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 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_avg_crd_input(self, selection='all', amber=False, firstter=None, lastter=None):
if self.type_na == 'arna+arna':
supplement1 = None
supplement2 = None
else:
supplement1 = get_patch(self.seq1, 1)
supplement2 = get_patch(self.seq2, 2)
f_inp = path.join(self.charmminp_folder, 'write_no_h_avg_crd.inp')
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(self.crd)
inp.read_traj(self.dcd_out)
inp.calculate_avg(selection=selection)
inp.coor_copy()
inp.write_crd(self.avg_crd, comp=True)
inp.end()
def make_no_h_dcd_input(self, crd_inp, mass_weighted=True, amber=False, begin=1, frame_num=10000, firstter=None, lastter=None):
if self.type_na == 'arna+arna':
supplement1 = None
supplement2 = None
else:
supplement1 = get_patch(self.seq1, 1)
supplement2 = get_patch(self.seq2, 2)
f_inp = path.join(self.charmminp_folder, 'write_no_h_dcd.inp')
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.dcd_in)
inp.open_write_traj(self.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()
def write_make_enm_crd_input(self, amber=True, firstter=None, lastter=None):
rtfprm_folder = '/Users/alayah361/fluctmatch'
inp_file = path.join(self.charmminp_folder, 'make_enm_crd.inp')
outcrd = path.join(self.input_folder, 'na_enm.crd')
na = 'bdna'
supplement1 = get_patch(self.seq1, 1)
supplement2 = get_patch(self.seq2, 2)
inp = Script(inp_file)
inp.write_bomlev()
inp.initialize_rtf_prm(rtfprm_folder=rtfprm_folder, amber=amber)
inp.write_seq(self.seq1, firstter=firstter, lastter=lastter, segid='strand1')
inp.write_supplement(supplement1)
inp.write_seq(self.seq2, firstter=firstter, lastter=lastter, segid='strand2')
inp.write_supplement(supplement2)
inp.gen_angle_dihedral()
inp.delete_selection()
inp.read_crd(self.crd)
inp.proc_enm_topology_from_allatom()
inp.write_crd(outcrd)
inp.end()
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()