Expose a streaming read/write interface about mdtraj HOT 7 CLOSED

+1

I have a DCD that is too big for me to read.

What do you want this to look like? Arbitrary slicing for reads? Append for writes?

from mdtraj.

no arbitrary slicing. something like

class DCDFile(object):
    def __init__(self, filename, mode='r'):
        """Open a DCD file"""

    def read_frames(n_frames=1):
        """Return the next n frames of the trajectory"""

    def close():
        """Close the file"""

from mdtraj.

I suppose a related feature would be to read only a subset of the atoms.

from mdtraj.

I need to look in the source, but I don't think that's possible with the DCD binary format. If you're doing a streaming analysis on a small number of frames at a time, then thats really how you're going to get the memory win.

from mdtraj.

Well, to me there's no reason why we couldn't implement this on the (c/p)ython side of things. I agree it might require an extra copy...

from mdtraj.

Yeah, it's not possible to actually load (and malloc space for) only some of the atoms. The DCD reader can give you the appearance of this by pre-slicing the results, but I don't think this is a good idea.

from mdtraj.

Okay, I take that back. You could, but you have to hack the binary format of the DCD file, instead of using the c-level dcd file reader functions. This is not worth it.

from mdtraj.