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 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')
log.verbose()
###################### 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)
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')
###################### MODEL RANDOMIZATION ######################
# Select the flexible atoms
# flexible: "those that are not fixed neither belong to to a rigid body"
# Only the flexible atoms are randomized
flexible_atoms = []
for n in sel_mobile:
flexible = True
for m in sel_rigid:
if n in m:
flexible = False
break
if(flexible):
# print "flexible atom ...",n
flexible_atoms.append(n)
print("number of flexible atoms ...",len(flexible_atoms))
sel_flex=selection(flexible_atoms)
sel_flex.randomize_xyz(deviation=1.0)
# randomize the rigid bodies if requested
seed()
max_trans = 10
max_ang = 30
for num in sel_rigid:
if rand_rigid[sel_rigid.index(num)]==1:
rand_rot_x = uniform(-1,1)
rand_rot_y = uniform(-1,1)
rand_rot_z = uniform(-1,1)
rand_ang = uniform(0,max_ang)
rand_trans_x = uniform(-max_trans,max_trans)
rand_trans_y = uniform(-max_trans,max_trans)
rand_trans_z = uniform(-max_trans,max_trans)
num.rotate_mass_center([rand_rot_x,rand_rot_y,rand_rot_z],
rand_ang)
num.translate([rand_trans_x,rand_trans_y,rand_trans_z])
# Write final randomized model
mdl.write(file=self.code+'_rand.pdb')
###################### CG MINIMIZATION ######################
print("Conjugate_gradients")
print("directory num %s" % self.run_num)
trc_step=5
trc_file = open('CG'+self.run_num+'.trc', "a")
i=0
# trim the schedule
self.sched.make_for_model(mdl)
for step in self.sched:
i = i+1
step.optimize(sel_all, output='REPORT', max_iterations=200,
actions=actions.trace(trc_step,trc_file))
# Write PDB file each optimization step
pdb_file='cg'+self.run_num+'_'+str(i)+'.pdb'
sel_all.write(file=pdb_file)
trc_file.close()
###################### PRINT FINAL ENERGY AND CCC ######################
print("final energy all ")
scal = physical.values(default=1.0, em_density=10000)
eval = sel_all.energy(schedule_scale=scal)
print("final cc ")
scal = physical.values(default=0.0, em_density=1.0)
eval = sel_all.energy(schedule_scale=scal)
# Write final model
sel_all.write(file='final'+self.run_num+'_cg.pdb')
os.system("rm -f *.MRC")
