General concept¶

In most case, to use pytraj, you just need to rember this format

import pytraj as pt
traj = pt.iterload(...)
data = pt.method_name(traj, mask=mask, ref=ref, frame_indices=frame_indices ...)

traj can be a Trajectory-like (having 3D coordinates and a Topology) or it can be any iterable object that produces pytraj.Frame (a single snapshot):

# a Trajectory
import pytraj as pt
traj = pt.iterload('traj.nc', 'traj.prmtop')
pt.radgyr(traj)

# an iterable object
def create_iterator(traj):
    for frame in traj:
        frame.xyz += 2.
        yield frame

fi = create_iterator(traj)
pt.radgyr(fi, top=traj.top)

# a FrameIterator
fi2 = pt.iterframe(traj, frame_indices=[0, 8, 3], mask='@CA')
pt.radgyr(fi2)

ref can be a single Frame or a Trajectory or an integer. If it’s a Trajectory, first conformation is always picked up. If it’s an integer, pytraj will do slicing the corresponding Trajectory:
```
frame = traj[3]
traj2 = traj[3:4]
pt.rmsd(traj, ref=frame)
pt.rmsd(traj, ref=3)
pt.rmsd(traj, ref=traj2)
```

mask follows Amber mask syntax (eg. :3-18@CA) or an atom index array (eg. [0, 3, 5]). If mask is a string (amber mask), the index is 1-based (counting from 1). If mass is an array-like, the index is 0-based (counting from 0):
```
# mask is a string
pt.radgyr(traj, '@CA')

# mask is a list of integers (atom indices)
pt.radgyr(traj, mask=[0, 3, 5, 7])
```

frame_indices is frame indices for calculation. It’s optional. If no frame_indices is provided, the calculation will be performed for whole trajectory:
```
# only compute radgyr for 3 frames (0, 3, and 7-th)
pt.radgyr(traj, frame_indices=[0, 3, 7])
```

Real world example¶

# calculate radius of gyration for whole trajectory, all atoms
In [1]: import pytraj as pt

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

In [3]: traj
Out[3]: 
pytraj.TrajectoryIterator, 101 frames: 
Size: 0.000503 (GB)
<Topology: 223 atoms, 13 residues, 1 mols, non-PBC>
           

In [4]: data = pt.radgyr(traj)

# calculate radius of gyration for whole trajectory, @CA atoms
In [5]: data = pt.radgyr(traj, mask='@CA')

# calculate radius of gyration for whole trajectory, for atom indices of [0, 3, 5, 100]
In [6]: data = pt.radgyr(traj, mask=[0, 3, 5, 100])

# calculate radius of gyration for whole trajectory, all atoms, only for 0, 7, and 8-th frames
In [7]: data = pt.radgyr(traj, frame_indices=[0, 7, 8])

# calculate rmsd with reference as 0-th frame, all atoms
In [8]: data = pt.rmsd(traj, ref=0)

# calculate rmsd with reference as 0-th frame, backbone heavy atoms
In [9]: data = pt.rmsd(traj, ref=0, mask='@C,CA,N,O')

# calculate rmsd with reference as last frame, CA atoms
In [10]: data = pt.rmsd(traj, ref=-1, mask='@CA')

In [11]: data
Out[11]: array([ 4.832 ,  5.168 ,  4.7418, ...,  1.0441,  1.3155,  0.    ])