def make_crd_input(self, amber=False, firstter=None, lastter=None):
if self.type_na == 'arna+arna':
na = 'arna'
supplement1 = None
supplement2 = None
elif self.type_na == 'bdna+bdna':
na = 'bdna'
supplement1 = get_patch(self.seq1, 1)
supplement2 = get_patch(self.seq2, 2)
crd1 = path.join(self.mkcrd_folder, '{0}1.crd'.format(na))
inp1 = Script(path.join(self.mkcrd_folder, '{0}1.inp'.format(na)))
inp1.write_bomlev()
inp1.initialize_rtf_prm(amber=amber)
inp1.write_seq(self.seq1, firstter=firstter, lastter=lastter, segid='strand1')
if supplement1 is not None:
inp1.write_supplement(supplement1)
inp1.gen_angle_dihedral()
inp1.read_pdb(path.join(self.mkcrd_folder, '{0}1.1.pdb'.format(na)))
inp1.write_crd(crd1)
inp1.end()
crd2 = path.join(self.mkcrd_folder, '{0}2.crd'.format(na))
inp2 = Script(path.join(self.mkcrd_folder, '{0}2.inp'.format(na)))
inp2.write_bomlev()
inp2.initialize_rtf_prm(amber=amber)
inp2.write_seq(self.seq2, firstter=firstter, lastter=lastter, segid='strand2')
if supplement2 is not None:
inp2.write_supplement(supplement2)
inp2.gen_angle_dihedral()
inp2.read_pdb(path.join(self.mkcrd_folder, '{0}2.1.pdb'.format(na)))
inp2.write_crd(crd2)
inp2.end()
inp3 = Script(path.join(self.mkcrd_folder, '{0}.inp'.format(self.type_na)))
inp3.write_bomlev()
inp3.initialize_rtf_prm(amber=amber)
inp3.write_seq(self.seq1, firstter=firstter, lastter=lastter, segid='strand1')
if supplement1 is not None:
inp3.write_supplement(supplement1)
inp3.write_seq(self.seq2, firstter=firstter, lastter=lastter, segid='strand2')
if supplement2 is not None:
inp3.write_supplement(supplement2)
inp3.gen_angle_dihedral()
inp3.read_crd(crd1, selection='segid strand1', ignore=True)
inp3.read_crd(crd2, selection='segid strand2', ignore=True)
inp3.write_crd(path.join(self.mkcrd_folder, '{0}.crd'.format(self.type_na)))
inp3.end()
def make_no_h_crd_input(self, 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_crd.inp')
crd_inp = path.join(self.mkcrd_folder, '{0}.crd'.format(self.type_na))
crd_out = path.join(self.heavy_folder, '{0}.nohydrogen.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.read_crd(crd_inp)
inp.delete_selection()
inp.write_crd(crd_out)
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 fit_dcd_to_avg_input(self, amber=False, begin=1, frame_num=10000, massweighted=False, firstter=None, lastter=None, dcd_out=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, 'fit_dcd_to_avg.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.dcd'.format(self.type_na))
if dcd_out is None:
dcd_out = path.join(self.heavy_folder, '{0}.nohydrogen.fitavg.dcd'.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.coor_copy()
inp.read_traj(dcd_inp)
inp.open_write_traj(dcd_out)
inp.write_noh_dcd(begin=begin, frame_num=frame_num, mass_weighted=massweighted)
inp.close_unit(21)
inp.close_unit(30)
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_convert_avg_to_dcd_input(self,
amber=False,
supplement1=None,
supplement2=None,
firstter=None,
lastter=None):
f_inp = path.join(self.inp_folder, 'convert_avgcrd_avgdcd.inp')
crd_inp = path.join(self.heavy_folder,
'{0}.nohydrogen.avg.crd'.format(self.type_na))
dcd_out = path.join(self.mode_traj_folder, 'aa.avg.dcd')
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.convert_avg_to_dcd(dcd_out)
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_covariance_mat_input(self, modeid=0):
f_inp = path.join(self.inp_folder, 'write_covar_mat.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(modeid)))
crd_out = path.join(self.covar_folder,
'covar.{0}.crd'.format(str(modeid)))
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.read_traj(dcd_inp)
inp.write_covar_mat_crd(crd_out)
inp.close_unit(15)
inp.close_unit(21)
inp.end()
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_gen_diff_crd(self,
mode=1,
n_frame=1000,
firstter=None,
lastter=None):
f_inp = path.join(self.inp_folder, 'gen_diff_crd.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)))
dcd_out = path.join(self.diff_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.coor_copy()
inp.make_diff_to_avg(dcd_inp, dcd_out, n_frame)
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_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()
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_avg_crd_input(self,
selection='all',
amber=False,
supplement1=None,
supplement2=None,
firstter=None,
lastter=None):
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_no_h_dcd_input(self,
mass_weighted=True,
amber=False,
supplement1=None,
supplement2=None,
begin=1,
frame_num=10000,
firstter=None,
lastter=None):
f_inp = path.join(self.inp_folder, 'write_no_h_dcd.inp')
crd_inp = path.join(self.mkcrd_folder, '{0}.crd'.format(self.type_na))
dcd_out = path.join(self.heavy_folder,
'{0}.nohydrogen.dcd'.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.read_crd(crd_inp)
inp.coor_copy()
inp.read_traj(self.inp_dcd)
inp.open_write_traj(dcd_out)
inp.write_noh_dcd(mass_weighted=mass_weighted,
begin=begin,
frame_num=frame_num)
inp.close_unit(21)
inp.close_unit(30)
inp.end()