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util.py
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util.py
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import numpy as np
from constants import DISTANCE_STRANDS, RESIDUE_LENGTH, CO_BOND, CC_BOND
from functions import caca_vector, co_vector, orientation_vector, rotation_matrix
from pyrosetta import *
pyrosetta.init(silent=True)
def sheet_numbering(parameters):
res_beta = list(list(zip(*parameters))[2])
count = 0
strands = []
for p in parameters:
count += int(p[2])
residues = list(range(1, count+1))
for i in res_beta:
beta = []
for j in range(int(i)):
beta.append(residues[0])
residues.pop(0)
strands.append(beta)
return strands
def beta_strand(strand, phi=-140.0, psi=130.0):
pose = pose_from_sequence(strand)
for uid,i in enumerate(strand):
res_id = uid + 1
# phi = random.uniform(-150.0, -130.0)
# psi = random.uniform(120.0, 140.0)
pose.set_phi(res_id, phi)
pose.set_psi(res_id, psi)
return pose
def parallel_strand(pose, strand, nbeta, nres):
ref_pose = pose.clone()
add_pose = beta_strand(strand)
trans_vector = co_vector(ref_pose)
pyrosetta.bindings.pose.translate(add_pose, trans_vector * (DISTANCE_STRANDS*(nbeta-1)))
pyrosetta.rosetta.core.pose.append_pose_to_pose(pose, add_pose)
return pose
def antiparallel_strand(pose, strand, nbeta, nres, quadruple = True):
length = RESIDUE_LENGTH * nres
ref_pose = beta_strand(strand)
trans_vector = co_vector(ref_pose)
back_vector = caca_vector(ref_pose)
orien_vector = orientation_vector(ref_pose)
rotation = rotation_matrix(trans_vector)
add_pose = beta_strand(strand)
if (nres % 2) == 0:
orien_rotation = rotation_matrix(orien_vector, theta=90)
trans_vector = co_vector(ref_pose)
elif (nres % 2) != 0:
orien_rotation = rotation_matrix(orien_vector, theta=-90)
pyrosetta.bindings.pose.rotate(add_pose, orien_rotation)
pyrosetta.bindings.pose.rotate(add_pose, rotation)
pyrosetta.bindings.pose.translate(add_pose, np.array(back_vector) * length)
pyrosetta.bindings.pose.translate(add_pose, np.array(trans_vector) * (DISTANCE_STRANDS*(nbeta-1)))
pyrosetta.rosetta.core.pose.append_pose_to_pose(pose, add_pose)
return pose
def tidy_pdb(in_pdb, nres1, nres2, ori1, ori2):
chid = "A"
strand1 = list(range(nres2+1))[1:]
strand2 = list(range(strand1[-1]+1, strand1[-1]+1+nres2))
strand3 = list(range(strand2[-1]+1, strand2[-1]+1+nres1))
strand4 = list(range(strand3[-1]+1, strand3[-1]+1+nres1))
strand5 = list(range(strand4[-1]+1, strand4[-1]+1+nres2))
strand6 = list(range(strand5[-1]+1, strand5[-1]+1+nres1))
strand7 = list(range(strand6[-1]+1, strand6[-1]+1+nres1))
topology = [strand7, strand6, strand3, strand4, strand1, strand2, strand5]
topology = [item for sublist in topology for item in sublist]
ini_res = 1
end_res = strand7[-1]
res_lis = list(range(ini_res, end_res+1))
renumbered_lis = []
sorted_lis = []
with open(in_pdb, "r") as inpdb:
for line in inpdb:
for i, resid in enumerate(res_lis):
if line.startswith("ATOM"):
if line[24:26].strip() == str(resid):
renumbered_lis.append(line[:21] + chid + str(topology[i]).rjust(4) + line[26:])
for line in sorted(renumbered_lis, key=lambda line: line[22:26]):
sorted_lis.append(line)
return sorted_lis
def sort_pdb(in_pdb, out_pdb):
with open(in_pdb, "r") as lines:
with open(out_pdb, "w") as outfile:
for line in sorted(lines, key=lambda line: line[22:26]):
outfile.write(line)
def arch_distance(sandwich_pdb):
pose = pose_from_pdb(sandwich_pdb)
xyz_a = pose.residue(18).xyz("C")
xyz_b = pose.residue(19).xyz("N")
d2_3 = math.sqrt(((xyz_b[0]-xyz_a[0])**2 + (xyz_b[1]-xyz_a[1])**2 + (xyz_b[2]-xyz_a[2])**2))
xyz_a = pose.residue(36).xyz("C")
xyz_b = pose.residue(37).xyz("N")
d4_5 = math.sqrt(((xyz_b[0]-xyz_a[0])**2 + (xyz_b[1]-xyz_a[1])**2 + (xyz_b[2]-xyz_a[2])**2))
xyz_a = pose.residue(45).xyz("C")
xyz_b = pose.residue(46).xyz("N")
d5_6 = math.sqrt(((xyz_b[0]-xyz_a[0])**2 + (xyz_b[1]-xyz_a[1])**2 + (xyz_b[2]-xyz_a[2])**2))
return str(round(d2_3,1)), str(round(d4_5,1)), str(round(d5_6,1))
def split(word):
return [char for char in word]