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()