Output files (out)

The out command is meant for writing output files. Bept provides two default output files which is always outputted. These are .bept and a {NAME}_bept.csv file which consists of ALL the information about each atom present in the structure.

The out command inputs two files COMPULSARILY which are .pqr and .dx file of the protein structure which you can obtain with the help of other COMMANDS of bept.

You can run the out command by running the following command in the terminal -

bept out -q /path/to/pqr_file -d /path/to/dx_file

To see the help message, you can run bept out --help in your terminal.

Calculation of the Gradients

We calculate the gradients of the electric field at each atom in the structure. The gradient is calculated using the algorithms used by numpy.gradient function. To know more about how we implement the gradient calculation, check out the Gradient Calculation documentation on our repository.

Format of {protein}_bept.csv

The data extracted from PQR file, apbs potential dx file is taken and mapped to each of the atom present in the PQR file. This data is now written to a .csv file making it easier for the user to use the data for the future. Here are the following columns present in the .csv file -

  1. Type - Denoting ATOM, HETATM, etc.

  2. Num - The serial number of atom from top as present in PQR file.

  3. Atom - The name of the atom, based on nomenclature provided by PQR file.

  4. Resi - The residue to which the atom belongs.

  5. Chain - The chain to which the residue belongs.

  6. Resi_Seq - The sequence number of the residue.

  7. Cx - The x-coordinate of the atom in the grid w.r.t origin.

  8. Cy - The y-coordinate of the atom in the grid w.r.t origin.

  9. Cz - The z-coordinate of the atom in the grid w.r.t origin.

  10. Q - The estimated charge of the atom.

  11. R - The radius of the atom.

  12. X - The grid position of the atom in x-direction w.r.t (0,0,0). Always integer.

  13. Y - The grid position of the atom in y-direction w.r.t (0,0,0). Always integer.

  14. Z - The grid position of the atom in z-direction w.r.t (0,0,0). Always integer.

  15. Ex - The electric field in x-direction at the atom.

  16. Ey - The electric field in y-direction at the atom.

  17. Ez - The electric field in z-direction at the atom.

  18. Potential - The potential value of the atom.

You can use this data for further analysis or for plotting graphs.

[!Important] This file is generated in the .bept directory present in your current working directory.

Format of .bept

The .bept file is a simple text file which contains a HEADER containing some metadata which are -

  1. Protein Structure Name - Path of input PDB file.

  2. The origin coordinates of the structure - Extracted from the PDB file.

  3. Grid size(x, y, z) of structure - which encloses the protein structure.

  4. Grid length of the box (hx, hy, hz) - The length of 1 unit along (x, y, z) respectively.

  5. The paths of reference PQR and Potential DX file inputted.

The .bept file is simply a tabulated neat looking representation of the .csv file.

[!Important] This file will be generated in your current working directory.

Further analysis and generation of other files

Bept currently supports production of the following file types other than mentioned above -

  1. .xyz - File containing the coordinates of the atoms in the structure.

  1. .cube - File containing the potential values of the atoms in the structure.

You can interactively select which file types to generate by using the interactive or -i flag as follows -

  1. Surface Residues data with their potential values.

Bept provides a list of surface residues in the protein along with their Potential value, using biopython library. The potential value used here is extracted from the bept.csv file generated.

V = Sum of potential of atoms on residue / Number of atoms in residue

[!Important] The data is written in a .csv file stored in the .bept directory as well as a well tabulated protein_surface_data.txt file too.

  1. SASA - Solvent Accessible Surface Area for protein.

Bept calculates the SASA value for the protein structure and prints to the terminal. To know more into how SASA values is calculated, check out the SASA Calculation documentation on our repository.

[!Note] For generation 3 and 4, PDB file paths is necessary.

Usage

The out command has -d and -q as required flags for providing potential .dx and .pqr file respectively. Optionally (and recommended) is to add -p path for providing the .pdb file.

bept out -q /path/to/pqr_file -d /path/to/dx_file -i

To generate all supported files, use the -all | --all-types flag for the same.

bept out -q /path/to/pqr_file -d /path/to/dx_file -p /path/to/pdb_file -all

You can also specify the output path of the files by using the -o flag as follows -

bept out -q /path/to/pqr_file -d /path/to/dx_file -o /path/to/output/directory

The output files will be generated in the specified directory, please do not provide a file name for output path.