def write_pdb(gaulog, scan_pts, opt_pts, args):
# get the bytes
chosen_bytes = []
if scan_pts == 'all':
for sbytes in gaulog.grep_bytes['orientation:']:
if opt_pts == 'all':
for byte in sbytes:
chosen_bytes.append(byte) # this is crazy
else:
chosen_bytes.append(sbytes[opt_pts])
else:
sbytes = gaulog.grep_bytes['orientation:'][scan_pts]
if opt_pts == 'all':
for byte in sbytes:
chosen_bytes.append(byte) # this is reasonable
else:
chosen_bytes.append(sbytes[opt_pts])
# produce txt output
txt = ''
txtf = {}
model_number = 0
for byte in chosen_bytes:
model_number += 1
xyz = gaulog.read_coordinates('all', byte)
counter = 0
txtd = {}
txt += 'MODEL %d\n' % model_number
for (coords, atom) in zip(xyz, gaulog.atoms_list):
counter += 1 # consistent with gaussian line number
atom.SetVector(coords[0], coords[1], coords[2])
atom.set_pdbinfo(atoms.PDBinfo('ATOM', counter))
if atom.oniom and args.files:
layermask = (atom.oniom.layer, atom.oniom.mask)
if layermask not in txtd:
txtd[layermask] = []
txtd[layermask].append(iolines.atom2pdb(atom))
elif atom.oniom and args.altloc:
atom.pdbinfo.altloc = atom.oniom.layer
txt += iolines.atom2pdb(atom)
txt += 'ENDMDL\n'
if model_number == 1:
for layermask in txtd:
txtf[layermask] = ''
for layermask in txtd:
txtf[layermask] += 'MODEL %d\n' % model_number
for line in txtd[layermask]:
txtf[layermask] += line
txtf[layermask] += 'ENDMDL\n'
return txt, txtf
def write_pdb(gaulog, scan_pts, opt_pts, args):
# get the bytes
chosen_bytes = []
if scan_pts == 'all':
for sbytes in gaulog.grep_bytes['orientation:']:
if opt_pts == 'all':
for byte in sbytes:
chosen_bytes.append(byte) # this is crazy
else:
chosen_bytes.append(sbytes[opt_pts])
else:
sbytes = gaulog.grep_bytes['orientation:'][scan_pts]
if opt_pts == 'all':
for byte in sbytes:
chosen_bytes.append(byte) # this is reasonable
else:
chosen_bytes.append(sbytes[opt_pts])
# produce txt output
txt = ''
txtf = {}
model_number = 0
for byte in chosen_bytes:
model_number += 1
xyz = gaulog.read_coordinates('all', byte)
counter = 0
txtd = {}
txt += 'MODEL %d\n' % model_number
for (coords, atom) in zip(xyz, gaulog.atoms_list):
counter += 1 # consistent with gaussian line number
atom.SetVector(coords[0],coords[1],coords[2])
atom.set_pdbinfo(atoms.PDBinfo('ATOM', counter))
if atom.oniom and args.files:
layermask = (atom.oniom.layer, atom.oniom.mask)
if layermask not in txtd:
txtd[layermask] = []
txtd[layermask].append(iolines.atom2pdb(atom))
elif atom.oniom and args.altloc:
atom.pdbinfo.altloc = atom.oniom.layer
txt += iolines.atom2pdb(atom)
txt += 'ENDMDL\n'
if model_number == 1:
for layermask in txtd:
txtf[layermask] = ''
for layermask in txtd:
txtf[layermask] += 'MODEL %d\n' % model_number
for line in txtd[layermask]:
txtf[layermask] += line
txtf[layermask] += 'ENDMDL\n'
return txt, txtf
def write_pdb(filename, atoms_list):
with open(filename, 'w') as o:
for (i, atom) in enumerate(atoms_list):
o.write(iolines.atom2pdb(atom))
def main():
args = get_args()
# .com file ?
if args.ext == '.com':
gaucom = GAUCOM(args.gau)
txt = ''
txtf = {}
for (i, at) in enumerate(gaucom.atoms_list):
at.set_pdbinfo(atoms.PDBinfo('ATOM', i))
if at.oniom and args.files:
layermask = (at.oniom.layer, at.oniom.mask)
if layermask not in txtf:
txtf[layermask] = ''
txtf[layermask] += iolines.atom2pdb(at)
if at.oniom.layer == 'H':
print at.x()
if at.oniom and args.altloc:
at.pdbinfo.altloc = at.oniom.layer
txt += iolines.atom2pdb(at)
else:
txt += iolines.atom2pdb(at)
if not args.files:
with open(args.pdb, 'w') as o:
o.write(txt)
if args.files:
for layermask in txtf:
l, m = layermask
with open('%s.%s.%d.pdb' % (args.base, l, m), 'w') as o:
o.write(txtf[layermask])
return 0
# Gaussian .log
gaulog = GAULOG(args.gau)
txt, txtf = write_pdb(gaulog, args.scan_step, args.opt_step, args)
if not args.files:
with open(args.pdb, 'w') as o:
o.write(txt)
else:
for layermask in txtf:
l, m = layermask
with open('%s.%s.%d.pdb' % (args.base, l, m), 'w') as o:
o.write(txtf[layermask])
# Alignment Pymol
if 'all' not in [args.scan_step, args.opt_step] or not args.align:
return 0
print('Aligning with pymol...')
# MORE MAGIC: Use pymol for alignment
o = args.pdb
b = os.path.splitext(o)[0]
txt = 'cmd.load("%s", format="pdb", multiplex=0)\n' % o
txt += 'cmd.intra_fit("%s", state=0)\n' % b
txt += 'cmd.save("%s", selection="%s", state=0, format="pdb")\n' % (o, b)
txt += 'cmd.quit\n'
with open('.temp_pymolscript.pml', "w") as temp_pymolscript:
temp_pymolscript.write(txt)
subprocess.call('pymol -qc .temp_pymolscript.pml', shell=True)
subprocess.call('rm .temp_pymolscript.pml', shell=True)
return 0
def main():
args = get_args()
# .com file ?
if args.ext == '.com':
gaucom = GAUCOM(args.gau)
txt = ''
txtf = {}
for (i,at) in enumerate(gaucom.atoms_list):
at.set_pdbinfo(atoms.PDBinfo('ATOM', i))
txt += iolines.atom2pdb(at)
if at.oniom and args.files:
layermask = (at.oniom.layer, at.oniom.mask)
if layermask not in txtf:
txtf[layermask] = ''
txtf[layermask] += iolines.atom2pdb(at)
if at.oniom and args.altloc:
at.pdbinfo.altloc = at.oniom.layer
txt += iolines.atom2pdb(at)
if not args.files:
with open(args.pdb, 'w') as o:
o.write(txt)
if args.files:
for layermask in txtf:
l, m = layermask
with open('%s.%s.%d.pdb' % (args.base, l, m), 'w') as o:
o.write(txtf[layermask])
return 0
# Gaussian .log
gaulog = GAULOG(args.gau)
txt, txtf = write_pdb(gaulog, args.scan_step, args.opt_step, args)
if not args.files:
with open(args.pdb, 'w') as o:
o.write(txt)
else:
for layermask in txtf:
l, m = layermask
with open('%s.%s.%d.pdb' % (args.base, l, m), 'w') as o:
o.write(txtf[layermask])
# Alignment Pymol
if 'all' not in [args.scan_step, args.opt_step] or not args.align:
return 0
print ('Aligning with pymol...')
# MORE MAGIC: Use pymol for alignment
o = args.pdb
b = os.path.splitext(o)[0]
txt = 'cmd.load("%s", format="pdb", multiplex=0)\n' % o
txt += 'cmd.intra_fit("%s", state=0)\n' % b
txt += 'cmd.save("%s", selection="%s", state=0, format="pdb")\n' % (o, b)
txt += 'cmd.quit\n'
with open('.temp_pymolscript.pml', "w") as temp_pymolscript:
temp_pymolscript.write(txt)
subprocess.call('pymol -qc .temp_pymolscript.pml', shell=True)
subprocess.call('rm .temp_pymolscript.pml', shell=True)
return 0
def write_pdb(filename, atoms_list):
with open(filename, 'w') as o:
for (i, atom) in enumerate(atoms_list):
o.write(iolines.atom2pdb(atom))
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")
