Package schrodinger :: Package application :: Package desmond :: Package packages :: Module traj

Module traj

Molecular dynamics trajectory handling module Define common APIs for various trajectory formats. Basic trajectory handling algorithms are also implemented here.

Classes

[hide private]

Source

DtrSource

Frame
This class, as its name suggests, represents a single trajectory frame.

Functions

[hide private]

_newid()
Ensurance: All IDs issued by this function are unique integer numbers > -1.

read_traj(inp, format="dtr")

write_traj(tr, fname, format="dtr")

merge(*arg)
Merge a list of trajectories.

concat(first_time, delta_time, *arg)
Concatenate a list of trajectories and reassign the chemical time for each frame.

list

extract_subsystem(tr, gids)
Extract the subsystem as specified by the gids for each frame in the given trajectory tr, and return a new trajectory for the subsystem.

Variables

[hide private]

_id_count = 0

Function Details

[hide private]

write_traj(tr, fname, format="dtr")

Parameters:

fname (str) - Output file name
format (str) - Trajectory file format. Valid values: "dtr"

merge(*arg)

Merge a list of trajectories. If there is any overlapped frames among these trajectories, the ones from the latter trajectory (higher index in the arg list) will be kept.

concat(first_time, delta_time, *arg)

Concatenate a list of trajectories and reassign the chemical time for each frame.

Parameters:

first_time (float) - Chemical time of the first frame.
delta_time (float) - The chemical time interval between two successive frames.

extract_subsystem(tr, gids)

Extract the subsystem as specified by the gids for each frame in the given trajectory tr, and return a new trajectory for the subsystem. The original trajectory is not mutated in any way by this function.

Parameters:

tr (list) - Original trajectory
gids (list of ints) - A list of gids that specifies the subsystem.

Returns: list

A new trajectory for the subsystem