def refine(atmsel): # at T=1000, max_atom_shift for 4fs is cca 0.15 A. md = molecular_dynamics(cap_atom_shift=0.39, md_time_step=4.0, md_return='FINAL') init_vel = True for (its, equil, temps) in ((200, 20, (150.0, 250.0, 400.0, 700.0, 1000.0)), (200, 600, (1000.0, 800.0, 600.0, 500.0, 400.0, 300.0))): for temp in temps: md.optimize(atmsel, init_velocities=init_vel, temperature=temp, max_iterations=its, equilibrate=equil) init_vel = False
def Optimizemodel(pdb_file):
"""
This functions returns a file with the optimized model from the input pdb.
It also returns the energies.
"""
env = environ()
env.io.atom_files_directory = ['../atom_files']
env.edat.dynamic_sphere = True
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
code, ext = pdb_file.split('.')
mdl = complete_pdb(env, pdb_file)
mdl.write(file=code + '.ini')
# Select all atoms:
atmsel = selection(mdl)
mpdf2 = atmsel.energy()
# Generate the restraints:
#mdl.restraints.make(atmsel, restraint_type='improper', spline_on_site=False)
#mdl.restraints.make(atmsel, restraint_type='bond', spline_on_site=False)
#mdl.restraints.make(atmsel, restraint_type='sphere', spline_on_site=False)
mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False)
mdl.restraints.write(file=code + '.rsr')
mpdf1 = atmsel.energy()
# Create optimizer objects and set defaults for all further optimizations
cg = conjugate_gradients(output='REPORT')
md = molecular_dynamics(output='REPORT')
# Open a file to get basic stats on each optimization
trcfil = open(code + '.D00000001', 'w')
# Run CG on the all-atom selection; write stats every 5 steps
cg.optimize(atmsel, max_iterations=20, actions=actions.trace(5, trcfil))
# Run MD; write out a PDB structure (called '1fas.D9999xxxx.pdb') every
# 10 steps during the run, and write stats every 10 steps
md.optimize(atmsel,
temperature=300,
max_iterations=50,
actions=[
actions.write_structure(10, code + '.D9999%04d.pdb'),
actions.trace(10, trcfil)
])
#refine(atmsel, code, trcfil)
# Finish off with some more CG, and write stats every 5 steps
cg.optimize(atmsel, max_iterations=20, actions=[actions.trace(5, trcfil)])
mpdf = atmsel.energy()
print("The initial energy of " + code + " is " + str(mpdf1[0]))
print("The final energy of " + code + " is " + str(mpdf[0]))
print("The final energy of " + code + " is " + str(mpdf2[0]))
mdl.write(file=code + '_optimized.pdb')
def refine(atmsel):
# at T=1000, max_atom_shift for 4fs is cca 0.15 A.
md = molecular_dynamics(cap_atom_shift=0.39, md_time_step=4.0,
md_return='FINAL')
init_vel = True
for (its, equil, temps) in ((200, 20, (150.0, 250.0, 400.0, 700.0, 1000.0)),
(200, 600,
(1000.0, 800.0, 600.0, 500.0, 400.0, 300.0))):
for temp in temps:
md.optimize(atmsel, init_velocities=init_vel, temperature=temp,
max_iterations=its, equilibrate=equil)
init_vel = False
def Optimizemodel(pdb_file, optimize):
print("Calculating the energy of the model...")
output_path_optimized = "/".join(pdb_file.split('/')[:-1])
sys.stdout = open(os.devnull, 'w')
env = environ()
env.io.atom_files_directory = ['../atom_files']
env.edat.dynamic_sphere = True
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
filename = pdb_file.split("/")[-1]
code = filename.split('.')[0]
mdl = complete_pdb(env, pdb_file)
mdl.write(file=output_path_optimized + "/" + code + '.ini')
# Select all atoms:
atmsel = selection(mdl)
mpdf2 = atmsel.energy()
sys.stdout = sys.__stdout__
if optimize:
print('Optimizing the model...')
sys.stdout = open(os.devnull, 'w')
# Generate the restraints:
mdl.restraints.make(atmsel,
restraint_type='stereo',
spline_on_site=False)
mdl.restraints.write(file=output_path_optimized + "/" + code + '.rsr')
# Create optimizer objects and set defaults for all further optimizations
cg = conjugate_gradients(output='REPORT')
md = molecular_dynamics(output='REPORT')
# Run CG on the all-atom selection
cg.optimize(atmsel, max_iterations=20)
# Run MD
md.optimize(atmsel, temperature=300, max_iterations=50)
# Finish off with some more CG
cg.optimize(atmsel, max_iterations=20)
mpdf = atmsel.energy()
# Create .pdb
mdl.write(file=output_path_optimized + "/" + code + '_optimized.pdb')
# Remove interdmediate files
os.remove(output_path_optimized + "/" + code + ".ini")
os.remove(output_path_optimized + "/" + code + ".rsr")
sys.stdout = sys.__stdout__
return mpdf2[0], mpdf[0]
else:
os.remove(output_path_optimized + "/" + code + '.ini')
return mpdf2[0]
def sgmdrefine(atmsel, actions, cap, timestep, equil_its, equil_equil,
equil_temps, sampl_its, sampl_equil, sampl_temps):
from modeller.optimizers import molecular_dynamics
mdl = atmsel.get_model()
md = molecular_dynamics(cap_atom_shift=cap, md_time_step=timestep,
md_return='FINAL', output=mdl.optimize_output,
actions=actions,friction=0,guide_factor=0,guide_time=0)
init_vel = True
# First run for equilibration, the second for sampling:
for (its, equil, temps) in ((equil_its, equil_equil, equil_temps),(sampl_its, sampl_equil, sampl_temps)):
for temp in temps:
md.optimize(atmsel, max_iterations=its, equilibrate=equil,
temperature=temp, init_velocities=init_vel)
init_vel=False
def optimize(directory, number):
log.none()
env = environ()
env.io.atom_files_directory = ['../atom_files']
env.edat.dynamic_sphere = True
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
filename = directory + "/model_" + str(number) + ".pdb"
#read model files
code = directory + "/model_" + str(number)
mdl = complete_pdb(env, filename)
# Select all atoms:
atmsel = selection(mdl)
# Generate the restraints:
mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False)
# Create optimizer objects and set defaults for all further optimizations
cg = conjugate_gradients(output='NO_REPORT')
md = molecular_dynamics(output='NO_REPORT')
if not os.path.exists(directory + '/optimization_stats'):
os.makedirs(directory + '/optimization_stats')
# Open a file to get basic stats on each optimization
trcfil = open(
directory + '/optimization_stats/model_' + str(number) + '.D00000001',
'w')
# Run CG on the all-atom selection; write stats every 5 steps
cg.optimize(atmsel, max_iterations=20, actions=actions.trace(5, trcfil))
# Run MD; write out a PDB structure (called '1fas.D9999xxxx.pdb') every
# 10 steps during the run, and write stats every 10 steps
md.optimize(atmsel,
temperature=300,
max_iterations=50,
actions=[actions.trace(10, trcfil)])
# Finish off with some more CG, and write stats every 5 steps
cg.optimize(atmsel, max_iterations=20, actions=[actions.trace(5, trcfil)])
#mpdf = atmsel.energy()
mdl.write(file=code + '.pdb')
def optimize(pdb, pdb_path):
print(1, pdb_path)
# Environ data
env = environ(0)
env.io.atom_files_directory = ['../atom_files']
env.edat.dynamic_sphere = True
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
code = pdb.split('.')[0]
mdl = complete_pdb(env, pdb)
mdl.write(file=code+'.ini')
# Select all atoms:
atmsel = selection(mdl)
# Generate the restraints:
mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False)
mdl.restraints.write(file=code+'.rsr')
mpdf_prior = atmsel.energy()
# Create optimizer objects and set defaults for all further optimizations
cg = conjugate_gradients(output='REPORT')
md = molecular_dynamics(output='REPORT')
# Open a file to get basic stats on each optimization
trcfil = open(code+'.D00000001', 'w')
# Run CG on the all-atom selection; write stats every 5 steps
cg.optimize(atmsel, max_iterations=20, actions=actions.trace(5, trcfil))
# Run MD; write out a PDB structure (called '1fas.D9999xxxx.pdb') every
# 10 steps during the run, and write stats every 10 steps
md.optimize(atmsel, temperature=300, max_iterations=50,
actions=[actions.write_structure(10, code+'.D9999%04d.pdb'),
actions.trace(10, trcfil)])
# Finish off with some more CG, and write stats every 5 steps
cg.optimize(atmsel, max_iterations=20,
actions=[actions.trace(5, trcfil)])
mpdf_after = atmsel.energy()
mdl.write(file=os.path.join(pdb_path, 'optimized.pdb'))
return (mpdf_prior, mpdf_after)
def refine(atmsel):
# at T=1000, max_atom_shift for 4fs is cca 0.15 A.
md = molecular_dynamics(
cap_atom_shift=0.39,
md_time_step=
4.0, ## cap_atom_shifts limita a distância (A) de movimento ao longo de um eixo
md_return='FINAL'
) ## estrutura final pode não ser a mínima de toda a trajectória - 'MINIMAL'
init_vel = True
for (its, equil,
temps) in ((200, 20, (150.0, 250.0, 400.0, 700.0, 1000.0)),
(200, 600, (1000.0, 800.0, 600.0, 500.0, 400.0, 300.0))):
for temp in temps:
md.optimize(
atmsel,
init_velocities=init_vel,
temperature=temp,
max_iterations=its,
equilibrate=equil
) ## equilibrate = re-escalonamento das velocidades após equil passos (200 < 600???)
init_vel = False ## usa as mesmas velocidades da corrida anterior
code = '1fas'
mdl = complete_pdb(env, code)
mdl.write(file=code+'.ini')
# Select all atoms:
atmsel = selection(mdl)
# Generate the restraints:
mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False)
mdl.restraints.write(file=code+'.rsr')
mpdf = atmsel.energy()
# Create optimizer objects and set defaults for all further optimizations
cg = conjugate_gradients(output='REPORT')
md = molecular_dynamics(output='REPORT')
# Open a file to get basic stats on each optimization
trcfil = file(code+'.D00000001', 'w')
# Run CG on the all-atom selection; write stats every 5 steps
cg.optimize(atmsel, max_iterations=20, actions=actions.trace(5, trcfil))
# Run MD; write out a PDB structure (called '1fas.D9999xxxx.pdb') every
# 10 steps during the run, and write stats every 10 steps
md.optimize(atmsel, temperature=300, max_iterations=50,
actions=[actions.write_structure(10, code+'.D9999%04d.pdb'),
actions.trace(10, trcfil)])
# Finish off with some more CG, and write stats every 5 steps
cg.optimize(atmsel, max_iterations=20,
actions=[actions.trace(5, trcfil)])
dih_lib_only=True)
mdl.restraints.make(all_atoms, aln=aln,
restraint_type='PHI_DIHEDRAL',spline_on_site=True,
dih_lib_only=True)
mdl.restraints.make(all_atoms, aln=aln,
restraint_type='PSI_DIHEDRAL',spline_on_site=True,
dih_lib_only=True)
mdl.restraints.condense()
# energy data
env.edat.dynamic_lennard = True
# Prepare optimizer
scaling_factors = physical.values(default=1.0, em_density=0)
MD = molecular_dynamics(output='REPORT',cap_atom_shift=0.0001,
md_time_step=0.05,temperature=params.temperature,
init_velocities=True,md_return=params.md_return,
equilibrate = params.equilibrate,
schedule_scale=scaling_factors)
w=actions.write_structure(params.skip_its_for_writing, 'md-%03d.pdb',
write_all_atoms=True, first=True, last=True, start=0)
# optimize
MD.optimize(all_atoms, max_iterations=params.max_iterations,actions=[w])
for c in mdl.chains:
c.name = 'A'
mdl.remark =""
mdl.reorder_atoms()
mdl.write(params.output_pdb_file, model_format='PDB')
# Generate two copies of a segment:
mdl = complete_pdb(env, '2abx', model_segment=('1:A', '74:B'))
mdl.rename_segments(segment_ids=('A', 'B'), renumber_residues=(1, 1))
myedat = energy_data(dynamic_sphere=False)
atmsel = selection(mdl)
atmsel.energy(edat=myedat)
atmsel.randomize_xyz(deviation=6.0)
# Define the two segments (chains in this case) to be identical:
defsym(mdl, seg1=('1:A', '74:A'), seg2=('1:B', '74:B'))
# Create optimizer objects
cg = conjugate_gradients()
md = molecular_dynamics(md_return='FINAL')
# Make them identical by optimizing the initial randomized structure
# without any other restraints:
atmsel.energy(edat=myedat)
mdl.write(file='define_symmetry-1.atm')
cg.optimize(atmsel, max_iterations=300, edat=myedat)
mdl.write(file='define_symmetry-2.atm')
atmsel.energy(edat=myedat)
# Now optimize with stereochemical restraints so that the
# result is not so distorted a structure (still distorted
# because optimization is not thorough):
myedat.dynamic_sphere = True
mdl.restraints.make(atmsel,
restraint_type='stereo',
def run(self):
int_seed=randint(0,2**8)
env = environ(rand_seed=int_seed)
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
###################### reading the density ######################
den = density(env, file=self.path + '/' + self.em_map_file,
em_density_format=self.format, em_map_size=self.box_size,
density_type='GAUSS', voxel_size=self.apix,
resolution=self.res,px=self.x,py=self.y,pz=self.z)
env.edat.density = den
env.edat.dynamic_sphere = True
###################### read pdb file ######################
aln = alignment(env)
mdl2 = model(env, file=self.input_pdb_file)
aln.append_model(mdl2, align_codes=self.input_pdb_file,
atom_files=self.input_pdb_file)
mdl = model(env, file=self.input_pdb_file)
aln.append_model(mdl, align_codes=self.code, atom_files=self.code)
aln.align(gap_penalties_1d=(-600, -400))
mdl.clear_topology()
mdl.generate_topology(aln[self.input_pdb_file])
mdl.transfer_xyz(aln)
mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')
####################### Remove chain names ######################
for c in mdl.chains:
c.name = ' '
mdl.write(file=self.code+'_ini.pdb')
###################### Select the mobile atoms ######################
sel_all = selection(mdl)
sel_fixed=[]
if(self.fixed_filename!=''):
# read the list of fixed residues
read_selection_list(self.path,mdl,sel_fixed,self.fixed_filename)
# select the non fixed, those ones that are going to be optimized
mobile_atoms = []
for n in sel_all:
mobile =True
for m in sel_fixed:
if n in m:
mobile=False
break
if mobile:
mobile_atoms.append(n)
# print "mobile atom ..",n
print "number of mobile atoms ..",len(mobile_atoms)
sel_mobile=selection(mobile_atoms) # selection of mobile residues
###################### RESTRAINTS FOR MOBILE ATOMS ############
# STEREOCHEMICAL restraints (based on the model)
mdl.restraints.make(sel_mobile, restraint_type='STEREO',
spline_on_site=False)
# MAINCHAIN homology restraints forcing to look in the library
# (dih_lib_only = True) and ignore the template.
mdl.restraints.make(sel_mobile, aln=aln,
restraint_type='PHI-PSI_BINORMAL',spline_on_site=True,
dih_lib_only=True)
mdl.restraints.make(sel_mobile, aln=aln,
restraint_type='OMEGA_DIHEDRAL',spline_on_site=True,
dih_lib_only=True)
# SIDECHAIN homology restraints forcing to look in the library
# (dih_lib_only = True) and ignore the template.
mdl.restraints.make(sel_mobile, aln=aln,
restraint_type='CHI1_DIHEDRAL',spline_on_site=True,
dih_lib_only=True)
mdl.restraints.make(sel_mobile, aln=aln,
restraint_type='CHI2_DIHEDRAL',spline_on_site=True,
dih_lib_only=True)
###################### define rigid bodies ######################
sel_rigid=[]
rand_rigid=[]
if(self.rigid_filename != ''):
load_rigid(self.path,mdl,sel_rigid,rand_rigid,self.rigid_filename)
for n in sel_rigid:
include_it=True
# Only add not fixed rigid bodies. Adding fixed ones is superfluous
for m in sel_fixed:
if(n in m):
include_it=False
break
if(include_it):
print "Considering rigid body ...",n
# for at in n:
# print "atom ...",at
mdl.restraints.rigid_bodies.append(rigid_body(n))
# Remove duplicated restraints
mdl.restraints.unpick_redundant()
# Write all the restraints to a file
mdl.restraints.write(file=self.code+'.rsr')
###################### MOLECULAR DYNAMICS ANNEALING ################
print "MD annealing"
scal_for_annealing = physical.values(default=1.0, em_density=10000)
cap=0.39
timestep=5.0
icount=0
trc_file = open('MD'+self.run_num+'.trc', "a")
###################### loop for number of cycles
a,b = 1,self.cycles
while a <= b:
equil_its=self.equil_its_for_heating
equil_equil=20
equil_temps= self.equil_temps_for_heating
trc_step=5
init_vel = True
# during heating simulations, FINAL structure is always returned.
# If the MINIMAL would be returned, no heating would be achieved.
MD = molecular_dynamics(cap_atom_shift=cap, md_time_step=timestep,
md_return='FINAL', output='REPORT',
schedule_scale=scal_for_annealing)
###################### heating the system
for (its, equil, temps) in [(equil_its, equil_equil, equil_temps)]:
for temp in temps:
# optimize the mobile atoms
MD.optimize(sel_mobile, max_iterations=its,
temperature=temp, init_velocities=init_vel,
equilibrate=equil,
actions=[actions.trace(trc_step,trc_file)])
# print progress
scal = physical.values(default=0.0, em_density=1.0)
(molpdf, terms) = sel_all.energy(schedule_scale=scal)
print "HEATING: iteration number= %s step= %d %d "\
"temp= %d EM score= %.3f" %(a,icount,its,int(temp),-molpdf)
icount=icount+equil_its
init_vel=False
###################### cooling the system
equil_its=self.equil_its_for_cooling
equil_temps= self.equil_temps_for_cooling
# during the cooling MD simulations the structure returned can be
# FINAL or MINIMAL acording to the option selected
MD = molecular_dynamics(cap_atom_shift=cap, md_time_step=timestep,
md_return=self.md_return, output='REPORT',
schedule_scale=scal_for_annealing)
for (its, equil, temps) in [(equil_its, equil_equil, equil_temps)]:
for temp in temps:
MD.optimize(sel_mobile, max_iterations=its,
temperature=temp, init_velocities=init_vel,
equilibrate=equil,
actions=[actions.trace(trc_step,trc_file)])
scal = physical.values(default=0.0, em_density=1.0)
(molpdf, terms) = sel_all.energy(schedule_scale=scal)
print "COOLING: iteration number= %s step= %d %d " \
"temp= %d EM score= %.3f" %(a,icount,its,int(temp),-molpdf)
icount=icount+equil_its
filename='md'+self.run_num+'_'+str(a)+'.pdb'
sel_all.write(file=filename)
a+=1
trc_file.close()
print "MD FINAL: step= %d: energy all (with scaling 1:10000)" % icount
eval = sel_all.energy(schedule_scale=scal_for_annealing)
################## final minimization with and without CC restraints.
################## Optimize all atoms for refinement
CG = conjugate_gradients()
print " final conjugate_gradients"
CG.optimize(sel_all, output='REPORT', max_iterations=200,
schedule_scale=scal_for_annealing)
eval = sel_all.energy(schedule_scale=scal_for_annealing)
scal = physical.values(default=1.0, em_density=0.0)
CG.optimize(sel_all, output='REPORT', max_iterations=200,
schedule_scale=scal)
eval = sel_all.energy(schedule_scale=scal)
sel_all.write(file='final'+self.run_num+'_mdcg.pdb')
os.system("rm -f *.MRC")
def Optimizemodel(pdb_file):
"""
It creates a PDB file with the optimized model from the input pdb,
with its energies and restraint contributions. Also it will create pdbs on
every step of the Molecular Dynamics optimization. The energy is returned as
the total value of Modeller's objective function, molpdf.
It also shows the topt 10 contributors to the molpdf before and after optimization
"""
# Setting up
env = environ()
env.io.atom_files_directory = ['../atom_files']
env.edat.dynamic_sphere = True
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
code, ext = pdb_file.split('.')
# Complete the pdb and make a model
mdl = complete_pdb(env, pdb_file)
mdl.write(file=code + '.ini')
# Select all atoms from the model, make restraints and save them in a file
atmsel = selection(mdl)
mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False)
mdl.restraints.write(file=code + '.rsr')
# Check the energy before optimization and save it in a var
initial_mpdf = atmsel.energy()
# Create optimizer objects
cg = conjugate_gradients(output='REPORT')
md = molecular_dynamics(output='REPORT')
# Open a file to get basic stats on each optimization
stats_file = open(code + '_opt.stats', 'w')
# Run MD. Write out a PDB structure every 10 steps during the run.
# Write stats every 10 steps
md.optimize(atmsel,
temperature=300,
max_iterations=50,
actions=[
actions.write_structure(10, code + '.MD%04d.pdb'),
actions.trace(10, stats_file)
])
# Run CG, and write stats every 5 steps
cg.optimize(atmsel,
max_iterations=50,
actions=[actions.trace(5, stats_file)])
# Final energy
final_mpdf = atmsel.energy()
# Assess DOPE
atmsel.assess_dope(output='ENERGY_PROFILE NO_REPORT',
file='TvLDH.profile',
normalize_profile=True,
smoothing_window=15)
# Print the energies and the contributions
initial_cont_all = dict(initial_mpdf[1])
top_init_conts = dict(
sorted(initial_cont_all.items(), key=itemgetter(1), reverse=True)[:5])
l.info("\n\nThe initial energy of " + code + " is " + str(initial_mpdf[0]))
print("\n\nThe initial energy of " + code + " is " + str(initial_mpdf[0]))
print("The top 10 initial contributions the restraints are:\n")
for keys, values in top_init_conts.items():
print(keys, ":", values)
final_cont_all = dict(final_mpdf[1])
top_final_conts = dict(
sorted(final_cont_all.items(), key=itemgetter(1), reverse=True)[:5])
l.info("\n\nThe final energy of " + code + " is " + str(final_mpdf[0]))
print("\n\nThe final energy of " + code + " is " + str(final_mpdf[0]))
print("Final contributions the restraints are:\n")
for keys, values in top_final_conts.items():
print(keys, ":", values)
mdl.write(file=code + '_optimized.pdb')
def optimization(pdb_file, options):
"""This function needs as an input a PDB file (the model), and gives as an output the optimized model."""
env = environ()
env.io.atom_files_directory = ['../atom_files']
env.edat.dynamic_sphere = True
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
path, ext = pdb_file.split('.')
list = path.split('/')
#if results/4g83/4g83model.pdb list[0]=results list[1]=4g83 list[2]=4g83model
dir = list[0] + "/" + list[1]
code = list[2]
mdl = complete_pdb(env, pdb_file)
mdl.write(file=path + '.ini')
atmsel = selection(mdl)
mpdf_ini = atmsel.energy()
z_score_ini = mdl.assess_normalized_dope()
mdl_ep_ini = atmsel.get_dope_profile()
mdl_ep_ini_smoothed = mdl_ep_ini.get_smoothed()
energy_profile_txt_path = dir + '/' + code + '_DOPE_EnergyProfile.txt'
mdl_ep_ini_smoothed.write_to_file(energy_profile_txt_path)
print("The unoptimized model's energy of " + code + " is: " +
str(mpdf_ini[0]))
print("The unoptimized Z-score of " + code + " is: " + str(z_score_ini))
energy_profile_txt_path_opt = None
if options.optimize:
cg = conjugate_gradients(output='REPORT')
md = molecular_dynamics(output='REPORT')
trcfil = open(path + '.D00000001', 'w')
cg.optimize(atmsel,
max_iterations=20,
actions=actions.trace(5, trcfil))
md.optimize(atmsel,
temperature=300,
max_iterations=50,
actions=[
actions.write_structure(10, path + '.D9999%04d.pdb'),
actions.trace(10, trcfil)
])
cg.optimize(atmsel,
max_iterations=20,
actions=[actions.trace(5, trcfil)])
mpdf = atmsel.energy()
z_score = mdl.assess_normalized_dope()
print("The final model energy of " + path + " is " + str(mpdf[0]))
print("The final model energy of " + path + " is " + str(mpdf_ini[0]))
print("The final z-score of " + code + " is: " + str(z_score))
mdl.write(file=path + '_optimized.pdb')
mdl_final = atmsel.get_dope_profile()
mdl_final_smoothed = mdl_final.get_smoothed(window=50)
energy_profile_txt_path_opt = dir + '/' + code + '_optimized_DOPE_EnergyProfile.txt'
mdl_final_smoothed.write_to_file(energy_profile_txt_path_opt)
mdl.write(file=dir + '/' + code + '_optimized.pdb')
energy_profile_plot(options, dir, code, energy_profile_txt_path,
energy_profile_txt_path_opt)