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loop_closure.py
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loop_closure.py
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import os
import random
from blueprint import *
from chiralities import codes, chiralities
from filters import check_short_hairpins, check_long_hairpins
from logger import LoggingManager
from protocols import blueprint_hairpins
from pyrosetta import *
pyrosetta.init()
def close_hairpins(initial_backbone, nres1, nres2, code, suffix):
ref_pose = pose_from_pdb(initial_backbone)
bp_hairpins = f"hp_{suffix}.bp"
bp_backbone = f"bb_{suffix}.bp"
log_file = f"sandwich_{suffix}.log"
hairpins = []
log = LoggingManager.get_logger("close_hairpins", file_name=log_file)
log.info("HAIRPINS")
chiral = chiralities[codes.index(code)]
chiral1 = chiral[0]
chiral2 = chiral[1]
chiral3 = chiral[2]
if chiral1 == "R":
lh = 5
abego_string = "BAAGB"
pyrosetta.init("-vall filtered.vall.hp5")
elif chiral1 == "L":
lh = 2
abego_string = None
pyrosetta.init("-vall filtered.vall.hp2")
blueprint_hairpins(nres1, nres2, lh, bp_hairpins, abego_string)
bdr = pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR()
censcorefxn = pyrosetta.create_score_function("fldsgn_cen.wts")
bdr.scorefunction(censcorefxn)
bdr.ss_from_blueprint(True)
bp = Blueprint(bp_hairpins)
if lh == 5:
bp.bp_data[nres1+2][1] = "G"
bp.bp_data[nres1+3][1] = "G"
bp.bp_data[nres1+4][1] = "G"
bp.dump_blueprint(bp_hairpins)
bdr.set_blueprint(bp_hairpins)
for i in range(10):
log.info(f"HAIRPIN_1: TRYING LENGTH {lh}")
idx = nres2
pose1 = ref_pose.clone()
bdr.apply(pose1)
try:
if lh == 5:
check, abego = check_long_hairpins(pose1, idx)
elif lh == 2:
check, abego = check_short_hairpins(pose1, idx)
except:
continue
if check == True:
idx = idx + lh
nres_total = nres1*4 + nres2*3 + lh
log.info(f"HAIRPIN_1: {i+1} ATTEMPTS WITH ABEGO {abego}")
hairpins.append(lh)
break
if pose1.size() == nres_total:
if chiral2 == "R":
lh = 5
abego_string = "BAAGB"
pyrosetta.init("-vall filtered.vall.hp5")
elif chiral2 == "L":
lh = 2
abego_string = None
pyrosetta.init("-vall filtered.vall.hp2")
idx = idx + nres2 + nres1
bdr = pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR()
bdr.scorefunction(censcorefxn)
bdr.ss_from_blueprint(True)
bp = Blueprint(bp_hairpins)
bp.add_loop_between_segments(idx=idx+1, length=lh, abego_string=abego_string)
if lh == 5:
bp.bp_data[idx+2][1] = "G"
bp.bp_data[idx+3][1] = "G"
bp.bp_data[idx+4][1] = "G"
bp.dump_blueprint(bp_hairpins)
bdr.set_blueprint(bp_hairpins)
for i in range(10):
log.info(f"HAIRPIN_2: TRYING LENGTH {lh}")
pose2 = pose1.clone()
bdr.apply(pose2)
try:
if lh == 5:
check, abego = check_long_hairpins(pose2, idx)
elif lh == 2:
check, abego = check_short_hairpins(pose2, idx)
except:
continue
if check == True:
idx = idx + lh
nres_total = nres_total + lh
log.info(f"HAIRPIN_2: {i+1} ATTEMPTS WITH ABEGO {abego}")
hairpins.append(lh)
break
if pose2.size() == nres_total:
if chiral3 == "R":
lh = 5
abego_string = "BAAGB"
pyrosetta.init("-vall filtered.vall.hp5")
elif chiral3 == "L":
lh = 2
abego_string = None
pyrosetta.init("-vall filtered.vall.hp2")
idx = idx + nres1*2 + nres2
bdr = pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR()
bdr.scorefunction(censcorefxn)
bdr.ss_from_blueprint(True)
bp = Blueprint(bp_hairpins)
bp.add_loop_between_segments(idx=idx+1, length=lh, abego_string=abego_string)
if lh == 5:
bp.bp_data[idx+2][1] = "G"
bp.bp_data[idx+3][1] = "G"
bp.bp_data[idx+4][1] = "G"
bp.dump_blueprint(bp_hairpins)
bdr.set_blueprint(bp_hairpins)
for i in range(10):
log.info(f"HAIRPIN_3: TRYING LENGTH {lh}")
pose3 = pose2.clone()
bdr.apply(pose3)
try:
if lh == 5:
check, abego = check_long_hairpins(pose3, idx)
elif lh == 2:
check, abego = check_short_hairpins(pose3, idx)
except:
continue
if check == True:
bp.reindex_blueprint(0)
bp.freeze_all()
bp.bp_data[0][-2] = "R"
bp.bp_data[-1][-2] = "R"
bp.dump_blueprint(bp_backbone)
os.remove(bp_hairpins)
log.info(f"HAIRPIN_3: {i+1} ATTEMPTS WITH ABEGO {abego}")
log.info("HAIRPINS COMPLETED")
hairpins.append(lh)
return pose3, bp_backbone, hairpins
break
def close_arches(pose, nres1, nres2, bp_backbone, suffix):
pyrosetta.init()
nres_total_ref = pose.size()
bp_arch1 = f"ac1_{suffix}.bp"
bp_arch2 = f"ac2_{suffix}.bp"
bp_sandwich = f"sandwich_{suffix}.bp"
log_file = f"sandwich_{suffix}.log"
arches = []
cbreak = pyrosetta.rosetta.protocols.simple_filters.ChainBreak()
log = LoggingManager.get_logger("close_arches", file_name=log_file)
log.info("ARCHES")
for i in range(10):
pose1 = pose.clone()
# ARCH 5-6
bp = Blueprint(bp_backbone)
idx = bp.segment_dict["E3"].bp_data[0][0]+nres1+nres2
l = random.sample([3, 4, 5, 6], 1)[0]
log.info(f"ARCH_5-6: TRYING LENGTH {l}")
bp.add_loop_between_segments(idx=idx, length=l)
bp.dump_blueprint(bp_arch1)
bdr = pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR()
censcorefxn = pyrosetta.create_score_function("fldsgn_cen.wts")
bdr.scorefunction(censcorefxn)
bdr.ss_from_blueprint(True)
bdr.set_blueprint(bp_arch1)
bdr.apply(pose1)
if pose1.size() == nres_total_ref + l:
nres_total = pose1.size()
abego = list(rosetta.core.sequence.get_abego(pose1))[idx:idx+l]
bp.reindex_blueprint(0)
bp.freeze_all()
bp.bp_data[0][-2] = "R"
bp.bp_data[-1][-2] = "R"
bp.dump_blueprint(bp_arch1)
log.info(f"ARCH_5-6: {i+1} ATTEMPTS WITH LENGTH {l} AND ABEGO {abego}")
arches.append(l)
break
elif i == 9:
os.remove(bp_backbone)
os.remove(bp_arch1)
os.remove(bp_arch2)
log.info("ARCHE5_6: FAILED")
if nres_total == nres_total_ref + l:
for i in range(10):
pose2 = pose1.clone()
# MODEL BOTH ARCHES (2-3 / 4-5) AT THE SAME TIME
bp = Blueprint(bp_arch1)
idx = bp.segment_dict["E2"].bp_data[0][0]+nres2
other_idx = bp.segment_dict["E3"].bp_data[0][0]+nres1+l
l = random.sample([3, 4, 5, 6], 1)[0]
other_l = random.sample([3, 4, 5, 6], 1)[0]
log.info(f"ARCH_2-3: TRYING LENGTH {l}")
log.info(f"ARCH_4-5: TRYING LENGTH {other_l}")
bp.add_loop_between_segments(idx=idx, length=l, other_idx=other_idx, other_length=other_l)
bp.dump_blueprint(bp_arch2)
bdr = pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR()
censcorefxn = pyrosetta.create_score_function("fldsgn_cen.wts")
bdr.scorefunction(censcorefxn)
bdr.ss_from_blueprint(True)
bdr.set_blueprint(bp_arch2)
bdr.apply(pose2)
# Apply chain break filter
break_filter = cbreak.report_sm(pose2)
if pose2.size() == nres_total+l+other_l and break_filter == 0.0:
abego = list(rosetta.core.sequence.get_abego(pose2))[idx:idx+l]
other_abego = list(rosetta.core.sequence.get_abego(pose2))[other_idx:other_idx+other_l]
bp.reindex_blueprint(0)
bp.freeze_all()
bp.bp_data[0][-2] = "R"
bp.bp_data[-1][-2] = "R"
bp.dump_blueprint(bp_sandwich)
os.remove(bp_backbone)
os.remove(bp_arch1)
os.remove(bp_arch2)
log.info(f"ARCH_2-3: {i+1} ATTEMPTS WITH LENGTH {l} AND ABEGO {abego}")
log.info(f"ARCH_4-5: {i+1} ATTEMPTS WITH LENGTH {other_l} AND ABEGO {other_abego}")
log.info("ARCHES: COMPLETED")
arches.append(l)
arches.append(other_l)
return pose2, nres_total+l+other_l, arches
break
elif i == 9:
os.remove(bp_backbone)
os.remove(bp_arch1)
os.remove(bp_arch2)
log.info("ARCHES2_3/4_5: FAILED")