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)
def do_restart(gl, gver='d'):
comname = os.path.splitext(gl.name)[0] + '.com'
gc = GC(comname)
for atom,xyz in zip(gc.atoms_list, gl.final_geometry):
atom.SetVector(xyz.GetVector())
newcomname = misc.increment_filename(comname)
# reduce scan steps accordingly
steps_done = len(gl.bytedict['orientation:'])-1
print steps_done
if steps_done:
print steps_done
for modred in gc.modreds:
if modred.action == 'S':# this FAILs for multi- scans
modred.scan_num_pts -= steps_done
gc.write_to_file(newcomname)
queue = guess_queue(newcomname)
gsub(newcomname, queue, gver)
def main():
try:
opts, args = getopt.gnu_getopt(sys.argv[1:], 'f:o:m:wd:', ['keep='])
except getopt.GetoptError as err:
sys.stderr.write(err + '\n')
usage()
sys.exit(2)
if len(args) < 1:
usage()
print('missing:')
print(' gaussian_input.com')
sys.exit(2)
elif len(args) > 1:
usage()
print('too many args:')
print(' %s' % (','.join(args)))
filein = args[0]
basename, input_extension = splitext(filein)
if input_extension != '.com':
print('WARNING:')
print(' inputname suffix is: %s' % input_extension)
# defaults
outputname = basename + '.frost.com'
freeze_angs = False
freeze_mm_wat = False
del_wat_angs = False
keep_N_wat = False
MASK = -1
# provided input
for o, a in opts:
if o == '-f': freeze_angs = float(a)
elif o == '-o': outputname = a
elif o == '-w': freeze_mm_wat = True
elif o == '-m': MASK = int(a)
elif o == '-d': del_wat_angs = float(a)
elif o == '--keep': keep_N_wat = int(a)
# input
gaucom = GAUCOM(filein)
resID_dict = build_resID_dict(gaucom.atoms_list)
# get xyz tuples
highlayer_xyz = []
all_xyz = []
non_wat_xyz = []
for i, atom in enumerate(gaucom.atoms_list):
if atom.oniom.layer == 'H':
highlayer_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
if not atom.resinfo.resname == 'WAT' or atom.oniom.layer == 'H':
non_wat_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
all_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
if not len(highlayer_xyz) and freeze_angs:
print('WELL WELL...')
print(' no highlayer defined, freezing nothing')
sys.exit()
elif freeze_angs == False:
freeze_idx = [False for _ in all_xyz]
if freeze_mm_wat:
for (i, xyz) in enumerate(all_xyz):
atom = gaucom.atoms_list[i]
freeze_idx[i] = (atom.oniom.layer == 'L'
and atom.resinfo.resname == 'WAT')
else:
# indexes to freeze
CUTOFF = freeze_angs + 1.0
freeze_idx = [False for _ in all_xyz]
for (i, xyz) in enumerate(all_xyz):
atom = gaucom.atoms_list[i]
tofreeze = min_dist([xyz], highlayer_xyz, CUTOFF) >= freeze_angs
tofreeze = tofreeze or (freeze_mm_wat and atom.oniom.layer == 'L'
and atom.resinfo.resname == 'WAT')
freeze_idx[i] = tofreeze
# byres
freeze_idx = byres(resID_dict, freeze_idx)
# freeze now
for (i, at) in enumerate(gaucom.atoms_list):
if freeze_idx[i]:
at.oniom.mask = MASK
# delete waters?
del_idx = [False for _ in all_xyz]
if del_wat_angs:
CUTOFF = del_wat_angs + 1.0
for (i, xyz) in enumerate(all_xyz):
atom = gaucom.atoms_list[i]
del_idx[i] = (
(min_dist([xyz], highlayer_xyz, CUTOFF) <= del_wat_angs)
and (atom.resinfo.resname == 'WAT')
and (atom.oniom.layer == 'L'))
del_idx = byresTrue(resID_dict, del_idx)
if keep_N_wat:
dists = []
for resID in resID_dict:
if resID[0] == 'WAT':
waters = [gaucom.atoms_list[i] for i in resID_dict[resID]]
if 'H' not in [a.oniom.layer for a in waters]:
xyz = [(atom.GetX(), atom.GetY(), atom.GetZ())
for a in waters]
dists.append((resID, min_dist(xyz, non_wat_xyz)))
if (i + 1) % 1001 == 0:
print(i)
dists.sort(key=lambda x: x[1])
# update del_idx
for (resID, dist) in dists[keep_N_wat:]:
for i in resID_dict[resID]:
del_idx[i] = True
if keep_N_wat or del_wat_angs:
del_idx = byres(resID_dict, del_idx)
print('Deleted atoms: %d' % (del_idx.count(True)))
# delete atoms
new_atoms_list = []
deleted = []
for (i, atom) in enumerate(gaucom.atoms_list):
if not del_idx[i]:
new_atoms_list.append(atom)
else:
atom.set_pdbinfo(atoms.PDBinfo('ATOM', i))
atom.pdbinfo.altloc = atom.oniom.layer
deleted.append(atom)
# write pdb with deleted atoms
write_pdb('%s.delwat.pdb' % (outputname), deleted)
# update atoms list
gaucom.atoms_list = new_atoms_list
gaucom.redo_connectivity_list() # works for TS structures?
# print pdb copy of model by mask
topdb_dict = {}
for (i, atom) in enumerate(gaucom.atoms_list):
mask = atom.oniom.mask
atom.set_pdbinfo(atoms.PDBinfo('ATOM', i))
atom.pdbinfo.altloc = atom.oniom.layer
if mask not in topdb_dict:
topdb_dict[mask] = []
topdb_dict[mask].append(atom)
for mask in topdb_dict:
write_pdb('%s.%d.pdb' % (outputname, mask), topdb_dict[mask])
# write output
gaucom.write_to_file(outputname)
return 0
def main():
try:
opts, args = getopt.gnu_getopt(sys.argv[1:], 'f:d:')
except getopt.GetoptError as err:
sys.stderr.write(str(err) + '\n')
if len(args) < 1:
usage()
print('Missing:')
print(' gaussian_input.com')
sys.exit(2)
elif len(args) > 1:
usage()
print('Hey! Too many args:')
print(' %s' % (', '.join(args)))
gaussian_com_filename = args[0]
new_folder_name = 'residel'
freeze_angs = 15
for o, a in opts:
if o == '-f': freeze_angs = float(a)
if o == '-d': new_folder_name = a
if not os.path.exists("./{}".format(new_folder_name)):
os.makedirs(new_folder_name)
# input
gaussian_file = GaussianCom(gaussian_com_filename)
resID_dict = build_resID_dict(gaussian_file.atoms_list)
# get xyz tuples
highlayer_xyz = []
all_xyz = []
non_wat_xyz = []
for i,atom in enumerate(gaussian_file.atoms_list):
if atom.oniom.layer == 'H':
highlayer_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
if not atom.resinfo.resname == 'WAT' or atom.oniom.layer == 'H':
non_wat_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
all_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
if not len(highlayer_xyz):
print('WELL WELL...')
print(' no highlayer defined, freezing nothing')
else:
# indexes to freeze
CUTOFF = freeze_angs + 1.0
freeze_idx = [False for _ in all_xyz]
for (i,xyz) in enumerate(all_xyz):
atom = gaussian_file.atoms_list[i]
tofreeze = min_dist( [xyz] , highlayer_xyz, CUTOFF) <= freeze_angs
freeze_idx[i] = tofreeze
if atom.resinfo.resname == 'WAT' or atom.oniom.layer == 'H':
freeze_idx[i] = False
# byres
freeze_idx = byres(resID_dict, freeze_idx)
# residue selection
res_2_go = list(set(get_resID(gaussian_file.atoms_list[i]) for i in np.where(freeze_idx)[0]))
atoms_list = gaussian_file.atoms_list
residues_list = Molecule("protein", atoms_list).make_residues_list()
input_list = []
for no, residue in enumerate(residues_list):
if get_resID(residue[0]) not in res_2_go:
continue
residue_number_name = "{0.resinfo.resnum}_{0.resinfo.resname}".format(residue[0])
print(residue_number_name)
incomplete_residues_list = Molecule("protein", atoms_list).make_residues_list()
incomplete_residues_list.remove(residue)
new_atoms_list = []
for res in incomplete_residues_list:
new_atoms_list.extend(res)
gaussian_file.atoms_list = new_atoms_list
gaussian_file.redo_connectivity_list()
no_electrons = 0
# correct link atom number and count total number of electrons
for i, atom in enumerate(new_atoms_list):
no_electrons += atom.GetAtomicNum()
if atom.oniom.link_bound_to:
if int(atom.oniom.link_bound_to) > atoms_list.index(residue[0]):
atom.oniom.link_bound_to = str(int(atom.oniom.link_bound_to) - len(residue))
#correct charge and multiplicity
new_protein = Molecule("new_protein", new_atoms_list)
charge = sum([res.get_charge() for res in incomplete_residues_list])
no_electrons -= round(charge)
multiplicity = int(gaussian_file.multiplicity_line.split()[1])
if (no_electrons%2==0 and multiplicity-1%2!=0) or (no_electrons%2==1 and multiplicity-1%2!=1):
print("Number of electrons and multiplicity are not compatible. Charge increased arbitrarily by one")
charge += 1
gaussian_file.multiplicity_line = "{0} {1}\n".format(int(round(charge))," ".join(gaussian_file.multiplicity_line.split()[1:]))
gaussian_name = "{0}_{1}.com".format(gaussian_com_filename[:-4],residue_number_name)
gaussian_file.write_to_file("{0}/{1}".format(new_folder_name, gaussian_name))
input_list.append(gaussian_name)
script_file_name = "{0}/{1}".format(new_folder_name,"run.sh")
with open(script_file_name, 'w') as run_script:
for job in input_list:
out_name = job[:-4]+".log"
run_script.write("g09 {0} {1}\n".format(job,out_name))
def main():
gaussian_com_filename = sys.argv[1]
new_folder_name = os.path.splitext(sys.argv[1])[0]
freeze_angs = 15
if not os.path.exists("./{}".format(new_folder_name)):
os.makedirs(new_folder_name)
# input
gaussian_file = GaussianCom(gaussian_com_filename)
resID_dict = build_resID_dict(gaussian_file.atoms_list)
# get xyz tuples
highlayer_xyz = []
all_xyz = []
non_wat_xyz = [] #all MM and non waters
for i,atom in enumerate(gaussian_file.atoms_list):
if atom.oniom.layer == 'H':
highlayer_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
if not atom.resinfo.resname == 'WAT' or atom.oniom.layer == 'H':
non_wat_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
all_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
if not len(highlayer_xyz):
print('WELL WELL...')
print(' no highlayer defined, freezing nothing')
else:
# indexes to freeze [list of atoms to "freeze"]
CUTOFF = freeze_angs + 1.0
freeze_idx = [False for _ in all_xyz]
for (i,xyz) in enumerate(all_xyz):
atom = gaussian_file.atoms_list[i]
tofreeze = min_dist( [xyz] , highlayer_xyz, CUTOFF) <= freeze_angs
freeze_idx[i] = tofreeze
if atom.resinfo.resname == 'WAT' or atom.oniom.layer == 'H':
freeze_idx[i] = False
# byres - returns the same freeze_idx list, but if at least one atom is true, then changes all to True
freeze_idx = byres(resID_dict, freeze_idx)
# residue selection [list of tuples (resn, resid)]
res_2_go = list(set(get_resID(gaussian_file.atoms_list[i]) for i in np.where(freeze_idx)[0]))
old_atoms_list = gaussian_file.atoms_list
residues_list = Molecule("protein", old_atoms_list).make_residues_list()
# do the magic
for no, residue in enumerate(residues_list):
if get_resID(residue[0]) not in res_2_go:
continue
#NOTA: a lista de residues (residue[0]) parece uma [lista de residues[lista atoms]] devo conseguir descompactar isto
resname = residue[0].resinfo.resname
resid = residue[0].resinfo.resnum
residue_number_name = "{0}_{1}".format(resname,resid)
original_charges = zerate_res_charge(old_atoms_list, (resname, resid))
#print(residue_number_name)
gaussian_name = "{0}_{1}.com".format(
gaussian_com_filename[:-4],
residue_number_name
)
gaussian_file.write_to_file("{0}/{1}".format(
new_folder_name,
gaussian_name)
)
reset_res_charge(old_atoms_list, (resname, resid), original_charges)
elif not args.target and (args.nsteps and args.stepsize):
stepsize = args.stepsize
nsteps = args.nsteps
else:
sys.stderr.write('\nShould not be here, something went wrong :(\n\n')
sys.exit()
#print nsteps, stepsize
new_modred.append(ModRed('B %d %d S %d %.4f\n' % (i, j, nsteps, stepsize)))
if args.Bfreeze:
for i, j in args.Bfreeze:
new_modred.append(ModRed('B %d %d F\n' % (i, j)))
gc.modreds = new_modred
#gc.additional_input_dict['modred'] = [m.line for m in new_modred]
# add modred to opt in route_section if necessary
gc.route_section.keywords['opt'].set('modred')
# write new file
output = increment_gaucom_name(args.COM)
if not exists(output):
gc.write_to_file(output)
print '%s' % output
else:
sys.stderr.write('%s already exists... not doing anything\n' % output)
#print args
stepsize = args.stepsize
nsteps = args.nsteps
else:
sys.stderr.write('\nShould not be here, something went wrong :(\n\n')
sys.exit()
#print nsteps, stepsize
new_modred.append(ModRed('B %d %d S %d %.4f\n' % (i,j,nsteps,stepsize)))
if args.Bfreeze:
for i,j in args.Bfreeze:
new_modred.append(ModRed('B %d %d F\n' % (i,j)))
gc.modreds = new_modred
#gc.additional_input_dict['modred'] = [m.line for m in new_modred]
# add modred to opt in route_section if necessary
gc.route_section.keywords['opt'].set('modred')
# write new file
output = increment_gaucom_name(args.COM)
if not exists(output):
gc.write_to_file(output)
print '%s' % output
else:
sys.stderr.write('%s already exists... not doing anything\n' % output)
#print args
def main():
try:
opts, args = getopt.gnu_getopt(sys.argv[1:], 'f:o:m:wd:', ['keep='])
except getopt.GetoptError as err:
sys.stderr.write(err + '\n')
usage()
sys.exit(2)
if len(args) < 1:
usage()
print('missing:')
print(' gaussian_input.com')
sys.exit(2)
elif len(args) > 1:
usage()
print('too many args:')
print(' %s' % (','.join(args)))
filein = args[0]
basename, input_extension = splitext(filein)
if input_extension != '.com':
print('WARNING:')
print(' inputname suffix is: %s' % input_extension)
# defaults
outputname = basename + '.frost.com'
freeze_angs = False
freeze_mm_wat = False
del_wat_angs = False
keep_N_wat = False
MASK = -1
# provided input
for o, a in opts:
if o == '-f': freeze_angs = float(a)
elif o == '-o': outputname = a
elif o == '-w': freeze_mm_wat = True
elif o == '-m': MASK = int(a)
elif o == '-d': del_wat_angs = float(a)
elif o == '--keep': keep_N_wat = int(a)
# input
gaucom = GAUCOM(filein)
resID_dict = build_resID_dict(gaucom.atoms_list)
# get xyz tuples
highlayer_xyz = []
all_xyz = []
non_wat_xyz = []
for i,atom in enumerate(gaucom.atoms_list):
if atom.oniom.layer == 'H':
highlayer_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
if not atom.resinfo.resname == 'WAT' or atom.oniom.layer == 'H':
non_wat_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
all_xyz.append((atom.GetX(), atom.GetY(), atom.GetZ()))
if not len(highlayer_xyz) and freeze_angs:
print('WELL WELL...')
print(' no highlayer defined, freezing nothing')
sys.exit()
elif freeze_angs == False:
freeze_idx = [False for _ in all_xyz]
if freeze_mm_wat:
for (i,xyz) in enumerate(all_xyz):
atom = gaucom.atoms_list[i]
freeze_idx[i] = (atom.oniom.layer=='L' and
atom.resinfo.resname=='WAT')
else:
# indexes to freeze
CUTOFF = freeze_angs + 1.0
freeze_idx = [False for _ in all_xyz]
for (i,xyz) in enumerate(all_xyz):
atom = gaucom.atoms_list[i]
tofreeze = min_dist( [xyz] , highlayer_xyz, CUTOFF) >= freeze_angs
tofreeze = tofreeze or (freeze_mm_wat and
atom.oniom.layer=='L' and atom.resinfo.resname=='WAT')
freeze_idx[i] = tofreeze
# byres
freeze_idx = byres(resID_dict, freeze_idx)
# freeze now
for (i, at) in enumerate(gaucom.atoms_list):
if freeze_idx[i]:
at.oniom.mask = MASK
# delete waters?
del_idx = [False for _ in all_xyz]
if del_wat_angs:
CUTOFF = del_wat_angs + 1.0
for (i,xyz) in enumerate(all_xyz):
atom = gaucom.atoms_list[i]
del_idx[i] = (
(min_dist([xyz], highlayer_xyz, CUTOFF) <= del_wat_angs) and
(atom.resinfo.resname == 'WAT') and
(atom.oniom.layer == 'L')
)
del_idx = byresTrue(resID_dict, del_idx)
if keep_N_wat:
dists = []
for resID in resID_dict:
if resID[0] == 'WAT':
waters = [gaucom.atoms_list[i] for i in resID_dict[resID]]
if 'H' not in [a.oniom.layer for a in waters]:
xyz = [(atom.GetX(), atom.GetY(), atom.GetZ()) for a in waters]
dists.append((resID, min_dist(xyz, non_wat_xyz)))
if (i+1)%1001 == 0:
print(i)
dists.sort(key=lambda x: x[1])
# update del_idx
for (resID, dist) in dists[keep_N_wat:]:
for i in resID_dict[resID]:
del_idx[i] = True
if keep_N_wat or del_wat_angs:
del_idx = byres(resID_dict, del_idx)
print('Deleted atoms: %d' % (del_idx.count(True)))
# delete atoms
new_atoms_list = []
deleted = []
for (i,atom) in enumerate(gaucom.atoms_list):
if not del_idx[i]:
new_atoms_list.append(atom)
else:
atom.set_pdbinfo(atoms.PDBinfo('ATOM', i))
atom.pdbinfo.altloc = atom.oniom.layer
deleted.append(atom)
# write pdb with deleted atoms
write_pdb('%s.delwat.pdb' % (outputname), deleted)
# update atoms list
gaucom.atoms_list = new_atoms_list
gaucom.redo_connectivity_list() # works for TS structures?
# print pdb copy of model by mask
topdb_dict = {}
for (i,atom) in enumerate(gaucom.atoms_list):
mask = atom.oniom.mask
atom.set_pdbinfo(atoms.PDBinfo('ATOM', i))
atom.pdbinfo.altloc = atom.oniom.layer
if mask not in topdb_dict:
topdb_dict[mask] = []
topdb_dict[mask].append(atom)
for mask in topdb_dict:
write_pdb('%s.%d.pdb' % (outputname, mask), topdb_dict[mask])
# write output
gaucom.write_to_file(outputname)
return 0