def rotate_single_mab(single_molecule, trial_molecule, groups, group_masks,
number_of_groups, residues_in_groups, rotation_variables,
dihedral_parameters, flexible_residues,
residue_rotation_indices, residue_rotation_mask,
step_parameters, first_last_resid, cutoff):
frame = 0
seed = [1, 2] # if you want a set SEED
seed = [0, 8]
if (seed[0] == 1):
from numpy.random import RandomState
seed_object = RandomState(seed[1])
else:
seed_object = -1
nonbondflag = False
backward = True
rotate_type = 'protein_backbone_dihedral'
molecule_type = rotation_variables[0]
temperature = rotation_variables[1]
basis = rotation_variables[2]
number_of_ranges = rotation_variables[3]
reslow = rotation_variables[4]
numcont = rotation_variables[5]
dtheta = rotation_variables[6]
kb = 1.380658E-23 # J/K
beta = 1.0 / (temperature * kb)
pairdat = ['dum', 1, 1.0]
check = 1
all_atoms_basis = 'resid[i] < 100'
error, all_atoms_mask = single_molecule.get_subset_mask(all_atoms_basis)
check_error(error)
while (check == 1):
print ':',
sys.stdout.flush()
coor = single_molecule.coor()
vdi, vdf, indices, this_mask = step_parameters.chooser(
coor, trial_molecule, pairdat, dtheta, number_of_ranges, reslow,
numcont, dihedral_parameters, beta, residue_rotation_indices,
residue_rotation_mask, nonbondflag, first_last_resid,
molecule_type, seed_object)
angle = pairdat[0]
residue_to_rotate = pairdat[1]
theta = pairdat[2]
# HARDWIRED
if (residue_to_rotate < 7):
this_group = groups[0]
this_mask = group_masks[0]
group_to_rotate = 0
else:
this_group = groups[1]
this_mask = group_masks[1]
group_to_rotate = 1
group_rotation.rotate_a_group(this_group, rotate_type,
residue_to_rotate, angle, theta,
backward)
check = check_ball_overlap(trial_molecule, this_group, group_to_rotate,
cutoff)
if (check == 1):
trial_molecule.set_coor_using_mask(single_molecule, frame,
all_atoms_mask)
error = single_molecule.copy_molecule_using_mask(
this_group, this_mask, frame)
if (check == 0):
trial_molecule.set_coor_using_mask(this_group, frame, this_mask)
error = single_molecule.copy_molecule_using_mask(
this_group, this_mask, frame)
return
def rotate_single_mab(single_molecule, trial_molecule, groups, group_masks, number_of_groups, residues_in_groups, rotation_variables, dihedral_parameters, flexible_residues, residue_rotation_indices, residue_rotation_mask, step_parameters, first_last_resid, cutoff):
frame = 0
seed = [1, 2] # if you want a set SEED
seed = [0, 8]
if(seed[0] == 1):
from numpy.random import RandomState
seed_object = RandomState(seed[1])
else:
seed_object = -1
nonbondflag = False
backward = True
rotate_type = 'protein_backbone_dihedral'
molecule_type = rotation_variables[0]
temperature = rotation_variables[1]
basis = rotation_variables[2]
number_of_ranges = rotation_variables[3]
reslow = rotation_variables[4]
numcont = rotation_variables[5]
dtheta = rotation_variables[6]
kb = 1.380658E-23 # J/K
beta = 1.0 / (temperature * kb)
pairdat = ['dum', 1, 1.0]
check = 1
all_atoms_basis = 'resid[i] < 100'
error, all_atoms_mask = single_molecule.get_subset_mask(all_atoms_basis)
check_error(error)
while(check == 1):
print ':',
sys.stdout.flush()
coor = single_molecule.coor()
vdi, vdf, indices, this_mask = step_parameters.chooser(coor, trial_molecule, pairdat, dtheta, number_of_ranges, reslow, numcont,
dihedral_parameters, beta, residue_rotation_indices, residue_rotation_mask, nonbondflag, first_last_resid, molecule_type, seed_object)
angle = pairdat[0]
residue_to_rotate = pairdat[1]
theta = pairdat[2]
# HARDWIRED
if(residue_to_rotate < 7):
this_group = groups[0]
this_mask = group_masks[0]
group_to_rotate = 0
else:
this_group = groups[1]
this_mask = group_masks[1]
group_to_rotate = 1
group_rotation.rotate_a_group(
this_group, rotate_type, residue_to_rotate, angle, theta, backward)
check = check_ball_overlap(
trial_molecule, this_group, group_to_rotate, cutoff)
if(check == 1):
trial_molecule.set_coor_using_mask(
single_molecule, frame, all_atoms_mask)
error = single_molecule.copy_molecule_using_mask(
this_group, this_mask, frame)
if(check == 0):
trial_molecule.set_coor_using_mask(this_group, frame, this_mask)
error = single_molecule.copy_molecule_using_mask(
this_group, this_mask, frame)
return
def simulate_single_mab(single_molecule, number_of_steps, groups, group_masks,
number_of_groups, residues_in_groups,
rotation_variables, dihedral_parameters,
flexible_residues, residue_rotation_indices,
residue_rotation_mask, step_parameters,
first_last_resid, cutoff):
frame = 0
seed = [1, 2]
seed = [0, 2]
if (seed[0] == 1):
from numpy.random import RandomState
seed_object = RandomState(seed[1])
else:
seed_object = -1
nonbondflag = False
backward = True
rotate_type = 'protein_backbone_dihedral'
molecule_type = rotation_variables[0]
temperature = rotation_variables[1]
basis = rotation_variables[2]
number_of_ranges = rotation_variables[3]
reslow = rotation_variables[4]
numcont = rotation_variables[5]
dtheta = rotation_variables[6]
kb = 1.380658E-23 # J/K
beta = 1.0 / (temperature * kb)
pairdat = ['dum', 1, 1.0]
dcdoutfile = single_molecule.open_dcd_write('adum.dcd')
coor = single_molecule.coor()
taccepted = 0
nsteps = 0
count = 0
# debugging
da_outfile = open('dangles.txt', 'w')
# end debugging
for i in xrange(number_of_steps):
print '.',
sys.stdout.flush()
vdi, vdf, indices, this_mask = step_parameters.chooser(
coor, single_molecule, pairdat, dtheta, number_of_ranges, reslow,
numcont, dihedral_parameters, beta, residue_rotation_indices,
residue_rotation_mask, nonbondflag, first_last_resid,
molecule_type, seed_object)
angle = pairdat[0]
residue_to_rotate = pairdat[1]
theta = pairdat[2]
# debugging
#angle = 'psi'
#residue_to_rotate = 5
#theta = 5.0 * numpy.pi/180.0
# end debugging
# HARDWIRED
if (residue_to_rotate < 7):
this_group = groups[0]
this_mask = group_masks[0]
group_to_rotate = 0
else:
this_group = groups[1]
this_mask = group_masks[1]
group_to_rotate = 1
group_rotation.rotate_a_group(this_group, rotate_type,
residue_to_rotate, angle, theta,
backward)
check = check_ball_overlap(single_molecule, this_group,
group_to_rotate, cutoff)
if (check == 0):
# debugging
if (angle == 'psi'):
basis = '(resid[i] == ' + str(
residue_to_rotate
) + ' and (name[i] == "N" or name[i] == "CA" or name[i] == "C")) or (resid[i] == ' + str(
residue_to_rotate + 1) + ' and (name[i] == "C") )'
error, mask = single_molecule.get_subset_mask(basis)
check_error(error)
error, temp_coor = single_molecule.get_coor_using_mask(
frame, mask)
check_error(error)
lcoor = temp_coor[0]
d_angle = sasmath.dihedral_angle(lcoor[0], lcoor[1], lcoor[2],
lcoor[3])
print 'initial dihedral angle = ', d_angle
da_outfile.write("%lf\n" % (d_angle))
da_outfile.flush()
# end debugging
single_molecule.set_coor_using_mask(this_group, frame, this_mask)
# debugging
if (angle == 'psi'):
error, temp_coor = single_molecule.get_coor_using_mask(
frame, mask)
check_error(error)
lcoor = temp_coor[0]
d_angle = sasmath.dihedral_angle(lcoor[0], lcoor[1], lcoor[2],
lcoor[3])
print 'final dihedral angle = ', d_angle
port = 54321
flag = 0
single_molecule.send_coordinates_to_vmd(port, flag)
# end debugging
single_molecule.write_dcd_step(dcdoutfile, 0, taccepted + 1)
taccepted += 1
else:
# if(count == 10):
# print '.',
# dcdfile2 = dum_molecule.open_dcd_read('adum.dcd')
# nf=dcdfile2[2]
# my_frame = random.randint(0,nf)
# for j in xrange(my_frame):
# dum_molecule.read_dcd_step(dcdfile2,my_frame)
# dum_coor = dum_molecule.coor()[0]
# single_molecule.coor()[0] = dum_coor
# count = 0
count += 1
nsteps += 1
return
def simulate_single_mab(single_molecule, number_of_steps, groups, group_masks, number_of_groups, residues_in_groups, rotation_variables, dihedral_parameters, flexible_residues, residue_rotation_indices, residue_rotation_mask, step_parameters, first_last_resid, cutoff):
frame = 0
seed = [1, 2]
seed = [0, 2]
if(seed[0] == 1):
from numpy.random import RandomState
seed_object = RandomState(seed[1])
else:
seed_object = -1
nonbondflag = False
backward = True
rotate_type = 'protein_backbone_dihedral'
molecule_type = rotation_variables[0]
temperature = rotation_variables[1]
basis = rotation_variables[2]
number_of_ranges = rotation_variables[3]
reslow = rotation_variables[4]
numcont = rotation_variables[5]
dtheta = rotation_variables[6]
kb = 1.380658E-23 # J/K
beta = 1.0 / (temperature * kb)
pairdat = ['dum', 1, 1.0]
dcdoutfile = single_molecule.open_dcd_write('adum.dcd')
coor = single_molecule.coor()
taccepted = 0
nsteps = 0
count = 0
# debugging
da_outfile = open('dangles.txt', 'w')
# end debugging
for i in xrange(number_of_steps):
print '.',
sys.stdout.flush()
vdi, vdf, indices, this_mask = step_parameters.chooser(coor, single_molecule, pairdat, dtheta, number_of_ranges, reslow, numcont,
dihedral_parameters, beta, residue_rotation_indices, residue_rotation_mask, nonbondflag, first_last_resid, molecule_type, seed_object)
angle = pairdat[0]
residue_to_rotate = pairdat[1]
theta = pairdat[2]
# debugging
#angle = 'psi'
#residue_to_rotate = 5
#theta = 5.0 * numpy.pi/180.0
# end debugging
# HARDWIRED
if(residue_to_rotate < 7):
this_group = groups[0]
this_mask = group_masks[0]
group_to_rotate = 0
else:
this_group = groups[1]
this_mask = group_masks[1]
group_to_rotate = 1
group_rotation.rotate_a_group(
this_group, rotate_type, residue_to_rotate, angle, theta, backward)
check = check_ball_overlap(
single_molecule, this_group, group_to_rotate, cutoff)
if(check == 0):
# debugging
if(angle == 'psi'):
basis = '(resid[i] == ' + str(residue_to_rotate) + ' and (name[i] == "N" or name[i] == "CA" or name[i] == "C")) or (resid[i] == ' + str(
residue_to_rotate + 1) + ' and (name[i] == "C") )'
error, mask = single_molecule.get_subset_mask(basis)
check_error(error)
error, temp_coor = single_molecule.get_coor_using_mask(
frame, mask)
check_error(error)
lcoor = temp_coor[0]
d_angle = sasmath.dihedral_angle(
lcoor[0], lcoor[1], lcoor[2], lcoor[3])
print 'initial dihedral angle = ', d_angle
da_outfile.write("%lf\n" % (d_angle))
da_outfile.flush()
# end debugging
single_molecule.set_coor_using_mask(this_group, frame, this_mask)
# debugging
if(angle == 'psi'):
error, temp_coor = single_molecule.get_coor_using_mask(
frame, mask)
check_error(error)
lcoor = temp_coor[0]
d_angle = sasmath.dihedral_angle(
lcoor[0], lcoor[1], lcoor[2], lcoor[3])
print 'final dihedral angle = ', d_angle
port = 54321
flag = 0
single_molecule.send_coordinates_to_vmd(port, flag)
# end debugging
single_molecule.write_dcd_step(dcdoutfile, 0, taccepted + 1)
taccepted += 1
else:
# if(count == 10):
# print '.',
# dcdfile2 = dum_molecule.open_dcd_read('adum.dcd')
# nf=dcdfile2[2]
# my_frame = random.randint(0,nf)
# for j in xrange(my_frame):
# dum_molecule.read_dcd_step(dcdfile2,my_frame)
# dum_coor = dum_molecule.coor()[0]
# single_molecule.coor()[0] = dum_coor
# count = 0
count += 1
nsteps += 1
return
