Error with etable_atom_pair_energies()

[Anonymous]

I am new to Pyrosetta and programing and I am learning how to use Pyrosetta. So when I was practicing scoring with Workshop #3 bullet point 5, I came across a error, and I have no idea what’s wrong with.

Here is what I did. 

r1 = pose.residue(24)

r2 = pose.residue(20)

a1 = r1.atom(“N”)

a2 = r1.atom(“O”)

etable_atom_pair_energies(a1, a2, scorefxn)

And it came out this error:

TypeError: etable_atom_pair_energies() missing 2 required positional arguments: ‘ atom_index_2’ and ‘sfxn’

For line 2 and 3, the book uses ras.residue(), but for some reason it did not work for me but the pose did. 

So from what it looks like I have typed things wrong, and I don’t know what is going on. Can anyone help me with this problem? Thank you all a lot.

 

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Update:

I think I figured out how to use this function. Instead of following the book, I did the following trying to find the attractive energy between the N of residue 24 and O of the residue 20:

etable_atom_pair_energies(r1, a1, r2, a2, fa_atr)

But I came accross another error. 

AttributeError: ‘pyrosetta.rosetta.core.scoring.ScoreTypr’ object has no attribute ‘energy_method_options’

Can anyone help me with this?

 

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Update 2:

I guess I didn’t understand what can be put as sfxn in the function below. Can someone give any examples on what can be input as sfxn?

etable_atom_pair_energies(r1, a1, r2, a2, sfxn)

 

[Anonymous]

#!/usr/bin/env python

#-*- coding: utf-8 -*



from pyrosetta import *

from pyrosetta.teaching import *

from rosetta.core.scoring.hbonds import HBondSet

from pyrosetta.rosetta import core, protocols



init()

pose = pose_from_pdb("6q21.clean.pdb")

fa_scorefxn = get_fa_scorefxn()



## extract atom-pair energy;

r1 = pose.residue(24)

r2 = pose.residue(20)

a1 = r1.atom_index("N")

a2 = r2.atom_index("O")

print etable_atom_pair_energies(r1, a1, r2, a2, fa_scorefxn)

Returns:

tuple: values of the lj_atr, lj_rep, fa_solv, and fa_elec potentials.

see: https://graylab.jhu.edu/PyRosetta.documentation/pyrosetta.toolbox.atom_pair_energy.html?highlight=etable_atom_pair_energies#pyrosetta.toolbox.atom_pair_energy.etable_atom_pair_energies

[Anonymous]

Thank you so much for reply, that really helped. I guess I was really confused on which argument I should put in. Thank you again. 

[Author]

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