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_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 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 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()