MDTraj
Installation
New to Python
Examples
What’s New?
Trajectory Reference
Analysis Reference
Atom Selection Reference
Low-level API
OpenMM Reporters
MDTraj Utils
mdconvert
MDTraj HDF5 Format Specification
MDTraj
Out-of-core calculations with
md.iterload()
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Out-of-core calculations with
md.iterload()
An error occurred while executing the following cell: ------------------ first_frame = md.load_frame(traj_filename, 0) first_frame ------------------ [31m---------------------------------------------------------------------------[39m [31mOSError[39m Traceback (most recent call last) [36mCell[39m[36m [39m[32mIn[3][39m[32m, line 1[39m [32m----> [39m[32m1[39m first_frame = [43mmd[49m[43m.[49m[43mload_frame[49m[43m([49m[43mtraj_filename[49m[43m,[49m[43m [49m[32;43m0[39;49m[43m)[49m [32m 2[39m first_frame [36mFile [39m[32m~/checkouts/readthedocs.org/user_builds/mdtraj/envs/stable/lib/python3.11/site-packages/mdtraj/core/trajectory.py:338[39m, in [36mload_frame[39m[34m(filename, index, top, atom_indices, **kwargs)[39m [32m 336[39m [38;5;28;01mif[39;00m [38;5;129;01mnot[39;00m _is_url(filename): [32m 337[39m [38;5;28;01mif[39;00m loader.[34m__name__[39m [38;5;129;01mnot[39;00m [38;5;129;01min[39;00m [[33m"[39m[33mload_dtr[39m[33m"[39m]: [32m--> [39m[32m338[39m [43m_assert_files_exist[49m[43m([49m[43mfilename[49m[43m)[49m [32m 339[39m [38;5;28;01melse[39;00m: [32m 340[39m _assert_files_or_dirs_exist(filename) [36mFile [39m[32m~/checkouts/readthedocs.org/user_builds/mdtraj/envs/stable/lib/python3.11/site-packages/mdtraj/core/trajectory.py:116[39m, in [36m_assert_files_exist[39m[34m(filenames)[39m [32m 114[39m [38;5;28;01mfor[39;00m fn [38;5;129;01min[39;00m filenames: [32m 115[39m [38;5;28;01mif[39;00m [38;5;129;01mnot[39;00m (os.path.exists(fn) [38;5;129;01mand[39;00m os.path.isfile(fn)): [32m--> [39m[32m116[39m [38;5;28;01mraise[39;00m [38;5;167;01mOSError[39;00m([33m"[39m[33mNo such file: [39m[38;5;132;01m%s[39;00m[33m"[39m % fn) [31mOSError[39m: No such file: data/frame0.h5
(
iterload.ipynb
;
iterload_eval.ipynb
;
iterload.py
)