def main():
"""
Reads a structure from a Gaussian Log file and other parameters from a
Gaussian Com file and creates a new Gaussian Com.
"""
args = get_args()
gaulog = GaussianLog(args.log)
gaucom = GaussianCom(args.template_com)
atoms_log_coords = gaulog.read_geometry(args.opt_step, args.scan_step)
for no, atom in enumerate(gaucom.atoms_list):
atom.SetVector(atoms_log_coords[no].GetVector())
gaucom.write_to_file(args.new_com)
if len(sys.argv) == 1 or sys.argv[1] in ["-h", "--help"]:
print("Como usar: {0} file.log ").format(sys.argv[0])
sys.exit()
#ficheiro entrada (output do gaussian)
global filein
filein = sys.argv[1]
#transformar o ficheiro log aberto numa variavel global (ler com o GaussianLog)
############## INICIO ##############
main()
#ler os bytes de todo o ficheiro e fazer todos os atributos d
gaussianlog = GaussianLog(filein)
for i, scan_step in enumerate( gaussianlog.grep_bytes['Step number'] ):
print( "Scan", i, ": ", len(gaussianlog.grep_bytes['Step number'][i]), "opt steps" )
scan_step = input('Type "scan_step" that you which to extract. Options: scan_step="all": ')
opt_step = input('Type "opt_step" that you which to extract. Options: opt_step="all": ')
#verificar se existe o ficheiro
output = input('Type the name of the output file: ')
if path.exists(str(output) + '.pdb'):
raise RuntimeError('%s already exists' %(str(output)+".pdb"))
open_output = open(str(output) + ".pdb", "w")
#casos em que extraio todos os scans
if str(scan_step) == 'all':
print(len(gaussianlog.grep_bytes['orientation:']))
