def readxyz(ifile):
"""readxyz(ifile) => Molecule
if got errors, raise FormatError
"""
mol = Molecule()
connects = []
line = ifile.readline()
match = re.compile(r'^ *(\d+) *(.*)$').match(line)
atmnum = int(match.group(1))
comment = match.group(2).strip()
if comment:
mol.comment = comment
for i in range(atmnum):
words = ifile.readline().split()
atom = Atom(words[1], int(words[5]))
coord = [float(x) for x in words[2:5]]
mol.addatom(atom, coord)
connects.append(words[6:])
for i, connect in enumerate(connects):
for j in connect:
mol.buildconnect(i, int(j)-1)
assert atmnum == len(mol)
return mol
def readgjf(ifile_or_ifname):
if isinstance(ifile_or_ifname, str):
ifile = file(ifile_or_ifname)
else:
ifile = ifile_or_ifname
blanklines = 0
mol = Molecule()
while blanklines < 2:
line = ifile.readline().strip()
if line == '':
blanklines += 1
ifile.readline() #跳过 '0 1' 这一行
for line in ifile:
line = line.strip()
if line == '':
break
words = line.split()
x = []
for word in words:
x.extend(word.split(','))
atom = Atom(x[0])
#Can deal with two types gjf file: 'H 0.1 0.2 0.3' and 'H 0 0.1 0.2 0.3'
coord = [float(coord) for coord in x[-3:]]
mol.addatom(atom, coord)
ifile.close()
return mol