def write_ic_fluct_inp(f_out, host, type_na, time_label, cutoff, rootfolder):
inp = charmm_fluct.Script(f_out)
inp.write_bomlev()
inp.initialize_variables(rootfolder, host, type_na, time_label)
inp.read_rtf(cutoff)
inp.read_seq()
inp.read_crd()
inp.stream_str(cutoff)
inp.read_traj()
inp.icfluct()
inp.write_icfluct(cutoff)
inp.end()
def write_nmainit_inp(f_out, host, type_na, cutoff, rootfolder, scratchfolder):
inp = charmm_fluct.Script(f_out)
inp.write_bomlev()
inp.initialize_variables_nma(rootfolder, scratchfolder, host, type_na,
cutoff)
inp.read_rtf(cutoff)
inp.read_prm()
inp.read_seq()
inp.read_crd_nma()
inp.set_mass_1()
inp.minimization()
inp.stream_str_nma()
inp.nma()
inp.end()
def write_ic_avg_inp(f_out,
host,
type_na,
cutoff,
rootfolder,
distance_average=False):
inp = charmm_fluct.Script(f_out)
inp.write_bomlev()
inp.initialize_variables(rootfolder, host, type_na)
inp.read_rtf(cutoff)
inp.read_seq()
inp.read_crd()
inp.stream_str(cutoff)
inp.read_traj()
inp.icavg(distance_average=distance_average)
inp.write_icavg(cutoff)
inp.end()