Datafiles¶
Location of data files for Pytim examples and tests¶
Real MD simulation data are stored in the
data/
subdirectory.Example: load an example trajectory
>>> import MDAnalysis as mda >>> import pytim >>> import numpy as np >>> from pytim.datafiles import * >>> u = mda.Universe(WATER_GRO,WATER_XTC) >>> print(u) <Universe with 12000 atoms>Example: list all configurations
>>> for config in sorted(pytim_data.config): ... print("{:20s} {:s}".format(config,pytim_data.description[config])) CCL4_WATER_GRO Carbon tetrachloride/TIP4p water interface DPPC_GRO DPPC bilayer FULLERENE_PDB fullerene GLUCOSE_PDB solvated beta-d-glucose LJ_GRO Lennard-Jones liquid/vapour interface MICELLE_PDB DPC micelle WATERSMALL_GRO small SPC water/vapour interface WATER_520K_GRO SPC/E water/vapour interface, 520K WATER_550K_GRO SPC/E water/vapour interface, 550K WATER_DROPLET_CYLINDRICAL_GRO cylindrical water droplet on graphite WATER_GRO SPC water/vapour interface WATER_PDB SPC water/vapour interface WATER_XYZ SPC water/vapour interfaceExample: list all topologies
>>> print(np.sort(pytim_data.topol)) ['AMBER03_TOP' 'CHARMM27_TOP' 'G43A1_TOP' 'WATER_LMP_DATA']Example: list all trajectories
>>> print (np.sort(pytim_data.traj)) ['LJ_SHORT_XTC' 'WATER_DROPLET_CYLINDRICAL_XTC' 'WATER_LMP_XTC' 'WATER_XTC']Example: list all files, file type, file format and description
>>> for label in pytim_data.label: ... type = pytim_data.type[label] ... format = pytim_data.format[label] ... description = pytim_data.description[label]