def _check_molecule_format(val):
"""If it seems to be zmatrix rather than xyz format we convert before returning"""
atoms = [x.strip() for x in val.split(';')]
if atoms is None or len(atoms) < 1:
raise QiskitChemistryError('Molecule format error: ' + val)
# Anx xyz format has 4 parts in each atom, if not then do zmatrix convert
parts = [x.strip() for x in atoms[0].split(' ')]
if len(parts) != 4:
try:
zmat = []
for atom in atoms:
parts = [x.strip() for x in atom.split(' ')]
z = [parts[0]]
for i in range(1, len(parts), 2):
z.append(int(parts[i]))
z.append(float(parts[i + 1]))
zmat.append(z)
xyz = z2xyz(zmat)
new_val = ""
for i in range(len(xyz)):
atm = xyz[i]
if i > 0:
new_val += "; "
new_val += "{} {} {} {}".format(atm[0], atm[1], atm[2], atm[3])
return new_val
except Exception as exc:
raise QiskitChemistryError('Failed to convert atom string: ' +
val) from exc
return val
def _check_molecule_format(val):
"""If it seems to be zmatrix rather than xyz format we convert before returning"""
atoms = [x.strip() for x in val.split(";")]
if atoms is None or len(atoms) < 1: # pylint: disable=len-as-condition
raise QiskitNatureError("Molecule format error: " + val)
# An xyz format has 4 parts in each atom, if not then do zmatrix convert
# Allows dummy atoms, using symbol 'X' in zmatrix format for coord computation to xyz
parts = [x.strip() for x in atoms[0].split(" ")]
if len(parts) != 4:
try:
zmat = []
for atom in atoms:
parts = [x.strip() for x in atom.split(" ")]
z = [parts[0]]
for i in range(1, len(parts), 2):
z.append(int(parts[i]))
z.append(float(parts[i + 1]))
zmat.append(z)
xyz = z2xyz(zmat)
new_val = ""
for atm in xyz:
if atm[0].upper() == "X":
continue
if new_val:
new_val += "; "
new_val += "{} {} {} {}".format(atm[0], atm[1], atm[2], atm[3])
return new_val
except Exception as exc:
raise QiskitNatureError("Failed to convert atom string: " +
val) from exc
return val
def test_convert(self):
self.assertTrue(cartesians_equal(z2xyz([['H']]),
[['H',0.0,0.0,0.0]]))
self.assertTrue(cartesians_equal(z2xyz([['H'], ['H', 1, 0.7]]),
[['H',0.0,0.0,0.0],['H',0.7,0.0,0.0]]))
self.assertTrue(cartesians_equal(z2xyz([['O'],['H',1,1.0],['H',1,1.0,2,90.0]]),
[['O',0.0,0.0,0.0],['H',1.0,0.0,0.0],['H',0.0,1.0,0.0]]))
self.assertTrue(cartesians_equal(z2xyz([['H'],['O',1,1],['O',2,1,1,90.],['H',3,1,2,90.,1,180.]]),
[['H',0,0,0],['O',1,0,0],['O',1,1,0],['H',2,1,0]]))
self.assertTrue(cartesians_equal(z2xyz([['H'],['O',1,1],['O',2,1,1,90.],['H',3,1,2,90.,1,0.]]),
[['H',0,0,0],['O',1,0,0],['O',1,1,0],['H',0,1,0]]))
self.assertTrue(cartesians_equal(z2xyz([['H'],['O',1,1],['O',2,1,1,90.],['H',3,1,2,90.,1,90.]]),
[['H',0,0,0],['O',1,0,0],['O',1,1,0],['H',1,1,-1]]))
self.assertTrue(cartesians_equal(z2xyz([['H'],['O',1,1],['O',2,1,1,90.],['H',3,1,2,90.,1,-90.]]),
[['H',0,0,0],['O',1,0,0],['O',1,1,0],['H',1,1,1]]))
return
def _check_molecule_format(val: str) -> str:
"""If it seems to be zmatrix rather than xyz format we convert before returning"""
# pylint: disable=import-error
from pyquante2.geo.zmatrix import z2xyz
atoms = [x.strip() for x in val.split(";")]
if atoms is None or len(atoms) < 1:
raise QiskitNatureError("Molecule format error: " + val)
# An xyz format has 4 parts in each atom, if not then do zmatrix convert
# Allows dummy atoms, using symbol 'X' in zmatrix format for coord computation to xyz
parts = [x.strip() for x in atoms[0].split()]
if len(parts) != 4:
try:
zmat = []
for atom in atoms:
parts = [x.strip() for x in atom.split()]
z: List[Union[str, int, float]] = [parts[0]]
for i in range(1, len(parts), 2):
z.append(int(parts[i]))
z.append(float(parts[i + 1]))
zmat.append(z)
xyz = z2xyz(zmat)
new_val = ""
for atm in xyz:
if atm[0].upper() == "X":
continue
if new_val:
new_val += "; "
new_val += f"{atm[0]} {atm[1]} {atm[2]} {atm[3]}"
return new_val
except Exception as exc:
raise QiskitNatureError("Failed to convert atom string: " +
val) from exc
return val