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

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_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.

list of frame

dehydrate(tr, solute_gids, water_gids_per_frame)
This function retains the GIDs of the solute atoms and the specified waters atoms, effectively removing the majority of the bulk waters from the trajectory.

Variables

[hide private]

_id_count = 0
hash(x)

__package__ = 'schrodinger.application.desmond.packages'

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

Returns: list

A new trajectory for the subsystem

dehydrate(tr, solute_gids, water_gids_per_frame)

This function retains the GIDs of the solute atoms and the specified waters atoms, effectively removing the majority of the bulk waters from the trajectory.

Parameters:

tr (list of Frame) - Input trajectory
solute_gids (list of ints) - A list of gids that specifies the subsystem.
water_gids_per_frame (list of lists of ints) - A list of gids that specifies the subsystem.

Returns: list of frame

A new, 'dehydrated' trajectory

Module traj

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

merge(*arg)

concat(first_time, delta_time, *arg)

extract_subsystem(tr, gids)

dehydrate(tr, solute_gids, water_gids_per_frame)

write_traj(tr, fname, format=`'dtr'`)