def main(args):
geom_patt = re.compile("([A-Z][a-z]*)((?:\s+-?\d+\.?\d*){3})")
float_patt = re.compile("-?\d+\.?\d*")
all_names = []
atoms = []
name = None
for i, page in enumerate(extract_pages(args.infile)):
print("parsing page {: 4d} please wait...".format(i + 1), end="\r")
for element in page:
last_line = None
if hasattr(element, "get_text"):
for line in element:
text = line.get_text()
match = geom_patt.search(text)
if not match and last_line and atoms:
name_match = geom_patt.search(name)
if name_match:
geom = Geometry(all_names[-1] + ".xyz")
geom.atoms.extend(atoms)
else:
geom = Geometry(atoms)
geom.name = name
geom.comment = name
if args.directory != "CURRENTDIR":
geom.name = os.path.join(
args.directory, geom.name)
orig_name = geom.name
i = 2
while geom.name in all_names:
geom.name = "{}_{:03d}".format(orig_name, i)
i += 1
if args.sort:
geom.refresh_connected()
geom.refresh_ranks()
geom.atoms = geom.reorder()[0]
geom.write()
all_names.append(geom.name)
atoms = []
name = None
# print()
# print(geom.name, len(geom.atoms))
# print(geom)
if match:
if not name:
name = last_line
element = match.group(1)
coords = float_patt.findall(match.group(2))
atoms.append(Atom(element, [float(c) for c in coords]))
last_line = text.strip()
prev_conf = conf
bad_subs = []
print_geom = geom
if args.remove_clash:
print_geom = Geometry([a.copy() for a in geom])
# print_geom.update_geometry(geom.coordinates.copy())
sub_list = [
Substituent(print_geom.find([at.name for at in sub]),
detect=False,
end=print_geom.find_exact(sub.end.name)[0])
for sub in substituents
]
bad_subs = print_geom.remove_clash(sub_list)
# somehow the atoms get out of order
print_geom.atoms = sorted(print_geom.atoms,
key=lambda a: float(a.name))
if args.skip_clash:
if bad_subs:
skipped += 1
continue
clashing = False
for j, a1 in enumerate(print_geom.atoms):
for a2 in print_geom.atoms[:j]:
if a2 not in a1.connected and a1.is_connected(a2):
clashing = True
break
if clashing:
break
