grm = restraints.get_grm(file_name = file_name)

r = model_statistics.geometry(

pdb_hierarchy = grm.pdb_hierarchy,

restraints_manager = grm.restraints_manager,

molprobity_scores = True)

# XXX very runtime inefficient

distances = flex.double()

xyz = grm.pdb_hierarchy.atoms().extract_xyz()

bond_proxies_simple = grm.restraints_manager.geometry.pair_proxies(

sites_cart = xyz).bond_proxies.simple

for i, site_i in enumerate(xyz):

for j, site_j in enumerate(xyz):

if(j>i):

bonded = False

for proxy in bond_proxies_simple:

p1 = list(proxy.i_seqs)

p2 = [i,j]

p1.sort()

p2.sort()

if(p1==p2): bonded=True

if(not bonded):

dist_ij = math.sqrt(

(site_i[0]-site_j[0])**2+

(site_i[1]-site_j[1])**2+

(site_i[2]-site_j[2])**2)

distances.append(dist_ij)

min_nonbonded_distance = flex.min(distances)

# bond(rmsd), bond(max), angle(rmsd), angle(max), etc..

#print r.b_mean, r.b_max, r.a_min, r.a_max, r.clashscore, min_nonbonded_distance

total_start_time = time.time()

# These are the 4 strategies

# Quantum REFINE Classical Refine Quantum Optimization Classical Optimization

strategies = {"refine_cctbx":"restraints=cctbx ","refine_qm":"restraints=qm ","opt_qm":"restraints=qm data_weight=0","opt_cctbx":"restraints=cctbx data_weight=0 "}

print "Strategies selected are: "

# This gives us the ability to direct the output PDBs of the script

results_prefix = "../p26/04_results/"

perturbed_prefix="../p26/03_perturbed/"

mtz_prefix="../p26/02_mtz/"

p26_pdb_prefix="../p26/01d_fixSplit_GFA/"

#

folder_name=results_prefix

make_folder(folder_name)

#Loop over refinement or optimization strategies

strategy_start_time = 0

print "structure_name","success_number","mc_cycles","cal_time","cal_steps",\

"rmsd_to_p26","restraint_scale_end","R_start","R_end","rmsd(b)_start","rmsd(b)_end"

for strategy_name,strategy in strategies.iteritems():

if(strategy_name=="refine_qm" or strategy_name=="refine_cctbx" ):

print "["+strategy_name+"]"

strategy_start_time = time.time()

folder_name=results_prefix+strategy_name

make_folder(folder_name)

file_out_prefix = [results_prefix]

file_out_prefix.append(strategy_name)

#Loop over data files

data_files = os.listdir(mtz_prefix)

# print "p26_file_name ", " minimum_nobond", " maximum_rms_deltas(b)", "maximum_rms_deltas(a)"

# for data_file in data_files:

# data_file_start_time = time.time()

# if(data_file.endswith(".mtz")):

# data_file_name = data_file[:-4] # drop the .mtz extension

# p26_pdb_file = p26_pdb_prefix+data_file_name+".pdb"

# stat_object = get_model_stat(file_name = p26_pdb_file)

# print p26_pdb_file, stat_object

for data_file in data_files:

data_file_start_time = time.time()

if(data_file.endswith(".mtz")):

data_file_name = data_file[:-4] # drop the .mtz extension

p26_pdb_file = p26_pdb_prefix+data_file_name+".pdb"

p26_pdb_xray = iotbx.pdb.input(

file_name = p26_pdb_file).xray_structure_simple()

folder_name=results_prefix+strategy_name+"/"+data_file_name

make_folder(folder_name)

file_out_prefix.append(data_file_name)

pertubations = os.listdir(perturbed_prefix+data_file_name+"/")

for pertubation in pertubations:

if(os.path.isdir(perturbed_prefix+"/"+data_file_name+"/"+pertubation)):

file_out_prefix.append(pertubation)

make_folder(results_prefix+strategy_name+"/"+data_file_name+"/"+pertubation)

#Loop over Snapshots

snapshotdir_name=perturbed_prefix+data_file_name+"/"+pertubation+"/"

snapshots = os.listdir(snapshotdir_name)

mc_cycles, cal_time, cal_steps,rmsd_to_p26,restraint_scale_end,R_start,\

R_end,rmsd_b_start,rmsd_b_end=0,0,0,0,0,0,0,0,0

job_failed=False

geometry_error=False

convergence_failed=True

counter=10.0

for snapshot in snapshots:

if(snapshot.endswith("pdb")):

snapshot_file_name = snapshot[:-4]

file_out_prefix.append(snapshot_file_name)

output=results_prefix+strategy_name+"/"+data_file_name+"/"+\

pertubation+"/"+snapshot_file_name

result_pdb= output+".pdb"

result_log=output+".log"

structure_name=data_file_name+"/"+pertubation+"/"+snapshot_file_name

result_pdb_exists=os.path.exists(result_pdb)

if(result_pdb_exists != True):

job_failed=True

print structure_name, " The job failed"

counter=counter-1.0

continue

else:

#minimum_nobond=0#=??

#maximum_rms_deltas_b=0#=??

minimum_nobond, maximum_rms_deltas_b, maximum_rms_deltas_a=get_model_stat(result_pdb)

if(minimum_nobond <1.3 or maximum_rms_deltas_b > 0.3 or maximum_rms_deltas_a>30):

geometry_error=True

print structure_name, "geometry error"

counter=counter-1.0

continue

log_file = open(result_log,"r").readlines()

cal_time=float((log_file[-1].split())[1])+cal_time

data_start=0

data_end=0

for line in log_file:

if 'End of input processing' in line:

data_start=log_file.index(line)+1

if "see the result structure" in line:

data_end=log_file.index(line)-1

if "Convergence reached" in line:

convergence_failed=False

if(convergence_failed==True):

print structure_name,"not converged"

counter=counter-1.0

continue

cols=[]

for line in log_file[data_start:data_end]:

line= line.replace("="," ")

col=line.split()

cols.append(col)

R_start=float(cols[0][3])+R_start

R_end=float(cols[-1][3])+R_end

rmsd_b_start=float(cols[3][2])+rmsd_b_start

rmsd_b_end=float(cols[-1][5])+rmsd_b_end

restraint_scale_end=float(cols[-1][7])+restraint_scale_end

mc_cycles=int(cols[-1][1])+1+mc_cycles

minimization_steps=[]

for col in cols[4:]:

minimization_steps.append(int(col[-1]))

cal_steps=sum(minimization_steps)+cal_steps

result_pdb_xray = iotbx.pdb.input(

file_name = result_pdb).xray_structure_simple()

rmsd_to_p26 = p26_pdb_xray.sites_cart().rms_difference(

result_pdb_xray.sites_cart())+rmsd_to_p26

# print (structure_name,geometry_error,minimum_nobond,

# maximum_rms_deltas_b,maximum_rms_deltas_a,mc_cycles,cal_time,cal_steps,

# rmsd_to_p26,restraint_scale_end,R_start,R_end,

# rmsd_b_start,rmsd_b_end)

#if (job_failed==False and geometry_error==False and convergence_failed==False):

if (counter!=0):

print data_file_name+"/"+pertubation, counter ,mc_cycles/counter,cal_time/counter,cal_steps/counter,rmsd_to_p26/counter,\

restraint_scale_end/counter,R_start/counter,R_end/counter,rmsd_b_start/counter,rmsd_b_end/counter

strategy_time = time.time() - strategy_start_time

print "Time taken for " ,strategy ,"was ", strategy_time

total_time = time.time() - total_start_time