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_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 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]
bilayer = u.select_atoms("resname DPPC DUPC")
com_traj = COMTraj.COMTraj(u.trajectory, bilayer)
# -----------------------