Package molfile

Structure and coordinate file manipulation library.

Reading a structure file:

   reader = molfile.mae.read('/path/to/foo.mae')

Iterating through the frames in a file:

   for frame in molfile.dtr.read('/path/to/foo.dtr').frames():
       function( frame.pos, frame.vel, frame.time, frame.box )

Random access to frames (only dtr files support this currently):

   f27 = molfile.dtr.read('/path/to/foo.dtr').frame(27) # 0-based index

Convert an mae file to a pdb file:

   input=molfile.mae.read('foo.mae')
   output=molfile.pdb.write('foo.pdb', atoms=input.atoms)
   output.frame(input.frames().next())
   output.close()

Write every 10th frame in a dtr to a trr:

   input=molfile.dtr.read('big.dtr')
   output=molfile.trr.write('out.trr, natoms=input.natoms)
   for i in range(0,input.nframes, 10):
       output.frame( input.frame(i) )
   output.close()

Write a frame with a specified set of gids:

   f = molfile.Frame(natoms, with_gids=True
   f.gid[:] = my_gids
   f.pos[:] = my_positions
   w.frame(f)

Read the raw fields from a frameset (dtr):

   dtr = molfile.DtrReader('input.dtr')    # also works for stk
   for i in range(dtr.nframes):
       f = dtr.frame(i)
       keyvals = dict()
       frame = dtr.frame(i, keyvals=keyvals)
       ## use data in keyvals

Write raw fields to a frameset (dtr):

   dtr = molfile.DtrWriter('output.dtr', natoms=natoms)
   keyvals = dict( s = "a string",
                   f = positions.flatten(),    # must be 1d arrays
                   i = numpy.array([1,2,3]),
                   )
   dtr.append( time = my_time, keyvals = keyvals )