pyRIF

Using Rotamer Interaction Fields from RIFGen/Dock in python

Installation

pip install pyRIF

Requirements

PyRosetta installed in python environment
RIFDock for generating RIFs

generating HDF5s of RIFs from RIFGen

include -dump_rifgen_hdf5 in your rifgen.flag file when running RIFGen. this will produce rif.h5 in your output directory. Then run python tools/convert_rif_h5.py rif.h5. This will produce py_rif.h5. This is the HDF5 file that will be needed to initialize RotamerInteractionField(). You will also need the path to the rotamer_index_spec.txt and target.pdb.gz created by RIFGen. These will be in the output directory you specified in rifgen.flag.

Pose Example

Moves your input pose into the region of the RIF, by aligning the target_selector residues onto the model specified with L_AA_RIF['target']

import glob
import pyrosetta
from pyrosetta.rosetta.core.select.residue_selector import ChainSelector

from pyRIF import RotamerInteractionField

pyrosetta.init()


# dictionary pointing to RIFGen outputs
L_AA_RIF = {
    'HDF5'   : '/path/to/py_rif.h5',
    'rots'   : '/path/to/rotamer_index_spec.txt',
    'target' : '/path/to/target.pdb.gz',
}


# residue selectors to select target and binder residues
target_selector = ChainSelector('A')
binder_selector = ChainSelector('B')


# create RIF object outside of loop
RIF = RotamerInteractionField(
    L_AA_RIF_kwargs=L_AA_RIF,
    residue_selector=binder_selector,
    target_selector=target_selector,
)

for PDB in glob.iglob('/path/to/pdbs/*.pdb'):
    pose = pyrosetta.io.pose_from_pdb(PDB)

    # apply the RIF
    STATUS, RIF_score, sequence_mapping = RIF.apply(pose)

    if STATUS:
        print(f'pass, {RIF_SCORE}\n{sequence_mapping}')
        # continue with remainder of protocol
    else:
        print('fail')

Numpy Example

Assumes your XYZs are already within the region of the RIF

import glob
import numpy as np
import pyrosetta

from pyRIF import RotamerInteractionField
pyrosetta.init()


# dictionary pointing to RIFGen outputs
L_AA_RIF = {
    'HDF5'   : '/path/to/py_rif.h5',
    'rots'   : '/path/to/rotamer_index_spec.txt',
    'target' : '/path/to/target.pdb.gz',
}


# create RIF object outside of loop
RIF = RotamerInteractionField(
    L_AA_RIF_kwargs=L_AA_RIF,
)

binder_xyzs = np.random.rand(1000, 100, 3, 3)# [(1000 proteins), (100 residues), (N CA C), (X Y Z)]

for i in range(binder_xyzs.shape[0]):

    STATUS, RIF_score, sequence_mapping = RIF.search_xyzs(binder_xyzs[i, :, :, :])

    if STATUS:
        print(f'pass, {RIF_SCORE}\n{sequence_mapping}')
        # continue with remainder of protocol
    else:
        print('fail')

Note about packing

Right now, packing is done by first pruning rotamers at a hit where the rotamer clashes in a voxel grid with the N CA C atoms of the binder (semi-equivalent to 1-body). Each pair of pruned rotamers at position i and j are then clashed checked against one another in the same voxel grid (semi-equivalent to 2-body). The lowest RIF_score set of rotamers at each hit position that survives these voxel clash checks is taken as the output sequence, and the sum of their RIF_scores is the output RIF_score for this pose/xyzs. This score is not the same as the RIF_score output by RIFDock.

Note about homog

If you are getting an error on import pyRIF, this is due to a bug in the package homog. See this pull-request for the fix. In short, on line 11 of homog/util.py change nopython=1, fastmath=1 to nopython=True, fastmath=True.