid_as_scatter(xyzc_mean, save=False, show=False, colorbar=True)
analyzer.reps['lipid_grid'].curvature()
return
def test_lipid_grid_opt():
sel_string = "resname POPC DOPE TLCL2"
name_dict = {'DOPE': ['P'], 'POPC': ['P'], 'TLCL2': ['P1', 'P3']}
analyzer = 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'] = name_dict
#analyzer._analysis_protocol.use_objects['lipid_grid'] = True
# adjust the number of bins for gridding
nbins = 100
#analyzer.rep_settings['lipid_grid']['n_xbins'] = nbins
#analyzer.rep_settings['lipid_grid']['n_ybins'] = nbins
analyzer.set_frame_range(0, 1, 1)
i = 0
zgrid = None
for _frame in analyzer:
lipid_grid = lg.LipidGrids(analyzer.reps['com_frame'],
analyzer.reps['leaflets'], [0, 1],
nxbins=nbins,
nybins=nbins)
lipid_grid_opt = lgo.LipidGrids(analyzer.reps['com_frame'],
analyzer.reps['leaflets'], [0, 1],
nxbins=nbins,
nybins=nbins)
lg_u = lipid_grid.leaf_grid['upper'].lipid_grid
lgo_u = lipid_grid_opt.leaf_grid['upper'].lipid_grid
lg_l = lipid_grid.leaf_grid['lower'].lipid_grid
lgo_l = lipid_grid_opt.leaf_grid['lower'].lipid_grid
print((np.array_equal(lg_u, lgo_u)))
print((np.array_equal(lg_l, lgo_l)))
comp_l = lg_l == lgo_l
wh = np.where(comp_l == False)
print(wh)
print((lg_l[wh]))
print((lgo_l[wh]))
# break
return
def test_leaflet_builder():
sel_string = "resname POPC DOPE TLCL2"
name_dict = {'DOPE': ['P'], 'POPC': ['P'], 'TLCL2': ['P1', 'P3']}
analyzer = BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection="resname POPC DOPE TLCL2")
analyzer.rep_settings['com_frame']['name_dict'] = name_dict
# Assign the leaflets using the 'avg_norm' method. (This is actually the
# default).
analyzer.adjust_rep_setting('leaflets', 'assign_method', 'avg_norm')
analyzer.run_analysis()
analyzer.reset()
# Now redo it using the 'orientation' mehtod to assign leaflets.""
analyzer.adjust_rep_setting('leaflets', 'assign_method', 'orientation')
analyzer.adjust_rep_setting('leaflets', 'orientation_atoms', {
'DOPE': ['C218', 'P'],
'POPC': ['C218', 'P'],
'TLCL2': ['CA18', 'P1']
})
analyzer.run_analysis()
return
def test_input_options():
print("testing various input options...")
#initialize analyzer with keyword options--and default analysis
print("Initialize using keyword options:")
sel_string = "segid MEMB"
ba = BilayerAnalyzer(
structure='../pybilt/sample_bilayer/sample_bilayer.psf',
trajectory='../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
selection=sel_string,
)
#add analysis by string input
ba.add_analysis('msd msd_2 leaflet upper resname POPC')
#add plot by string -- currenlty only available
ba.add_plot('msd msd_p msd_1 DOPE-U msd_2 POPC-U')
#add analysis by list/tuple input
ba.add_analysis(['msd', 'msd_3', {'resname': 'POPC', 'leaflet': 'lower'}])
#add analysis by dictionary input
analysis_in_dict = dict()
analysis_in_dict['analysis_key'] = 'msd'
analysis_in_dict['analysis_id'] = 'msd_4'
analysis_in_dict['analysis_settings'] = {'resname': 'DOPE', 'leaflet': 'lower'}
ba.add_analysis(analysis_in_dict)
# run the analyses
ba.run_analysis()
#initialize analyzer using input script
print("Initialize with an input script:")
ba = BilayerAnalyzer(input_file='sample_1.in')
#run analysis
ba.run_analysis()
#now initialize with an input dictionary
# define the input dictionary
input_dict = {'structure' : '../pybilt/sample_bilayer/sample_bilayer.psf',
'trajectory' : '../pybilt/sample_bilayer/sample_bilayer_10frames.dcd',
'selection' : 'segid MEMB'
}
#now initialize the analyzer
print("Initializing using input dictionary:")
ba = BilayerAnalyzer(input_dict=input_dict)
ba.add_analysis('msd msd_b resname DOPE leaflet upper')
ba.run_analysis()
return
from tqdm import tqdm # tqdm
import seaborn as sns
# pybilt modules
from pybilt.bilayer_analyzer import BilayerAnalyzer
from pybilt.bilayer_analyzer import print_valid_analyses
from pybilt.com_trajectory import COMTraj
from pybilt.lipid_grid.lipid_grid import grid_curvature
from pybilt.lipid_grid.lipid_grid import LipidGrid2d
from pybilt.lipid_grid.lipid_grid_opt import LipidGrids
sel_string = "resname DPPC or resname DUPC"
ba = BilayerAnalyzer(
structure='../replicate.gro',
trajectory='../md.xtc',
selection=sel_string,
)
ba.add_analysis('ndcorr ndcorr_1')
#ba.run_analysis()
#ndcorr_1Dat = ba.get_analysis_data('ndcorr_1')
# Separate Curvature analysis
u = mda.Universe('../replicate.gro', '../md.xtc')
lipids = u.select_atoms("resname DPPC DUPC")
lipidindices = lipids.indices
#G = [u.select_atoms("resid {}".format(index)) for index in lipidindices]
#COM = [i.center_of_mass() for i in G]