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Residue Pair Energy

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Residue Pair Energy



After protein interface design some of the residues are showing a significant difference In relative residue energy (difference between control and design in REU) . Therefore I wish to know about the residue pair energies and also the atom interaction that is contributing to the change in the total energy of the designed residue at the interface. I am using the following command line in pyrosetta after loading the PDB by the pose


pyrosetta.toolbox.atom_pair_energy.print_residue_pair_energies (50, pose, sfxn='REF2015', score_type="total_score", threshold=0.0)


pyrosetta.toolbox.atom_pair_energy.print_atom_pair_energy_table (sfxn=' REF2015', score_type="total_score", 50, 55, pose, threshold=0.0)


However it is not working. Kindly let me know if at all I am using the correct syntax and if there is another alternative for the same.


I am getting the following error



pyrosetta.toolbox.atom_pair_energy.print_residue_pair_energies (50, pose, sfxn='REF2015', score_type= 'total_score', threshold=0)
AttributeError                            Traceback (most recent call last)
<ipython-input-29-df17b5b63b20> in <module>()
----> 1 pyrosetta.toolbox.atom_pair_energy.print_residue_pair_energies (50, pose, sfxn='REF2015', score_type= 'total_score', threshold=0)

/usr/local/lib/python2.7/dist-packages/pyrosetta-2017-py2.7-linux-x86_64.egg/pyrosetta/toolbox/atom_pair_energy.pyc in print_residue_pair_energies(res, pose, sfxn, score_type, threshold)
    212     """
    213     for res_idx, score in _reisude_pair_energies(
--> 214         res, pose, sfxn, score_type, threshold
    215     ):
    216         print("{0} {1}  {2}".format(pose.residue(res_idx).name1(), res_idx, score))

/usr/local/lib/python2.7/dist-packages/pyrosetta-2017-py2.7-linux-x86_64.egg/pyrosetta/toolbox/atom_pair_energy.pyc in _reisude_pair_energies(res, pose, sfxn, score_type, threshold)
    170             residue i with the user-specified residue, res.
    171     """
--> 172     sfxn.score(pose)
    173     for i in range(1, pose.total_residue() + 1):
    174         emap = rosetta.core.scoring.EMapVector()

AttributeError: 'str' object has no attribute 'score'

Thanking you




Post Situation: 
Thu, 2020-02-13 03:36