To conclude:
this small workaround works - but great care must be taken into
checking the structures:
--------------------------------------------------
import pybel, openbabel
mol=pybel.readfile("cdx", "benzene_acs.cdx").next()
factor=1.39/1.89 # this is the error of the bond length: real
value/wrong one
for each in mol.atoms:
x=each.coords[0]*factor
y=each.coords[1]*factor
z=each.coords[2]*factor
each.OBAtom.SetVector(x,y,z)
mol.addh()
output = pybel.Outputfile("mol2", "benzene_acs.mol2","overwrite=True")
output.write(mol)
output.close()
--------------------------------------------------
hope this will help
thank you guys for this wonderful software and those lovely python
libraries! :)
andrea
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