Command line usage

Run isopeptide bond prediction from command line.

Usage

Example:

$ isopeptor tests/data/test_structures/

protein_name        probability     chain   r1_bond r_cat   r2_bond r1_bond_name    r_cat_name      r2_bond_name    bond_type       rmsd    r_asa   template
8beg                0.987           A       590     636     729     LYS             ASP             ASN             CnaA-like       0.0     0.004   8beg_A_590_636_729
8beg                0.987           A       756     806     894     LYS             ASP             ASN             CnaA-like       0.0     0.028   8beg_A_756_806_894
8beg                0.987           A       922     973     1049    LYS             ASP             ASN             CnaA-like       0.0     0.015   8beg_A_922_973_1049
8beg                0.987           A       1076    1123    1211    LYS             ASP             ASN             CnaA-like       0.0     0.015   8beg_A_1076_1123_1211
7woi                0.987           A       57      158     195     LYS             GLU             ASN             CnaB-like       0.001   0.019   7woi_A_57_158_195
7woi                0.987           A       203     246     318     LYS             ASP             ASN             CnaA-like       0.0     0.012   7woi_A_203_246_318
5dz9                0.987           A       556     606     703     LYS             ASP             ASN             CnaA-like       0.0     0.009   4z1p_A_3_53_150
5dz9                0.987           A       730     776     861     LYS             ASP             ASN             CnaA-like       0.0     0.019   4z1p_A_177_223_308
4z1p                0.987           A       3       53      150     LYS             ASP             ASN             CnaA-like       0.0     0.009   4z1p_A_3_53_150
4z1p                0.987           A       177     223     308     LYS             ASP             ASN             CnaA-like       0.0     0.019   4z1p_A_177_223_308
6to1_af             0.505           A       13      334     420     LYS             ASP             ASN             CnaA-like       0.548   0.002   4uzg_A_187_225_330

To redirect the output to a .tsv file use:

$ isopeptor tests/data/test_structures/ > output.tsv

Full command line options are:

$ isopeptor -h

usage: isopeptor [-h] [--distance DISTANCE] [--fixed_r_asa FIXED_R_ASA] [--eval_geometry] path_to_structure_files

Run isopeptide bond prediction from command line. Usage: isopeptor path/to pdb files/ > isopeptide_bonds.csv

positional arguments:
path_to_structure_files
                        Path to directory containing .pdb/.cif files.

options:
-h, --help            show this help message and exit
--distance DISTANCE   Specifies permissivity of jess search. The higher, the more permissive.
--fixed_r_asa FIXED_R_ASA
                        Fixes the relative solvent accessible area using a value between 0 and 1 to speed up the prediction.
--eval_geometry       Run geometric evaluation of isopeptide bonds.

Note

Specifying –fixed_r_asa with a relative solvent accessibile area between 0 and 1 allows skipping this time-consuming calculation. The downside of it is that the prediction is less reliable. It is useful for very high throughput screenings where high precision is not required.

Note

To run a geometric evaluation use the –eval_geometry flag. This will report bond length, dihedral angles (pseudo-psi,phi and psi) and statistical measures. See the workflow:Geometric evaluation section for more information.