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View Code? Open in Web Editor NEWScripts to analyse MD trajectories of pure water as well as confined in nanotubes or by flat sheets (graphene, hBN)
Scripts to analyse MD trajectories of pure water as well as confined in nanotubes or by flat sheets (graphene, hBN)
Make use of full MDAnalysis trajectory capability and support other formats and filenames.
e.g. example form mlp-score using mdtraj:
def load_with_cell(filename_or_filenames, **kwargs):
"""Load a trajectory and inject cell dimensions from a topology PDB file if not present.
All arguments and keyword arguments are passed on to `mdtraj.load`. The `top`
keyword argument is used load a PDB file and get cell information from it.
"""
# load the "topology frame" to get cell dimensions
top = kwargs.get("top")
if top is not None and isinstance(top, str):
# load topology frame - just the first one from the file, in case there are more frames
frame_top = mdt.load_frame(top, 0)
unitcell_lengths = frame_top.unitcell_lengths
unitcell_angles = frame_top.unitcell_angles
if (unitcell_lengths is None) or (unitcell_angles is None):
raise ValueError("Frame providing topology is missing cell information.")
else:
raise ValueError("Provide a PDB with cell dimensions.")
# load the trajectory itself
trj = mdt.load(filename_or_filenames, **kwargs)
# inject the cell information
len_trj = len(trj)
trj.unitcell_lengths = unitcell_lengths.repeat(len_trj, axis=0)
trj.unitcell_angles = unitcell_angles.repeat(len_trj, axis=0)
return trj
findpeaks package is not available on conda
replace findpeaks package with different 2D peak finder
remove dependence on matplotlib widget and other jupyter magic functions
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