def get_angles(dcd_file_name, pdb_file_name, first_last_resid, flex_file, nf=0):
from dna.ds_dna_monte_carlo import read_flex_resids
txtOutput = []
out_file = open(dcd_file_name[:-4] + '.ddat', 'w')
# read flex file
# flex_file = pdb_file_name[:-3] + 'flex'
(segnames, flex_resids) = read_flex_resids(flex_file)
segname = segnames[0]
numranges = 0
resid_old = -999.999 # any number that is not an int
for resid_new in flex_resids[:, 0]:
if resid_new != resid_old + 1:
numranges += 1
resid_old = resid_new
res_low = [flex_resids[0, 0]]
n_cont = [len(flex_resids[:, 0])]
flexible_residues = dmc.get_flexible_residues(numranges, res_low, n_cont)
molecule_type = "dna"
mol = sasmol.SasMol(0)
mol.read_pdb(pdb_file_name)
residue_rotation_indices, residue_rotation_mask = dmc.get_rotation_indices(
mol, molecule_type, flexible_residues, txtOutput)
# print "residue_rotation_indices = ",residue_rotation_indices
# first_last_resid = [flexible_residues[0], flexible_residues[-1]]
alpha = []
beta = []
gamma = []
delta = [] # <--- significant
epsilon = []
zeta = []
chi = [] # <--- significant
all_alpha = []
all_beta = []
all_gamma = []
all_delta = [] # <--- significant
all_epsilon = []
all_zeta = []
all_chi = [] # <--- significant
dcdfile = mol.open_dcd_read(dcd_file_name)
if nf == 0:
nf = dcdfile[2] # number of frames
# reslist = range(first_last_resid[0],first_last_resid[1]+1)
# print 'reslist = ',reslist
st1 = "# base\talpha\tbeta\tgamma\tdelta\tepsilon\tzeta\tchi\n"
out_file.write("%s" % (st1))
res_mol = sasmol.SasMol(0)
for i in xrange(nf):
mol.read_dcd_step(dcdfile, i)
coor = mol.coor()
out_file.write("# frame %d\n" % (i + 1))
for res in xrange(n_cont[0]):
q0 = res_low[0] + res
error, res_mask = mol.get_subset_mask(
"(resid[i] == " + str(q0) + ")")
mol.copy_molecule_using_mask(res_mol, res_mask, 0)
st = '%s %d' % (res_mol.resname()[0][0], q0)
# get the indices and mask for this residue
indices = residue_rotation_indices[q0]
this_mask = numpy.array(residue_rotation_mask[q0])
# alpha
alpha_angle = dr.measure(coor, indices, "alpha", this_mask, q0,
first_last_resid, molecule_type)
str_alpha_angle = '%.1f' % alpha_angle
all_alpha.append(alpha_angle)
st = st + '\t' + str_alpha_angle
logging.debug('alpha: ' + str_alpha_angle)
# beta
beta_angle = dr.measure(coor, indices, "beta", this_mask, q0,
first_last_resid, molecule_type)
str_beta_angle = '%.1f' % (beta_angle)
all_beta.append(beta_angle)
st = st + '\t' + str_beta_angle
logging.debug('beta: ' + str_beta_angle)
# gamma
gamma_angle = dr.measure(coor, indices, "gamma", this_mask, q0,
first_last_resid, molecule_type)
str_gamma_angle = '%.1f' % (gamma_angle)
all_gamma.append(gamma_angle)
st = st + '\t' + str_gamma_angle
logging.debug('gamma: ' + str_gamma_angle)
# delta
delta_angle = dr.measure(coor, indices, "delta", this_mask, q0,
first_last_resid, molecule_type)
str_delta_angle = '%.1f' % (delta_angle)
all_delta.append(delta_angle)
st = st + '\t' + str_delta_angle
logging.debug('delta: ' + str_delta_angle)
# epsilon
epsilon_angle = dr.measure(coor, indices, "epsilon", this_mask, q0,
first_last_resid, molecule_type)
str_epsilon_angle = '%.1f' % (epsilon_angle)
all_epsilon.append(epsilon_angle)
st = st + '\t' + str_epsilon_angle
logging.debug('epsilon: ' + str_epsilon_angle)
# zeta
zeta_angle = dr.measure(coor, indices, "zeta", this_mask, q0,
first_last_resid, molecule_type)
str_zeta_angle = '%.1f' % (zeta_angle)
all_zeta.append(zeta_angle)
st = st + '\t' + str_zeta_angle
logging.debug('zeta: ' + str_zeta_angle)
# chi
chi_angle = dr.measure(coor, indices, "chi", this_mask, q0,
first_last_resid, molecule_type)
str_chi_angle = '%.1f' % (chi_angle)
all_chi.append(chi_angle)
st = st + '\t' + str_chi_angle
logging.debug('alpha: ' + str_alpha_angle)
out_file.write("%s\n" % (st))
all_angles = [all_alpha, all_beta, all_gamma, all_delta, all_epsilon,
all_zeta, all_chi]
out_file.close()
print '\nsuccessfully finished calculating dihedrals \_/'
return all_angles
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