def make_quasi_mode_input(self, mode=1, firstter=None, lastter=None):
f_inp = path.join(self.inp_folder, 'quasi_mode.inp')
crd_inp = path.join(self.heavy_folder,
'{0}.nohydrogen.avg.crd'.format(self.type_na))
dcd_inp = path.join(self.mode_traj_folder,
'mode.{0}.dcd'.format(str(mode)))
inp = Script(f_inp)
inp.write_bomlev()
inp.initialize_rtf_prm()
inp.write_seq(self.seq1,
firstter=firstter,
lastter=lastter,
segid='strand1')
inp.write_seq(self.seq2,
firstter=firstter,
lastter=lastter,
segid='strand2')
inp.gen_angle_dihedral()
inp.delete_selection()
inp.read_crd(crd_inp)
inp.read_traj(dcd_inp)
inp.calculate_avg()
inp.coor_copy()
inp.write_quasi(vect=False)
inp.quasi_end()
inp.close_unit(21)
inp.end()
def make_avg_crd_input(self, selection='all', amber=False, firstter=None, lastter=None):
if self.type_na == 'arna+arna':
supplement1 = None
supplement2 = None
elif self.type_na == 'bdna+bdna':
supplement1 = get_patch(self.seq1, 1)
supplement2 = get_patch(self.seq2, 2)
f_inp = path.join(self.inp_folder, 'write_no_h_avg_crd.inp')
crd_inp = path.join(self.heavy_folder, '{0}.nohydrogen.crd'.format(self.type_na))
dcd_inp = path.join(self.heavy_folder, '{0}.nohydrogen.dcd'.format(self.type_na))
crd_out = path.join(self.heavy_folder, '{0}.nohydrogen.avg.crd'.format(self.type_na))
inp = Script(f_inp)
inp.write_bomlev()
inp.initialize_rtf_prm(amber=amber)
inp.write_seq(self.seq1, firstter=firstter, lastter=lastter, segid='strand1')
if supplement1 is not None:
inp.write_supplement(supplement1)
inp.write_seq(self.seq2, firstter=firstter, lastter=lastter, segid='strand2')
if supplement2 is not None:
inp.write_supplement(supplement2)
inp.gen_angle_dihedral()
inp.delete_selection()
inp.read_crd(crd_inp)
inp.read_traj(dcd_inp)
inp.calculate_avg(selection=selection)
inp.coor_copy()
inp.write_crd(crd_out, comp=True)
inp.end()
def make_quasi_input(self,
mass_all_same=False,
amber=False,
supplement1=None,
supplement2=None,
begin=1,
stop=10000,
firstter=None,
lastter=None):
f_inp = path.join(self.inp_folder, 'quasi.inp')
crd_inp = path.join(self.heavy_folder,
'{0}.nohydrogen.avg.crd'.format(self.type_na))
dcd_inp = path.join(self.heavy_folder,
'{0}.nohydrogen.fitavg.dcd'.format(self.type_na))
crd_out = path.join(self.nm_folder, 'quasi.nmvector.crd')
inp = Script(f_inp)
inp.write_bomlev()
inp.initialize_rtf_prm(amber=amber)
inp.write_seq(self.seq1,
firstter=firstter,
lastter=lastter,
segid='strand1')
if supplement1 is not None:
inp.write_supplement(supplement1)
inp.write_seq(self.seq2,
firstter=firstter,
lastter=lastter,
segid='strand2')
if supplement2 is not None:
inp.write_supplement(supplement2)
inp.gen_angle_dihedral()
inp.delete_selection()
if mass_all_same:
inp.set_all_mass_same()
inp.read_crd(crd_inp)
inp.read_traj(dcd_inp)
inp.calculate_avg(begin=begin, stop=stop)
inp.coor_copy()
inp.write_quasi()
inp.write_quasi_mode_crd(crd_out)
inp.quasi_end()
inp.close_unit(21)
inp.end()