def read_trajectory(self, fn):
"""
Reads a trr-trajectory, resolves periodic boundary conditions
with L{PbcResolver} and calculates internal coordinates.
@param fn: filename of a gromacs trr trajectory.
@return: L{InternalArray}
"""
required_atoms = set(sum([c.atoms for c in self], ()))
atoms_start = min(required_atoms)
atoms_end = max(required_atoms) + 1
f_trr = TrrFile(fn)
(frames_x, frames_box) = f_trr.read_frames(atoms_start,
atoms_end,
read_boxes=True)
f_trr.close()
pbc = PbcResolver(frames_box)
def dx_provider(atom1, atom2):
ai = frames_x[:, atom1 - atoms_start, :]
aj = frames_x[:, atom2 - atoms_start, :]
return (pbc.rvec_sub(ai, aj))
array = np.column_stack([c.from_externals(dx_provider) for c in self])
return (InternalArray(self, array))
def main():
if(len(sys.argv) != 3):
print("Takes a trr-trajectory and converts it into a mat-file for matlab.")
print("Usage: trr2mat.py <trr-input-file> <mat-output-file>")
sys.exit(1)
trr_fn = sys.argv[1]
mat_fn = sys.argv[2]
print("Opening: %s"%trr_fn)
f = TrrFile(trr_fn)
data = f.read_frames()
f.close()
print("Loaded trr-file with shape: "+str(data.shape))
print("Writing: %s"%mat_fn)
savemat(mat_fn, {"trr":data})
def read_trajectory(self, fn):
"""
Reads a trr-trajectory, resolves periodic boundary conditions
with L{PbcResolver} and calculates internal coordinates.
@param fn: filename of a gromacs trr trajectory.
@return: L{InternalArray}
"""
required_atoms = set(sum([c.atoms for c in self], () ))
atoms_start = min(required_atoms)
atoms_end = max(required_atoms) + 1
f_trr = TrrFile(fn)
(frames_x, frames_box) = f_trr.read_frames(atoms_start, atoms_end, read_boxes=True)
f_trr.close()
pbc = PbcResolver(frames_box)
def dx_provider(atom1, atom2):
ai = frames_x[:,atom1-atoms_start,:]
aj = frames_x[:,atom2-atoms_start,:]
return(pbc.rvec_sub(ai, aj))
array = np.column_stack([ c.from_externals(dx_provider) for c in self ])
return( InternalArray(self, array) )
