Collate Analysis Data

The collate function of MD Davis uses HDF5 file format to store the heterogeneous data obtained from consolidating and organizing the data from multiple calculations using the h5py Python module. HDF5 being an open binary format, allows users to open these files directly in C, C++, or FORTRAN programs. It is much smaller to store and faster to load than text files. Moreover, the data can be inspected with the HDF View GUI.

Step 1: Create a TOML file (input.toml) as shown below specifying the output files from GROMACS.

name = 'protein_name_no_spaces'
output = 'protein_data.h5'
label = 'Protein from <i>some organism</i>'
text_label = 'Protein Name'

trajectory = 'trajectory.xtc'
structure = 'structure.pdb'

[timeseries]
    rmsd = 'rmsd.xvg'
    rg = 'rg.xvg'

[dihedral]
    chunk = 101         # Number of frames to read at a time

[residue_property]
    secondary_structure = 'sec_str.dat'
    rmsf = 'rmsf.xvg'
    sasa = 'resarea.xvg'

If the chunk under dihedral is provided, MD DaVis will calculate backbone dihedral angles for all frames and the torsional flexibility (circular standard deviation) of each dihedral angle.

In case, the RMSF for each chain was calculated separately, the files may be provided with rmsf key as follows:

[residue_property]
    rmsf = ['rmsf_chain_A.xvg', 'rmsf_chain_B.xvg']

Step 2: Collect all the data from the output files into a single HDF file using the following command:

md-davis collate input.toml

Multiple input files can also be provided.

md-davis collate input1.toml input2.toml

Note

The command can be run multiple times to incrementally add data into a HDF5 file by modifying the TOML file. For example, first adding the RMSD and Rg then adding dihedral and so no. However, sometimes if a variable or group already exists in the HDF5 file then h5py will fail to create the file. Please the delete the exisintg file and rerun the command by providing all data at once.