distpair = tuple([int(x) for x in line.split()])
dists.append(distpair)
input_file_list = sys.argv[2:] #com files
results_dict = OrderedDict([])
for input_file in input_file_list:
input_file_no_suf = input_file[:-4]
results_dict[input_file_no_suf] = []
#print(input_file)
if input_file.endswith(".com"):
gaussian_file = GaussianCom(input_file)
structure = gaussian_file.atoms_list
else:
gaussian_file = GaussianLog(input_file)
structure = gaussian_file.final_geometry
for pair in dists:
atom_a = structure[pair[0] - 1]
atom_b = structure[pair[1] - 1]
this_dist = atom_a.distance(atom_b)
if len(pair) == 2:
results_dict[input_file_no_suf].append(
"{0:7.5f}".format(this_dist))
#print("{0:>3}{2[0]:<4}-{1:>3}{2[1]:<4} : {3:7.3f}".format(atom_a,atom_b,pair,this_dist))
elif len(pair) == 3:
atom_c = structure[pair[2] - 1]
this_angle = atom_b.angle(atom_a, atom_c)
this_angle = math.degrees(this_angle)
results_dict[input_file_no_suf].append(
"{0:7.3f}".format(this_angle))
from gaussian import GaussianCom, GaussianLog
print("Trying to read qm_modred_gen.com, a simple gassian.com file")
gaussian_file_name = "qm_modred_gen.com"
gaussian_com = GaussianCom(gaussian_file_name)
print("List of atoms:\n", gaussian_com.atoms_list)
print("Everything seems ok\n\n")
print("Trying to read oniom.com, a simple ONIOM gassian.com file")
gaussian_file_name = "oniom.com"
gaussian_com = GaussianCom(gaussian_file_name)
print("List of atoms:\n", gaussian_com.atoms_list[0:100], " ... ")
print("Everything seems ok\n\n")
print("Trying to read oniom_pdb.com, a ONIOM gassian.com file with pdb info")
gaussian_file_name = "oniom_pdb.com"
gaussian_com = GaussianCom(gaussian_file_name)
print("List of atoms:\n", gaussian_com.atoms_list[0:100], " ... ")
print("Everything seems ok\n\n")
print("Trying to read oniom_pdb.log, a ONIOM gassian.log file with pdb info")
gaussian_file_name = "oniom_pdb.log"
gaussian_log = GaussianLog(gaussian_file_name)
print("Everything seems ok\n\n")
print("Trying to read big_scan_oniom.log, a 1.2 GB ONIOM gassian.log file")
gaussian_file_name = "big_scan_oniom.log"
gaussian_log = GaussianLog(gaussian_file_name)
print("Everything seems ok\n\n")
from elements_database import ATOMIC_NUMBER_DICT
try:
reactants_folder = sys.argv[1]
ts_folder = sys.argv[2]
original_ts_energy = float(sys.argv[3])
except:
print(
"Usage: residel_energies.py <reactants_folder> <ts_folder> <ts_energy>"
)
sys.exit()
for reactants_filename in os.listdir(reactants_folder):
if reactants_filename.endswith(".log"):
try:
reactants_energy = GaussianLog("{0}/{1}"\
.format(reactants_folder,reactants_filename)).energies_list[-1][-1]
except IndexError:
reactants_energy = None
try:
ts_filenames = os.listdir(ts_folder)
ts_filename_end = "_".join(reactants_filename.split("_")[-2:])
ts_filename = ts_folder + "_" + ts_filename_end
ts_energy = GaussianLog("{0}/{1}"\
.format(ts_folder,ts_filename)).energies_list[-1][-1]
except IndexError:
ts_energy = None
if reactants_energy and ts_energy:
print(
ts_filename_end[:-4],