def writepdbfile(atoms, filename):
with open(filename, 'w') as f:
for atom in atoms:
if atom == 'TER\n':
f.write('TER\n')
else:
f.write(iolines.atom2pdb(atom))
def writepdbfile(atoms, filename):
with open(filename, 'w') as f:
for atom in atoms:
if atom == 'TER\n':
f.write('TER\n')
else:
f.write(iolines.atom2pdb(atom))
print 'Writ:oniom_line7-', new_line7
# 8
check_oniom8(oniom_line8, 'read')
atom8 = iolines.zmat2atom(oniom_line8)
new_line8 = iolines.atom2zmat(atom8)
check_oniom8(new_line8, 'write')
print 'Read:oniom_line8-', oniom_line8
print 'Writ:oniom_line8-', new_line8
#xyzpdb_line
check_xyzpdb(xyzpdb_line, 'read')
atom_xyzpdb = iolines.zmat2atom(xyzpdb_line)
new_linexyzpdb = iolines.atom2zmat(atom_xyzpdb)
check_xyzpdb(xyzpdb_line, 'write')
print 'Read:xyzpdb_line-', xyzpdb_line
print 'Writ:xyzpdb_line-', new_linexyzpdb
# mm
check_mm(mm_line, 'read')
atom_mm = iolines.zmat2atom(mm_line)
new_line_mm = iolines.atom2zmat(atom_mm)
check_mm(new_line_mm, 'write')
# print pdb oniom8
atom8 = iolines.zmat2atom(oniom_line8)
p = atoms.PDBinfo('HETATM', 27)
atom8.set_pdbinfo(p)
print(iolines.atom2pdb(atom8))
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])):
atoms_structure = gaussianlog.read_geometry(i, scan_step)
for j,atom in enumerate(atoms_structure):
pdb_obj = atoms.PDBinfo('ATOM', j+1)
atom.set_pdbinfo(pdb_obj)
atom.pdbinfo.altloc = atom.oniom.layer
open_output.write(iolines.atom2pdb(atom))
open_output.write("END\n")