Rotamer information from pose

Thank you so much for your kindly providing this information. Basically I would like to know the index of the rotamer in the Dunbrack library for a particular residue in a packed protein pose in PyRosetta. The function or method rotamer_from_chi is defined as: void core::pack::dunbrack::rotamer_from_chi (chemical::ResidueType const & rsd_type, ChiVector const & chi,RotVector & rot). In the function rotamer_from_chi which has three inputs, what is the first input “ResidueType”? Is it the amino acid type? So can I give a string ‘M’ or ‘MET’ as the first input? I know how to get the chi angle using the pose.chi(1,7) for getting the chi angle for residue 7 in chain 1 in the pose. Finally, the last input is RotVector, which is a list. Can I just define an empty list rotv = list()? I am getting an error in my code in the iPyRosetta command line below:

In [1]: import rosetta

In [2]: import rosetta.core.pack.task

In [3]: from rosetta import *

In [4]: init()
PYROSETTA_DATABASE environment variable was set to: /home/ayushgoyal/Code/PyRosetta.Ubuntu-12.04LTS-r55722.64Bit/rosetta_database; using it….
PyRosetta 3.4.0 [Rosetta-3.4 55721:55721:812a1e7baefddf32ce551097c8aabf494e5983a2] retrieved from:
(C) Copyright Rosetta Commons Member Institutions.
Created in JHU by Sergey Lyskov and PyRosetta Team.

core.init: Rosetta version from
core.init: command: PyRosetta -ex1 -ex2aro -database /home/ayushgoyal/Code/PyRosetta.Ubuntu-12.04LTS-r55722.64Bit/rosetta_database
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-41651338 seed_offset=0 real_seed=-41651338
core.init.random: RandomGenerator:init: Normal mode, seed=-41651338 RG_type=mt19937

In [5]: native_pdb = ‘/home/ayushgoyal/Proteins/1PGA/1PGA.pdb’

In [6]: native_pose = Pose()

In [7]: pose_from_pdb(native_pose, native_pdb);
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 9172 residue types
core.pack.task: Packer task: initialize from command line()

In [8]: native_pose.chi(1,7)
Out[8]: -55.53287780791491

In [9]: native_pose.residue_type(7)
Out[9]:

In [10]: from rosetta.core.pack.dunbrack import *

In [11]: rotv = list()

In [12]: rotamer_from_chi(native_pose.residue_type(7),native_pose.chi(1,7),rotv)

---

ArgumentError Traceback (most recent call last)
in ()
—-> 1 rotamer_from_chi(native_pose.residue_type(7),native_pose.chi(1,7),rotv)

ArgumentError: Python argument types in
rosetta.core.pack.dunbrack.__dunbrack_all_at_once_.rotamer_from_chi(ResidueType, float, list)
did not match C++ signature:
rotamer_from_chi(core::conformation::Residue rsd, utility::vector1 > {lvalue} rot)
rotamer_from_chi(core::chemical::ResidueType rsd_type, utility::vector1 > chi, utility::vector1 > {lvalue} rot)

Thank you again so much rmoretti for your kind help. For residue 1 in the pose created from the 1PGA.pdb, I got the Chi angles as [-68.3503, 176.299, 151.646, ] and the rotamer vector as [3, 2, 2, ]. For residue 2, I got the Chi angles are [-58.6313, 3.4e-05, ] and rotamer vector as [3, 0, ]. I was wondering how there could be more than one rotamer or conformational isomerism for a given residue? I am getting as many rotamers as the chi angles? Or does the rotamer vector of [3,2,2] define the rotamer?

I have written the following script GetRotamer.py to print the rotamer of a particular residue in a pose:

import rosetta
import rosetta.core.pack.task
from rosetta import *
from rosetta.core.pack.dunbrack import *

init()

native_pose = Pose()
native_pdb = ‘/home/ayushgoyal/Proteins/1PGA/1PGA.pdb’
pose_from_pdb(native_pose, native_pdb);

residue_number = 1;
residueType = native_pose.residue_type(residue_number);
angles = native_pose.residue(residue_number).chi();
rotv = rosetta.utility.vector1_Size();
rotamer_from_chi(residueType,angles,rotv)

print ‘nChi angles are ‘, angles
print ‘nRotamer vectors are ‘, rotv

When I ran this script, the output was as follows:

In [3]: run GetRotamer.py
PYROSETTA_DATABASE environment variable was set to: /home/ayushgoyal/Code/PyRosetta.Ubuntu-12.04LTS-r55722.64Bit/rosetta_database; using it….
PyRosetta 3.4.0 [Rosetta-3.4 55721:55721:812a1e7baefddf32ce551097c8aabf494e5983a2] retrieved from:
(C) Copyright Rosetta Commons Member Institutions.
Created in JHU by Sergey Lyskov and PyRosetta Team.

core.init: Rosetta version from
core.init: command: PyRosetta -ex1 -ex2aro -database /home/ayushgoyal/Code/PyRosetta.Ubuntu-12.04LTS-r55722.64Bit/rosetta_database
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1906108914 seed_offset=0 real_seed=1906108914
core.init.random: RandomGenerator:init: Normal mode, seed=1906108914 RG_type=mt19937
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 9172 residue types
core.pack.task: Packer task: initialize from command line()
core.pack.dunbrack: Dunbrack 2010 library took 0.1 seconds to load from binary

Chi angles are [-68.3503, 176.299, 151.646, ]

Rotamer vectors are [3, 2, 2, ]

I was wondering how there could be more than one rotamer or conformational isomerism for a given residue?

Thank you so much for your kind advice. The reason I wanted to know the rotamers for a residue is so I could calculate the self-energies and the table of pairwise energies between rotamers of mutable (molten or changeable) residues in a side-chain packing problem and redesign problem. I basically am trying to figure out how to get the tables of pairwise rotamer-to-rotamer energies between mutable residues. I want the pairwise rotamer-to-rotamer energy table between mutable residues where the residue can change to all possible amino acid types and thus all possible rotamers of all possible amino acid types. I want to include all rotamers of all possible amino acid types in the mutable residues because I am trying to extend the side chain packing (only rotamers of a single amino acid type allowed) to redesign (all rotamers of all amino acid types allowed). I am modifying code from Jason Pacheco of Brown University (I changed the rotamer_set_for_moltenresidue function to FixbbRotamerSets function to try to include all rotamers of all amino acid types but it is giving the following error – AttributeError: ‘RotamerSets’ object has no attribute ‘FixbbRotamerSets’):

import numpy as np
import optparse # for option sorting
import rosetta
import rosetta.core.pack.task

from rosetta import *
from scipy.sparse import *
from rosetta.core.pack.rotamer_set import *
from rosetta.core.pack import *
from rosetta.core.pack.interaction_graph import *
from rosetta.core.pack.task import * # for using resfiles

init()

## FUNCTIONS ############################################

def get_rotamer_etable( ig, rotsets, moltenresI, moltenresJ ):
“””Computes rotamer-rotamer energy table between two residues.”””

# check edge exists
if not ig.get_edge_exists(moltenresI, moltenresJ):
return None

# get etable
rotsI = rotsets.FixbbRotamerSets()
rotsJ = rotsets.FixbbRotamerSets()
n_rots_I = rotsI.num_rotamers()
n_rots_J = rotsJ.num_rotamers()
E = np.zeros((n_rots_I,n_rots_J))
for s_i in range(1, n_rots_I+1):
for s_j in range(1, n_rots_J+1):
E[s_i-1,s_j-1] = ig.get_two_body_energy_for_edge(moltenresI, moltenresJ, s_i, s_j)
return E

Please kindly guide me.
Thank you so much.