Trajectories

Trajectory

class traj(file_input=None[, frame=None, begin=None, end=None, increment=1, units=None, verbose=True])

All data related with a trajectory and the coordinates of a system is sort in this class. Although this class can be independently initalized, it is recommended the use of the method msystem.load_traj() for the same sake.

Parameters:

• file_input (str) – Name of trajectory file in the following formats: pdb, gro, xtc, trr, dcd.
• frame (int or list.) – Index of frames to be loaded.
• begin (int.) – Frame to start the loading process.
• end (int.) – Frame to finish the loading process.
• increment (int.) – Interval to load frames.
• units (str.) – Units for “begin”, “end” and “increment”. [only units=’frames’ available]
• verbose (bool) – Prints out general information.

Returns:

None

Prints out:

general information if verbose=True.

traj.name

Name of the input file with the trajectory. (String)

traj.type

Extension of the topology file: pdb, gro, xtc, trr, dcd. (String)

traj.title

Title or header of the file if there exist. (String)

traj.num_frames

Number of frames loaded from the input file and thereby saved in the list traj.frame. (int)

traj.total_frames

Total number of frames in the input file. (int)

traj.precision

Precision of the coordinates found in the input file. (float)

traj.frame

List of frames. Each fream is an object of frame class. (List)

traj.io_opened

Input/Output control variable: 1 -if the file is opened- or 0 -if it is closed-. (int)

traj.io_end

Input/Output control variable: 1 -if the file is at the end- or 0 -if it is not-. (int)

traj.io_err

Input/Output contro variable: 1 -if the i/o found and error- or 0 -if not-. (int)

Frame

Frames are represented by objects of class frame with common attributes and methods:

class frame

frame.time

Time value of frame for this frame. (float)

frame.step

Integration step found in the trajectory for this frame.

frame.precision

Precision of coordinates as it was found in the trajectory.

frame.lam

–

frame.model

Index of model if the input file is a pdb with different models.

frame.coors

Array with the coordinates in the frame. (numpy.ndarray(shape=(num_atoms,3),dtype=float))

frame.box

Array with dimensions of the box in the frame. (numpy.ndarray(shape=(3,3),dtype=float))

frame.cell

Array with dimensions and angles of the unit chell for the frame. (numpy.ndarray(shape=(3,3),dtype=float))

frame.orthogonal

Control variable: 1 -if the box is orthogonal- or 0 -if not-. (int)

frame.volume

Volume of the box. (float)

Box and Cell

In frame, class trajectory, box is the orthorombic set of vectors and cell (unit cell) has the length of three vectors vi in the elements cell[i,i] and the angles alpha, beta and gamma in cell[1,2], cell[1,3] and cell[2,3] respectively.

See: http://www.mail-archive.com/gmx-users@gromacs.org/msg28019.html See also: SUBROUTINE TRICLINIC (cell,box) in libdcdfile.f90

Pynoramix sets the box always in the positive cuadrant. This way any atom is always in {[0,Lx),[0,Ly),[0,Lz)}. It implies that molecules can be split if they are over the cell edges.