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)
#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:']))
#falta meter aqui a opcao opt_step =='all' , mas neste caso nao faz muito sentido
#if opt_step == 'all':
opt_step = int(opt_step)
print(len(gaussianlog.grep_bytes['orientation:']))
for i in range(len(gaussianlog.grep_bytes['orientation:'])):
atoms_structure = gaussianlog.read_geometry(opt_step, i)
for j,atom in enumerate(atoms_structure):
pdb_obj = atoms.PDBinfo('ATOM', j+1 )
#res_obj = atoms.RESinfo(atom.element,'',0,'') #quando nao ha info pdb
#atom.set_resinfo(res_obj)
atom.set_pdbinfo(pdb_obj)
atom.pdbinfo.altloc = atom.oniom.layer
open_output.write(iolines.atom2pdb(atom))
open_output.write("END\n")
#casos em que so extraio de um scan
else:
scan_step = int(scan_step)
#todos os opt
if opt_step == 'all':
for i in range(len(gaussianlog.grep_bytes['orientation:'][scan_step])):
