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 measure(coor, indices, an, this_mask, q0, first_last_resid, molecule_type):
ind = numpy.nonzero(this_mask * numpy.arange(1, len(this_mask) + 1))[0]
this_frame_coor = coor[0, :, :]
lcoor = numpy.take(this_frame_coor[:, :], ind, 0)
error = []
if (molecule_type == 'protein'):
if (an == 'phi'):
angle = sasmath.dihedral_angle(lcoor[0, :], lcoor[1, :],
lcoor[2, :], lcoor[3, :])
elif (an == 'psi'):
if (q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[0, :], lcoor[1, :],
lcoor[2, :], lcoor[3, :])
else:
angle = sasmath.dihedral_angle(lcoor[1, :], lcoor[2, :],
lcoor[3, :], lcoor[4, :])
else:
angle = 0.0
message = 'error (in rotate.measure): no phi/psi angle specified'
error.append(message)
print 'unknown angle specified: %s\nnow exiting' % an
sys.exit()
#
# OPEN Stub for error handling
#
elif (molecule_type == 'rna'):
if (an == 'alpha'):
angle = sasmath.dihedral_angle(lcoor[0, :], lcoor[1, :],
lcoor[2, :], lcoor[3, :])
elif (an == 'beta'):
if (q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[0, :], lcoor[1, :],
lcoor[2, :], lcoor[3, :])
else:
angle = sasmath.dihedral_angle(lcoor[1, :], lcoor[2, :],
lcoor[3, :], lcoor[4, :])
elif (an == 'gamma'):
if (q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[1, :], lcoor[2, :],
lcoor[3, :], lcoor[4, :])
else:
angle = sasmath.dihedral_angle(lcoor[2, :], lcoor[3, :],
lcoor[4, :], lcoor[5, :])
elif (an == 'delta'):
if (q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[2, :], lcoor[3, :],
lcoor[4, :], lcoor[5, :])
else:
angle = sasmath.dihedral_angle(lcoor[3, :], lcoor[4, :],
lcoor[5, :], lcoor[6, :])
elif (an == 'epsilon'):
if (q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[3, :], lcoor[4, :],
lcoor[5, :], lcoor[6, :])
else:
angle = sasmath.dihedral_angle(lcoor[4, :], lcoor[5, :],
lcoor[6, :], lcoor[7, :])
elif (an == 'eta'):
if (q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[4, :], lcoor[5, :],
lcoor[6, :], lcoor[7, :])
else:
angle = sasmath.dihedral_angle(lcoor[5, :], lcoor[6, :],
lcoor[7, :], lcoor[8, :])
else:
angle = 0.0
message = 'error (in rotate.measure): no alpha/beta/delta/epsilon/eta angle specified'
error.append(message)
print 'unknown angle specified: %s\nnow exiting' % an
sys.exit()
elif (molecule_type == 'dna'):
if (first_last_resid[0] == first_last_resid[1]):
print 'only given one base for calculating angles'
print 'code needs revision in order to enable this'
return 0
i = {
"O3'-1": 0,
"P": 1,
"O5'": 2,
"C5'": 3,
"C4'": 4,
"O4'": 5,
"C1'": 6,
"chi3": 7,
"chi4": 8,
"C3'": 9,
"O3'": 10,
"P+1": 11,
"O5'+1": 12
}
if q0 == first_last_resid[0] and len(lcoor) == 12:
first_last_coor = numpy.zeros((13, 3))
first_last_coor[1:] = lcoor
lcoor = numpy.copy(first_last_coor)
if (an == 'alpha'):
if (q0 == first_last_resid[0]):
angle = 0
else:
angle = sasmath.dihedral_angle(lcoor[i["O3'-1"], :],
lcoor[i["P"], :],
lcoor[i["O5'"], :],
lcoor[i["C5'"], :])
elif (an == 'beta'):
angle = sasmath.dihedral_angle(lcoor[i["P"], :],
lcoor[i["O5'"], :],
lcoor[i["C5'"], :],
lcoor[i["C4'"], :])
elif (an == 'gamma'):
angle = sasmath.dihedral_angle(lcoor[i["O5'"], :],
lcoor[i["C5'"], :],
lcoor[i["C4'"], :],
lcoor[i["C3'"], :])
elif (an == 'delta'):
angle = sasmath.dihedral_angle(lcoor[i["C5'"], :],
lcoor[i["C4'"], :],
lcoor[i["C3'"], :],
lcoor[i["O3'"], :])
elif (an == 'epsilon'):
if (q0 == first_last_resid[1]):
angle = 0
else:
angle = sasmath.dihedral_angle(lcoor[i["C4'"], :],
lcoor[i["C3'"], :],
lcoor[i["O3'"], :],
lcoor[i["P+1"], :])
elif (an == 'zeta'):
if (q0 == first_last_resid[1]):
angle = 0
else:
angle = sasmath.dihedral_angle(lcoor[i["C3'"], :],
lcoor[i["O3'"], :],
lcoor[i["P+1"], :],
lcoor[i["O5'+1"], :])
elif (an == 'chi'):
angle = sasmath.dihedral_angle(lcoor[i["O4'"], :],
lcoor[i["C1'"], :],
lcoor[i["chi3"], :],
lcoor[i["chi4"], :])
else:
angle = 0.0
message = 'error (in rotate.measure): no alpha/beta/delta/epsilon/eta angle specified'
error.append(message)
print 'unknown angle specified: %s\nnow exiting' % an
return angle
def measure(coor, indices, an, this_mask, q0, first_last_resid, molecule_type):
ind = numpy.nonzero(this_mask * numpy.arange(1, len(this_mask) + 1))[0]
this_frame_coor = coor[0, :, :]
lcoor = numpy.take(this_frame_coor[:, :], ind, 0)
error = []
if(molecule_type == 'protein'):
if(an == 'phi'):
angle = sasmath.dihedral_angle(
lcoor[0, :], lcoor[1, :], lcoor[2, :], lcoor[3, :])
elif(an == 'psi'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(
lcoor[0, :], lcoor[1, :], lcoor[2, :], lcoor[3, :])
else:
angle = sasmath.dihedral_angle(
lcoor[1, :], lcoor[2, :], lcoor[3, :], lcoor[4, :])
else:
angle = 0.0
message = 'error (in rotate.measure): no phi/psi angle specified'
error.append(message)
print 'unknown angle specified: %s\nnow exiting' % an
sys.exit()
#
# OPEN Stub for error handling
#
elif(molecule_type == 'rna'):
if(an == 'alpha'):
angle = sasmath.dihedral_angle(
lcoor[0, :], lcoor[1, :], lcoor[2, :], lcoor[3, :])
elif(an == 'beta'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(
lcoor[0, :], lcoor[1, :], lcoor[2, :], lcoor[3, :])
else:
angle = sasmath.dihedral_angle(
lcoor[1, :], lcoor[2, :], lcoor[3, :], lcoor[4, :])
elif(an == 'gamma'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(
lcoor[1, :], lcoor[2, :], lcoor[3, :], lcoor[4, :])
else:
angle = sasmath.dihedral_angle(
lcoor[2, :], lcoor[3, :], lcoor[4, :], lcoor[5, :])
elif(an == 'delta'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(
lcoor[2, :], lcoor[3, :], lcoor[4, :], lcoor[5, :])
else:
angle = sasmath.dihedral_angle(
lcoor[3, :], lcoor[4, :], lcoor[5, :], lcoor[6, :])
elif(an == 'epsilon'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(
lcoor[3, :], lcoor[4, :], lcoor[5, :], lcoor[6, :])
else:
angle = sasmath.dihedral_angle(
lcoor[4, :], lcoor[5, :], lcoor[6, :], lcoor[7, :])
elif(an == 'eta'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(
lcoor[4, :], lcoor[5, :], lcoor[6, :], lcoor[7, :])
else:
angle = sasmath.dihedral_angle(
lcoor[5, :], lcoor[6, :], lcoor[7, :], lcoor[8, :])
else:
angle = 0.0
message = 'error (in rotate.measure): no alpha/beta/delta/epsilon/eta angle specified'
error.append(message)
print 'unknown angle specified: %s\nnow exiting' % an
sys.exit()
elif(molecule_type == 'dna'):
if(first_last_resid[0] == first_last_resid[1]):
print 'only given one base for calculating angles'
print 'code needs revision in order to enable this'
return 0
i = {"O3'-1": 0, "P": 1, "O5'": 2, "C5'": 3, "C4'": 4, "O4'": 5,
"C1'": 6, "chi3": 7, "chi4": 8, "C3'": 9,
"O3'": 10, "P+1": 11, "O5'+1": 12}
if q0 == first_last_resid[0] and len(lcoor) == 12:
first_last_coor = numpy.zeros((13, 3))
first_last_coor[1:] = lcoor
lcoor = numpy.copy(first_last_coor)
if(an == 'alpha'):
if(q0 == first_last_resid[0]):
angle = 0
else:
angle = sasmath.dihedral_angle(
lcoor[i["O3'-1"], :], lcoor[i["P"], :], lcoor[i["O5'"], :], lcoor[i["C5'"], :])
elif(an == 'beta'):
angle = sasmath.dihedral_angle(
lcoor[i["P"], :], lcoor[i["O5'"], :], lcoor[i["C5'"], :], lcoor[i["C4'"], :])
elif(an == 'gamma'):
angle = sasmath.dihedral_angle(
lcoor[i["O5'"], :], lcoor[i["C5'"], :], lcoor[i["C4'"], :], lcoor[i["C3'"], :])
elif(an == 'delta'):
angle = sasmath.dihedral_angle(
lcoor[i["C5'"], :], lcoor[i["C4'"], :], lcoor[i["C3'"], :], lcoor[i["O3'"], :])
elif(an == 'epsilon'):
if(q0 == first_last_resid[1]):
angle = 0
else:
angle = sasmath.dihedral_angle(
lcoor[i["C4'"], :], lcoor[i["C3'"], :], lcoor[i["O3'"], :], lcoor[i["P+1"], :])
elif(an == 'zeta'):
if(q0 == first_last_resid[1]):
angle = 0
else:
angle = sasmath.dihedral_angle(
lcoor[i["C3'"], :], lcoor[i["O3'"], :], lcoor[i["P+1"], :], lcoor[i["O5'+1"], :])
elif(an == 'chi'):
angle = sasmath.dihedral_angle(
lcoor[i["O4'"], :], lcoor[i["C1'"], :], lcoor[i["chi3"], :], lcoor[i["chi4"], :])
else:
angle = 0.0
message = 'error (in rotate.measure): no alpha/beta/delta/epsilon/eta angle specified'
error.append(message)
print 'unknown angle specified: %s\nnow exiting' % an
return angle
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