def initialize_system(m1, molecule_type, basis, numranges, reslow, numcont):
resid = m1.resid()
first_last_resid = [resid[0], resid[-1]]
print 'first_last_resid = ', first_last_resid
print 'resid = ', resid
txtOutput = None
if(molecule_type == 'protein'):
basis_filter = 'name[i] == "' + basis + '"'
error, basis_mask = m1.get_subset_mask(basis_filter)
check_error(error)
basis_m1 = sasmol.SasMol(1)
error = m1.copy_molecule_using_mask(basis_m1, basis_mask, 0)
check_error(error)
basis_resname = basis_m1.resname()
basis_resid = basis_m1.resid()
print 'reslow = ', reslow
print 'numcont = ', numcont
print 'numranges = ', numranges
print 'basis_resname = ', basis_resname
print 'basis_resid = ', basis_resid
respsi = []
resphi = []
dihedral_energy.protein_initialization(
respsi, resphi, basis_resid, basis_resname, numranges, reslow, numcont, first_last_resid, txtOutput)
dihedral_parameters = [respsi, resphi]
elif(molecule_type == 'rna'):
#rna_filter = 'name[i] == "P"'
#rna_filter = 'name[i] == "O5\'"'
rna_filter = 'name[i] == "' + basis + '"'
error, basis_mask = m1.get_subset_mask(rna_filter)
basis_m1 = sasmol.SasMol(1)
error = m1.copy_molecule_using_mask(basis_m1, basis_mask, 0)
basis_resname = basis_m1.resname()
basis_resid = basis_m1.resid()
print 'sum(basis_mask) rna = ', sum(basis_mask)
print 'len(resid) rna = ', len(resid)
resalpha = []
resbeta = []
resgamma = []
resdelta = []
resepsilon = []
reseta = []
dihedral_energy.rna_initialization(resalpha, resbeta, resgamma, resdelta, resepsilon,
reseta, basis_resid, basis_resname, numranges, reslow, numcont, first_last_resid, txtOutput)
dihedral_parameters = [
resalpha, resbeta, resgamma, resdelta, resepsilon, reseta]
print 'dihedral parameters = ', dihedral_parameters
flexible_residues = dihedral_monte_carlo.get_flexible_residues(
numranges, reslow, numcont)
print 'molecule_type = ', molecule_type
residue_rotation_indices, residue_rotation_mask = dihedral_monte_carlo.get_rotation_indices(
m1, molecule_type, flexible_residues, txtOutput)
step_parameters = step.Setup()
return dihedral_parameters, flexible_residues, residue_rotation_indices, residue_rotation_mask, step_parameters, first_last_resid
def initialize_system(m1, molecule_type, basis, numranges, reslow, numcont):
resid = m1.resid()
first_last_resid = [resid[0], resid[-1]]
print 'first_last_resid = ', first_last_resid
print 'resid = ', resid
txtOutput = None
if (molecule_type == 'protein'):
basis_filter = 'name[i] == "' + basis + '"'
error, basis_mask = m1.get_subset_mask(basis_filter)
check_error(error)
basis_m1 = sasmol.SasMol(1)
error = m1.copy_molecule_using_mask(basis_m1, basis_mask, 0)
check_error(error)
basis_resname = basis_m1.resname()
basis_resid = basis_m1.resid()
print 'reslow = ', reslow
print 'numcont = ', numcont
print 'numranges = ', numranges
print 'basis_resname = ', basis_resname
print 'basis_resid = ', basis_resid
respsi = []
resphi = []
dihedral_energy.protein_initialization(respsi, resphi, basis_resid,
basis_resname, numranges,
reslow, numcont,
first_last_resid, txtOutput)
dihedral_parameters = [respsi, resphi]
elif (molecule_type == 'rna'):
#rna_filter = 'name[i] == "P"'
#rna_filter = 'name[i] == "O5\'"'
rna_filter = 'name[i] == "' + basis + '"'
error, basis_mask = m1.get_subset_mask(rna_filter)
basis_m1 = sasmol.SasMol(1)
error = m1.copy_molecule_using_mask(basis_m1, basis_mask, 0)
basis_resname = basis_m1.resname()
basis_resid = basis_m1.resid()
print 'sum(basis_mask) rna = ', sum(basis_mask)
print 'len(resid) rna = ', len(resid)
resalpha = []
resbeta = []
resgamma = []
resdelta = []
resepsilon = []
reseta = []
dihedral_energy.rna_initialization(resalpha, resbeta, resgamma,
resdelta, resepsilon, reseta,
basis_resid, basis_resname,
numranges, reslow, numcont,
first_last_resid, txtOutput)
dihedral_parameters = [
resalpha, resbeta, resgamma, resdelta, resepsilon, reseta
]
print 'dihedral parameters = ', dihedral_parameters
flexible_residues = dihedral_monte_carlo.get_flexible_residues(
numranges, reslow, numcont)
print 'molecule_type = ', molecule_type
residue_rotation_indices, residue_rotation_mask = dihedral_monte_carlo.get_rotation_indices(
m1, molecule_type, flexible_residues, txtOutput)
step_parameters = step.Setup()
return dihedral_parameters, flexible_residues, residue_rotation_indices, residue_rotation_mask, step_parameters, first_last_resid
def dihedralgenerate(variables, txtOutput):
runname, dcdfile, path, pdbfile, trials, goback, temp, molecule_type, numranges, dtheta, reslow, numcont, lowres1, highres1, basis, cutoff, lowrg, highrg, zflag, zcutoff, cflag, confile, nonbondflag, nonbondscale, psffilepath, psffilename, parmfilepath, parmfilename, plotflag, directedmc, seed = unpack_variables(
variables)
alignflag = '1'
saveflag = '0'
pdbfilename = pdbfile
if(runname[-1] == '/'):
lin = len(runname)
runname = runname[:lin - 1]
direxist = os.path.exists(runname)
if(direxist == 0):
os.system('mkdir -p ' + runname)
genpath = runname + '/generate'
genpaths = genpath + '/'
direxist = os.path.exists(genpath)
if(direxist == 0):
os.system('mkdir -p ' + genpath)
if(path != ""):
if path[-1] != "/":
path += '/'
cpfile = os.path.join(path, pdbfilename)
cpst = 'cp ' + cpfile + ' ' + genpaths
os.system(cpst)
parmfilepath += '/'
fileexist = os.path.exists('.last_sas')
if(fileexist == 1):
os.system('mv -f .last_sas .last_sas_bu')
lastsasfile = open('./.last_sas', 'w')
lastsasfile.write('run_name\t' + runname + '\n')
lastsasfile.write('pdb_name\t' + pdbfile + '\n')
lastsasfile.write('dcd_name\t' + dcdfile + '\n')
kb = 1.380658E-23 # J/K
beta = 1.0 / (temp * kb)
m1 = sasmol.SasMol(0)
m2 = sasmol.SasMol(1)
m1.read_pdb(path + pdbfile, saspdbrx_topology=True)
nf1 = m1.number_of_frames()
m1.calccom(0)
dcdoutfile = m1.open_dcd_write(genpaths + dcdfile)
resid = m1.resid()
first_last_resid = [resid[0], resid[-1]]
print 'first_last_resid = ', first_last_resid
cutoff_array = []
vdw_factor = 0.3
if(molecule_type == 'protein'):
if(basis.lower() == 'all'):
print 'setting up all atom overlap arrays'
m1.set_average_vdw()
npairs = m1.natoms() * (m1.natoms() - 1) / 2
cutoff_array = numpy.zeros(npairs, numpy.float)
pairs.pairs(m1.atom_vdw(), cutoff_array)
basis_filter = 'not name[i] == None'
elif(basis.lower() == 'backbone'):
basis_filter = 'name[i] == "N" or name[i] == "CA" or name[i] == "C" '
elif(basis.lower() == 'heavy'):
basis_filter = 'not name[i][0] == "H" '
else:
string_basis = string.split(basis, ",")
number_basis_types = len(string_basis)
for i in xrange(number_basis_types):
if(i == 0):
basis_filter = 'name[i] == "' + string_basis[i] + '" '
else:
basis_filter = basis_filter + \
' or name[i] == "' + string_basis[i] + '" '
print 'basis_filter = ', basis_filter
error, basis_mask = m1.get_subset_mask(basis_filter)
basis_atom = "CA"
setup_basis_filter = 'name[i] == "' + basis_atom + '"'
error, setup_basis_mask = m1.get_subset_mask(setup_basis_filter)
basis_m1 = sasmol.SasMol(1)
error = m1.copy_molecule_using_mask(basis_m1, setup_basis_mask, 0)
basis_resname = basis_m1.resname()
basis_resid = basis_m1.resid()
respsi = []
resphi = []
dihedral_energy.protein_initialization(
respsi, resphi, basis_resid, basis_resname, numranges, reslow, numcont, first_last_resid, txtOutput)
dihedral_parameters = [respsi, resphi]
elif(molecule_type == 'rna'):
# ATOM N1 NN2 -0.13 ! \
# ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \
# ATOM H6 HN3 0.17 ! | | \ / \ \
# ATOM C5 CN3 -0.13 ! -P-O5'-C5'---C4' C1'
# ATOM H5 HN3 0.07 ! | | \ / \
# ATOM C2 CN1 0.52 ! O2P H5'' C3'--C2' H1'
# ATOM O2 ON1C -0.49 ! / \ / \
# ATOM N3 NN3 -0.66 ! O3' H3' O2' H2''
# ATOM C4 CN2 0.65 ! | |
# ATOM N4 NN1 -0.75 ! H2'
if(basis.lower() == 'all'):
print 'setting up all atom overlap arrays'
m1.set_average_vdw()
npairs = m1.natoms() * (m1.natoms() - 1) / 2
cutoff_array = numpy.zeros(npairs, numpy.float)
pairs.pairs(m1.atom_vdw(), cutoff_array)
basis_filter = 'not name[i] == None'
elif(basis.lower() == 'backbone'):
basis_filter = 'name[i] == "P" or name[i] == "O5\'" or name[i] == "C5\'" or name[i] == "C4\'" or name[i] == "C3\'" or name[i] == "O3\'" '
elif(basis.lower() == 'heavy'):
basis_filter = 'not name[i][0] == "H" '
else:
string_basis = string.split(basis, ",")
number_basis_types = len(string_basis)
for i in xrange(number_basis_types):
if(i == 0):
basis_filter = 'name[i] == "' + string_basis[i] + '" '
else:
basis_filter = basis_filter + \
' or name[i] == "' + string_basis[i] + '" '
error, basis_mask = m1.get_subset_mask(basis_filter)
basis_atom = "P"
setup_basis_filter = 'name[i] == "' + basis_atom + '"'
error, setup_basis_mask = m1.get_subset_mask(setup_basis_filter)
basis_m1 = sasmol.SasMol(1)
error = m1.copy_molecule_using_mask(basis_m1, setup_basis_mask, 0)
basis_resname = basis_m1.resname()
basis_resid = basis_m1.resid()
resalpha = []
resbeta = []
resgamma = []
resdelta = []
resepsilon = []
reseta = []
dihedral_energy.rna_initialization(resalpha, resbeta, resgamma, resdelta, resepsilon,
reseta, basis_resid, basis_resname, numranges, reslow, numcont, first_last_resid, txtOutput)
dihedral_parameters = [
resalpha, resbeta, resgamma, resdelta, resepsilon, reseta]
else:
print 'molecule_type = ', molecule_type
print 'm1.moltype() = ', m1.moltype()
message = 'rotation basis is not setup for molecule type = ' + \
m1.moltype()[0]
message += ' : stopping here'
print_failure(message, txtOutput)
return
if(cflag == 1):
filter_flag = 0
error, constraint_basis1_array, constraint_basis2_array, distance_array, type_array = constraints.read_constraints(
m1, confile, filter_flag)
mask_a_array = []
mask_b_array = []
for i in xrange(len(distance_array)):
print constraint_basis1_array[i]
print constraint_basis2_array[i]
print distance_array[i]
print type_array[i]
error, local_mask_a_array = m1.get_subset_mask(
constraint_basis1_array[i])
error, local_mask_b_array = m1.get_subset_mask(
constraint_basis2_array[i])
mask_a_array.append(local_mask_a_array)
mask_b_array.append(local_mask_b_array)
# testing code is below (to the end of this loop) ... remove at
# some point
test_filename1 = 'dum_a_' + str(i) + '.pdb'
test_filename2 = 'dum_b_' + str(i) + '.pdb'
new_beta = m1.beta()
m1.setBeta('0.00')
value = '1.00'
error = m1.set_descriptor_using_mask(
local_mask_a_array, beta, value)
m1.write_pdb(test_filename1, 0, 'w')
value = '0.00'
error = m1.set_descriptor_using_mask(
local_mask_a_array, beta, value)
value = '1.00'
error = m1.set_descriptor_using_mask(
local_mask_b_array, beta, value)
m1.write_pdb(test_filename2, 0, 'w')
value = '0.00'
error = m1.set_descriptor_using_mask(
local_mask_b_array, beta, value)
else:
mask_a_array = []
mask_b_array = []
distance_array = []
type_array = []
if(nonbondflag == 1):
message = '> energy implementation is not implemented in this version '
message += ' : stopping here'
print_failure(message, txtOutput)
return
else:
charge = []
exclusionlist = []
onefourlist = []
vdwparam = []
angleparam = []
dihedralparam = []
angleoutfile = open(genpaths + runname + '.angle_energies.txt', 'a')
hrg = 0.0
lowestrg = 1000.0
accepted = 0
over = 0
badrg = 0
nsteps = 0
arg = 0.0
trg = 0.0
badz = 0
badc = 0
pairdat = ['dum', 1, 1.0]
all_rg_tally = []
accepted_rg_tally = []
if(plotflag == 1):
graph = Gnuplot.Gnuplot(debug=1)
graph.clear()
graph('set title "Rg Results"')
graph.xlabel('Structure Number')
graph.ylabel('Rg (Angstrom^2)')
failtally = 0
acc = 0
oofile = 'objects.txt'
lineintxtOutput = ''.join(['=' for x in xrange(60)])
ttxt = time.ctime()
txtOutput.put("\n%s \n" % (lineintxtOutput))
txtOutput.put("DATA FROM RUN: %s \n\n" % (ttxt))
coor = m1.coor()
frame = 0
flexible_residues = get_flexible_residues(numranges, reslow, numcont)
print 'molecule_type = ', molecule_type
residue_rotation_indices, residue_rotation_mask = get_rotation_indices(
m1, molecule_type, flexible_residues, txtOutput)
name = m1.name()
step_parameters = step.Setup()
# get alignment sub molecule
#align_filter = 'name[i] == "'+basis+'" and (resid[i] >= '+str(lowres1)+' and resid[i] <= '+str(highres1)+')'
align_filter = 'name[i] == "' + basis_atom + \
'" and (resid[i] >= ' + str(lowres1) + \
' and resid[i] <= ' + str(highres1) + ')'
error, align_mask = m1.get_subset_mask(align_filter)
sub_m1 = sasmol.SasMol(2)
error = m1.copy_molecule_using_mask(sub_m1, align_mask, 0)
com_sub_m1 = sub_m1.calccom(0)
sub_m1.center(0)
coor_sub_m1 = sub_m1.coor()[0]
sub_m2 = sasmol.SasMol(4)
error = m1.copy_molecule_using_mask(sub_m2, align_mask, 0)
# MAIN LOOP
if(seed[0] == 1):
from numpy.random import RandomState
seed_object = RandomState(seed[1])
else:
seed_object = -1
minx = []
miny = []
minz = []
maxx = []
maxy = []
maxz = []
if(directedmc > 0):
rg_difference_list = []
directed_rg_list = []
accepted_rg_list = []
rg_list_length = 10 # hardwired
for i in range(trials):
print '.',
sys.stdout.flush()
# print i ; sys.stdout.flush()
vdi, vdf, indices, this_mask = step_parameters.chooser(
coor, m1, pairdat, dtheta, numranges, reslow, numcont, dihedral_parameters, beta, residue_rotation_indices, residue_rotation_mask, nonbondflag, first_last_resid, molecule_type, seed_object)
an = pairdat[0]
q0 = pairdat[1]
th = pairdat[2]
nsteps += 1
re = [0, 0, 0, 0.0, 0.0, lowestrg, hrg, 0, 0, []]
this_first_coor_x = m1.coor()[0, 0, 0]
this_first_coor_y = m1.coor()[0, 0, 1]
this_first_coor_z = m1.coor()[0, 0, 2]
this_final_coor_x = m1.coor()[0, -1, 0]
this_final_coor_y = m1.coor()[0, -1, 1]
this_final_coor_z = m1.coor()[0, -1, 2]
if(this_first_coor_x == this_final_coor_x and this_first_coor_y == this_final_coor_y and this_first_coor_z == this_final_coor_z):
print 'this_first_coor_x = ', this_first_coor_x
print 'this_first_coor_y = ', this_first_coor_y
print 'this_first_coor_z = ', this_first_coor_z
print 'this_final_coor_x = ', this_final_coor_x
print 'this_final_coor_y = ', this_final_coor_y
print 'this_final_coor_z = ', this_final_coor_z
if(i > 0):
print 'previous_first_coor = ', previous_first_coor
print 'previous_final_coor = ', previous_final_coor
print 'failtally = ', failtally
print 'goback = ', goback
print '>>> STOPPING NOW'
sys.stdout.flush()
sys.exit()
else:
previous_first_coor = m1.coor()[0, 0, :]
previous_final_coor = m1.coor()[0, -1, :]
newafile = dihedral_rotate.rotate(coor, m1, q0, th, an, cutoff, lowrg, highrg, re, accepted, zflag, zcutoff, cflag, dcdoutfile, indices, this_mask, basis_mask,
sub_m2, align_mask, coor_sub_m1, com_sub_m1, mask_a_array, mask_b_array, distance_array, type_array, first_last_resid, molecule_type, cutoff_array, vdw_factor)
# print 'back from dihedral_rotate'; sys.stdout.flush()
accepted = accepted + re[0]
over = over + re[1]
badrg = badrg + re[2]
rg_value = re[3]
trg = trg + re[3]
arg = arg + re[4]
lowestrg = re[5]
hrg = re[6]
badz = badz + re[7]
badc = badc + re[8]
if(len(re[9]) > 0):
minmax = re[9]
minx.append(minmax[0][0])
miny.append(minmax[0][1])
minz.append(minmax[0][2])
maxx.append(minmax[1][0])
maxy.append(minmax[1][1])
maxz.append(minmax[1][2])
all_rg_tally.append([i, rg_value])
if(re[0] == 1):
accepted_rg_tally.append([i, accepted, rg_value])
if(directedmc > 0):
if(len(rg_difference_list) <= rg_list_length):
this_rg_difference = abs(rg_value - directedmc)
rg_difference_list.append(this_rg_difference)
directed_rg_list.append(rg_value)
accepted_rg_list.append(accepted)
else:
this_rg_difference = abs(rg_value - directedmc)
evaluate_rg(rg_difference_list, directed_rg_list,
accepted_rg_list, this_rg_difference, rg_value, accepted)
if(re[0] == 0):
if(failtally == goback):
failtally = 0
if(accepted > 0):
if(seed[0] == 1):
ran_num = seed_object.rand()
dum = int(accepted * ran_num) - 1
elif(directedmc > 0):
local_rg_list_length = len(directed_rg_list)
ran_num = random.randrange(0, local_rg_list_length)
dum = accepted_rg_list[ran_num]
else:
dum = int(accepted * random.random()) - 1
if(dum == -1):
print '\nreloading coordinates from original starting structure'
m1.read_pdb(
path + pdbfile, fastread=True, saspdbrx_topology=True)
coor = m1.coor()
print 'accepted = ', accepted
print 'dum = ', dum
else:
print '\nreloading coordinates from a previously accepted structure'
# print 'accepted = ',accepted
#dum = int(accepted*1)-1
# print 'dum = ',dum
# print 'dum+1 = ',dum+1
m1.read_single_dcd_step(genpaths + dcdfile, dum + 1)
# m1.read_single_dcd_step(genpaths+dcdfile,dum)
coor = m1.coor()
else:
print '\n>>>>>reloading coordinates from original starting structure'
m1.read_pdb(
path + pdbfile, fastread=True, saspdbrx_topology=True)
coor = m1.coor()
else:
failtally = failtally + 1
if(((i + 1) % (float(trials) / 100.0) == 0 or (trials < 10))):
fraction_done = (float(i + 1) / float(trials))
progress_string = '\nCOMPLETED ' + \
str(i + 1) + ' of ' + str(trials) + ' : ' + \
str(fraction_done * 100.0) + ' % done'
print('%s\n' % progress_string)
print accepted, ' configurations accepted out of ', nsteps, (float(accepted) / nsteps) * 100.0, ' %\n\n'
report_string = 'STATUS\t' + str(fraction_done)
txtOutput.put(report_string)
if(i > 9):
if((i + 1) % (trials / 10) == 0 and accepted > 0 and i + 1 > 10):
if(plotflag == 1):
graph.plot(Gnuplot.Data(all_rg_tally, using='1:2 w p ps 4', title='all Rg'), Gnuplot.Data(
accepted_rg_tally, using='1:3 w lp pt 5 ps 2', title='accepted'))
fraction_done = (float(i + 1) / float(trials))
report_string = 'STATUS\t' + str(fraction_done)
txtOutput.put(report_string)
elif(accepted > 0):
if(plotflag == 1):
graph.plot(Gnuplot.Data(all_rg_tally, using='1:2 w p ps 4', title='all Rg'), Gnuplot.Data(
accepted_rg_tally, using='1:3 w lp pt 5 ps 2', title='accepted'))
fraction_done = (float(i + 1) / float(trials))
report_string = 'STATUS\t' + str(fraction_done)
txtOutput.put(report_string)
# print 'finished loop for i = ',i,'\n' ; sys.stdout.flush()
m1.close_dcd_write(dcdoutfile)
rgplot = open(
'./' + runname + '/generate/' + dcdfile + '.all_rg_results_data.txt', 'a')
rgplot.write('# structure number (structure 1 = 1; not 0), Rg (all)\n')
for ii in range(len(all_rg_tally)):
rgplot.write('%i\t%f\n' %
(all_rg_tally[ii][0] + 1, all_rg_tally[ii][1]))
rgplot.close()
rgplot = open(
'./' + runname + '/generate/' + dcdfile + '.accepted_rg_results_data.txt', 'a')
rgplot.write(
'# structure number (structure 1 = 1; not 0), Rg (accepted), trial number\n')
for ii in range(len(accepted_rg_tally)):
rgplot.write('%i\t%f\t%i\n' % (accepted_rg_tally[ii][
1] + 0, accepted_rg_tally[ii][2], accepted_rg_tally[ii][0] + 1))
rgplot.close()
outfile7 = open(genpaths + dcdfile + '.stats', 'a')
outfile7.write('%s\t%f\t%s\t%f\n' %
('lowest Rg = ', lowestrg, 'highest Rg = ', hrg))
outfile7.write('%s\t%i\t%s\t%i\t%s\t%f%s\n' % ('accepted ', accepted,
' out of ', nsteps, ' moves : ', (accepted / float(nsteps)) * 99.0, ' %'))
outfile7.write('%s\t%i\t%s\t%i\t%s\t%f%s\n' % (
'overlapped ', over, ' out of ', nsteps, ' moves : ', (over / float(nsteps)) * 100.0, ' %'))
outfile7.write('%s\t%i\t%s\t%i\t%s\t%f%s\n' % (
'bad rg2 ', badrg, ' out of ', nsteps, ' moves : ', (badrg / float(nsteps)) * 100.0, ' %'))
if(zflag == 1):
outfile7.write('%s\t%i\t%s\t%i\t%s\t%f%s\n' % (
'bad zcut ', badz, ' out of ', nsteps, ' moves : ', (badz / float(nsteps)) * 100.0, ' %'))
if(cflag == 1):
outfile7.write('%s\t%i\t%s\t%i\t%s\t%f%s\n' % ('constraint filter rejected ',
badc, ' out of ', nsteps, ' moves : ', (badz / float(nsteps)) * 100.0, ' %'))
if(accepted > 0):
outfile7.write('%s\t%f\n' %
('average accepted rg2 = ', arg / (accepted)))
else:
outfile7.write('%s\t%f\n' % ('average accepted rg2 = ', 0.0))
outfile7.write('%s\t%f\n' %
('average total rg2 of ensemble = ', trg / (nsteps)))
lastsasfile.close()
angleoutfile.close()
if(accepted > 0):
txtOutput.put("Average accepted rg2 = %lf\n" % (arg / (accepted)))
txtOutput.put(
"\nConfigurations and statistics saved in %s directory\n\n" % ('./' + genpaths))
else:
txtOutput.put(
"\n NO ACCEPTED MOVES\n\n Statistics saved in %s directory\n\n" % (genpaths))
txtOutput.put("lowest Rg = %lf\t highest Rg = %lf\n" % (lowestrg, hrg))
txtOutput.put("accepted %d out of %d : %lf percent\n" %
(accepted, nsteps, (accepted / float(nsteps)) * 100.0))
txtOutput.put("overlapped %d out of %d moves : %lf percent\n" %
(over, nsteps, (float(over) / float(nsteps)) * 100.0))
txtOutput.put("bad rg2 %d out of %d moves : %lf percent\n\n\n" %
(badrg, nsteps, (float(badrg) / float(nsteps)) * 100.0))
if(zflag == 1):
txtOutput.put("bad zcut %d out of %d moves : %lf percent\n\n\n" % (
badz, nsteps, (float(badz) / float(nsteps)) * 100.0))
if(cflag == 1):
txtOutput.put("constraint filter rejected %d out of %d moves : %lf percent\n\n\n" % (
badc, nsteps, (float(badc) / float(nsteps)) * 100.0))
if(len(minx) > 0 and len(miny) > 0 and len(minz) > 0 and len(maxx) > 0 and len(maxy) > 0 and len(maxz) > 0):
min_x = numpy.min(minx)
min_y = numpy.min(miny)
min_z = numpy.min(minz)
max_x = numpy.max(maxx)
max_y = numpy.max(maxy)
max_z = numpy.max(maxz)
txtOutput.put("minimum x = %lf\t maximum x = %lf -> range: %lf Angstroms\n" %
(min_x, max_x, (max_x - min_x)))
txtOutput.put("minimum y = %lf\t maximum y = %lf -> range: %lf Angstroms\n" %
(min_y, max_y, (max_y - min_y)))
txtOutput.put("minimum z = %lf\t maximum z = %lf -> range: %lf Angstroms\n\n" %
(min_z, max_z, (max_z - min_z)))
outfile7.write("\nminimum x = %lf\t maximum x = %lf -> range: %lf Angstroms\n" %
(min_x, max_x, (max_x - min_x)))
outfile7.write("minimum y = %lf\t maximum y = %lf -> range: %lf Angstroms\n" %
(min_y, max_y, (max_y - min_y)))
outfile7.write("minimum z = %lf\t maximum z = %lf -> range: %lf Angstroms\n\n" %
(min_z, max_z, (max_z - min_z)))
outfile7.close()
else:
outfile7.close()
txtOutput.put("\n%s \n" % (lineintxtOutput))
time.sleep(1.0)
if(plotflag == 1):
wait('\n')
print 'DIHEDRAL IS DONE'
return()