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_get_eigenvector_input(self,
modeid=1,
firstter=None,
lastter=None):
f_inp = path.join(self.inp_folder, 'get_eigenvectors.inp')
crd_inp = path.join(self.heavy_folder,
'{0}.nohydrogen.avg.crd'.format(self.type_na))
mode_inp = path.join(self.nm_folder, 'quasi.nmvector.crd')
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_normal_mode(mode_inp)
inp.print_eigenvector(modeid)
inp.quasi_end()
inp.end()
def make_gen_mode_input(self,
modeid,
phase='3.6',
ncyc=10,
temp=310,
tfre=1,
amber=False,
supplement1=None,
supplement2=None,
firstter=None,
lastter=None):
f_inp = path.join(self.inp_folder, 'gen_mode.inp')
crd_inp = path.join(self.heavy_folder,
'{0}.nohydrogen.avg.crd'.format(self.type_na))
mode_inp = path.join(self.nm_folder, 'quasi.nmvector.crd')
dcd_out = path.join(self.mode_traj_folder,
'mode.{0}.dcd'.format(str(modeid)))
inp = Script(f_inp,
mode='write',
description='generate mode {0}'.format(modeid))
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_normal_mode(mode_inp)
inp.write_quasi_mode_dcd(dcd_out,
modeid,
phase=phase,
ncyc=ncyc,
temp=temp,
tfre=tfre)
inp.quasi_end()
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()
def make_gen_mode_superimpose_input(self, modeid):
f_inp = path.join(self.inp_folder, 'gen_mode.inp')
crd_inp = path.join(self.heavy_folder,
'{0}.nohydrogen.avg.crd'.format(self.type_na))
mode_inp = path.join(self.nm_folder, 'quasi.nmvector.crd')
dcd_out = path.join(self.mode_traj_folder,
'mode.1to{0}.dcd'.format(str(modeid)))
inp = Script(f_inp,
mode='write',
description='generate mode {0}'.format(modeid))
inp.write_bomlev()
inp.initialize_rtf_prm()
inp.write_seq(self.seq1, segid='strand1')
inp.write_seq(self.seq2, segid='strand2')
inp.gen_angle_dihedral()
inp.delete_selection()
inp.read_crd(crd_inp)
inp.read_normal_mode(mode_inp)
inp.write_quasi_mode_supe_dcd(dcd_out, modeid)
inp.quasi_end()
inp.end()
def make_proj_md_to_mode_input(self, mode):
f_inp = path.join(self.inp_folder, 'proj_md_to_mode.inp')
crd_inp = path.join(self.heavy_folder,
'{0}.nohydrogen.avg.crd'.format(self.type_na))
mode_inp = path.join(self.nm_folder, 'quasi.nmvector.crd')
dcd_inp = path.join(self.diff_folder, 'mode.0.dcd')
crd_out = path.join(self.coef_folder,
'proj.md.onto.mode.{0}.crd'.format(str(mode)))
inp = Script(f_inp)
inp.write_bomlev()
inp.initialize_rtf_prm()
inp.write_seq(self.seq1, segid='strand1')
inp.write_seq(self.seq2, segid='strand2')
inp.gen_angle_dihedral()
inp.delete_selection()
inp.read_crd(crd_inp)
# inp.coor_copy()
inp.read_traj(dcd_inp)
inp.read_normal_mode(mode_inp)
inp.write_proj_mode_crd(crd_out, mode)
inp.quasi_end()
inp.close_unit(21)
inp.end()
def make_get_eigenvector_input_v1(self,
modeid=1,
amber=False,
supplement1=None,
supplement2=None,
firstter=None,
lastter=None):
f_inp = path.join(self.inp_folder, 'get_eigenvectors.inp')
crd_inp = path.join(self.heavy_folder,
'{0}.nohydrogen.avg.crd'.format(self.type_na))
mode_inp = path.join(self.nm_folder, 'quasi.nmvector.crd')
crd_out = path.join(self.nm_single_folder,
'mode.{0}.crd'.format(modeid))
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_normal_mode(mode_inp)
inp.write_quasi_single_mode_crd(modeid, crd_out)
inp.quasi_end()
inp.end()
