filename : str
Path to the PDB file on disk. The string could be a URL. Valid URL
schemes include http and ftp.
stride : int, default=None
Only read every stride-th model from the file
atom_indices : array_like, default=None
If not None, then read only a subset of the atoms coordinates from the
file. These indices are zero-based (not 1 based, as used by the PDB
format). So if you want to load only the first atom in the file, you
would supply atom_indices = np.array([0]).
frame : int, default=None
Use this option to load only a single frame from a trajectory on disk.
If frame is None, the default, the entire trajectory will be loaded.
If supplied, stride will be ignored.
no_boxchk : bool, default=False
By default, a heuristic check based on the particle density will be
performed to determine if the unit cell dimensions are absurd. If the
particle density is >1000 atoms per nm^3, the unit cell will be
discarded. This is done because all PDB files from RCSB contain a CRYST1
record, even if there are no periodic boundaries, and dummy values are
filled in instead. This check will filter out those false unit cells and
avoid potential errors in geometry calculations. Set this variable to
True in order to skip this heuristic check.
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