Frequently Asked Questions

Why do most of examples use pytraj.iterload instead of pytraj.load

Because we encourage user to use out-of-core calculation for memory saving. Most of the time we don’t need change trajecotry’s coordinate, so it’s OK to just use immutable trajectory.

So does not pytraj support much for in-memory calculation?

Yes, pytraj does support in-memory calculation very well. Just consider pytraj.Trajectory as a mutable Python’s list and pytraj.TrajectoryIterator as immutable Python’s tuple.

The difference between traj[1:11:2] and traj(1, 11, 2)?

traj[1:11:2] returns a new pytraj.Trajectory while traj(1, 11, 2) returns a FrameIterator for lazy loading. You can use both for analysis.

In [1]: import pytraj as pt

In [2]: traj = pt.iterload('', 'tz2.parm7')

In [3]: traj[1:11:2]
pytraj.Trajectory, 5 frames: 
Size: 0.000025 (GB)
<Topology: 223 atoms, 13 residues, 1 mols, non-PBC>

In [4]: pt.radgyr(traj[1:11:2])
Out[4]: array([ 9.5746,  9.9404,  8.9159,  8.0262,  8.6852])

In [5]: traj(1, 11, 2)
<FrameIterator with start=1, stop=11, step=2, n_frames=5, 
mask=None, autoimage=False, rmsfit=None, copy=False> 

In [6]: pt.radgyr(traj(1, 11, 2))
Out[6]: array([ 9.5746,  9.9404,  8.9159,  8.0262,  8.6852])

It’s too slow to convert to numpy array, about 3 us for only 10 atom-Frame

It’s constant time to cast to numpy array. It takes similar time to cast from 1 million-atom Frame too. This is not problem since you only need cast once without making extra data copying.

What’s the idiom to load data to memory for specific atoms?

In [7]: import pytraj as pt

In [8]: traj = pt.iterload('', 'tz2.parm7')

In [9]: traj
pytraj.TrajectoryIterator, 101 frames: 
Size: 0.000503 (GB)
<Topology: 223 atoms, 13 residues, 1 mols, non-PBC>

In [10]: traj[:8, '@CA']
pytraj.Trajectory, 8 frames: 
Size: 0.000002 (GB)
<Topology: 12 atoms, 12 residues, 12 mols, non-PBC>

List comprehensions give identical frames when iterating trajecotry

This is our intention for memory saving. Use copy method. (But what do you need list comprehensions for in this case?)

# same frames
[frame for frame in traj]

# different frames
[frame.copy() for frame in traj]

Get undefined symbol error when import pytraj

Probably you use old libcpptraj. You can export LD_LIBRARY_PATH

# supposed you have libcpptraj in /home/lib/cpptraj/, do
$ export LD_LIBRARY_PATH=/home/lib/cpptraj/:$LD_LIBRARY_PATH

Error: Could not determine trajectory format ”.nc”

libcpptraj needs to be installed with NetCDF library. If you encouter this, send us email or open issue on github

ImportError: cannot open shared object file

Something is wrong with conda. Try conda install libnetcdf.

ValueError: Big-endian buffer not supported on little-endian compiler

When you are using memoryview, make sure to use correct type. Just google this error.

ImportError after cpptraj update


ImportError ... undefined symbol


since pytraj requires cpptraj at both compiling and running time, if you update, you need to rebbuild pytraj from fresh.

# supposed you are in pytraj home folder (having, tests, ...)
rm -rf build
python install

ValueError: Buffer not C contiguous


File "pytraj/cyutils.pyx", line 76, in _fast_iterptr (pytraj/cyutils.cpp:5078)...
ValueError: Buffer not C contiguous.


For very fast trajectory iterating, pytraj require coords must be stored in a C contiguous memory block.
You should try `np.ascontiguousarray`: `xyz = np.ascontiguousarray(xyz)`