2. Reading the simulations

This doc page will guide you through preparing your data in the package expected structure and present a function for reading and storing them.

2.1. Directory Structure

Our reader function expects a specific directory structure.

input_directory/
  Agonists/
    Ligand1_/
      trajectory_.xtc
      topology_.pdb
      sasa.xvg *
      salts/ *
    Ligand2_
       .
       .
       .
  Antagonists/
     .
     .
     .

On the above structure everything followed by an underscore _ can have a different name.

Agonists and Antagonists were the class labels of my use case. Currently, you must follow the same names as class labels. Should fixed, so as class label is also a variable.

Note

sasa.xvg and salts/ are explained in SASA and Salt Bridges.

As an example this was my actual input directory named New_AI_MD:

2.2. Reading Function

Reads the simulations (topologies, trajectories and sasa.xvg, salts if available) and stores them in a dictionary structure. The dictionary structure called analysis_actors_dict is the core structure that our functions take as an argument.

Example:

from MDSimsEval.utils import create_analysis_actor_dict
analysis_actors_dict = create_analysis_actor_dict('path_to_data_directory/')

analysis_actors_dict['Agonists'][0].info()
Out:
    <<< Info of 5-MeOT >>>
    Number of Frames: 2500
    Number of Atoms: 4743
    Number of Residues: 291

param root_directory

The path of the input directory having the expected structure on the documentation

type root_directory

str

returns

analysis_actors_dict:

Dict(
    "Agonists": List[AnalysisActor.class]
    "Antagonists": List[AnalysisActor.class]
  )

2.3. SASA and Salt Bridges

These two features have a different way of being calculated outside of this package.

Concerning SASA we must first create a sasa.xvg file for each simulation and keep it next to the topology and the trajectory. The GROMACS command is:

gmx sasa -f trajecotry.xtc -s topology.pdb -o sasa.xvg
# Select Group 1 (Protein)

Concerning the salt bridges you must use a VMD plugin and copy the whole outputted directory named salts/ next to the trajectory files.

Note

Currently no analysis functions uses salt bridges in this package.