Relative path

../fullrmc/Examples/docking/

Description

Here a single molecule is used to demonstrate how to use rotate and translate a group towards another. This example was used to generate the docking video example as seen in the online documentation. When running this example several files will be generated where all moved are saved. If VMD. is installed, the trajectory of all moves will be automatically visualized.

Files

1. system.pdb: The single constituted of two molecules
2. run.py: The script file used to run the simulation

run.py explained

IMPORTING USEFUL DEFINITIONS:

All useful packages, modules and definitions are imported.

SHUT DOWN LOGGING:

Set logger minimum level to maximum possible integer value. This will mute all non-error logging.

CREATE ENGINE:

Create the engine and the needed inter-molecular distance constraints.

DIFFERENT RUNS:

Define functions to run fitting engine. All of the following functions finish running the engine using Engine.run method. A trajectory of all moves is saved to the disk by setting XYZPath argument not to None.

1. move_towards: Groups are using engine set_groups_as_molecules method. Then only first group is kept in the engine keeping the other as fixed. A collection of move generators MoveGeneratorCollector is created and set to the remaining group. RotationGenerator and TranslationTowardsCenterGenerator are added to this collection.

RUN SIMULATION:

move_towards function is called.

VISUALIZE SIMULATION:

Reset initial pdb to engine instance. Visualize engine along with all saved four trajectories “trajectory.xyz”.