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filters.py
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filters.py
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import numpy as np
from pyrosetta import *
pyrosetta.init()
def check_chirality(pose, nres1, nres2, reverse=False):
"Check chiralities of hairpins as defined in Lin. PNAS. 2015"
chiralities = {
"h1": "",
"h2": "",
"h3": ""
}
# Check h1
com1 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, 1, 2)
com2 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, nres2-1, nres2)
u = np.array(com2 - com1)
u = u / np.linalg.norm(u)
com1 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, 1, nres2)
com2 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, nres2+1, nres2*2)
v = np.array(com2 - com1)
v = v / np.linalg.norm(v)
uv = np.cross(u, v)
uv = uv / np.linalg.norm(uv)
ca = pose.residue(1).xyz("CA")
cb = pose.residue(1).xyz("CB")
w = np.array(cb - ca)
w = w / np.linalg.norm(w)
if np.dot(uv,w) > 0:
chiralities["h1"] = "R"
else:
chiralities["h1"] = "L"
# Check h2
com1 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, nres2*2+1, nres2*2+2)
com2 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, nres2*2+nres1-1, nres2*2+nres1)
u = np.array(com2 - com1)
u = u / np.linalg.norm(u)
com1 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, nres2*2+1, nres2*2+nres1)
com2 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, nres2*2+nres1+1, nres2*2+nres1*2)
v = np.array(com2 - com1)
v = v / np.linalg.norm(v)
uv = np.cross(u, v)
uv = uv / np.linalg.norm(uv)
ca = pose.residue(nres2*2+nres1).xyz("CA")
cb = pose.residue(nres2*2+nres1).xyz("CB")
w = np.array(cb - ca)
w = w / np.linalg.norm(w)
if np.dot(uv,w) > 0:
chiralities["h2"] = "R"
else:
chiralities["h2"] = "L"
# Check h3
com1 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, nres2*3+nres1*2+1, nres2*3+nres1*2+2)
com2 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, nres2*3+nres1*3-1, nres2*3+nres1*3)
u = np.array(com2 - com1)
u = u / np.linalg.norm(u)
com1 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, nres2*3+nres1*2+1, nres2*3+nres1*3)
com2 = pyrosetta.rosetta.protocols.geometry.center_of_mass(pose, nres2*3+nres1*3+1, nres2*3+nres1*4)
v = np.array(com2 - com1)
v = v / np.linalg.norm(v)
uv = np.cross(u, v)
uv = uv / np.linalg.norm(uv)
ca = pose.residue(nres2*3+nres1*3).xyz("CA")
cb = pose.residue(nres2*3+nres1*3).xyz("CB")
w = np.array(cb - ca)
w = w / np.linalg.norm(w)
if np.dot(uv,w) > 0:
chiralities["h3"] = "R"
else:
chiralities["h3"] = "L"
return chiralities
def check_short_hairpins(pose, idx):
lh = 2
abego = list(rosetta.core.sequence.get_abego(pose))
aa = ["A", "A"]
bg = ["B", "G"]
ea = ["E", "A"]
gg = ["G", "G"]
h = abego[idx:idx+lh]
if h != aa and h != bg and h != ea and h != gg:
return False
else:
return True, h
def check_long_hairpins(pose, idx):
lh = 5
abego = list(rosetta.core.sequence.get_abego(pose))
aa = ["B", "A", "A", "G", "B"]
h = abego[idx:idx+lh]
if h != aa:
return False
else:
return True, h