本文整理汇总了Python中openbabel.OBConversion方法的典型用法代码示例。如果您正苦于以下问题：Python openbabel.OBConversion方法的具体用法？Python openbabel.OBConversion怎么用？Python openbabel.OBConversion使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类openbabel的用法示例。
在下文中一共展示了openbabel.OBConversion方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: _crd2mul
# 需要导入模块: import openbabel [as 别名]
# 或者: from openbabel import OBConversion [as 别名]
def _crd2mul(symbols, crds):
atomnumber = len(symbols)
xyzstring = ''.join((f"{atomnumber}\nDPGEN\n", "\n".join(
['{:2s} {:22.15f} {:22.15f} {:22.15f}'.format(s, x, y, z)
for s, (x, y, z) in zip(symbols, crds)])))
conv = openbabel.OBConversion()
conv.SetInAndOutFormats('xyz', 'gjf')
mol = openbabel.OBMol()
conv.ReadString(mol, xyzstring)
gjfstring = conv.WriteString(mol)
try:
mul = int(gjfstring.split('\n')[4].split()[1])
except IndexError:
# openbabel 3.0
mul = int(gjfstring.split('\n')[5].split()[1])
return mul 示例2: to_mol2
# 需要导入模块: import openbabel [as 别名]
# 或者: from openbabel import OBConversion [as 别名]
def to_mol2(infile,outfile):
conv = ob.OBConversion()
conv.SetInAndOutFormats("sdf","mol2")
mol = ob.OBMol()
conv.ReadFile(mol, infile)
conv.WriteFile(mol, outfile) 示例3: openbabel_force_field_on_rdkit_conformers
# 需要导入模块: import openbabel [as 别名]
# 或者: from openbabel import OBConversion [as 别名]
def openbabel_force_field_on_rdkit_conformers(label, rd_mol, force_field='MMFF94s', optimize=True):
"""
Optimize RDKit conformers by OpenBabel using a force field (MMFF94 or MMFF94s are recommended).
This is a fall back method when RDKit fails to generate force field optimized conformers.
Args:
label (str): The species' label.
rd_mol (RDKit RDMol): The RDKit molecule with embedded conformers to optimize.
force_field (str, optional): The type of force field to use.
optimize (bool, optional): Whether to first optimize the conformer using FF. True to optimize.
Returns:
list: Entries are optimized xyz's in a dictionary format.
Returns:
list: Entries are float numbers representing the energies (in kJ/mol).
"""
xyzs, energies = list(), list()
# Set up Openbabel input and output format
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats('xyz', 'xyz')
# Set up Openbabel force field
ff = ob.OBForceField.FindForceField(force_field)
symbols = [rd_atom.GetSymbol() for rd_atom in rd_mol.GetAtoms()]
for i in range(rd_mol.GetNumConformers()):
# Convert RDKit conformer to xyz string
conf = rd_mol.GetConformer(i)
xyz_str = f'{conf.GetNumAtoms()}\n\n'
for j in range(conf.GetNumAtoms()):
xyz_str += symbols[j] + ' '
pt = conf.GetAtomPosition(j)
xyz_str += ' '.join([str(pt.x), str(pt.y), str(pt.z)]) + '\n'
# Build OpenBabel molecule from xyz string
ob_mol = ob.OBMol()
obconversion.ReadString(ob_mol, xyz_str)
ff.Setup(ob_mol)
# Optimize the molecule if needed
if optimize:
ff.ConjugateGradients(2000)
# Export xyzs and energies
ob_mol.GetCoordinates()
ff.GetCoordinates(ob_mol)
energies.append(ff.Energy())
xyz_str = '\n'.join(obconversion.WriteString(ob_mol).splitlines()[2:])
xyzs.append(converter.str_to_xyz(xyz_str))
return xyzs, energies