3. AnalysisActor

class MDSimsEval.AnalysisActorClass.AnalysisActor(topology, trajectory, drug_name, sasa_file='', salts_directory='')

The AnalysisActor is the core object which inputs a single topology and trajectory and performs the analysis.

The class will be responsible for reading, running calculations and storing the results. The role of the class is mainly “structural” since it is the base input of all of our analysis functions. In the future a caching mechanism should be added so as to not have to perform multiple times the same calculations and instead read them from disk.

Note

Solvent Accessible Surface Area (SASA) and Salt bridges are calculated outside of the package. More info on SASA and Salt Bridges.

Example

Example on calculating RMSF and PCA on the whole analysis_actors_dict

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

for ligand in analysis_actors_dict['Agonists'] + analysis_actors_dict['Antagonists']:
    ligand.perform_analysis(metrics=["RMSF", "PCA"])
Parameters

  • topology (str) – The topology filepath (.pdb, .gro etc)

  • trajectory (str) – The trajectory filepath (.xtc etc)

  • drug_name (str) – The name of the agonist or antagonist

  • sasa_file (str, optional) – Full path of the sasa.xvg file generated by Gromacs

  • salts_directory (str, optional) – Full path of the salts directory generated by the vmd extension

uni

The universe of atoms created by MDAnalysis tool (MDAnalysis.core.universe)

mdtraj

The trajectory of atoms created by MDTraj tool (mdtraj.Trajectory)

drug_name

The ligand name initialized in the construction of the object

Type

str

rg_res

Radius of gyration of each frame (MDAnalysisRg)

Type

list of double

rmsf_res

RMSF of each atom of the protein (MDAnalysisRMSF)

Type

list of double

pca_res

Object containing eigenvectors and eigenvalues of CA atoms covariance matrix (MDAnalysis.analysis.pca.PCA)

pca_xyz

The coordinates of the atoms selected for PCA

Type

ndarray[#atoms_selected * 3, #frames]

sasa_res

The calculation currently is performed outside of the pipeline using gromacs.

Type

ndarray[2, #frames]

hbonds

A list containing the atom indices involved in each of the identified hydrogen bonds at each frame. Each element in the list is an array where each row contains three integer indices, (d_i, h_i, a_i), such that d_i is the index of the donor atom, h_i the index of the hydrogen atom, and a_i the index of the acceptor atom involved in a hydrogen bond which occurs in that frame. (MDtraj)

Type

ndarray[#frames, #hbonds_of_frame, 3]

salt_bridges_df

A pd.DataFrame with the first two columns [“Residue1”, “Residue2”] being the residue names that form the salt bridge and the next #frames column the distance between these two residues (VMD plugin)

Type

pd.DataFrame[#NumberOfSaltBridges, 2 + DistancesPerFrame]

salt_bridges_over_time

A vector of size #frames containing the number of active salt bridges per frame

Type

ndarray[#frames]

get_frames_number()

Returns the number of frames of the trajectory

info()

Prints basic info of the simulation

perform_analysis(metrics=())

Runs the analysis methods for calculating the metrics specified by metrics argument

Parameters

metrics (List[str]) –

A list of the metrics to be calculated. Available:
Empty List []: All of the available metrics will be calculated (default)
’Rg’: Radius of Gyration
’RMSF’: Root Mean Square Fluctuations
’SASA’: Solvent Accessible Surface Area
’PCA’: Principal Component Analysis
’Hbonds’: Hydrogen Bonds
’Salt’: Calculate number of salt bridges