jyesselm/abg

Tools for computing alpha beta gamma euler angles to describe the orientation of RNA motifs.

How to install

python setup.py install

How to compute the euler angles

Should generate the module abg and the script calc_abg

If you only want to compute the alpha beta gamma angles use the script. Use 3 basepairs whenever possible.

# using 3 base pairs above and below the motif of interest
calc_abg -helix_1_res "3,4,5,25,26,27" -helix_2_res "10,11,12,21,22,23" examples/ens-1.pdb

# using 2
calc_abg -helix_1_res "4,5,25,26" -helix_2_res "10,11,22,23" examples/ens-1.pdb

# using 1
calc_abg -helix_1_res "5,25" -helix_2_res "10,23" examples/ens-1.pdb

Output looks like

2022-05-28 19:13:18,043 - abg.main - INFO - residues in helix 1: [3, 4, 5, 25, 26, 27]
2022-05-28 19:13:18,043 - abg.main - INFO - residues in helix 2: [10, 11, 12, 21, 22, 23]
2022-05-28 19:13:18,043 - abg.main - INFO - examples/ens-1.pdb is determined to be in PDB format
   a     b      g    rmsd1    rmsd2      x     y      z
----  ----  -----  -------  -------  -----  ----  -----
68.4  20.1  -19.2     0.44     0.66  -5.65  8.92  -11.5

where rmsd1 and rmsd 2 is how well your bottom and top stem can be overlayed with an idealized helix.

You can also supply a csv file and calculate abg on every pdb in the csv file. Ensure your pdb path is supplied the 'pdb' column

calc_abg -helix_1_res "3,4,5,25,26,27" -helix_2_res "10,11,12,21,22,23" examples/test.csv 

How to call the package in another script

import abg.compute

pdb_path = "examples/ens-1.pdb"
helix_1_resi = [3, 4, 5, 25, 26, 27]
helix_2_resi = [10, 11, 12, 21, 22, 23]

abg_computer = abg.compute.ABGComputer()
r = abg_computer.compute(pdb_path, helix_1_resi, helix_2_resi)

print(r.a, r.b, r.g, r.rmsd1, r.rmsd2, r.x, r.y, r.z)